Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold297
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 119839
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33
Found at i:12371 original size:15 final size:15
Alignment explanation
Indices: 12348--12378 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
12338 TACCTTCTTC
12348 TTTAATCACTTACCT
1 TTTAATCACTTACCT
*
12363 TTTACTCACTTACCT
1 TTTAATCACTTACCT
12378 T
1 T
12379 CTTTCTTACC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.23, C:0.29, G:0.00, T:0.48
Consensus pattern (15 bp):
TTTAATCACTTACCT
Found at i:12650 original size:46 final size:49
Alignment explanation
Indices: 12544--12659 Score: 139
Period size: 50 Copynumber: 2.4 Consensus size: 49
12534 TGTCTTCGAC
** * * *
12544 ATGGACTTACATGAATTATTCCTGTCTCCAATGCCATATATATATCTAAT
1 ATGGACTTACATGGCTCATTCCTATCTCCAAAGCCA-ATATATATCTAAT
* *
12594 ATGGGCTTACATGGCTCATTCCTATCTCCAAAGCC-ATATAT-T-TGAT
1 ATGGACTTACATGGCTCATTCCTATCTCCAAAGCCAATATATATCTAAT
12640 ATGGACTTACATGGCTCATT
1 ATGGACTTACATGGCTCATT
12660 TCTGTCCTGT
Statistics
Matches: 58, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
46 22 0.38
47 1 0.02
48 6 0.10
50 29 0.50
ACGTcount: A:0.28, C:0.22, G:0.14, T:0.36
Consensus pattern (49 bp):
ATGGACTTACATGGCTCATTCCTATCTCCAAAGCCAATATATATCTAAT
Found at i:19678 original size:28 final size:29
Alignment explanation
Indices: 19641--19731 Score: 107
Period size: 29 Copynumber: 3.2 Consensus size: 29
19631 AAGACTACAT
*
19641 ACATGCATATGGCCCACTAGGCCC-AATC
1 ACATTCATATGGCCCACTAGGCCCAAATC
* *
19669 TCATTCATATGGCCCATTAGGCCCAAATC
1 ACATTCATATGGCCCACTAGGCCCAAATC
* *
19698 ACATTCATATAGCCCATCT-GGCCCGAATC
1 ACATTCATATGGCCCA-CTAGGCCCAAATC
19727 A-ATTC
1 ACATTC
19732 CAAGCCATGT
Statistics
Matches: 54, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
28 25 0.46
29 28 0.52
30 1 0.02
ACGTcount: A:0.29, C:0.33, G:0.14, T:0.24
Consensus pattern (29 bp):
ACATTCATATGGCCCACTAGGCCCAAATC
Found at i:22131 original size:16 final size:17
Alignment explanation
Indices: 22110--22142 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
22100 CACATTGAAG
22110 TGTTTT-TTGAAAACCT
1 TGTTTTATTGAAAACCT
22126 TGTTTTCATTGAAAACC
1 TGTTTT-ATTGAAAACC
22143 CTTCTTTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
18 9 0.60
ACGTcount: A:0.27, C:0.15, G:0.12, T:0.45
Consensus pattern (17 bp):
TGTTTTATTGAAAACCT
Found at i:22760 original size:11 final size:11
Alignment explanation
Indices: 22744--22769 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
22734 CGAAGCCCAC
22744 ATCACAATAAT
1 ATCACAATAAT
22755 ATCACAATAAT
1 ATCACAATAAT
22766 ATCA
1 ATCA
22770 AACATGCAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.54, C:0.19, G:0.00, T:0.27
Consensus pattern (11 bp):
ATCACAATAAT
Found at i:25510 original size:15 final size:16
Alignment explanation
Indices: 25487--25520 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
25477 ATAGCCAGAC
25487 TTTCAAC-TTTTGGCA
1 TTTCAACTTTTTGGCA
*
25502 TTTCGACTTTTTGGCA
1 TTTCAACTTTTTGGCA
25518 TTT
1 TTT
