diff --git a/.gitignore b/.gitignore
index f1fb212b..ce2df748 100755
--- a/.gitignore
+++ b/.gitignore
@@ -70,3 +70,6 @@ docs/_build/
 target/
 
 .eggs
+
+# mac files
+.DS_Store
diff --git a/poetry.lock b/poetry.lock
index 327195a9..5e73246c 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -1,4 +1,4 @@
-# This file is automatically @generated by Poetry 1.7.1 and should not be changed by hand.
+# This file is automatically @generated by Poetry 1.6.1 and should not be changed by hand.
 
 [[package]]
 name = "alabaster"
@@ -132,51 +132,6 @@ files = [
 [package.dependencies]
 numpy = "*"
 
-[[package]]
-name = "build"
-version = "1.0.3"
-description = "A simple, correct Python build frontend"
-optional = false
-python-versions = ">= 3.7"
-files = [
-    {file = "build-1.0.3-py3-none-any.whl", hash = "sha256:589bf99a67df7c9cf07ec0ac0e5e2ea5d4b37ac63301c4986d1acb126aa83f8f"},
-    {file = "build-1.0.3.tar.gz", hash = "sha256:538aab1b64f9828977f84bc63ae570b060a8ed1be419e7870b8b4fc5e6ea553b"},
-]
-
-[package.dependencies]
-colorama = {version = "*", markers = "os_name == \"nt\""}
-importlib-metadata = {version = ">=4.6", markers = "python_version < \"3.10\""}
-packaging = ">=19.0"
-pyproject_hooks = "*"
-tomli = {version = ">=1.1.0", markers = "python_version < \"3.11\""}
-
-[package.extras]
-docs = ["furo (>=2023.08.17)", "sphinx (>=7.0,<8.0)", "sphinx-argparse-cli (>=1.5)", "sphinx-autodoc-typehints (>=1.10)", "sphinx-issues (>=3.0.0)"]
-test = ["filelock (>=3)", "pytest (>=6.2.4)", "pytest-cov (>=2.12)", "pytest-mock (>=2)", "pytest-rerunfailures (>=9.1)", "pytest-xdist (>=1.34)", "setuptools (>=42.0.0)", "setuptools (>=56.0.0)", "setuptools (>=56.0.0)", "setuptools (>=67.8.0)", "wheel (>=0.36.0)"]
-typing = ["importlib-metadata (>=5.1)", "mypy (>=1.5.0,<1.6.0)", "tomli", "typing-extensions (>=3.7.4.3)"]
-virtualenv = ["virtualenv (>=20.0.35)"]
-
-[[package]]
-name = "cachecontrol"
-version = "0.13.1"
-description = "httplib2 caching for requests"
-optional = false
-python-versions = ">=3.7"
-files = [
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-    {file = "cachecontrol-0.13.1.tar.gz", hash = "sha256:f012366b79d2243a6118309ce73151bf52a38d4a5dac8ea57f09bd29087e506b"},
-]
-
-[package.dependencies]
-filelock = {version = ">=3.8.0", optional = true, markers = "extra == \"filecache\""}
-msgpack = ">=0.5.2"
-requests = ">=2.16.0"
-
-[package.extras]
-dev = ["CacheControl[filecache,redis]", "black", "build", "cherrypy", "mypy", "pytest", "pytest-cov", "sphinx", "tox", "types-redis", "types-requests"]
-filecache = ["filelock (>=3.8.0)"]
-redis = ["redis (>=2.10.5)"]
-
 [[package]]
 name = "cai2"
 version = "1.0.5"
@@ -195,13 +150,13 @@ scipy = "*"
 
 [[package]]
 name = "certifi"
-version = "2023.11.17"
+version = "2024.2.2"
 description = "Python package for providing Mozilla's CA Bundle."
 optional = false
 python-versions = ">=3.6"
 files = [
-    {file = "certifi-2023.11.17-py3-none-any.whl", hash = "sha256:e036ab49d5b79556f99cfc2d9320b34cfbe5be05c5871b51de9329f0603b0474"},
-    {file = "certifi-2023.11.17.tar.gz", hash = "sha256:9b469f3a900bf28dc19b8cfbf8019bf47f7fdd1a65a1d4ffb98fc14166beb4d1"},
+    {file = "certifi-2024.2.2-py3-none-any.whl", hash = "sha256:dc383c07b76109f368f6106eee2b593b04a011ea4d55f652c6ca24a754d1cdd1"},
+    {file = "certifi-2024.2.2.tar.gz", hash = "sha256:0569859f95fc761b18b45ef421b1290a0f65f147e92a1e5eb3e635f9a5e4e66f"},
 ]
 
 [[package]]
@@ -367,21 +322,6 @@ files = [
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-[[package]]
-name = "cleo"
-version = "2.1.0"
-description = "Cleo allows you to create beautiful and testable command-line interfaces."
-optional = false
-python-versions = ">=3.7,<4.0"
-files = [
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-
-[package.dependencies]
-crashtest = ">=0.4.1,<0.5.0"
-rapidfuzz = ">=3.0.0,<4.0.0"
-
 [[package]]
 name = "click"
 version = "8.1.7"
@@ -487,8 +427,8 @@ files = [
 
 [package.dependencies]
 numpy = [
-    {version = ">=1.16,<2.0", markers = "python_version <= \"3.11\""},
     {version = ">=1.26.0rc1,<2.0", markers = "python_version >= \"3.12\""},
+    {version = ">=1.16,<2.0", markers = "python_version <= \"3.11\""},
 ]
 
 [package.extras]
@@ -565,71 +505,6 @@ tomli = {version = "*", optional = true, markers = "python_full_version <= \"3.1
 [package.extras]
 toml = ["tomli"]
 
-[[package]]
-name = "crashtest"
-version = "0.4.1"
-description = "Manage Python errors with ease"
-optional = false
-python-versions = ">=3.7,<4.0"
-files = [
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-
-[[package]]
-name = "cryptography"
-version = "42.0.2"
-description = "cryptography is a package which provides cryptographic recipes and primitives to Python developers."
-optional = false
-python-versions = ">=3.7"
-files = [
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-
-[package.dependencies]
-cffi = {version = ">=1.12", markers = "platform_python_implementation != \"PyPy\""}
-
-[package.extras]
-docs = ["sphinx (>=5.3.0)", "sphinx-rtd-theme (>=1.1.1)"]
-docstest = ["pyenchant (>=1.6.11)", "readme-renderer", "sphinxcontrib-spelling (>=4.0.1)"]
-nox = ["nox"]
-pep8test = ["check-sdist", "click", "mypy", "ruff"]
-sdist = ["build"]
-ssh = ["bcrypt (>=3.1.5)"]
-test = ["certifi", "pretend", "pytest (>=6.2.0)", "pytest-benchmark", "pytest-cov", "pytest-xdist"]
-test-randomorder = ["pytest-randomly"]
-
 [[package]]
 name = "cycler"
 version = "0.12.1"
@@ -683,17 +558,6 @@ files = [
     {file = "decorator-5.1.1.tar.gz", hash = "sha256:637996211036b6385ef91435e4fae22989472f9d571faba8927ba8253acbc330"},
 ]
 
-[[package]]
-name = "distlib"
-version = "0.3.8"
-description = "Distribution utilities"
-optional = false
-python-versions = "*"
-files = [
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-
 [[package]]
 name = "docutils"
 version = "0.20.1"
@@ -705,93 +569,6 @@ files = [
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 ]
 
-[[package]]
-name = "dulwich"
-version = "0.21.7"
-description = "Python Git Library"
-optional = false
-python-versions = ">=3.7"
-files = [
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-
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-fastimport = ["fastimport"]
-https = ["urllib3 (>=1.24.1)"]
-paramiko = ["paramiko"]
-pgp = ["gpg"]
-
 [[package]]
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 version = "1.2.0"
@@ -834,22 +611,6 @@ files = [
 [package.extras]
 devel = ["colorama", "json-spec", "jsonschema", "pylint", "pytest", "pytest-benchmark", "pytest-cache", "validictory"]
 
-[[package]]
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-
 [[package]]
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 version = "4.47.2"
@@ -996,17 +757,6 @@ files = [
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-
 [[package]]
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 version = "0.19.1"
@@ -1116,21 +848,6 @@ docs = ["Jinja2 (==2.11.3)", "MarkupSafe (==1.1.1)", "Pygments (==2.8.1)", "alab
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-
 [[package]]
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@@ -1229,30 +946,6 @@ traitlets = ">=5.3"
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-
 [[package]]
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 version = "1.4.5"
@@ -1383,71 +1076,71 @@ tornado = {version = "*", markers = "python_version > \"2.7\""}
 
 [[package]]
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 typing = ["typing-extensions"]
 xmp = ["defusedxml"]
 
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-
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@@ -2639,20 +2052,6 @@ six = "*"
 fixture = ["fixtures"]
 test = ["fixtures", "mock", "purl", "pytest", "requests-futures", "sphinx", "testtools"]
 
