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matrix-clustering_demo_peak-motifs_result.tf
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AC oligos_7nt_mkv4_m1
XX
ID oligos_7nt_mkv4_m1
XX
DE tsatATGCAAATgwry
PO A C G T
1 49 21 45 111
2 39 74 71 42
3 150 6 14 56
4 37 26 12 151
5 223 1 0 2
6 0 1 1 224
7 2 0 219 5
8 0 210 2 14
9 215 0 4 7
10 202 6 6 12
11 224 1 1 0
12 1 8 3 214
13 48 17 143 18
14 77 48 38 63
15 80 43 68 35
16 53 63 52 58
XX
CC program: feature
CC matrix.nb: 1
CC matrix.nb: 1
CC sites: 226
CC consensus.strict: tcatATGCAAATgaac
CC consensus.strict.rc: GTTCATTTGCATATGA
CC consensus.IUPAC: tsatATGCAAATgwry
CC consensus.IUPAC.rc: RYWCATTTGCATATSA
CC consensus.regexp: t[cg]atATGCAAATg[at][ag][ct]
CC consensus.regexp.rc: [AG][CT][AT]CATTTGCATAT[CG]A
XX
//
AC oligos_7nt_mkv4_m2
XX
ID oligos_7nt_mkv4_m2
XX
DE cyhcATTTGCATAACAAwrr
PO A C G T
1 33 51 36 35
2 24 45 34 52
3 41 44 22 48
4 20 91 18 26
5 128 7 11 9
6 2 2 1 150
7 8 12 2 133
8 20 3 0 132
9 9 5 139 2
10 2 152 0 1
11 154 0 1 0
12 3 2 0 150
13 110 11 21 13
14 129 5 2 19
15 4 121 17 13
16 148 3 1 3
17 148 1 5 1
18 50 3 6 96
19 53 17 72 13
20 39 34 67 15
XX
CC program: feature
CC matrix.nb: 2
CC matrix.nb: 2
CC sites: 155
CC consensus.strict: cttcATTTGCATAACAAtgg
CC consensus.strict.rc: CCATTGTTATGCAAATGAAG
CC consensus.IUPAC: cyhcATTTGCATAACAAwrr
CC consensus.IUPAC.rc: YYWTTGTTATGCAAATGDRG
CC consensus.regexp: c[ct][act]cATTTGCATAACAA[at][ag][ag]
CC consensus.regexp.rc: [CT][CT][AT]TTGTTATGCAAATG[AGT][AG]G
XX
//
AC oligos_7nt_mkv4_m3
XX
ID oligos_7nt_mkv4_m3
XX
DE wtATGCTAATww
PO A C G T
1 60 14 22 63
2 33 26 26 74
3 156 1 2 0
4 0 0 0 159
5 1 1 155 2
6 8 138 3 10
7 5 1 2 151
8 158 0 1 0
9 158 1 0 0
10 24 7 10 118
11 48 22 39 50
12 43 34 35 47
XX
CC program: feature
CC matrix.nb: 3
CC matrix.nb: 3
CC sites: 159
CC consensus.strict: ttATGCTAATtt
CC consensus.strict.rc: AAATTAGCATAA
CC consensus.IUPAC: wtATGCTAATww
CC consensus.IUPAC.rc: WWATTAGCATAW
CC consensus.regexp: [at]tATGCTAAT[at][at]
CC consensus.regexp.rc: [AT][AT]ATTAGCATA[AT]
XX
//
AC oligos_7nt_mkv4_m4
XX
ID oligos_7nt_mkv4_m4
XX
DE TtTGCATgACAATrr
PO A C G T
1 25 28 14 186
2 53 52 31 117
3 41 8 5 199
4 24 16 206 7
5 5 247 0 1
6 250 1 2 0
7 3 0 1 249
8 53 13 165 22
9 248 1 0 4
10 8 221 10 14
