diff --git a/src/consensus.rs b/src/consensus.rs
index 0dfd232..56fc0ba 100644
--- a/src/consensus.rs
+++ b/src/consensus.rs
@@ -197,6 +197,8 @@ mod tests {
                 chrom: "chr1".to_string(),
                 start: 1,
                 end: 100,
+                id: "".to_string(),
+                motifs: "CA".to_string(),
             },
         );
         println!("Consensus: {}", cons.seq.unwrap());
diff --git a/src/genotype.rs b/src/genotype.rs
index 11df3f6..e84a96c 100644
--- a/src/genotype.rs
+++ b/src/genotype.rs
@@ -330,6 +330,8 @@ mod tests {
             chrom: String::from("chr7"),
             start: 154654404,
             end: 154654432,
+            id: String::from("test-repeat"),
+            motifs: "CA".to_string(),
         };
         let flanking = 2000;
         let minlen = 5;
@@ -369,6 +371,8 @@ mod tests {
             chrom: String::from("chr7"),
             start: 154654404,
             end: 154654432,
+            id: "TEST".to_string(),
+            motifs: "CA".to_string(),
         };
         let args = Cli {
             bam: String::from("test_data/small-test-phased.bam"),
@@ -397,6 +401,8 @@ mod tests {
             chrom: String::from("chr7"),
             start: 154654404,
             end: 154654432,
+            id: "TEST".to_string(),
+            motifs: "CA".to_string(),
         };
         let args = Cli {
             bam: String::from("test_data/small-test-phased.bam"),
@@ -441,6 +447,8 @@ mod tests {
             chrom: String::from("chr7"),
             start: 154654404,
             end: 154654432,
+            id: "TEST".to_string(),
+            motifs: "CA".to_string(),
         };
         let mut bam = parse_bam::create_bam_reader(&args.bam, &args.fasta);
         let genotype = genotype_repeat(&repeat, &args, &mut bam);
@@ -469,6 +477,8 @@ mod tests {
             chrom: String::from("chr7"),
             start: 154654404,
             end: 154654432,
+            id: "TEST".to_string(),
+            motifs: "CA".to_string(),
         };
         let mut bam = parse_bam::create_bam_reader(&args.bam, &args.fasta);
         let genotype = genotype_repeat(&repeat, &args, &mut bam);
@@ -498,6 +508,8 @@ mod tests {
             chrom: String::from("chr7"),
             start: 154654404,
             end: 154654432,
+            id: "TEST".to_string(),
+            motifs: "CA".to_string(),
         };
         let mut bam = parse_bam::create_bam_reader(&args.bam, &args.fasta);
         let genotype = genotype_repeat(&repeat, &args, &mut bam);
diff --git a/src/motif.rs b/src/motif.rs
index cdffdb5..123f765 100644
--- a/src/motif.rs
+++ b/src/motif.rs
@@ -5,6 +5,20 @@ fn create_motif(seq: &str) -> String {
     unimplemented!()
 }
 