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-content-hash = "dda87bcb19ab2cfd245697f1041342119359a31a3d13e9edf32156e1054697a8"
+python-versions = ">=3.8,<4.0"
+content-hash = "596f6112da03f3e5b4ef570338171cd957ee434fecf8ed71534df25617ef53b0"
diff --git a/pyproject.toml b/pyproject.toml
index 51049527..b57332d7 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,102 +1,105 @@
 [project]
-name = "pydna"
-dynamic = ["version"]
-description = "Representing double stranded DNA and functions for simulating cloning and homologous recombination between DNA molecules."
 authors = ["Björn F. Johansson<bjornjobb@gmail.com>"]
+classifiers = [
+  "Development Status :: 4 - Beta",
+  "Environment :: Console",
+  "Intended Audience :: Education",
+  "Intended Audience :: Developers",
+  "Intended Audience :: Science/Research",
+  "License :: OSI Approved :: BSD License",
+  "Operating System :: OS Independent",
+  "Programming Language :: Python :: 3.8",
+  "Programming Language :: Python :: 3.9",
+  "Programming Language :: Python :: 3.10",
+  "Programming Language :: Python :: 3.11",
+  "Programming Language :: Python :: 3.12",
+  "Topic :: Education",
+  "Topic :: Scientific/Engineering :: Bio-Informatics",
+]
+description = "Representing double stranded DNA and functions for simulating cloning and homologous recombination between DNA molecules."
+dynamic = ["version"]
+name = "pydna"
 readme = "README.md"
-classifiers=["Development Status :: 4 - Beta",
-             "Environment :: Console",
-             "Intended Audience :: Education",
-             "Intended Audience :: Developers",
-             "Intended Audience :: Science/Research",
-             "License :: OSI Approved :: BSD License",
-             "Operating System :: OS Independent",
-             "Programming Language :: Python :: 3.8",
-             "Programming Language :: Python :: 3.9",
-             "Programming Language :: Python :: 3.10",
-             "Programming Language :: Python :: 3.11",
-             "Programming Language :: Python :: 3.12",
-             "Topic :: Education",
-             "Topic :: Scientific/Engineering :: Bio-Informatics", ]
 [tool.poetry.urls]
 Changelog = "https://github.com/BjornFJohansson/pydna/blob/master/docs/CHANGELOG.md#changelog"
 [tool.poetry]
-name = "pydna"
-version = "6.0.0-a.24.post.17+b7b559bd66"
-description = "Representing double stranded DNA and functions for simulating cloning and homologous recombination between DNA molecules."
 authors = ["BjornFJohansson <bjornjobb@gmail.com>"]
+description = "Representing double stranded DNA and functions for simulating cloning and homologous recombination between DNA molecules."
+documentation = "https://pydna.readthedocs.io/?badge=latest"
+homepage = "https://github.com/BjornFJohansson/pydna#-pydna"
 license = "BSD"
+name = "pydna"
 readme = "README.md"
-homepage = "https://github.com/BjornFJohansson/pydna#-pydna"
-documentation = "https://pydna.readthedocs.io/?badge=latest"
 repository = "https://github.com/BjornFJohansson/pydna/tree/dev_bjorn"
+version = "6.0.0-a.24.post.17+b7b559bd66"
 [tool.poetry.dependencies]
-python = ">=3.8, <4.0"
 appdirs = ">=1.4.4"
 biopython = ">=1.80"
+cai2 = {version = ">=1.0.5", optional = true}
+matplotlib = {version = ">=3.4.3", optional = true}
 networkx = ">=2.8.8"
-pydivsufsort = ">=0.0.14"
-seguid = ">=0.0.3"
-prettytable = ">=3.5.0"
-pyfiglet = "0.8.post1"
 numpy = [
-    {version = ">=1.24.4", python = ">=3.8,<3.9"},
-    {version = ">=1.26.3", python = ">=3.9"}
+  {version = ">1.26", python = ">=3.9"},
+  {version = "<1.24", python = "<3.9"},
 ]
-pyperclip = { version = ">=1.8.2", optional = true }
+pillow = {version = ">=8.4.0", optional = true}
+prettytable = ">=3.5.0"
+pydivsufsort = ">=0.0.11"
+pyfiglet = "0.8.post1"
+pyparsing = {version = ">=2.4.7", optional = true}
+pyperclip = {version = ">=1.8.2", optional = true}
+python = ">=3.8,<4.0"
+requests = {version = ">=2.26.0", optional = true}
 scipy = [
-    {version = ">=1.9.3", python = ">=3.8,<3.9",  optional = true },
-    {version = ">=1.11.4", python = ">=3.9",  optional = true }
+  {version = ">=1.11.3", python = ">=3.12", optional = true},
+  {version = ">=1.9.3", python = "<3.12", optional = true},
 ]
-matplotlib = { version = ">=3.4.3", optional = true }
-pillow = { version = ">=8.4.0", optional = true }
-pyparsing = { version = ">=2.4.7", optional = true }
-requests = { version = ">=2.26.0", optional = true }
-cai2 = { version = ">=1.0.5", optional = true }
-poetry = "^1.7.1"
+seguid = "^0.0.3"
 [tool.poetry.extras]
 clipboard = ["pyperclip"]
-gel = ["scipy", "matplotlib", "pillow"]
 download = ["pyparsing", "requests"]
 express = ["cai2"]
+gel = ["scipy", "matplotlib", "pillow"]
 [build-system]
-requires = ["poetry-core",
-            "poetry-dynamic-versioning"]
 build-backend = "poetry_dynamic_versioning.backend"
+requires = [
+  "poetry-core",
+  "poetry-dynamic-versioning",
+]
 [tool.poetry-dynamic-versioning]
 enable = true
-vcs = "git"
 style = "semver"
+vcs = "git"
 [tool.poetry-dynamic-versioning.substitution]
 folders = [
-  { path = "src"}
+  {path = "src"},
 ]
 [tool.poetry.group.test] # This part can be left out
 [tool.poetry.group.test.dependencies]
+coverage = ">=7.1.0"
+nbval = ">=0.9.6"
 pytest = ">=7.2.0"
 pytest-cov = ">=4.0.0"
 pytest-doctestplus = ">=0.12.1"
 pytest-profiling = ">=1.7.0"
-coverage = ">=7.1.0"
-nbval = ">=0.9.6"
 requests-mock = ">=1.10.0"
 
 [tool.poetry.group.docs.dependencies]
-sphinx-autobuild = "^2021.3.14"
 numpydoc = "^1.6.0"
+sphinx-autobuild = "^2021.3.14"
 sphinx-rtd-theme = ">=1.3,<3.0"
 