11 252 0 0 1
12 251 0 1 1
13 58 6 5 184
14 80 21 129 23
15 68 60 105 20
XX
CC program: feature
CC matrix.nb: 4
CC matrix.nb: 4
CC sites: 253
CC consensus.strict: TtTGCATgACAATgg
CC consensus.strict.rc: CCATTGTCATGCAAA
CC consensus.IUPAC: TtTGCATgACAATrr
CC consensus.IUPAC.rc: YYATTGTCATGCAAA
CC consensus.regexp: TtTGCATgACAAT[ag][ag]
CC consensus.regexp.rc: [CT][CT]ATTGTCATGCAAA
XX
//
AC oligos_7nt_mkv4_m5
XX
ID oligos_7nt_mkv4_m5
XX
DE ccCCCCCACCCCcmc
PO A C G T
1 74 198 51 81
2 65 187 81 71
3 32 310 34 28
4 6 372 15 11
5 11 371 12 10
6 8 378 10 8
7 7 380 12 5
8 276 55 45 28
9 10 374 12 8
10 8 374 9 13
11 7 372 11 14
12 9 372 17 6
13 79 230 51 44
14 102 167 68 67
15 79 183 69 73
XX
CC program: feature
CC matrix.nb: 5
CC matrix.nb: 5
CC sites: 404
CC consensus.strict: ccCCCCCACCCCccc
CC consensus.strict.rc: GGGGGGGTGGGGGGG
CC consensus.IUPAC: ccCCCCCACCCCcmc
CC consensus.IUPAC.rc: GKGGGGGTGGGGGGG
CC consensus.regexp: ccCCCCCACCCCc[ac]c
CC consensus.regexp.rc: G[GT]GGGGGTGGGGGGG
XX
//
AC positions_7nt_m1
XX
ID positions_7nt_m1
XX
DE kkcyTTTGTTATGCAAATGvarkc
PO A C G T
1 10 11 18 15
2 8 12 17 17
3 1 36 8 9
4 2 33 3 16
5 12 1 1 40
6 0 2 0 52
7 0 0 1 53
8 5 2 47 0
9 0 2 0 52
10 3 8 4 39
11 51 0 2 1
12 0 0 0 54
13 0 0 53 1
14 1 50 1 2
15 45 1 0 8
16 45 1 6 2
17 51 1 0 2
18 2 3 4 45
19 6 3 40 5
20 14 15 15 10
21 27 8 12 7
22 14 5 22 13
23 6 12 18 18
24 9 21 11 13
XX
CC program: feature
CC matrix.nb: 1
CC matrix.nb: 1
CC sites: 54
CC consensus.strict: ggccTTTGTTATGCAAATGcaggc
CC consensus.strict.rc: GCCTGCATTTGCATAACAAAGGCC
CC consensus.IUPAC: kkcyTTTGTTATGCAAATGvarkc
CC consensus.IUPAC.rc: GMYTBCATTTGCATAACAAARGMM
CC consensus.regexp: [gt][gt]c[ct]TTTGTTATGCAAATG[acg]a[ag][gt]c
CC consensus.regexp.rc: G[AC][CT]T[CGT]CATTTGCATAACAAA[AG]G[AC][AC]
XX
//
AC positions_7nt_m2
XX
ID positions_7nt_m2
XX
DE hrydcATTTGCATATGcAAATgwr
PO A C G T
1 6 5 2 5
2 7 2 5 4
3 0 5 3 10
4 5 0 8 5
5 1 12 1 4
6 14 0 2 2
7 0 3 0 15
8 3 0 0 15
9 0 0 0 18
10 3 0 15 0
11 1 17 0 0
12 17 0 1 0
13 1 0 0 17
14 15 1 1 1
15 0 0 0 18
16 0 0 18 0
17 3 12 1 2
18 18 0 0 0
19 16 0 0 2
20 16 0 2 0
21 2 1 2 13
22 3 2 12 1
23 6 2 3 7
24 7 3 7 1
XX
CC program: feature
CC matrix.nb: 2
CC matrix.nb: 2
CC sites: 18
CC consensus.strict: aatgcATTTGCATATGcAAATgta