25521 TAAGATTTGC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 6 0.35
16 11 0.65
ACGTcount: A:0.15, C:0.18, G:0.15, T:0.53
Consensus pattern (16 bp):
TTTCAACTTTTTGGCA
Found at i:31907 original size:28 final size:29
Alignment explanation
Indices: 31867--31921 Score: 85
Period size: 29 Copynumber: 1.9 Consensus size: 29
31857 CTGTATCTGA
*
31867 CCCATTAAGCCC-AATCATATTCATATGG
1 CCCATTAAGCCCAAATCACATTCATATGG
*
31895 CCCATTAGGCCCAAATCACATTCATAT
1 CCCATTAAGCCCAAATCACATTCATAT
31922 TCATGCTCAC
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 11 0.46
29 13 0.54
ACGTcount: A:0.33, C:0.31, G:0.09, T:0.27
Consensus pattern (29 bp):
CCCATTAAGCCCAAATCACATTCATATGG
Found at i:32158 original size:16 final size:15
Alignment explanation
Indices: 32137--32166 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
32127 CAAACTTTCA
32137 GCTTTTCGGCATTTTT
1 GCTTTTCGGC-TTTTT
32153 GCTTTTCGGCTTTT
1 GCTTTTCGGCTTTT
32167 GCCAATTCAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.03, C:0.20, G:0.20, T:0.57
Consensus pattern (15 bp):
GCTTTTCGGCTTTTT
Found at i:33269 original size:11 final size:11
Alignment explanation
Indices: 33255--33281 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
33245 TATTTTTATT
33255 TAATTAAACTA
1 TAATTAAACTA
33266 TAATTAAACTA
1 TAATTAAACTA
33277 TAATT
1 TAATT
33282 CATTTATTCC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.52, C:0.07, G:0.00, T:0.41
Consensus pattern (11 bp):
TAATTAAACTA
Found at i:39086 original size:15 final size:15
Alignment explanation
Indices: 39066--39134 Score: 84
Period size: 15 Copynumber: 4.6 Consensus size: 15
39056 GTATCTTGGG
39066 TTTCTTTATCCTGGA
1 TTTCTTTATCCTGGA
* *
39081 TCTCTTTATTCTGGA
1 TTTCTTTATCCTGGA
* *
39096 TTTCTTTATTCTGGG
1 TTTCTTTATCCTGGA
* *
39111 TTTCTCTATCTTGGA
1 TTTCTTTATCCTGGA
39126 TTTCTTTAT
1 TTTCTTTAT
39135 TCGGTTTTCT
Statistics
Matches: 45, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 45 1.00
ACGTcount: A:0.12, C:0.17, G:0.13, T:0.58
Consensus pattern (15 bp):
TTTCTTTATCCTGGA
Found at i:39135 original size:30 final size:30
Alignment explanation
Indices: 39057--39144 Score: 99
Period size: 30 Copynumber: 3.0 Consensus size: 30
39047 CATAGTATCG
* * * *
39057 TATCTTGGGTTTCTTTATCCTGGATCTCTT
1 TATCTTGGATTTCTTTATTCTGGATTTCTC
*
39087 TAT-TCTGGATTTCTTTATTCTGGGTTTCTC
1 TATCT-TGGATTTCTTTATTCTGGATTTCTC
*
39117 TATCTTGGATTTCTTTATTC-GGTTTTCT
1 TATCTTGGATTTCTTTATTCTGGATTTCT
39145 TGTTATCTTT
Statistics
Matches: 50, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
29 8 0.16
30 41 0.82
31 1 0.02
ACGTcount: A:0.10, C:0.17, G:0.16, T:0.57
Consensus pattern (30 bp):
TATCTTGGATTTCTTTATTCTGGATTTCTC
Found at i:41588 original size:46 final size:46
Alignment explanation
Indices: 41532--41709 Score: 196
Period size: 46 Copynumber: 3.8 Consensus size: 46
41522 GATGGTTGAG
*
41532 CATCCAAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA
1 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA
* * *** * * * *
41578 TATCTGAACTCGTTGAGTTGAGTCCGAGTTCGAGAGATGTA-ACTAGG