 [tool.pytest.ini_options]
 minversion = "6.0.2"
 python_files = "test_*.py"
 testpaths = [
-    "tests",
-    "src",
+  "tests",
+  "src",
 ]
 [tool.black]
+include = '\.pyi?$'
 line-length = 119
 target-version = ["py38", "py39", "py310", "py311", "py312"]
-include = '\.pyi?$'
 # 'extend-exclude' excludes files or directories in addition to the defaults
 extend-exclude = '''
 # A regex preceded with ^/ will apply only to files and directories
diff --git a/scripts/cutsite_pairs.ipynb b/scripts/cutsite_pairs.ipynb
new file mode 100644
index 00000000..ac26e9b4
--- /dev/null
+++ b/scripts/cutsite_pairs.ipynb
@@ -0,0 +1,276 @@
+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "# New cut implementation\n",
+    "\n",
+    "The most important thing is that cuts are now represented as `((cut_watson, ovhg), enz)`:\n",
+    "\n",
+    "- `cut_watson` is a positive integer contained in `[0,len(seq))`, where `seq` is the sequence that will be cut. It represents the position of the cut on the watson strand, using the full sequence as a reference. By \"full sequence\" I mean the one you would get from `str(Dseq)`. See example below.\n",
+    "- `ovhg` is the overhang left after the cut. It has the same meaning as `ovhg` in the `Bio.Restriction` enzyme objects, or pydna's `Dseq` property.\n",
+    "- `enz` is the enzyme object. It's not necessary to perform the cut, but can be used to keep track of which enzyme was used.\n",
+    "\n",
+    "The new implementation of `Dseq.cut` now looks like this:\n",
+    "\n",
+    "```python\n",
+    "cutsites = self.get_cutsites(*enzymes)\n",
+    "cutsite_pairs = self.get_cutsite_pairs(cutsites)\n",
+    "return tuple(self.apply_cut(*cs) for cs in cutsite_pairs)\n",
+    "```\n",
+    "\n",
+    "Let's go through it step by step"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 1,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "get_cutsites output: [((3, -4), EcoRI), ((11, -4), EcoRI)]\n",
+      "EcoRI.search output: [4, 12] < (positions are 1-based)\n",
+      "EcoRI.ovhg: -4\n",
+      "\n",
+      "get_cutsites output: [((6, -4), EcoRI)]\n",
+      "EcoRI.search output: [7] < (positions are 1-based)\n",
+      "EcoRI.ovhg: -4\n",
+      "\n",
+      "get_cutsites output: [((1, 2), PacI)]\n",
+      "PacI.search output: [2] < (positions are 1-based)\n",
+      "PacI.ovhg: 2\n",
+      "\n"
+     ]
+    }
+   ],
+   "source": [
+    "from pydna.dseq import Dseq\n",
+    "from Bio.Restriction import EcoRI, PacI\n",
+    "\n",
+    "dseq = Dseq('aaGAATTCaaGAATTCaa')\n",
+    "\n",
+    "# what this function does is basically handle the format of the enzymes, and return the cut positions\n",
+    "# that are returned by enz.search, along with the enzyme name and overhang. Positions are made zero-base\n",
+    "# instead of one-based\n",
+    "\n",
+    "print('get_cutsites output:', dseq.get_cutsites([EcoRI]))\n",
+    "print('EcoRI.search output:', EcoRI.search(dseq), '< (positions are 1-based)')\n",
+    "print('EcoRI.ovhg:', EcoRI.ovhg)\n",
+    "print()\n",
+    "\n",
+    "# Below are two examples of circular sequences with a cutsite that spans the origin.\n",
+    "dseq = Dseq('TTCaaGAA', circular=True)\n",
+    "print('get_cutsites output:', dseq.get_cutsites([EcoRI]))\n",
+    "print('EcoRI.search output:', EcoRI.search(dseq, linear=False), '< (positions are 1-based)')\n",
+    "print('EcoRI.ovhg:', EcoRI.ovhg)\n",
+    "print()\n",
+    "\n",
+    "dseq = Dseq('TTAAaaTTAA', circular=True)\n",
+    "print('get_cutsites output:', dseq.get_cutsites([PacI]))\n",
+    "print('PacI.search output:', PacI.search(dseq, linear=False), '< (positions are 1-based)')\n",
+    "print('PacI.ovhg:', PacI.ovhg)\n",
+    "print()\n"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "Note in the above printed output how if the ovhg is negative, for an origin spanning cutsite, the position lies on the left side of the origin, and viceversa.\n",
+    "\n",
+    "Below, you can see that the `cut_watson` is defined with respect to the \"full sequence\""
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 2,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "Dseq(-10)\n",
+      "aaGAATTCaa\n",
+      " tCTTAAGtt\n",
+      "ovhg: -1 >> [((3, -4), EcoRI)]\n",
+      "\n",
+      "Dseq(-10)\n",
+      "aaGAATTCaa\n",
+      "ttCTTAAGtt\n",
+      "ovhg: 0 >> [((3, -4), EcoRI)]\n",
+      "\n",
+      "Dseq(-10)\n",
+      " aGAATTCaa\n",
+      "ttCTTAAGtt\n",
+      "ovhg: 1 >> [((3, -4), EcoRI)]\n",
+      "\n"
+     ]
+    }
+   ],
+   "source": [
+    "# `cut_watson` is defined with respect to the \"full sequence\"\n",
+    "for ovhg in [-1, 0, 1]:\n",
+    "    dseq = Dseq.from_full_sequence_and_overhangs('aaGAATTCaa', ovhg, 0)\n",
+    "    print(dseq.__repr__())\n",
+    "    print('ovhg:', ovhg, '>>', dseq.get_cutsites([EcoRI]))\n",
+    "    print()\n"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "Cuts are only returned if the recognition site and overhang are on the double-strand part of the sequence."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 8,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "[((1, -4), EcoRI)]\n",
+      "[]\n"
+     ]
+    }
+   ],
+   "source": [
+    "\n",
+    "seq = Dseq('GAATTC')\n",
+    "print(seq.get_cutsites([EcoRI]))\n",
+    "\n",
+    "seq = Dseq.from_full_sequence_and_overhangs('GAATTC', -1, 0)\n",
+    "print(seq.get_cutsites([EcoRI]))"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "\n",
+    "\n",
+    "## Pairing cutsites\n",
+    "\n",
+    "A fragment produced by restriction is represented by a tuple of length 2 that may contain cutsites or `None`:\n",
+    "\n",
+    "- Two cutsites: represents the extraction of a fragment between those two cutsites, in that orientation. To represent the opening of a circular molecule with a single cutsite, we put the same cutsite twice. See below.\n",
+    "- `None`, cutsite: represents the extraction of a fragment between the left edge of linear sequence and the cutsite.\n",
+    "- cutsite, `None`: represents the extraction of a fragment between the cutsite and the right edge of a linear sequence.\n",
+    "\n",
+    "## Generating the sequence\n",
+    "\n",
+    "To get the fragment, we use the function `dseq.apply_cut`, passing the two elements of the tuple as arguments."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 6,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "> None, cutsite : (None, ((3, -4), EcoRI))\n",
+      "Dseq(-7)\n",
+      "aaG\n",
+      "ttCTTAA\n",
+      "\n",
+      "> cutsite, cutsite : (((3, -4), EcoRI), ((11, -4), EcoRI))\n",
+      "Dseq(-12)\n",
+      "AATTCaaG\n",
+      "    GttCTTAA\n",
+      "\n",
+      "> cutsite, None : (((11, -4), EcoRI), None)\n",
+      "Dseq(-7)\n",
+      "AATTCaa\n",
+      "    Gtt\n",
+      "\n",
+      "Circular molecule\n",
+      "> cutsite, cutsite : (((6, -4), EcoRI), ((6, -4), EcoRI))\n",
+      "Dseq(-12)\n",
+      "AATTCaaG\n",
+      "    GttCTTAA\n"
+     ]
+    }
+   ],
+   "source": [
+    "dseq = Dseq('aaGAATTCaaGAATTCaa')\n",
+    "cutsites = dseq.get_cutsites([EcoRI])\n",
+    "\n",
+    "cutsite_pairs = dseq.get_cutsite_pairs(cutsites)\n",
+    "pair_types = ['None, cutsite', 'cutsite, cutsite', 'cutsite, None']\n",
+    "\n",
+    "for pair, pair_type in zip(cutsite_pairs, pair_types):\n",
+    "    print('>', pair_type, ':',pair)\n",
+    "    print(dseq.apply_cut(*pair).__repr__())\n",
+    "    print()\n",
+    "\n",
+    "# Opening a circular sequence\n",
+    "print('Circular molecule')\n",
+    "dseq = Dseq('TTCaaGAA', circular=True)\n",
+    "cutsites = dseq.get_cutsites([EcoRI])\n",
+    "cutsite_pairs = dseq.get_cutsite_pairs(cutsites)\n",
+    "print('> cutsite, cutsite :', cutsite_pairs[0])\n",
+    "print(dseq.apply_cut(*cutsite_pairs[0]).__repr__())"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 7,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "Dseq(-7)\n",
+      " aG\n",
+      "ttCTTAA\n",
+      "\n",
+      "Dseq(-7)\n",
+      "AATTCaa\n",
+      "    Gt\n"
+     ]
+    }
+   ],
+   "source": [
+    "# Note that the cutsite respects the ovhg of the parent sequence:\n",
+    "dseq = Dseq.from_full_sequence_and_overhangs('aaGAATTCaaGAATTCaa', 1, 1)\n",
+    "f1, f2, f3 = dseq.cut([EcoRI])\n",
+    "print(f1.__repr__())\n",
+    "print()\n",
+    "print(f3.__repr__())\n"
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": ".venv",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.11.6"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 2
+}
diff --git a/src/pydna/amplify.py b/src/pydna/amplify.py
index 200cfb7b..042a50a6 100644
--- a/src/pydna/amplify.py
+++ b/src/pydna/amplify.py
@@ -354,7 +354,10 @@ def products(self):
                     tpl = self.template
                 else:
                     continue
-                prd = _Dseqrecord(fp) + tpl[fp.position : rp.position] + _Dseqrecord(rp).reverse_complement()
+                if tpl.circular and fp.position == rp.position:
+                    prd = _Dseqrecord(fp) + _Dseqrecord(rp).reverse_complement()
+                else:
+                    prd = _Dseqrecord(fp) + tpl[fp.position : rp.position] + _Dseqrecord(rp).reverse_complement()
                 prd.features = feats
                 full_tmpl_features = [
                     f for f in self.template.features if f.location.start == 0 and f.location.end == len(self.template)
diff --git a/src/pydna/dseq.py b/src/pydna/dseq.py
index cb5f788c..5b3b4736 100644
--- a/src/pydna/dseq.py
+++ b/src/pydna/dseq.py
@@ -22,7 +22,6 @@
 import math as _math
 
 from pydna.seq import Seq as _Seq
-from Bio.Restriction import FormattedSeq as _FormattedSeq
 from Bio.Seq import _translate_str
 
 from pydna._pretty import pretty_str as _pretty_str
@@ -31,12 +30,14 @@
 
 from pydna.utils import rc as _rc
 from pydna.utils import flatten as _flatten
-from pydna.common_sub_strings import common_sub_strings as _common_sub_strings
+from pydna.utils import cuts_overlap as _cuts_overlap
 
-from operator import itemgetter as _itemgetter
+from pydna.common_sub_strings import common_sub_strings as _common_sub_strings
 from Bio.Restriction import RestrictionBatch as _RestrictionBatch
 from Bio.Restriction import CommOnly
 
+from typing import Tuple
+
 
 class Dseq(_Seq):
     """Dseq holds information for a double stranded DNA fragment.
@@ -813,7 +814,7 @@ def shifted(self, shift):
             raise TypeError("DNA is not circular.")
         shift = shift % len(self)
         if not shift:
-            return self
+            return _copy.deepcopy(self)
         else:
             return (self[shift:] + self[:shift]).looped()
 
@@ -1440,116 +1441,302 @@ def cut(self, *enzymes):
 
         """
 
-        pad = "n" * 50
+        cutsites = self.get_cutsites(*enzymes)
+        cutsite_pairs = self.get_cutsite_pairs(cutsites)
+        return tuple(self.apply_cut(*cs) for cs in cutsite_pairs)
+
+    def cutsite_is_valid(self, cutsite):
+        """Returns False if:
+        - Cut positions fall outside the sequence (could be moved to Biopython)
+        - Overhang is not double stranded
+        - Recognition site is not double stranded or is outside the sequence
+        - For enzymes that cut twice, it checks that at least one possibility is valid
+        """
 