CC consensus.strict.rc: TACATTTGCATATGCAAATGCATT
CC consensus.IUPAC: hrydcATTTGCATATGcAAATgwr
CC consensus.IUPAC.rc: YWCATTTGCATATGCAAATGHRYD
CC consensus.regexp: [act][ag][ct][agt]cATTTGCATATGcAAATg[at][ag]
CC consensus.regexp.rc: [CT][AT]CATTTGCATATGCAAATG[ACT][AG][CT][AGT]
XX
//
AC positions_7nt_m3
XX
ID positions_7nt_m3
XX
DE dbhyTbvTTATGCATAAbvArdvh
PO A C G T
1 1 0 1 2
2 0 1 1 2
3 1 2 0 1
4 0 1 0 3
5 0 0 0 4
6 0 1 1 2
7 1 2 1 0
8 0 0 0 4
9 0 0 0 4
10 4 0 0 0
11 0 0 0 4
12 0 0 4 0
13 0 4 0 0
14 4 0 0 0
15 0 0 0 4
16 4 0 0 0
17 4 0 0 0
18 0 1 2 1
19 2 1 1 0
20 4 0 0 0
21 3 0 1 0
22 1 0 2 1
23 2 1 1 0
24 2 1 0 1
XX
CC program: feature
CC matrix.nb: 3
CC matrix.nb: 3
CC sites: 4
CC consensus.strict: ttctTtcTTATGCATAAgaAagaa
CC consensus.strict.rc: TTCTTTCTTATGCATAAGAAAGAA
CC consensus.IUPAC: dbhyTbvTTATGCATAAbvArdvh
CC consensus.IUPAC.rc: DBHYTBVTTATGCATAABVARDVH
CC consensus.regexp: [agt][cgt][act][ct]T[cgt][acg]TTATGCATAA[cgt][acg]A[ag][agt][acg][act]
CC consensus.regexp.rc: [AGT][CGT][ACT][CT]T[CGT][ACG]TTATGCATAA[CGT][ACG]A[AG][AGT][ACG][ACT]
XX
//
AC positions_7nt_m4
XX
ID positions_7nt_m4
XX
DE ygsATATGCGCATATGCArATrwr
PO A C G T
1 1 10 2 14
2 4 4 17 2
3 5 9 9 4
4 23 0 3 1
5 2 5 0 20
6 27 0 0 0
7 0 1 0 26
8 1 0 23 3
9 0 22 0 5
10 4 2 21 0
11 2 19 6 0
12 27 0 0 0
13 0 1 0 26
14 26 0 1 0
15 0 0 1 26
16 2 0 22 3
17 0 24 1 2
18 19 3 5 0
19 10 3 8 6
20 22 0 4 1
21 2 4 0 21
22 14 0 13 0
23 10 5 0 12
24 10 1 14 2
XX
CC program: feature
CC matrix.nb: 4
CC matrix.nb: 4
CC sites: 27
CC consensus.strict: tgcATATGCGCATATGCAaATatg
CC consensus.strict.rc: CATATTTGCATATGCGCATATGCA
CC consensus.IUPAC: ygsATATGCGCATATGCArATrwr
CC consensus.IUPAC.rc: YWYATYTGCATATGCGCATATSCR
CC consensus.regexp: [ct]g[cg]ATATGCGCATATGCA[ag]AT[ag][at][ag]
CC consensus.regexp.rc: [CT][AT][CT]AT[CT]TGCATATGCGCATAT[CG]C[AG]
XX
//
AC positions_7nt_m5
XX
ID positions_7nt_m5
XX
DE byATTGTcATGCAAATGcaaky
PO A C G T
1 7 20 19 27
2 6 31 8 28
3 51 3 2 17
4 0 3 1 69
5 1 2 2 68
6 3 9 58 3
7 8 0 3 62
8 9 44 6 14
9 71 0 0 2
10 0 0 0 73
11 0 0 72 1
12 1 64 4 4
13 69 0 1 3
14 63 1 5 4
15 72 0 1 0
16 8 2 4 59
17 9 4 53 7
18 15 27 18 13
19 43 12 10 8
20 35 10 18 10
21 16 13 23 21
22 13 25 15 20
XX
CC program: feature
CC matrix.nb: 5
CC matrix.nb: 5
CC sites: 73