1 CATCCGAACTCGTTGAGTTGAGTCCGAGTTC-ACTTATGGATGCGA-A
* *
41625 CATCCGAGCTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGCGAA
1 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA
** *
41671 CGCCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
41710 GCGGGTTACA
Statistics
Matches: 105, Mismatches: 24, Indels: 6
0.78 0.18 0.04
Matches are distributed among these distances:
46 71 0.68
47 34 0.32
ACGTcount: A:0.22, C:0.20, G:0.28, T:0.29
Consensus pattern (46 bp):
CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA
Found at i:41690 original size:93 final size:93
Alignment explanation
Indices: 41531--41701 Score: 270
Period size: 93 Copynumber: 1.8 Consensus size: 93
41521 GGATGGTTGA
* * *
41531 GCATCCAAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATATCTGAACTCGTTGAGT
1 GCATCCAAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACACCCGAACTCGTTGAGT
41596 TGAGTCCGAGTTCGAGAGATGTAACTAG
66 TGAGTCCGAGTTCGAGAGATGTAACTAG
* * * * *
41624 GCATCCGAGCTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCAAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACACCCGAACTCGTTGAGT
41689 TGAGTCCGAGTTC
66 TGAGTCCGAGTTC
41702 ACTTATGGGC
Statistics
Matches: 70, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
93 70 1.00
ACGTcount: A:0.22, C:0.20, G:0.29, T:0.29
Consensus pattern (93 bp):
GCATCCAAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACACCCGAACTCGTTGAGT
TGAGTCCGAGTTCGAGAGATGTAACTAG
Found at i:43953 original size:43 final size:43
Alignment explanation
Indices: 43905--43989 Score: 134
Period size: 43 Copynumber: 2.0 Consensus size: 43
43895 TAGGCTTGAG
* * *
43905 GGAGCAATTAAGGTACGTTTTTGACTCGTTTTTAATGATTTCA
1 GGAGCAATTAAGGAACGATTTTGACTCATTTTTAATGATTTCA
*
43948 GGAGCAATTAAGGAACGATTTTGATTCATTTTTAATGATTTC
1 GGAGCAATTAAGGAACGATTTTGACTCATTTTTAATGATTTC
43990 TACGTTTTTG
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
43 38 1.00
ACGTcount: A:0.28, C:0.11, G:0.20, T:0.41
Consensus pattern (43 bp):
GGAGCAATTAAGGAACGATTTTGACTCATTTTTAATGATTTCA
Found at i:44783 original size:22 final size:23
Alignment explanation
Indices: 44736--44786 Score: 61
Period size: 22 Copynumber: 2.3 Consensus size: 23
44726 TAGTTCGTGT
*
44736 GAGCTTACTGAATCAGCTCGAAA
1 GAGCTTAATGAATCAGCTCGAAA
*
44759 GAGCTTAATGTAT-AGCTC-AATA
1 GAGCTTAATGAATCAGCTCGAA-A
44781 GAGCTT
1 GAGCTT
44787 CTCGTTTCTA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 2 0.08
22 12 0.48
23 11 0.44
ACGTcount: A:0.33, C:0.18, G:0.22, T:0.27
Consensus pattern (23 bp):
GAGCTTAATGAATCAGCTCGAAA
Found at i:49197 original size:45 final size:44
Alignment explanation
Indices: 49132--49334 Score: 240
Period size: 45 Copynumber: 4.7 Consensus size: 44
49122 ATCGTACACC
** * *
49132 ACTATTCAAGCCTTTGAGCCTAGCAGGCTATGATGCCTGTGAAAT
1 ACTATTCGGGCCTTCGAGCCTAGCAGGCTATGATG-CGGTGAAAT
*
49177 ACTATTCGGGCCTTCAAGCCTAGCAGGCTATGATGCCGGTGAAAT
1 ACTATTCGGGCCTTCGAGCCTAGCAGGCTATGATG-CGGTGAAAT
*
49222 ACTATTCGGGCCTTCGAGCCTAGCAGGC--T-AT-CGGTGAGAT
1 ACTATTCGGGCCTTCGAGCCTAGCAGGCTATGATGCGGTGAAAT