+        assert cutsite != None, "cutsite is None"
+
+        enz = cutsite[1]
+        watson, crick, ovhg = self.get_cut_parameters(cutsite, True)
+
+        # The cut positions fall within the sequence
+        # This could go into Biopython
+        if not self.circular and crick < 0 or crick > len(self):
+            return False
+
+        # The overhang is double stranded
+        overhang_dseq = self[watson:crick] if ovhg < 0 else self[crick:watson]
+        if overhang_dseq.ovhg != 0 or overhang_dseq.watson_ovhg() != 0:
+            return False
+
+        # The recognition site is double stranded and within the sequence
+        start_of_recognition_site = watson - enz.fst5
+        if start_of_recognition_site < 0:
+            start_of_recognition_site += len(self)
+        end_of_recognition_site = start_of_recognition_site + enz.size
         if self.circular:
-            dsseq = Dseq.from_string(
-                self._data.decode("ASCII"),
-                # linear=True,
-                circular=False,
-            )
-        else:
-            dsseq = self.mung()
-
-        if len(enzymes) == 1 and hasattr(enzymes[0], "intersection"):
-            # argument is probably a RestrictionBatch
-            enzymecuts = []
-            for e in enzymes[0]:
-                cuts = e.search(
-                    _Seq(pad + dsseq.watson + dsseq.watson[: e.size - 1] + pad) if self.circular else dsseq
+            end_of_recognition_site %= len(self)
+        recognition_site = self[start_of_recognition_site:end_of_recognition_site]
+        if len(recognition_site) == 0 or recognition_site.ovhg != 0 or recognition_site.watson_ovhg() != 0:
+            if enz.scd5 is None:
+                return False
+            else:
+                # For enzymes that cut twice, this might be referring to the second one
+                start_of_recognition_site = watson - enz.scd5
+                if start_of_recognition_site < 0:
+                    start_of_recognition_site += len(self)
+                end_of_recognition_site = start_of_recognition_site + enz.size
+                if self.circular:
+                    end_of_recognition_site %= len(self)
+                recognition_site = self[start_of_recognition_site:end_of_recognition_site]
+                if (len(recognition_site) == 0 or recognition_site.ovhg != 0 or recognition_site.watson_ovhg() != 0):
+                    return False
+
+        return True
+
+    def get_cutsites(self, *enzymes):
+        """Returns a list of cutsites, represented represented as `((cut_watson, ovhg), enz)`:
+
+        - `cut_watson` is a positive integer contained in `[0,len(seq))`, where `seq` is the sequence
+          that will be cut. It represents the position of the cut on the watson strand, using the full
+          sequence as a reference. By "full sequence" I mean the one you would get from `str(Dseq)`.
+        - `ovhg` is the overhang left after the cut. It has the same meaning as `ovhg` in
+          the `Bio.Restriction` enzyme objects, or pydna's `Dseq` property.
+        - `enz` is the enzyme object. It's not necessary to perform the cut, but can be
+           used to keep track of which enzyme was used.
+
+        Cuts are only returned if the recognition site and overhang are on the double-strand
+        part of the sequence.
+
+        Parameters
+        ----------
+
+        enzymes : Union[_RestrictionBatch,list[_RestrictionType]]
+
+        Returns
+        -------
+        list[tuple[tuple[int,int], _RestrictionType]]
+
+        Examples
+        --------
+
+        >>> from Bio.Restriction import EcoRI
+        >>> from pydna.dseq import Dseq
+        >>> seq = Dseq('AAGAATTCAAGAATTC')
+        >>> seq.get_cutsites(EcoRI)
+        [((3, -4), EcoRI), ((11, -4), EcoRI)]
+
+        `cut_watson` is defined with respect to the "full sequence", not the
+        watson strand:
+
+        >>> dseq = Dseq.from_full_sequence_and_overhangs('aaGAATTCaa', 1, 0)
+        >>> dseq
+        Dseq(-10)
+         aGAATTCaa
+        ttCTTAAGtt
+        >>> dseq.get_cutsites([EcoRI])
+        [((3, -4), EcoRI)]
+
+        Cuts are only returned if the recognition site and overhang are on the double-strand
+        part of the sequence.
+
+        >>> Dseq('GAATTC').get_cutsites([EcoRI])
+        [((1, -4), EcoRI)]
+        >>> Dseq.from_full_sequence_and_overhangs('GAATTC', -1, 0).get_cutsites([EcoRI])
+        []
+
+        """
+
+        if len(enzymes) == 1 and isinstance(enzymes[0], _RestrictionBatch):
+                # argument is probably a RestrictionBatch
+                enzymes = [e for e in enzymes[0]]
+
+        enzymes = _flatten(enzymes)
+        out = list()
+        for e in enzymes:
+            # Positions of the cut on the watson strand. They are 1-based, so we subtract
+            # 1 to get 0-based positions
+            cuts_watson = [c - 1 for c in e.search(self, linear=(not self.circular))]
+
+            out += [((w, e.ovhg), e) for w in cuts_watson]
+
+        return sorted([cutsite for cutsite in out if self.cutsite_is_valid(cutsite)])
+
+    def left_end_position(self) -> Tuple[int, int]:
+        """The index in the full sequence of the watson and crick start positions.
+
+        full sequence (str(self)) for all three cases is AAA
+
+        ```
+        AAA              AA               AAT
+         TT             TTT               TTT
+        Returns (0, 1)  Returns (1, 0)    Returns (0, 0)
+        ```
+
+        """
+        if self.ovhg > 0:
+            return self.ovhg, 0
+        return 0, -self.ovhg
+
+    def right_end_position(self) -> Tuple[int, int]:
+        """The index in the full sequence of the watson and crick end positions.
+
+        full sequence (str(self)) for all three cases is AAA
+
+        ```
+        AAA               AA                   AAA
+        TT                TTT                  TTT
+        Returns (3, 2)    Returns (2, 3)       Returns (3, 3)
+        ```
+
+        """
+        if self.watson_ovhg() < 0:
+            return len(self) + self.watson_ovhg(), len(self)
+        return len(self), len(self) - self.watson_ovhg()
+
+    def get_cut_parameters(self, cut: tuple, is_left: bool):
+        """For a given cut expressed as ((cut_watson, ovhg), enz), returns
+        a tuple (cut_watson, cut_crick, ovhg).
+
+        - cut_watson: see get_cutsites docs
+        - cut_crick: equivalent of cut_watson in the crick strand
+        - ovhg: see get_cutsites docs
+
+        The cut can be None if it represents the left or right end of the sequence.
+        Then it will return the position of the watson and crick ends with respect
+        to the "full sequence". The `is_left` parameter is only used in this case.
+
+        """
+        if cut is not None:
+            watson, ovhg = cut[0]
+            crick = (watson - ovhg)
+            if self.circular:
+                crick %= len(self)
+            return watson, crick, ovhg
+
+        assert not self.circular, 'Circular sequences should not have None cuts'
+
+        if is_left:
+            return *self.left_end_position(), self.ovhg
+        # In the right end, the overhang does not matter
+        return *self.right_end_position(), self.watson_ovhg()
+
+    def apply_cut(self, left_cut, right_cut):
+        """Extracts a subfragment of the sequence between two cuts.
+
+        For more detail see the documentation of get_cutsite_pairs.
+
+        Parameters
+        ----------
+        left_cut : Union[tuple[tuple[int,int], _RestrictionType], None]
+        right_cut: Union[tuple[tuple[int,int], _RestrictionType], None]
+
+        Returns
+        -------
+        Dseq
+
+        Examples
+        --------
+        >>> from Bio.Restriction import EcoRI
+        >>> from pydna.dseq import Dseq
+        >>> dseq = Dseq('aaGAATTCaaGAATTCaa')
+        >>> cutsites = dseq.get_cutsites([EcoRI])
+        >>> cutsites
+        [((3, -4), EcoRI), ((11, -4), EcoRI)]
+        >>> p1, p2, p3 = dseq.get_cutsite_pairs(cutsites)
+        >>> p1
+        (None, ((3, -4), EcoRI))
+        >>> dseq.apply_cut(*p1)
+        Dseq(-7)
+        aaG
+        ttCTTAA
+        >>> p2
+        (((3, -4), EcoRI), ((11, -4), EcoRI))
+        >>> dseq.apply_cut(*p2)
+        Dseq(-12)
+        AATTCaaG
+            GttCTTAA
+        >>> p3
+        (((11, -4), EcoRI), None)
+        >>> dseq.apply_cut(*p3)
+        Dseq(-7)
+        AATTCaa
+            Gtt
+
+        >>> dseq = Dseq('TTCaaGAA', circular=True)
+        >>> cutsites = dseq.get_cutsites([EcoRI])
+        >>> cutsites
+        [((6, -4), EcoRI)]
+        >>> pair = dseq.get_cutsite_pairs(cutsites)[0]
+        >>> pair
+        (((6, -4), EcoRI), ((6, -4), EcoRI))
+        >>> dseq.apply_cut(*pair)
+        Dseq(-12)
+        AATTCaaG
+            GttCTTAA
+
+        """
+        if _cuts_overlap(left_cut, right_cut, len(self)):
+            raise ValueError("Cuts overlap")
+
+        left_watson, left_crick, ovhg_left = self.get_cut_parameters(left_cut, True)
+        right_watson, right_crick, _ = self.get_cut_parameters(right_cut, False)
+        return Dseq(
+                    str(self[left_watson:right_watson]),
+                    # The line below could be easier to understand as _rc(str(self[left_crick:right_crick])), but it does not preserve the case
+                    str(self.reverse_complement()[len(self) - right_crick:len(self) - left_crick]),
+                    ovhg=ovhg_left,
                 )
-                enzymecuts.append((cuts, e))
-            enzymecuts.sort()
-            enzymes = [e for (c, e) in enzymecuts if c]
-        else:
-            # argument is probably a list of restriction enzymes
-            enzymes = [
-                e
-                for e in list(dict.fromkeys(_flatten(enzymes)))
-                if e.search(_Seq(pad + dsseq.watson + dsseq.watson[: e.size - 1] + pad) if self.circular else dsseq)
-            ]  # flatten
 
-        if not enzymes:
-            return ()
+    def get_cutsite_pairs(self, cutsites):
+        """ Returns pairs of cutsites that render the edges of the resulting fragments.
+
+        A fragment produced by restriction is represented by a tuple of length 2 that
+        may contain cutsites or `None`:
 
+            - Two cutsites: represents the extraction of a fragment between those two
+              cutsites, in that orientation. To represent the opening of a circular
+              molecule with a single cutsite, we put the same cutsite twice.
+            - `None`, cutsite: represents the extraction of a fragment between the left
+              edge of linear sequence and the cutsite.
+            - cutsite, `None`: represents the extraction of a fragment between the cutsite
+              and the right edge of a linear sequence.
+
+        Parameters
+        ----------
+        cutsites : list[tuple[tuple[int,int], _RestrictionType]]
+
+        Returns
+        -------
+        list[tuple[tuple[tuple[int,int], _RestrictionType]|None],tuple[tuple[int,int], _RestrictionType]|None]
+
+        Examples
+        --------
+
+        >>> from Bio.Restriction import EcoRI
+        >>> from pydna.dseq import Dseq
+        >>> dseq = Dseq('aaGAATTCaaGAATTCaa')
+        >>> cutsites = dseq.get_cutsites([EcoRI])
+        >>> cutsites
+        [((3, -4), EcoRI), ((11, -4), EcoRI)]
+        >>> dseq.get_cutsite_pairs(cutsites)
+        [(None, ((3, -4), EcoRI)), (((3, -4), EcoRI), ((11, -4), EcoRI)), (((11, -4), EcoRI), None)]
+
+        >>> dseq = Dseq('TTCaaGAA', circular=True)
+        >>> cutsites = dseq.get_cutsites([EcoRI])
+        >>> cutsites
+        [((6, -4), EcoRI)]
+        >>> dseq.get_cutsite_pairs(cutsites)
+        [(((6, -4), EcoRI), ((6, -4), EcoRI))]
+        """
+        if len(cutsites) == 0:
+            return []
         if not self.circular:
-            frags = [self]
+            cutsites = [None, *cutsites, None]
         else:
-            ln = len(self)
-            for e in enzymes:
-                wpos = [x - len(pad) - 1 for x in e.search(_Seq(pad + self.watson + self.watson[: e.size - 1]) + pad)][
-                    ::-1
-                ]
-                cpos = [x - len(pad) - 1 for x in e.search(_Seq(pad + self.crick + self.crick[: e.size - 1]) + pad)][
-                    ::-1
-                ]
-
-                for w, c in _itertools.product(wpos, cpos):
-                    if w % len(self) == (self.length - c + e.ovhg) % len(self):
-                        frags = [
-                            Dseq(
-                                self.watson[w % ln :] + self.watson[: w % ln],
-                                self.crick[c % ln :] + self.crick[: c % ln],
-                                ovhg=e.ovhg,
-                                pos=min(w, len(dsseq) - c),
-                            )
-                        ]
-                        # breakpoint()
-                        break
-                else:
-                    continue
-                break
+            # Add the first cutsite at the end, for circular cuts
+            cutsites.append(cutsites[0])
 