CC consensus.strict: tcATTGTcATGCAAATGcaagc
CC consensus.strict.rc: GCTTGCATTTGCATGACAATGA
CC consensus.IUPAC: byATTGTcATGCAAATGcaaky
CC consensus.IUPAC.rc: RMTTGCATTTGCATGACAATRV
CC consensus.regexp: [cgt][ct]ATTGTcATGCAAATGcaa[gt][ct]
CC consensus.regexp.rc: [AG][AC]TTGCATTTGCATGACAAT[AG][ACG]
XX
//
AC MA0079.3
XX
ID SP1
XX
DE MA0079.3 SP1; from JASPAR
PO A C G T
1 857 1786 4271 1820
2 0 6215 642 1877
3 99 6703 0 1932
4 0 8734 0 0
5 0 8661 0 73
6 1359 0 4624 2751
7 0 8734 0 0
8 0 8734 0 0
9 0 6679 0 2055
10 1054 6357 0 1323
11 652 4969 734 2379
XX
CC program: jaspar
CC matrix.nb: 243
CC min.prior: 0.25
CC alphabet.size: 4
CC max.bits: 2
CC total.information: 9.22897315885212
CC information.per.column: 0.838997559895647
CC max.possible.info.per.col: 1.38629436111989
CC consensus.strict: gCCCCgCCCCc
CC consensus.strict.rc: GGGGGCGGGGC
CC consensus.IUPAC: gCCCCkCCCCy
CC consensus.IUPAC.rc: RGGGGMGGGGC
CC consensus.regexp: gCCCC[gt]CCCC[ct]
CC consensus.regexp.rc: [AG]GGGG[AC]GGGGC
CC residues.content.crude.freq: a:0.0419|c:0.7033|g:0.1069|t:0.1479
CC G+C.content.crude.freq: 0.810240023315361
CC residues.content.corrected.freq: a:0.0419|c:0.7033|g:0.1069|t:0.1479
CC G+C.content.corrected.freq: 0.810204506426601
XX
//
AC MA0162.2
XX
ID EGR1
XX
DE MA0162.2 EGR1; from JASPAR
PO A C G T
1 1098 5728 3083 2347
2 1506 6847 1359 2544
3 1160 6049 2250 2797
4 1335 10431 0 490
5 233 11574 0 449
6 2911 0 6840 2505
7 0 12256 0 0
8 0 11852 0 404
9 0 10154 611 1491
10 3652 8361 0 243
11 0 11952 0 304
12 2368 0 6599 3289
13 0 9849 1420 987
14 3026 5595 1913 1722
XX
CC program: jaspar
CC matrix.nb: 222
CC min.prior: 0.25
CC alphabet.size: 4
CC max.bits: 2
CC total.information: 9.6228979082673
CC information.per.column: 0.687349850590521
CC max.possible.info.per.col: 1.38629436111989
CC consensus.strict: cccCCgCCCCCgCc
CC consensus.strict.rc: GGCGGGGGCGGGGG
CC consensus.IUPAC: sccCCgCCCMCkCc
CC consensus.IUPAC.rc: GGMGKGGGCGGGGS
CC consensus.regexp: [cg]ccCCgCCC[AC]C[gt]Cc
CC consensus.regexp.rc: GG[AC]G[GT]GGGCGGGG[CG]
CC residues.content.crude.freq: a:0.1008|c:0.6449|g:0.1403|t:0.1141
CC G+C.content.crude.freq: 0.785172277135397
CC residues.content.corrected.freq: a:0.1008|c:0.6448|g:0.1403|t:0.1141
CC G+C.content.corrected.freq: 0.785149011060735
XX
//