* *
49262 ACTATTCGGGCCTTCGAGCCTAGTAGGCTATAATGCTGGTGAAAT
1 ACTATTCGGGCCTTCGAGCCTAGCAGGCTATGATGC-GGTGAAAT
*
49307 GA-TA-TCGGG-CTTCGAGCCTAGTAGGCTA
1 -ACTATTCGGGCCTTCGAGCCTAGCAGGCTA
49335 AATGCCGGTG
Statistics
Matches: 143, Mismatches: 9, Indels: 14
0.86 0.05 0.08
Matches are distributed among these distances:
40 35 0.24
42 3 0.02
43 22 0.15
44 6 0.04
45 76 0.53
46 1 0.01
ACGTcount: A:0.24, C:0.23, G:0.27, T:0.27
Consensus pattern (44 bp):
ACTATTCGGGCCTTCGAGCCTAGCAGGCTATGATGCGGTGAAAT
Found at i:49290 original size:85 final size:83
Alignment explanation
Indices: 49170--49334 Score: 242
Period size: 85 Copynumber: 2.0 Consensus size: 83
49160 TATGATGCCT
*
49170 GTGAAATACTATTCGGGCCTTCAAGCCTAGCAGGCTATGATGCCGGTGAAAT-ACTATTCGGGCC
1 GTGAAATACTATTCGGGCCTTCAAGCCTAGCAGGCTATAATGCCGGTGAAATGA-TA-TCGGG-C
49234 TTCGAGCCTAGCAGGCTATCG
63 TTCGAGCCTAGCAGGCTATCG
* * * *
49255 GTGAGATACTATTCGGGCCTTCGAGCCTAGTAGGCTATAATGCTGGTGAAATGATATCGGGCTTC
1 GTGAAATACTATTCGGGCCTTCAAGCCTAGCAGGCTATAATGCCGGTGAAATGATATCGGGCTTC
*
49320 GAGCCTAGTAGGCTA
66 GAGCCTAGCAGGCTA
49335 AATGCCGGTG
Statistics
Matches: 73, Mismatches: 6, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
83 18 0.25
84 5 0.07
85 49 0.67
86 1 0.01
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (83 bp):
GTGAAATACTATTCGGGCCTTCAAGCCTAGCAGGCTATAATGCCGGTGAAATGATATCGGGCTTC
GAGCCTAGCAGGCTATCG
Found at i:54215 original size:12 final size:13
Alignment explanation
Indices: 54187--54219 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
54177 TTATTTCTTT
54187 TTCTCCATCTACC
1 TTCTCCATCTACC
*
54200 TTCTCC-TCTTCC
1 TTCTCCATCTACC
54212 TTCTCCAT
1 TTCTCCAT
54220 AGCCGAACCC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
12 11 0.61
13 7 0.39
ACGTcount: A:0.09, C:0.45, G:0.00, T:0.45
Consensus pattern (13 bp):
TTCTCCATCTACC
Found at i:55298 original size:28 final size:28
Alignment explanation
Indices: 55266--55385 Score: 206
Period size: 28 Copynumber: 4.3 Consensus size: 28
55256 ATTTACTAGA
55266 ATACCCCTATGTATGCAAAATTACCATT
1 ATACCCCTATGTATGCAAAATTACCATT
55294 ATACCCCTATGTATGCAAAATTACCATT
1 ATACCCCTATGTATGCAAAATTACCATT
55322 ATACCCCTATGTATGCAAAATTACCATT
1 ATACCCCTATGTATGCAAAATTACCATT
* * *
55350 AT-CCCCTATGTGTGCAAAATGACCTTT
1 ATACCCCTATGTATGCAAAATTACCATT
55377 ATACCCCTA
1 ATACCCCTA
55386 GGGTTAATTT
Statistics
Matches: 88, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
27 24 0.27
28 64 0.73
ACGTcount: A:0.33, C:0.27, G:0.08, T:0.32
Consensus pattern (28 bp):
ATACCCCTATGTATGCAAAATTACCATT
Found at i:55381 original size:55 final size:56
Alignment explanation
Indices: 55266--55385 Score: 206
Period size: 55 Copynumber: 2.2 Consensus size: 56
55256 ATTTACTAGA
*
55266 ATACCCCTATGTATGCAAAATTACCATTATACCCCTATGTATGCAAAATTACCATT
1 ATACCCCTATGTATGCAAAATTACCATTATACCCCTATGTATGCAAAATGACCATT
* *
55322 ATACCCCTATGTATGCAAAATTACCATTAT-CCCCTATGTGTGCAAAATGACCTTT
1 ATACCCCTATGTATGCAAAATTACCATTATACCCCTATGTATGCAAAATGACCATT
55377 ATACCCCTA
1 ATACCCCTA
55386 GGGTTAATTT
Statistics
Matches: 61, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