+pub fn create_mc(motifs_string: &str, repeats: &str) -> String {
+     let motifs: Vec<String> = motifs_string.split(',').map(|s| s.to_string()).collect();
+
+     let mut motif_counts = vec![0; motifs.len()];
+     for motif in motifs.iter() {
+         let mut start = 0;
+         while let Some(index) = repeats[start..].find(motif) {
+             motif_counts[motifs.iter().position(|x| x == motif).unwrap()] += 1;
+             start += index + motif.len();
+         }
+     }
+     motif_counts.iter().map(|count| count.to_string()).collect::<Vec<String>>().join("_")
+ }
+
 #[cfg(test)]
 mod tests {
     use super::*;
@@ -17,4 +31,22 @@ mod tests {
             "(CAG)4(CGG)3(CAG)3"
         );
     }
+    #[test]
+    fn test_create_mc() {
+        let motifs = "ATG,CGT,GCA";
+        let repeat = "ATGCGTATGCGTAGCGT";
+        println!("{:?}", create_mc(&motifs, &repeat));
+        assert_eq!(
+            create_mc(&motifs, repeat), "2_3_0"
+        );
+    }
+    #[test]
+    fn test_create_mc_with_n() {
+        let motifs = "NCG";
+        let repeat = "ACGACGACGACG";
+
+        assert_eq!(
+            create_mc(&motifs, repeat), "4"
+        );
+    }
 }
diff --git a/src/parse_bam.rs b/src/parse_bam.rs
index 1465671..3ae0938 100644
--- a/src/parse_bam.rs
+++ b/src/parse_bam.rs
@@ -143,6 +143,8 @@ fn test_get_overlapping_reads() {
         chrom: String::from("chr7"),
         start: 154654404,
         end: 154654432,
+        id: "TEST".to_string(),
+        motifs: "CA".to_string(),
     };
     let unphased = false;
     let mut bam = create_bam_reader(&bam, &fasta);
@@ -157,6 +159,8 @@ fn test_get_overlapping_reads_url1() {
         chrom: String::from("chr20"),
         start: 154654404,
         end: 154654432,
+        id: "TEST".to_string(),
+        motifs: "CA".to_string(),
     };
     let unphased = false;
     let mut bam = create_bam_reader(&bam, &fasta);
@@ -171,6 +175,8 @@ fn test_get_overlapping_reads_url2() {
         chrom: String::from("chr20"),
         start: 154654404,
         end: 154654432,
+        id: "TEST".to_string(),
+        motifs: "CA".to_string(),
     };
     let unphased = false;
     let mut bam = create_bam_reader(&bam, &fasta);
@@ -185,6 +191,8 @@ fn test_get_overlapping_reads_url3() {
         chrom: String::from("chr20"),
         start: 154654404,
         end: 154654432,
+        id: "TEST".to_string(),
+        motifs: "CA".to_string(),
     };
     let unphased = false;
     let mut bam = create_bam_reader(&bam, &fasta);
@@ -199,6 +207,8 @@ fn test_get_overlapping_reads_url4() {
         chrom: String::from("chr20"),
         start: 154654404,
         end: 154654432,
+        id: "TEST".to_string(),
+        motifs: "CA".to_string(),
     };
     let unphased = false;
     let mut bam = create_bam_reader(&bam, &fasta);
diff --git a/src/phase_insertions.rs b/src/phase_insertions.rs
index b351139..6b6a3f2 100644
--- a/src/phase_insertions.rs
+++ b/src/phase_insertions.rs
@@ -332,6 +332,8 @@ mod tests {
                 chrom: "chr7".to_string(),
                 start: 154654404,
                 end: 154654432,
+                id: "TEST".to_string(),
+                motifs: "CA".to_string(),
             },
             false,
         );
@@ -372,6 +374,8 @@ mod tests {
                 chrom: "chr7".to_string(),
                 start: 154654404,
                 end: 154654432,
+                id: "TEST".to_string(),
+                motifs: "CA".to_string(),
             },
             false,
         );
@@ -411,6 +415,8 @@ mod tests {
                 chrom: "chr7".to_string(),
                 start: 154654404,
                 end: 154654432,
+                id: "TEST".to_string(),
+                motifs: "CA".to_string(),
             },
             false,
         );
@@ -453,6 +459,8 @@ mod tests {
                 chrom: "chr7".to_string(),
                 start: 154654404,
                 end: 154654432,
+                id: "TEST".to_string(),
+                motifs: "CA".to_string(),
             },
             false,
         );
@@ -493,6 +501,8 @@ mod tests {
                 chrom: "chr7".to_string(),
                 start: 154654404,
                 end: 154654432,
+                id: "TEST_RFC1".to_string(),
+                motifs: "CA".to_string(),
             },
             false,
         );
@@ -564,6 +574,8 @@ mod tests {
                 chrom: "chr7".to_string(),
                 start: 154654404,
                 end: 154654432,
+                id: "TEST_RFC1".to_string(),
+                motifs: "CA".to_string(),
             },
             false,
         );
diff --git a/src/repeats.rs b/src/repeats.rs
index bc8f86a..f799d24 100644
--- a/src/repeats.rs
+++ b/src/repeats.rs
@@ -21,7 +21,9 @@ impl RepeatIntervalIterator {
         let end: u32 = interval.split('-').collect::<Vec<&str>>()[1]
             .parse()
             .unwrap();
-        let repeat = RepeatInterval::new_interval(chrom, start, end, fasta)
+        let id = String::new();
+        let motifs = String::new();
+        let repeat = RepeatInterval::new_interval(chrom, start, end, fasta, id, motifs)
             .expect("Failed to create repeat interval");
         RepeatIntervalIterator {
             current_index: 0,
@@ -74,6 +76,8 @@ impl Clone for RepeatInterval {
             chrom: self.chrom.clone(),
             start: self.start,
             end: self.end,
+            id: self.id.clone(),
+            motifs: self.motifs.clone(),
         }
     }
 }
@@ -99,6 +103,8 @@ pub struct RepeatInterval {
     pub chrom: String,
     pub start: u32,
     pub end: u32,
+    pub id: String,
+    pub motifs: String,
 }
 