-        newfrags = []
-
-        # print(repr(frags[0]))
-        # print(frags[0].pos)
-
-        for enz in enzymes:
-            for frag in frags:
-                ws = [x - 1 for x in enz.search(_Seq(frag.watson + "n"))]
-                cs = [x - 1 for x in enz.search(_Seq(frag.crick + "n"))]
-
-                sitepairs = [
-                    (sw, sc)
-                    for sw, sc in _itertools.product(ws, cs[::-1])
-                    if (
-                        sw + max(0, frag.ovhg) - max(0, enz.ovhg)
-                        == len(frag.crick) - sc - min(0, frag.ovhg) + min(0, enz.ovhg)
-                    )
-                ]
-
-                sitepairs.append((self.length, 0))
-
-                w2, c1 = sitepairs[0]
-                newfrags.append(Dseq(frag.watson[:w2], frag.crick[c1:], ovhg=frag.ovhg, pos=frag.pos))
-
-                for (w1, c2), (w2, c1) in zip(sitepairs[:-1], sitepairs[1:]):
-                    newfrags.append(
-                        Dseq(
-                            frag.watson[w1:w2],
-                            frag.crick[c1:c2],
-                            ovhg=enz.ovhg,
-                            pos=frag.pos + w1 - max(0, enz.ovhg) + max(0, frag.ovhg),
-                        )
-                    )
-            frags = newfrags
-            newfrags = []
-
-        return tuple(frags)
-
-    def _firstcut(self, *enzymes):
-        rb = _RestrictionBatch(_flatten(enzymes))
-        watson = _FormattedSeq(_Seq(self.watson), linear=False)
-        crick = _FormattedSeq(_Seq(self.crick), linear=False)
-        enzdict = dict(sorted(rb.search(watson).items(), key=_itemgetter(1)))
-        ln = self.length
-        for enzyme, wposlist in enzdict.items():
-            for cpos in enzyme.search(crick)[::-1]:
-                for wpos in wposlist:
-                    if cpos == (ln - wpos + enzyme.ovhg + 2) or ln:
-                        return (wpos - 1, cpos - 1, enzyme.ovhg)
-        return ()
+        return list(zip(cutsites, cutsites[1:]))
 
 
 if __name__ == "__main__":
diff --git a/src/pydna/dseqrecord.py b/src/pydna/dseqrecord.py
index d02ff319..81b3c8cb 100644
--- a/src/pydna/dseqrecord.py
+++ b/src/pydna/dseqrecord.py
@@ -15,11 +15,12 @@
 from Bio.Restriction import CommOnly
 from pydna.dseq import Dseq as _Dseq
 from pydna._pretty import pretty_str as _pretty_str
-from pydna.utils import flatten as _flatten
+from pydna.utils import flatten as _flatten, location_boundaries as _location_boundaries
 
 # from pydna.utils import memorize as _memorize
 from pydna.utils import rc as _rc
 from pydna.utils import shift_location as _shift_location
+from pydna.utils import shift_feature as _shift_feature
 from pydna.common_sub_strings import common_sub_strings as _common_sub_strings
 from Bio.SeqFeature import SeqFeature as _SeqFeature
 from Bio import SeqIO
@@ -827,10 +828,22 @@ def __getitem__(self, sl):
         sl_stop = sl.stop or len(self.seq)  # 1
 
         if not self.circular or sl_start < sl_stop:
+            # TODO: special case for sl_end == 0 in circular sequences
+            # related to https://github.com/BjornFJohansson/pydna/issues/161
+            if self.circular and sl.stop == 0:
+                sl = slice(sl.start, len(self.seq), sl.step)
             answer.features = super().__getitem__(sl).features
         elif self.circular and sl_start > sl_stop:
             answer.features = self.shifted(sl_start).features
-            answer.features = [f for f in answer.features if f.location.parts[-1].end <= answer.seq.length]
+            # origin-spanning features should only be included after shifting
+            # in cases where the slice comprises the entire sequence, but then
+            # sl_start == sl_stop and the second condition is not met
+            answer.features = [f for f in answer.features if (
+                               _location_boundaries(f.location)[1] <= answer.seq.length and
+                               _location_boundaries(f.location)[0] < _location_boundaries(f.location)[1])]
+        elif self.circular and sl_start == sl_stop:
+            cut = ((sl_start, 0), None)
+            return self.apply_cut(cut, cut)
         else:
             answer = Dseqrecord("")
         identifier = "part_{id}".format(id=self.id)
@@ -1208,7 +1221,7 @@ def shifted(self, shift):
             raise TypeError("Sequence is linear, origin can only be " "shifted for circular sequences.\n")
         ln = len(self)
         if not shift % ln:
-            return self  # shift is a multiple of ln or 0
+            return _copy.deepcopy(self)  # shift is a multiple of ln or 0
         else:
             shift %= ln  # 0<=shift<=ln
         newseq = (self.seq[shift:] + self.seq[:shift]).looped()
@@ -1216,7 +1229,7 @@ def shifted(self, shift):
         for feature in newfeatures:
             feature.location = _shift_location(feature.location, -shift, ln)
         newfeatures.sort(key=_operator.attrgetter("location.start"))
-        answer = _copy.copy(self)
+        answer = _copy.deepcopy(self)
         answer.features = newfeatures
         answer.seq = newseq
         return answer
@@ -1258,47 +1271,82 @@ def cut(self, *enzymes):
 
 
         """
-        from pydna.utils import shift_location
 
-        features = _copy.deepcopy(self.features)
+        cutsites = self.seq.get_cutsites(*enzymes)
+        cutsite_pairs = self.seq.get_cutsite_pairs(cutsites)
+        return tuple(self.apply_cut(*cs) for cs in cutsite_pairs)
 
-        if self.circular:
-            try:
-                x, y, oh = self.seq._firstcut(*enzymes)
-            except ValueError:
-                return ()
-            dsr = _Dseq(
-                self.seq.watson[x:] + self.seq.watson[:x],
-                self.seq.crick[y:] + self.seq.crick[:y],
-                oh,
-            )
-            newstart = min(x, (self.seq.length - y))
-            for f in features:
-                f.location = shift_location(f.location, -newstart, self.seq.length)
-                f.location, *rest = f.location.parts
-                for part in rest:
-                    if 0 in part:
-                        f.location._end = part.end + self.seq.length
-                    else:
-                        f.location += part
-            frags = dsr.cut(enzymes) or [dsr]
+    def apply_cut(self, left_cut, right_cut):
+        dseq = self.seq.apply_cut(left_cut, right_cut)
+        # TODO: maybe remove depending on https://github.com/BjornFJohansson/pydna/issues/161
+
+        if left_cut == right_cut:
+            # Not really a cut, but to handle the general case
+            if left_cut is None:
+                features = _copy.deepcopy(self.features)
+            else:
+                # The features that span the origin if shifting with left_cut, but that do not cross
+                # the cut site should be included, and if there is a feature within the cut site, it should
+                # be duplicated. See https://github.com/BjornFJohansson/pydna/issues/180 for a practical example.
+                #
+                # Let's say we are going to open a circular plasmid like below (| inidicate cuts, numbers indicate
+                # features)
+                #
+                #    3333|3
+                #    1111
+                #     000
+                # XXXXatg|YYY
+                # XXX|tacYYYY
+                #     000
+                #     2222
+                #
+                left_watson, left_crick, left_ovhg = self.seq.get_cut_parameters(left_cut, True)
+                initial_shift = left_watson if left_ovhg < 0 else left_crick
+                features = self.shifted(initial_shift).features
+                # for f in features:
+                #     print(f.id, f.location, _location_boundaries(f.location))
+                # Here, we have done what's shown below (* indicates the origin).
+                # The features 0 and 2 have the right location for the final product:
+                #
+                #    3*3333
+                #    1*111
+                # XXXX*atgYYY
+                # XXXX*tacYYY
+                #      000
+                #      2222
+
+                features_need_transfer = [f for f in features if (_location_boundaries(f.location)[1] <= abs(left_ovhg))]
+                features_need_transfer = [_shift_feature(f, -abs(left_ovhg), len(self)) for f in features_need_transfer]
+                #                                           ^                ^^^^^^^^^
+                # Now we have shifted the features that end before the cut (0 and 1, but not 3), as if
+                # they referred to the below sequence (* indicates the origin):
+                #
+                #    1111
+                #     000
+                # XXXXatg*YYY
+                # XXXXtac*YYY
+                #
+                # The features 0 and 1 would have the right location if the final sequence had the same length
+                # as the original one. However, the final product is longer because of the overhang.
+
+                features += [_shift_feature(f, abs(left_ovhg), len(dseq)) for f in features_need_transfer]
+                #                             ^                ^^^^^^^^^
+                # So we shift back by the same amount in the opposite direction, but this time we pass the 
+                # length of the final product.
+                # print(*features, sep='\n')
+                # Features like 3 are removed here
+                features = [f for f in features if (
+                               _location_boundaries(f.location)[1] <= len(dseq) and
+                               _location_boundaries(f.location)[0] <= _location_boundaries(f.location)[1])]
         else:
-            frags = self.seq.cut(enzymes)
-            if not frags:
-                return ()
-        dsfs = []
-        for fr in frags:
-            dsf = Dseqrecord(fr, n=self.n)
-            start = fr.pos
-            end = fr.pos + fr.length
-            dsf.features = [
-                _copy.deepcopy(fe) for fe in features if start <= fe.location.start and end >= fe.location.end
-            ]
-            for feature in dsf.features:
-                feature.location += -start
-            dsfs.append(dsf)
-        return tuple(dsfs)
+            left_watson, left_crick, left_ovhg = self.seq.get_cut_parameters(left_cut, True)
+            right_watson, right_crick, right_ovhg = self.seq.get_cut_parameters(right_cut, False)
+
+            left_edge = left_crick if left_ovhg > 0 else left_watson
+            right_edge = right_watson if right_ovhg > 0 else right_crick
+            features = self[left_edge:right_edge].features
 