55 31 0.51
56 30 0.49
ACGTcount: A:0.33, C:0.27, G:0.08, T:0.32
Consensus pattern (56 bp):
ATACCCCTATGTATGCAAAATTACCATTATACCCCTATGTATGCAAAATGACCATT
Found at i:55534 original size:28 final size:27
Alignment explanation
Indices: 55501--55572 Score: 81
Period size: 27 Copynumber: 2.6 Consensus size: 27
55491 CTGGTGGCTA
**
55501 TGCCACAAATTATCTGTTCTAGTGGCCC
1 TGCCACAAA-TATCTGTTCTAGTGGAAC
**
55529 TGCCACGTATATCTGTTCTAGTGGAAC
1 TGCCACAAATATCTGTTCTAGTGGAAC
*
55556 AGCCACAAAATATCTGT
1 TGCCAC-AAATATCTGT
55573 ATCTGGTGAC
Statistics
Matches: 36, Mismatches: 7, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
27 21 0.58
28 15 0.42
ACGTcount: A:0.26, C:0.25, G:0.18, T:0.31
Consensus pattern (27 bp):
TGCCACAAATATCTGTTCTAGTGGAAC
Found at i:59235 original size:45 final size:44
Alignment explanation
Indices: 59170--59372 Score: 240
Period size: 45 Copynumber: 4.7 Consensus size: 44
59160 ATCGTACACC
** * *
59170 ACTATTCAAGCCTTTGAGCCTAGCAGGCTATGATGCCTGTGAAAT
1 ACTATTCGGGCCTTCGAGCCTAGCAGGCTATGATG-CGGTGAAAT
*
59215 ACTATTCGGGCCTTCAAGCCTAGCAGGCTATGATGCCGGTGAAAT
1 ACTATTCGGGCCTTCGAGCCTAGCAGGCTATGATG-CGGTGAAAT
*
59260 ACTATTCGGGCCTTCGAGCCTAGCAGGC--T-AT-CGGTGAGAT
1 ACTATTCGGGCCTTCGAGCCTAGCAGGCTATGATGCGGTGAAAT
* *
59300 ACTATTCGGGCCTTCGAGCCTAGTAGGCTATAATGCTGGTGAAAT
1 ACTATTCGGGCCTTCGAGCCTAGCAGGCTATGATGC-GGTGAAAT
*
59345 GA-TA-TCGGG-CTTCGAGCCTAGTAGGCTA
1 -ACTATTCGGGCCTTCGAGCCTAGCAGGCTA
59373 AATGCCGGTG
Statistics
Matches: 143, Mismatches: 9, Indels: 14
0.86 0.05 0.08
Matches are distributed among these distances:
40 35 0.24
42 3 0.02
43 22 0.15
44 6 0.04
45 76 0.53
46 1 0.01
ACGTcount: A:0.24, C:0.23, G:0.27, T:0.27
Consensus pattern (44 bp):
ACTATTCGGGCCTTCGAGCCTAGCAGGCTATGATGCGGTGAAAT
Found at i:59328 original size:85 final size:83
Alignment explanation
Indices: 59208--59372 Score: 242
Period size: 85 Copynumber: 2.0 Consensus size: 83
59198 TATGATGCCT
*
59208 GTGAAATACTATTCGGGCCTTCAAGCCTAGCAGGCTATGATGCCGGTGAAAT-ACTATTCGGGCC
1 GTGAAATACTATTCGGGCCTTCAAGCCTAGCAGGCTATAATGCCGGTGAAATGA-TA-TCGGG-C
59272 TTCGAGCCTAGCAGGCTATCG
63 TTCGAGCCTAGCAGGCTATCG
* * * *
59293 GTGAGATACTATTCGGGCCTTCGAGCCTAGTAGGCTATAATGCTGGTGAAATGATATCGGGCTTC
1 GTGAAATACTATTCGGGCCTTCAAGCCTAGCAGGCTATAATGCCGGTGAAATGATATCGGGCTTC
*
59358 GAGCCTAGTAGGCTA
66 GAGCCTAGCAGGCTA
59373 AATGCCGGTG
Statistics
Matches: 73, Mismatches: 6, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
83 18 0.25
84 5 0.07
85 49 0.67
86 1 0.01
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (83 bp):
GTGAAATACTATTCGGGCCTTCAAGCCTAGCAGGCTATAATGCCGGTGAAATGATATCGGGCTTC
GAGCCTAGCAGGCTATCG
Found at i:64255 original size:12 final size:13
Alignment explanation
Indices: 64227--64259 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
64217 TTATTTCTTT
64227 TTCTCCATCTACC
1 TTCTCCATCTACC
*
64240 TTCTCC-TCTTCC
1 TTCTCCATCTACC
64252 TTCTCCAT
1 TTCTCCAT
64260 AGCCGAACCC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
12 11 0.61
13 7 0.39
ACGTcount: A:0.09, C:0.45, G:0.00, T:0.45