 impl fmt::Display for RepeatInterval {
@@ -117,10 +123,25 @@ impl RepeatInterval {
         let chrom = rec.chrom().to_string();
         let start = rec.start().try_into().unwrap();
         let end = rec.end().try_into().unwrap();
-        RepeatInterval::new_interval(chrom, start, end, fasta)
+        let mut id = String::new();
+        let mut motifs = String::new();
+        if let Some(info) = rec.name() {
+            let key_value_pairs: Vec<&str> = info.split(';').collect();
+            // Find and extract the value associated with the "ID" key
+            for pair in key_value_pairs {
+                if pair.starts_with("ID=") {
+                    id = pair.trim_start_matches("ID=").to_string();
+                }
+                else if pair.starts_with("MOTIFS=") {
+                    motifs = pair.trim_start_matches("MOTIFS=").to_string();
+                    break;
+                }
+            }
+        }
+        RepeatInterval::new_interval(chrom, start, end, fasta, id, motifs)
     }
 
-    fn new_interval(chrom: String, start: u32, end: u32, fasta: &str) -> Option<Self> {
+    fn new_interval(chrom: String, start: u32, end: u32, fasta: &str, id: String, motifs: String) -> Option<Self> {
         if end < start {
             panic!("End coordinate is smaller than start coordinate for {chrom}:{start}-{end}")
         }
@@ -138,7 +159,7 @@ impl RepeatInterval {
                     .expect("Failed parsing chromosome length from fai file")
                     > end
             {
-                return Some(Self { chrom, start, end });
+                return Some(Self { chrom, start, end, id, motifs});
             }
         }
         // if the chromosome is not in the fai file or the end does not fit the interval, return None
@@ -146,11 +167,13 @@ impl RepeatInterval {
             "Chromosome {chrom} is not in the fasta file or the end coordinate is out of bounds"
         );
     }
-    pub fn new(chrom: &str, start: u32, end: u32) -> Self {
+    pub fn new(chrom: &str, start: u32, end: u32, id: &str, motifs: &str) -> Self {
         Self {
             chrom: chrom.to_string(),
             start,
             end,
+            id: id.to_string(),
+            motifs: motifs.to_string(),
         }
     }
 
diff --git a/src/vcf.rs b/src/vcf.rs
index 5f5960c..c7d9109 100644
--- a/src/vcf.rs
+++ b/src/vcf.rs
@@ -7,6 +7,8 @@ use std::cmp::Ordering;
 use std::fmt;
 use std::io::Read;
 
+use crate::motif::create_mc;
+
 pub struct Allele {
     pub length: String, // length of the consensus sequence minus the length of the repeat sequence
     pub full_length: String, // length of the consensus sequence
@@ -55,6 +57,9 @@ pub struct VCFRecord {
     pub ps: Option<u32>, // phase set identifier
     pub flags: String,
     pub allele: (String, String),
+    pub id: String,
+    pub motifs: String,
+    pub mc: (String, String),
 }
 
 impl VCFRecord {
@@ -87,6 +92,9 @@ impl VCFRecord {
             "Genotyping {repeat}:{repeat_ref_sequence} with {} and {}",
             allele1.seq, allele2.seq,
         );
+        let mc1 = create_mc(&repeat.motifs, &allele1.seq);
+        let mc2 = create_mc(&repeat.motifs, &allele2.seq);
+        println!("{:?} {:?} {:?} {:?} {:?} {:?}", &repeat, &repeat.motifs, &mc1, &mc2, &allele1.seq, &allele2.seq);
         // if the consensus is very similar to the reference the variant is considered ref
         // for this I use a threshold of 5% of the length of the repeat sequence in the reference
         // e.g. if the repeat is 300bp in the reference this will allow an edit distance of 15
@@ -158,6 +166,9 @@ impl VCFRecord {
             ps,
             flags,
             allele: (genotype1.to_string(), genotype2.to_string()),
+            id: repeat.id.clone(),
+            motifs: repeat.motifs.clone(),
+            mc: (mc1, mc2),
         }
     }
 