+        return Dseqrecord(dseq, features=features)
 
 if __name__ == "__main__":
     cache = _os.getenv("pydna_cache")
diff --git a/src/pydna/utils.py b/src/pydna/utils.py
index e7c8e221..08c593de 100644
--- a/src/pydna/utils.py
+++ b/src/pydna/utils.py
@@ -18,6 +18,8 @@
 import keyword as _keyword
 import collections as _collections
 import itertools as _itertools
+from copy import deepcopy as _deepcopy
+from typing import Union as _Union
 
 import sys as _sys
 import re
@@ -40,22 +42,36 @@ def shift_location(original_location, shift, lim):
     """docstring."""
     newparts = []
     strand = original_location.strand
+
     for part in original_location.parts:
-        ns = (part.start + shift) % lim
-        ne = (part.end + shift) % lim or lim
-        oe = newparts[-1].end if newparts else None
+        new_start = (part.start + shift) % lim
+        new_end = (part.end + shift) % lim or lim
+        old_start, old_end = (newparts[-1].start, newparts[-1].end) if len(newparts) else (None, None)
+
+        # The "join with old" cases are for features with multiple parts
+        # in which consecutive parts do not have any bases between them.
+        # This type of feature is generated to represent a feature that
+        # spans the origin of a circular sequence. See more details in
+        # https://github.com/BjornFJohansson/pydna/issues/195
+
         if len(part) == 0:
-            newparts.append(_sl(ns, ns, strand))
+            newparts.append(_sl(new_start, new_start, strand))
             continue
-        elif oe == ns:
+        # Join with old, case 1
+        elif strand != -1 and old_end == new_start:
             part = newparts.pop()
-            part._end = ne
-            ns = part.start
-        if ns < ne:
-            newparts.append(_sl(ns, ne, strand))
+            part._end = new_end
+            new_start = part.start
+        # Join with old, case 2
+        elif strand == -1 and old_start == new_end:
+            part = newparts.pop()
+            part._start = new_start
+            new_end = part.end
+        if new_start < new_end:
+            newparts.append(_sl(new_start, new_end, strand))
         else:
-            parttuple = (_sl(ns, lim, strand), _sl(0, ne, strand))
-            newparts.extend(parttuple if strand == 1 else parttuple[::-1])
+            parttuple = (_sl(new_start, lim, strand), _sl(0, new_end, strand))
+            newparts.extend(parttuple if strand != -1 else parttuple[::-1])
     try:
         newloc = _cl(newparts)
     except ValueError:
@@ -63,6 +79,14 @@ def shift_location(original_location, shift, lim):
     assert len(newloc) == len(original_location)
     return newloc
 
+def shift_feature(feature, shift, lim):
+    """Return a new feature with shifted location."""
+    # TODO: Missing tests
+    new_location = shift_location(feature.location, shift, lim)
+    new_feature = _deepcopy(feature)
+    new_feature.location = new_location
+    return new_feature
+
 
 # def smallest_rotation(s):
 #     """Smallest rotation of a string.
@@ -570,6 +594,37 @@ def eq(*args, **kwargs):
                 same = False
     return same
 
+def cuts_overlap(left_cut, right_cut, seq_len):
+    # Special cases:
+    if left_cut is None or right_cut is None or left_cut == right_cut:
+        return False
+
+    # This block of code would not be necessary if the cuts were
+    # initially represented like this
+    (left_watson, left_ovhg), _ = left_cut
+    (right_watson, right_ovhg), _ = right_cut
+    # Position of the cut on the crick strands on the left and right
+    left_crick = left_watson - left_ovhg
+    right_crick = right_watson - right_ovhg
+    if left_crick >= seq_len:
+        left_crick -= seq_len
+        left_watson -= seq_len
+    if right_crick >= seq_len:
+        right_crick -= seq_len
+        right_watson -= seq_len
+
+    # Convert into ranges x and y and see if ranges overlap
+    x = sorted([left_watson, left_crick])
+    y = sorted([right_watson, right_crick])
+    return (x[1] > y[0]) != (y[1] < x[0])
+
+def location_boundaries(loc: _Union[_sl,_cl]):
+
+    if loc.strand == -1:
+        return loc.parts[-1].start, loc.parts[0].end
+    else:
+        return loc.parts[0].start, loc.parts[-1].end
+
 
 if __name__ == "__main__":
     cached = _os.getenv("pydna_cached_funcs", "")
diff --git a/tests/test_module_dseq.py b/tests/test_module_dseq.py
index 9b0bbef0..524abd3a 100644
--- a/tests/test_module_dseq.py
+++ b/tests/test_module_dseq.py
@@ -62,7 +62,8 @@ def test_cut1():
 
     assert first + second + third + fourth == lds
 
-    assert (first.pos, second.pos, third.pos, fourth.pos) == (0, 4, 13, 22)
+    # TODO: remove
+    # assert (first.pos, second.pos, third.pos, fourth.pos) == (0, 4, 13, 22)
 
     frags2 = lds.cut((KpnI, ApaI, TaiI))
 
@@ -70,7 +71,8 @@ def test_cut1():
 
     assert first2 + second2 + third2 + fourth2 == lds
 
-    assert (first2.pos, second2.pos, third2.pos, fourth2.pos) == (0, 4, 13, 21)
+    # TODO: remove
+    # assert (first2.pos, second2.pos, third2.pos, fourth2.pos) == (0, 4, 13, 21)
 
 
 def test_cas9():
@@ -164,6 +166,7 @@ def cut_and_religate_Dseq(seq_string, enz, top):
         if not frags:
             return
         a = frags.pop(0)
+
         for f in frags:
             a += f
         if not top:
@@ -540,12 +543,12 @@ def test_dseq():
     assert obj.cut(rb) == obj.cut(BamHI, BglII) == obj.cut(BglII, BamHI)
 
     obj = Dseq("ggatccAGATCT", circular=True)
-
-    assert obj.cut(rb) == obj.cut(BamHI, BglII) != obj.cut(BglII, BamHI)
+    # TODO: address this test change Related to https://github.com/BjornFJohansson/pydna/issues/78
+    assert obj.cut(rb) == obj.cut(BamHI, BglII) == obj.cut(BglII, BamHI)
 
     obj = Dseq("AGATCTggatcc", circular=True)
 
-    assert obj.cut(rb) == obj.cut(BglII, BamHI) != obj.cut(BamHI, BglII)
+    assert obj.cut(rb) == obj.cut(BglII, BamHI) == obj.cut(BamHI, BglII)
 
 
 def test_Dseq_slicing():
@@ -574,7 +577,7 @@ def test_Dseq_slicing2():
     from Bio.Restriction import BamHI, EcoRI, KpnI
 
     a = Dseq("aaGGATCCnnnnnnnnnGAATTCccc", circular=True)
-
+    # TODO: address this test change Related to https://github.com/BjornFJohansson/pydna/issues/78
     assert (
         a.cut(
             EcoRI,
@@ -585,7 +588,7 @@ def test_Dseq_slicing2():
             BamHI,
             EcoRI,
             KpnI,
-        )[::-1]
+        )
     )
 
 
@@ -606,6 +609,12 @@ def test_Dseq___getitem__():
     assert s[9:1] == Dseq("")
     assert t[9:1] == Dseq("")
 
+    # Indexing of full circular molecule (https://github.com/BjornFJohansson/pydna/issues/161)
+    s = Dseq("GGATCC", circular=True)
+    str_seq = str(s)
+    for shift in range(len(s)):
+        assert str(s[shift : shift]) == str_seq[shift:] + str_seq[:shift]
+
 
 def test_cut_circular():
     from pydna.dseq import Dseq
@@ -706,6 +715,10 @@ def test_shifted():
     with pytest.raises(TypeError):
         b.shifted(1)
 
+    # Shifted with zero gives a copy of the sequence, not the same sequence
+    assert a.shifted(0) == a
+    assert a.shifted(0) is not a
+
 
 def test_misc():
     from pydna.dseq import Dseq
@@ -717,8 +730,8 @@ def test_misc():
     a, b = x.cut(NotI)
 
     z = (a + b).looped()
-
-    assert z.shifted(5) == x
+    # TODO: address this test change Related to https://github.com/BjornFJohansson/pydna/issues/78
+    assert z.shifted(-6) == x
 
 
 def test_cut_missing_enzyme():
@@ -785,5 +798,254 @@ def test_from_full_sequence_and_overhangs():
         assert dseq_2.watson_ovhg() == watson_ovhg
 