Consensus pattern (13 bp):
TTCTCCATCTACC
Found at i:65341 original size:28 final size:28
Alignment explanation
Indices: 65309--65428 Score: 206
Period size: 28 Copynumber: 4.3 Consensus size: 28
65299 ATTTACTAGA
65309 ATACCCCTATGTATGCAAAATTACCATT
1 ATACCCCTATGTATGCAAAATTACCATT
65337 ATACCCCTATGTATGCAAAATTACCATT
1 ATACCCCTATGTATGCAAAATTACCATT
65365 ATACCCCTATGTATGCAAAATTACCATT
1 ATACCCCTATGTATGCAAAATTACCATT
* * *
65393 AT-CCCCTATGTGTGCAAAATGACCTTT
1 ATACCCCTATGTATGCAAAATTACCATT
65420 ATACCCCTA
1 ATACCCCTA
65429 GGGTTAATTT
Statistics
Matches: 88, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
27 24 0.27
28 64 0.73
ACGTcount: A:0.33, C:0.27, G:0.08, T:0.32
Consensus pattern (28 bp):
ATACCCCTATGTATGCAAAATTACCATT
Found at i:65424 original size:55 final size:56
Alignment explanation
Indices: 65309--65428 Score: 206
Period size: 55 Copynumber: 2.2 Consensus size: 56
65299 ATTTACTAGA
*
65309 ATACCCCTATGTATGCAAAATTACCATTATACCCCTATGTATGCAAAATTACCATT
1 ATACCCCTATGTATGCAAAATTACCATTATACCCCTATGTATGCAAAATGACCATT
* *
65365 ATACCCCTATGTATGCAAAATTACCATTAT-CCCCTATGTGTGCAAAATGACCTTT
1 ATACCCCTATGTATGCAAAATTACCATTATACCCCTATGTATGCAAAATGACCATT
65420 ATACCCCTA
1 ATACCCCTA
65429 GGGTTAATTT
Statistics
Matches: 61, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
55 31 0.51
56 30 0.49
ACGTcount: A:0.33, C:0.27, G:0.08, T:0.32
Consensus pattern (56 bp):
ATACCCCTATGTATGCAAAATTACCATTATACCCCTATGTATGCAAAATGACCATT
Found at i:65575 original size:28 final size:27
Alignment explanation
Indices: 65534--65615 Score: 94
Period size: 28 Copynumber: 3.0 Consensus size: 27
65524 AGGAAGCGTC
65534 CTAGTGGCTA-TGCCACAAATTATCTGTT
1 CTAGTGGC-ACTGCCACAAA-TATCTGTT
* **
65562 CTAGTGGCCCTGCCACGTATATCTGTT
1 CTAGTGGCACTGCCACAAATATCTGTT
*
65589 CTAGTGGCACAGCCACAAAATATCTGT
1 CTAGTGGCACTGCCAC-AAATATCTGT
65616 ATCTGGTGAC
Statistics
Matches: 45, Mismatches: 7, Indels: 4
0.80 0.12 0.07
Matches are distributed among these distances:
27 22 0.49
28 23 0.51
ACGTcount: A:0.24, C:0.26, G:0.20, T:0.30
Consensus pattern (27 bp):
CTAGTGGCACTGCCACAAATATCTGTT
Found at i:69131 original size:44 final size:45
Alignment explanation
Indices: 68962--69125 Score: 251
Period size: 44 Copynumber: 3.7 Consensus size: 45
68952 TATCGTATAG
*
68962 TACTATTCGGGCCTTTGAGCCTAGCAAGCTATGATGCCGGTGAAA
1 TACTATTCGGGCCTTCGAGCCTAGCAAGCTATGATGCCGGTGAAA
* *
69007 TACTATTCGGGCCTTCGATCC-AGCAGGCTATGATGCCGGTGAAA
1 TACTATTCGGGCCTTCGAGCCTAGCAAGCTATGATGCCGGTGAAA
* * *
69051 TACTATTCAGGCCTTCGAGCCTAG-AGGCTATGATGCCGGTGAGA
1 TACTATTCGGGCCTTCGAGCCTAGCAAGCTATGATGCCGGTGAAA
*
69095 TACTATTCGCGCCTTCGAGCCTAGCAAGCTA
1 TACTATTCGGGCCTTCGAGCCTAGCAAGCTA
69126 AATGCCAGTG
Statistics
Matches: 108, Mismatches: 9, Indels: 4
0.89 0.07 0.03
Matches are distributed among these distances:
44 82 0.76
45 26 0.24
ACGTcount: A:0.23, C:0.25, G:0.26, T:0.26
Consensus pattern (45 bp):
TACTATTCGGGCCTTCGAGCCTAGCAAGCTATGATGCCGGTGAAA
Found at i:70118 original size:29 final size:30
Alignment explanation
Indices: 70067--70133 Score: 118