@@ -182,6 +193,9 @@ impl VCFRecord {
             ps: None,
             flags: "".to_string(),
             allele: (".".to_string(), ".".to_string()),
+            id: repeat.id.clone(),
+            motifs: repeat.motifs.clone(),
+            mc: (".".to_string(), ".".to_string()),
         }
     }
 }
@@ -191,12 +205,12 @@ impl fmt::Display for VCFRecord {
         match &self.alt_seq {
             Some(alts) => {
                 let (FORMAT, ps) = match self.ps {
-                    Some(ps) => ("GT:RB:FRB:SUP:SC:PS", format!(":{}", ps)),
-                    None => ("GT:RB:FRB:SUP:SC", "".to_string()),
+                    Some(ps) => ("GT:RB:FRB:SUP:MC:SC:PS", format!(":{}", ps)),
+                    None => ("GT:RB:FRB:SUP:MC:SC", "".to_string()),
                 };
                 write!(
                     f,
-                    "{chrom}\t{start}\t.\t{ref}\t{alt}\t.\t.\t{flags}END={end};STDEV={sd1},{sd2}{somatic}{outliers}\t{FORMAT}\t{genotype1}|{genotype2}:{l1},{l2}:{fl1},{fl2}:{sup1},{sup2}:{score1},{score2}{ps}",
+                    "{chrom}\t{start}\t.\t{ref}\t{alt}\t.\t.\t{flags}REPID={id};MOTIFS={motifs};END={end};STDEV={sd1},{sd2}{somatic}{outliers}\t{FORMAT}\t{genotype1}|{genotype2}:{l1},{l2}:{fl1},{fl2}:{sup1},{sup2}:{mc1},{mc2}:{score1},{score2}{ps}",
                     chrom = self.chrom,
                     start = self.start,
                     flags = self.flags,
@@ -217,12 +231,17 @@ impl fmt::Display for VCFRecord {
                     sup2 = self.support.1,
                     score1 = self.score.0,
                     score2 = self.score.1,
+                    id = self.id,
+                    motifs = self.motifs,
+                    mc1 = self.mc.0,
+                    mc2 = self.mc.1,
+                    
                 )
             }
             None => {
                 write!(
                     f,
-                    "{chrom}\t{start}\t.\t{ref}\t.\t.\t.\tEND={end};{somatic}\tGT:SUP\t{genotype1}|{genotype2}:{sup1},{sup2}",
+                    "{chrom}\t{start}\t.\t{ref}\t.\t.\t.\tREPID={id};MOTIFS={motifs};END={end};{somatic}\tGT:SUP\t{genotype1}|{genotype2}:{sup1},{sup2}:{mc1},{mc2}",
                     chrom = self.chrom,
                     start = self.start,
                     end = self.end,
@@ -232,6 +251,10 @@ impl fmt::Display for VCFRecord {
                     genotype2 = self.allele.1,
                     sup1 = self.support.0,
                     sup2 = self.support.1,
+                    id = self.id,
+                    motifs = self.motifs,
+                    mc1 = self.mc.0,
+                    mc2 = self.mc.1,
                 )
             }
         }
@@ -286,6 +309,12 @@ pub fn write_vcf_header(fasta: &str, bam: &str, sample: &Option<String>) {
         let length = contig.next().unwrap().parse::<usize>().unwrap();
         println!(r#"##contig=<ID={},length={}>"#, name, length);
     }
+    println!(
+        r#"##INFO=<ID=REPID,Number=1,Type=String,Description="Repeat ID">"#
+    );
+    println!(
+        r#"##INFO=<ID=MOTIFS,Number=1,Type=String,Description="Repeat motifs">"#
+    );
     println!(
         r#"##INFO=<ID=END,Number=1,Type=Integer,Description="End position of the repeat interval">"#
     );
@@ -310,6 +339,7 @@ pub fn write_vcf_header(fasta: &str, bam: &str, sample: &Option<String>) {
     );
     println!(r#"##FORMAT=<ID=PS,Number=1,Type=Integer,Description="Phase set identifier">"#);
     println!(r#"##FORMAT=<ID=SUP,Number=2,Type=Integer,Description="Read support per allele">"#);
+    println!(r#"##FORMAT=<ID=MC,Number=2,Type=String,Description="Motif count per allele">"#);
     println!(r#"##FORMAT=<ID=SC,Number=2,Type=Integer,Description="Consensus score per allele">"#);
     let name = match sample {
         Some(name) => name,