 
+def test_right_end_position():
+
+    from pydna.dseq import Dseq
+
+    test_cases = [
+        ("AAA", "TT", (3, 2)),
+        ("AA", "TTT", (2, 3)),
+        ("AAA", "TTT", (3, 3)),
+    ]
+    for watson, crick, expected in test_cases:
+        dseq = Dseq(watson, crick, ovhg=0, circular=False)
+        assert dseq.right_end_position() == expected
+
+def test_left_end_position():
+
+    from pydna.dseq import Dseq
+
+    test_cases = [
+        ("AAA", "TT", (0, 1), -1),
+        ("AA", "TTT", (1, 0), 1),
+        ("AAT", "TTT", (0, 0), 0),
+    ]
+    for watson, crick, expected, ovhg in test_cases:
+        dseq = Dseq(watson, crick, ovhg=ovhg, circular=False)
+        assert dseq.left_end_position() == expected
+
+
+def test_apply_cut():
+    from pydna.dseq import Dseq
+
+    seq = Dseq('aaGAATTCaa', circular=False)
+
+    # A cut where both sides are None returns the same sequence
+    assert seq.apply_cut(None, None) == seq
+
+    # A cut where one side is None leaves that side intact
+    EcoRI_cut = ((3, -4), None)
+    assert seq.apply_cut(None, EcoRI_cut) == Dseq.from_full_sequence_and_overhangs('aaGAATT', watson_ovhg=-4, crick_ovhg=0)
+    assert seq.apply_cut(EcoRI_cut, None) == Dseq.from_full_sequence_and_overhangs('AATTCaa', watson_ovhg=0, crick_ovhg=-4)
+
+    # It respects the original overhang
+    seq = Dseq.from_full_sequence_and_overhangs('aaGAATTCaa', watson_ovhg=1, crick_ovhg=1)
+    assert seq.apply_cut(None, EcoRI_cut) == Dseq.from_full_sequence_and_overhangs('aaGAATT', watson_ovhg=-4, crick_ovhg=1)
+    assert seq.apply_cut(EcoRI_cut, None) == Dseq.from_full_sequence_and_overhangs('AATTCaa', watson_ovhg=1, crick_ovhg=-4)
+
+    seq = Dseq.from_full_sequence_and_overhangs('aaGAATTCaa', watson_ovhg=-1, crick_ovhg=-1)
+    assert seq.apply_cut(None, EcoRI_cut) == Dseq.from_full_sequence_and_overhangs('aaGAATT', watson_ovhg=-4, crick_ovhg=-1)
+    assert seq.apply_cut(EcoRI_cut, None) == Dseq.from_full_sequence_and_overhangs('AATTCaa', watson_ovhg=-1, crick_ovhg=-4)
+
+    # A repeated cut in a circular molecule opens it up
+    seq = Dseq('aaGAATTCaa', circular=True)
+    assert seq.apply_cut(EcoRI_cut, EcoRI_cut) == Dseq.from_full_sequence_and_overhangs('AATTCaaaaGAATT', watson_ovhg=-4, crick_ovhg=-4)
+
+    # Two cuts extract a subsequence
+    seq = Dseq('aaGAATTCaaGAATTCaa', circular=True)
+    EcoRI_cut_2 = ((11, -4), None)
+    assert seq.apply_cut(EcoRI_cut, EcoRI_cut_2) == Dseq.from_full_sequence_and_overhangs('AATTCaaGAATT', watson_ovhg=-4, crick_ovhg=-4)
+
+    # Overlapping cuts should return an error
+    seq = Dseq('aaGAATTCaa', circular=True)
+    first_cuts = [
+        ((3, -4), None),
+        ((7, 4), None),
+        # Spanning the origin
+        ((9, -8), None),
+        ((8, 8), None),
+        ]
+    overlapping_cuts = [
+        ((4, -4), None),
+        ((2, -4), None),
+        ((2, -6), None),
+        ((8, 4), None),
+        ((6, 4), None),
+        ((8, 6), None),
+        # Spanning the origin
+        ((7, -8), None),
+        ((6, 8), None),
+    ]
+
+    for first_cut in first_cuts:
+        for second_cut in overlapping_cuts:
+            try:
+                seq.apply_cut(first_cut, second_cut)
+            except ValueError as e:
+                assert e.args[0] == 'Cuts overlap'
+            else:
+                print(first_cut, second_cut)
+                assert False, 'Expected ValueError'
+
+    # Rotating the sequence, apply the same cut
+    seq = Dseq('acgtATGaatt', circular=True)
+    for shift in range(len(seq)):
+        seq_shifted = seq.shifted(shift)
+        start = 4 - shift
+        if start < 0:
+            start += len(seq)
+        # Cut with negative ovhg
+        new_cut = ((start, -3), None)
+        out = seq_shifted.apply_cut(new_cut, new_cut)
+        assert str(out) == 'ATGaattacgtATG'
+
+        # Cut with positive ovhg
+        start = (start + 3) % len(seq)
+        new_cut = ((start, 3), None)
+        out = seq_shifted.apply_cut(new_cut, new_cut)
+        assert str(out) == 'ATGaattacgtATG'
+
+        # A blunt cut
+        start = 4 - shift
+        new_cut = ((start, 0), None)
+        out = seq_shifted.apply_cut(new_cut, new_cut)
+        assert str(out) == 'ATGaattacgt'
+
+
+def test_cutsite_is_valid():
+
+    from pydna.dseq import Dseq
+    from Bio.Restriction import EcoRI, BsaI, PacI, NmeDI, Acc65I, NotI, BamHI, EcoRV
+
+    # Works for circular case
+    seqs = ["GAATTC", "TTAATTAAC", "GATATC"]
+    enzs = [EcoRI, PacI, EcoRV]
+    for seq, enz in zip(seqs, enzs):
+        dseq = Dseq(seq, circular=True)
+        for shift in range(len(seq)):
+            dseq_shifted = dseq.shifted(shift)
+            cutsite, = dseq_shifted.get_cutsites([enz])
+            assert dseq_shifted.cutsite_is_valid(cutsite)
+
+    # Works for overhangs
+    seqs = ["GAATTC", "TTAATTAA", "GATATC"]
+    for seq, enz in zip(seqs, enzs):
+        for ovhg in [-1, 0, 1]:
+            dseq = Dseq.from_full_sequence_and_overhangs(seq, ovhg, 0)
+            if ovhg != 0:
+                assert len(dseq.get_cutsites([enz])) == 0
+            else:
+                assert len(dseq.get_cutsites([enz])) == 1
+
+            dseq = Dseq.from_full_sequence_and_overhangs(seq, 0, ovhg)
+            if ovhg != 0:
+                assert len(dseq.get_cutsites([enz])) == 0
+            else:
+                assert len(dseq.get_cutsites([enz])) == 1
+
+    # Special cases:
+    dseq = Dseq.from_full_sequence_and_overhangs('AAAAAAAAAAAAAGCCGGCAAAAAAAAAAAA', 0, 0)
+    assert len(dseq.get_cutsites([NmeDI])) == 2
+    # Remove left cutting place
+    assert len(dseq[2:].get_cutsites([NmeDI])) == 1
+    # Remove right cutting place
+    assert len(dseq[:-2].get_cutsites([NmeDI])) == 1
+    # Remove both cutting places
+    assert len(dseq[2:-2].get_cutsites([NmeDI])) == 0
+
+    # overhang left side
+    dseq = Dseq.from_full_sequence_and_overhangs('AAAAAAAAAAAAAGCCGGCAAAAAAAAAAAA', -2, 0)
+    assert len(dseq.get_cutsites([NmeDI])) == 1
+    dseq = Dseq.from_full_sequence_and_overhangs('AAAAAAAAAAAAAGCCGGCAAAAAAAAAAAA', 2, 0)
+    assert len(dseq.get_cutsites([NmeDI])) == 1
+
+    # overhang right side
+    dseq = Dseq.from_full_sequence_and_overhangs('AAAAAAAAAAAAAGCCGGCAAAAAAAAAAAA', 0, 2)
+    assert len(dseq.get_cutsites([NmeDI])) == 1
+    dseq = Dseq.from_full_sequence_and_overhangs('AAAAAAAAAAAAAGCCGGCAAAAAAAAAAAA', 0, -2)
+    assert len(dseq.get_cutsites([NmeDI])) == 1
+
+    # overhang both sides
+    dseq = Dseq.from_full_sequence_and_overhangs('AAAAAAAAAAAAAGCCGGCAAAAAAAAAAAA', 2, 2)
+    assert len(dseq.get_cutsites([NmeDI])) == 0
+    dseq = Dseq.from_full_sequence_and_overhangs('AAAAAAAAAAAAAGCCGGCAAAAAAAAAAAA', -2, -2)
+    assert len(dseq.get_cutsites([NmeDI])) == 0
+
+    # overhang on recognition site removes both cutting places
+    dseq = Dseq.from_full_sequence_and_overhangs('AAAAAAAAAAAAAGCCGGCAAAAAAAAAAAA', 16, 0)
+    assert len(dseq.get_cutsites([NmeDI])) == 0
+    dseq = Dseq.from_full_sequence_and_overhangs('AAAAAAAAAAAAAGCCGGCAAAAAAAAAAAA', 0, 16)
+    assert len(dseq.get_cutsites([NmeDI])) == 0
+
+def test_get_cutsite_pairs():
+    from pydna.dseq import Dseq
+
+    # in the test, we replace cuts by integers for clarity.
+
+    dseq = Dseq('A')
+
+    # Empty returns empty list
+    assert dseq.get_cutsite_pairs([]) == []
+
+    # Single cut on linear seq returns two fragments
+    assert dseq.get_cutsite_pairs([1]) == [(None, 1), (1, None)]
+
+    # Two cuts on linear seq return three fragments
+    assert dseq.get_cutsite_pairs([1, 2]) == [(None, 1), (1, 2), (2, None)]
+
+    dseq = Dseq('A', circular=True)
+
+    # Empty returns empty list
+    assert dseq.get_cutsite_pairs([]) == []
+
+    # Single cut on circular seq returns opened molecule
+    assert dseq.get_cutsite_pairs([1]) == [(1, 1)]
+
+    # Two cuts on circular seq return 2 fragments
+    assert dseq.get_cutsite_pairs([1, 2]) == [(1, 2), (2, 1)]
+
+def test_get_cut_parameters():
+
+    from pydna.dseq import Dseq
+
+    dseq = Dseq.from_full_sequence_and_overhangs('aaaACGTaaa', 3, 3)
+    assert dseq.get_cut_parameters(None, True) == (*dseq.left_end_position(), dseq.ovhg)
+    assert dseq.get_cut_parameters(None, False) == (*dseq.right_end_position(), dseq.watson_ovhg())
+
+    assert dseq.get_cut_parameters(((4, -2), None), True) == (4, 6, -2)
+    assert dseq.get_cut_parameters(((4, -2), None), False) == (4, 6, -2)
+    assert dseq.get_cut_parameters(((6, 2), None), True) == (6, 4, 2)
+    assert dseq.get_cut_parameters(((6, 2), None), False) == (6, 4, 2)
+
+    dseq = Dseq('aaaACGTaaa', circular=True)
+
+    # None cannot be used on circular molecules
+    try:
+        assert dseq.get_cut_parameters(None, True) == (*dseq.left_end_position(), dseq.ovhg)
+    except AssertionError as e:
+        assert e.args[0] == 'Circular sequences should not have None cuts'
+    else:
+        assert False, 'Expected AssertionError'
+
+    try:
+        assert dseq.get_cut_parameters(None, False) == (*dseq.right_end_position(), dseq.watson_ovhg())
+    except AssertionError as e:
+        assert e.args[0] == 'Circular sequences should not have None cuts'
+    else:
+        assert False, 'Expected AssertionError'
+
+    # "Normal" cuts
+    assert dseq.get_cut_parameters(((4, -2), None), True) == (4, 6, -2)
+    assert dseq.get_cut_parameters(((4, -2), None), False) == (4, 6, -2)
+    assert dseq.get_cut_parameters(((6, 2), None), True) == (6, 4, 2)
+    assert dseq.get_cut_parameters(((6, 2), None), False) == (6, 4, 2)
+
+    # Origin-spannign cuts
+    assert dseq.get_cut_parameters(((9, -2), None), True) == (9, 1, -2)
+    assert dseq.get_cut_parameters(((9, -2), None), False) == (9, 1, -2)
+    assert dseq.get_cut_parameters(((1, 2), None), True) == (1, 9, 2)
+    assert dseq.get_cut_parameters(((1, 2), None), False) == (1, 9, 2)
+
+
 if __name__ == "__main__":
     pytest.main([__file__, "-vv", "-s"])
diff --git a/tests/test_module_dseqrecord.py b/tests/test_module_dseqrecord.py
index 3dc47a21..da9fbdbf 100644
--- a/tests/test_module_dseqrecord.py
+++ b/tests/test_module_dseqrecord.py
@@ -1,7 +1,6 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
 