Period size: 29 Copynumber: 2.3 Consensus size: 30
70057 TACAAGTGGG
70067 GCCCGTGTGTCACACACGACCTAGGCATAC
1 GCCCGTGTGTCACACACGACCTAGGCATAC
*
70097 GCCCGTGTG-CACACACGGCCTAGGCATAC
1 GCCCGTGTGTCACACACGACCTAGGCATAC
70126 GCCCGTGT
1 GCCCGTGT
70134 ACCCAACCGT
Statistics
Matches: 36, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
29 27 0.75
30 9 0.25
ACGTcount: A:0.19, C:0.37, G:0.27, T:0.16
Consensus pattern (30 bp):
GCCCGTGTGTCACACACGACCTAGGCATAC
Found at i:84974 original size:43 final size:42
Alignment explanation
Indices: 84927--85031 Score: 104
Period size: 43 Copynumber: 2.5 Consensus size: 42
84917 TCCTAGATAG
* * *
84927 GGTCTTACACGAAATCTTATAAT-GATGCCAATGTCCCAAACAT
1 GGTCTTACACGAAATC--ACAATAAATGCCAAAGTCCCAAACAT
* * *
84970 GGTCTTACATGTAATCACAATACAATGCCAAAGTCCCAGACAT
1 GGTCTTACACGAAATCACAATA-AATGCCAAAGTCCCAAACAT
* *
85013 GGTCTTACATGTAATCACA
1 GGTCTTACACGAAATCACA
85032 TCTCGATAAC
Statistics
Matches: 54, Mismatches: 6, Indels: 4
0.84 0.09 0.06
Matches are distributed among these distances:
41 4 0.07
43 50 0.93
ACGTcount: A:0.35, C:0.24, G:0.14, T:0.27
Consensus pattern (42 bp):
GGTCTTACACGAAATCACAATAAATGCCAAAGTCCCAAACAT
Found at i:86722 original size:50 final size:50
Alignment explanation
Indices: 86638--86886 Score: 259
Period size: 50 Copynumber: 5.0 Consensus size: 50
86628 ATCACTCATT
* * * * * *
86638 TGGCCAAATATACAAGGTCAAATATAATAGCACATATGTGCTTACCGATA
1 TGGCCGAATATGCAAGATCAAATATAATATCACATATGTACTTACCTATA
* * *
86688 TCGCCGAATATGCAAGATCAAATTTAATATCACATATGTGCTTACCTATA
1 TGGCCGAATATGCAAGATCAAATATAATATCACATATGTACTTACCTATA
* * * * * *
86738 TAGACGAATATGAAAGATCAAATTTAACATCACATATGTACTTACTTATA
1 TGGCCGAATATGCAAGATCAAATATAATATCACATATGTACTTACCTATA
* * *
86788 TGGCCGAATATGCAA-ATTCAAATATAATATCTCATTTGTACATACCT-TCA
1 TGGCCGAATATGCAAGA-TCAAATATAATATCACATATGTACTTACCTAT-A
* * * * *
86838 TGGCCGAATATTCAAGATCCAATACAACATCACATATGTACATACCTAT
1 TGGCCGAATATGCAAGATCAAATATAATATCACATATGTACTTACCTAT
86887 GCGGCCAAAT
Statistics
Matches: 167, Mismatches: 28, Indels: 7
0.83 0.14 0.03
Matches are distributed among these distances:
49 2 0.01
50 163 0.98
51 2 0.01
ACGTcount: A:0.39, C:0.19, G:0.12, T:0.30
Consensus pattern (50 bp):
TGGCCGAATATGCAAGATCAAATATAATATCACATATGTACTTACCTATA
Found at i:89444 original size:129 final size:129
Alignment explanation
Indices: 89214--89471 Score: 464
Period size: 129 Copynumber: 2.0 Consensus size: 129
89204 GGATGAAAAG
* *
89214 TAGTACTAAAATTCCGTTTAGTACCTAATGTATCTTCGAGTTTCTTCCAAAACTGTGATGTAAAT
1 TAGTACTAAAATTCAGTTTAGTACCTAATGCATCTTCGAGTTTCTTCCAAAACTGTGATGTAAAT
*
89279 GTCAGATCTCTATCTGACACAATAGAAATAGGTACTCCGTGTAGTCTCACAATCTGAGAAACAT
66 CTCAGATCTCTATCTGACACAATAGAAATAGGTACTCCGTGTAGTCTCACAATCTGAGAAACAT
89343 TAGTACTAAAATTCAGTTTAGTACCTAATGCATCTTCGAGTTTCTTCCAAAACTGTGATGTAAAT
1 TAGTACTAAAATTCAGTTTAGTACCTAATGCATCTTCGAGTTTCTTCCAAAACTGTGATGTAAAT
*
89408 CTC-GAATCTCTATCTGACACAGTAGAAATAGGTACTCCGTGTAGTCTCACAATCTGAGAAACAT
66 CTCAG-ATCTCTATCTGACACAATAGAAATAGGTACTCCGTGTAGTCTCACAATCTGAGAAACAT
89472 ACAATTTAGC
Statistics