-import pydna
 import pytest
 from pydna import _PydnaWarning
 
@@ -801,6 +800,9 @@ def test_Dseqrecord_cutting_adding_2():
     for enz in enzymes:
         for f in a:
             b, c, d = f.cut(enz)
+            print(b.seq.__repr__())
+            print(c.seq.__repr__())
+            print(d.seq.__repr__())
             e = b + c + d
             assert str(e.seq).lower() == str(f.seq).lower()
 
@@ -1104,6 +1106,12 @@ def test_features_change_ori():
     from pydna.readers import read
     from pydna.utils import eq
 
+    # Shifted a sequence by zero returns a copy
+    s = Dseqrecord("GGATCC", circular=True)
+    assert s.shifted(0) == s
+    assert s.shifted(0) is not s
+
+
     s1 = read(
         """
         LOCUS       New_DNA                   13 bp ds-DNA     circular     08-JAN-2018
@@ -1597,30 +1605,32 @@ def test_figure():
     assert circularDseqrecord.extract_feature(0).seq == feat
 
     a22, b22 = circularDseqrecord.cut(KpnI, Bsp120I)
+
+    # Passes the tests if changed to "Dseqrecord(-18)\n    cgatcgatcG    \ncatg\x1b[48;5;11mgctagctagC\x1b[0mCCGG"
     assert (
         b22.figure()
-        == "Dseqrecord(-18)\n    cgatcgatcG    \ncatg\x1b[48;5;11mgctag\x1b[0m\x1b[48;5;11mctagC\x1b[0mCCGG"
+        == "Dseqrecord(-18)\n    cgatcgatcG    \ncatg\x1b[48;5;11mgctagctagC\x1b[0mCCGG"
     )
     assert b22.extract_feature(0).seq == feat
 
     a23, b23 = circularDseqrecord.cut(KpnI, ApaI)
     assert (
         b23.figure()
-        == "Dseqrecord(-18)\n    cgatcgatcGGGCC\ncatg\x1b[48;5;11mgctag\x1b[0m\x1b[48;5;11mctagC\x1b[0m    "
+        == "Dseqrecord(-18)\n    cgatcgatcGGGCC\ncatg\x1b[48;5;11mgctagctagC\x1b[0m    "
     )
     assert b23.extract_feature(0).seq == feat
 
     a24, b24 = circularDseqrecord.cut(Acc65I, Bsp120I)
     assert (
         b24.figure()
-        == "Dseqrecord(-18)\ngtaccgatcgatcG    \n    \x1b[48;5;11mgctag\x1b[0m\x1b[48;5;11mctagC\x1b[0mCCGG"
+        == "Dseqrecord(-18)\ngtaccgatcgatcG    \n    \x1b[48;5;11mgctagctagC\x1b[0mCCGG"
     )
     assert b24.extract_feature(0).seq == feat
 
     a25, b25 = circularDseqrecord.cut(Acc65I, ApaI)
     assert (
         b25.figure()
-        == "Dseqrecord(-18)\ngtaccgatcgatcGGGCC\n    \x1b[48;5;11mgctag\x1b[0m\x1b[48;5;11mctagC\x1b[0m    "
+        == "Dseqrecord(-18)\ngtaccgatcgatcGGGCC\n    \x1b[48;5;11mgctagctagC\x1b[0m    "
     )
     assert b25.extract_feature(0).seq == feat
 
@@ -1642,10 +1652,11 @@ def test_jan_glx():
     puc19_ = (bb + insert).looped().synced(puc19)
     assert puc19_.seguid() == "cdseguid-zhw8Yrxfo3FO5DDccx4PamBVPCQ"
 
-    # print(puc19_.extract_feature(2), "\n")
-    # print(puc19.extract_feature(6))
-
+    # Some features are lost because they spanned the cutting sites in puc19.
+    assert puc19_.extract_feature(0).seq == puc19.extract_feature(2).seq
+    assert puc19_.extract_feature(1).seq == puc19.extract_feature(4).seq
     assert puc19_.extract_feature(2).seq == puc19.extract_feature(6).seq
+    assert puc19_.extract_feature(3).seq == puc19.extract_feature(7).seq
 
 
 def test_synced():
@@ -1841,6 +1852,7 @@ def test__repr_pretty_():
 
 def test___getitem__():
     from pydna.dseqrecord import Dseqrecord
+    from Bio.SeqFeature import SeqFeature, SimpleLocation
 
     s = Dseqrecord("GGATCC", circular=False)
     assert s[1:-1].seq == Dseqrecord("GATC", circular=False).seq
@@ -1852,13 +1864,32 @@ def test___getitem__():
     assert s[1:5].seq == Dseqrecord("GATC", circular=False).seq
     assert s[5:1:-1].seq == Dseqrecord("CCTA", circular=False).seq
 
-    assert t[1:1].seq == Dseqrecord("").seq
+    assert t[1:1].seq == Dseqrecord("GATCCG").seq
     assert t[5:1].seq == Dseqrecord("CG", circular=False).seq
     assert t[9:1].seq == Dseqrecord("").seq
     assert t[1:9].seq == Dseqrecord("").seq
     assert t[9:10].seq == Dseqrecord("").seq
     assert t[10:9].seq == Dseqrecord("").seq
 
+    # Test how slicing works with features (using sequence as in test_features_change_ori)
+    seqRecord = Dseqrecord("aaagGTACCTTTGGATCcggg", circular=True)
+    f1 = SeqFeature(SimpleLocation(4, 17, 1), type="misc_feature")
+    f2 = SeqFeature(SimpleLocation(17, 21, 1) + SimpleLocation(0, 4, 1), type="misc_feature")
+    seqRecord.features = [f1, f2]
+
+    # Exact feature sliced for normal and origin-spanning features
+    assert len(seqRecord[4:17].features) == 1
+    assert len(seqRecord[17:4].features) == 1
+
+    # Partial feature sliced for normal and origin-spanning features
+    assert len(seqRecord[2:20].features) == 1
+    assert len(seqRecord[13:8].features) == 1
+
+    # Indexing of full circular molecule (https://github.com/BjornFJohansson/pydna/issues/161)
+    s = Dseqrecord("GGATCC", circular=True)
+    str_seq = str(s.seq)
+    for shift in range(len(s)):
+        assert str(s[shift : shift].seq) == str_seq[shift:] + str_seq[:shift]
 
 def test___eq__():
     from pydna.dseqrecord import Dseqrecord
@@ -2223,6 +2254,37 @@ def test_assemble_YEp24PGK_XK():
     assert YEp24PGK_XK_correct.seguid() == "cdseguid-hEldsrUV0mBpISw8_xpvnpfYi0g"
     assert eq(YEp24PGK_XK, YEp24PGK_XK_correct)
 
+def test_apply_cut():
+
+    from pydna.dseqrecord import Dseqrecord
+    from Bio.SeqFeature import SeqFeature, SimpleLocation
+    from pydna.utils import location_boundaries as _location_boundaries
+
+    def find_feature_by_id(f: Dseqrecord, id: str) -> SeqFeature:
+        return next(f for f in f.features if f.id == id)
+    # Single cut case, check that features are transmitted correctly.
+    for strand in [1, -1, None]:
+        seq = Dseqrecord("acgtATGaatt", circular=True)
+        seq.features.append(SeqFeature(SimpleLocation(4, 7,  strand), id='full_overlap'))
+        seq.features.append(SeqFeature(SimpleLocation(3, 7,  strand), id='left_side'))
+        seq.features.append(SeqFeature(SimpleLocation(4, 8,  strand), id='right_side'))
+        seq.features.append(SeqFeature(SimpleLocation(3, 10, strand), id='throughout'))
+        for shift in range(len(seq)):
+            seq_shifted = seq.shifted(shift)
+            cut_feature = find_feature_by_id(seq_shifted, 'full_overlap')
+            start, end = _location_boundaries(cut_feature.location)
+            # Cut leaving + and - overhangs in the feature full_overlap
+            for dummy_cut in (((start, -3), None), ((end, 3), None)):
+                open_seq = seq_shifted.apply_cut(dummy_cut, dummy_cut)
+                assert len(open_seq.features) == 4
+                new_locs = sorted(str(f.location) for f in open_seq.features)
+                assert str(open_seq.seq) == 'ATGaattacgtATG'
+                if strand == 1:
+                    assert new_locs == sorted(['[0:3](+)', '[0:4](+)', '[11:14](+)', '[10:14](+)'])
+                elif strand == -1:
+                    assert new_locs == sorted(['[0:3](-)', '[0:4](-)', '[11:14](-)', '[10:14](-)'])
+                if strand == None:
+                    assert new_locs == sorted(['[0:3]', '[0:4]', '[11:14]', '[10:14]'])
 
 if __name__ == "__main__":
     args = [
diff --git a/tests/test_module_utils.py b/tests/test_module_utils.py
index 2351f368..fe6b2f01 100644
--- a/tests/test_module_utils.py
+++ b/tests/test_module_utils.py
@@ -463,5 +463,18 @@ def close(self):
     assert mf(1, kw=1) == ((1,), {"kw": 1})
 
 
+def test_shift_location():
+    from pydna.utils import shift_location
+    from Bio.SeqFeature import SimpleLocation
+
+    # TODO: more tests here
+
+    # Shifting of locations should be reversible (https://github.com/BjornFJohansson/pydna/issues/195)
+    for strand in (1, -1, None):
+        loc = SimpleLocation(0, 2, strand)
+        assert shift_location(shift_location(loc, 1, 6), -1, 6) == loc
+
+
+
 if __name__ == "__main__":
     pytest.main([__file__, "-vv", "-s"])