Matches: 124, Mismatches: 4, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
128 1 0.01
129 123 0.99
ACGTcount: A:0.33, C:0.20, G:0.16, T:0.32
Consensus pattern (129 bp):
TAGTACTAAAATTCAGTTTAGTACCTAATGCATCTTCGAGTTTCTTCCAAAACTGTGATGTAAAT
CTCAGATCTCTATCTGACACAATAGAAATAGGTACTCCGTGTAGTCTCACAATCTGAGAAACAT
Found at i:94525 original size:50 final size:50
Alignment explanation
Indices: 94447--94712 Score: 284
Period size: 50 Copynumber: 5.3 Consensus size: 50
94437 ATCACTCATT
* * *
94447 TGGCCAAATATACAAGATCAAATATAATAGCACATATGTGCTTACCTATA
1 TGGCCGAATATACAAGATCAAATATAATATCACATATGTACTTACCTATA
* * * *
94497 TGGCCGAATATGCAAGATCAAATTTAATATCACATATGTGCTTAACTATA
1 TGGCCGAATATACAAGATCAAATATAATATCACATATGTACTTACCTATA
* * * * * *
94547 TAGCCGAATATGCAAGATCAAATTTAACATCACATATGTACTTACTTAGA
1 TGGCCGAATATACAAGATCAAATATAATATCACATATGTACTTACCTATA
* * *
94597 TGGCCGAATATACAA-ATTCAAATATAATATCAAATTTGTACATACCT-TCA
1 TGGCCGAATATACAAGA-TCAAATATAATATCACATATGTACTTACCTAT-A
* * * * * * *
94647 TGGCTGAATATTCAAGATCCAATACAACATCACATATGTACATACCTATG
1 TGGCCGAATATACAAGATCAAATATAATATCACATATGTACTTACCTATA
*
94697 TGGCTGAATATACAAG
1 TGGCCGAATATACAAG
94713 GTCATTTAGC
Statistics
Matches: 183, Mismatches: 29, Indels: 8
0.83 0.13 0.04
Matches are distributed among these distances:
49 1 0.01
50 180 0.98
51 2 0.01
ACGTcount: A:0.40, C:0.18, G:0.12, T:0.30
Consensus pattern (50 bp):
TGGCCGAATATACAAGATCAAATATAATATCACATATGTACTTACCTATA
Found at i:101600 original size:28 final size:28
Alignment explanation
Indices: 101568--101629 Score: 106
Period size: 28 Copynumber: 2.2 Consensus size: 28
101558 ATTTACTAGA
*
101568 ATACCCCTATGTATGCAAAATTACCATT
1 ATACCCCTATGTATGCAAAATGACCATT
*
101596 ATACCCCTATGTATGCAAAATGACCTTT
1 ATACCCCTATGTATGCAAAATGACCATT
101624 ATACCC
1 ATACCC
101630 TTAGGGTTAA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.34, C:0.27, G:0.08, T:0.31
Consensus pattern (28 bp):
ATACCCCTATGTATGCAAAATGACCATT
Found at i:102316 original size:19 final size:19
Alignment explanation
Indices: 102292--102330 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
102282 TTAATTATTT
* *
102292 TTTTATGGTTTTGTTTTAC
1 TTTTATGATTTTATTTTAC
*
102311 TTTTATTATTTTATTTTAC
1 TTTTATGATTTTATTTTAC
102330 T
1 T
102331 ATGATGAAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.15, C:0.05, G:0.08, T:0.72
Consensus pattern (19 bp):
TTTTATGATTTTATTTTAC
Found at i:103862 original size:20 final size:20
Alignment explanation
Indices: 103837--103882 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
103827 ATTGGGCATT
103837 GCCCATATT-AACACAGTTGG
1 GCCCATATTCAACACAGTT-G
*
103857 GCCCAT-TTCAATACAGTTG
1 GCCCATATTCAACACAGTTG
103876 GCCCATA
1 GCCCATA
103883 ACAAAGCAGT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
19 9 0.39
20 14 0.61
ACGTcount: A:0.28, C:0.28, G:0.17, T:0.26
Consensus pattern (20 bp):
GCCCATATTCAACACAGTTG
Found at i:114508 original size:49 final size:49
Alignment explanation
Indices: 114451--114550 Score: 166
Period size: 49 Copynumber: 2.0 Consensus size: 49
114441 CTTACCTGAC
* *
114451 CTTTCACTATTCATAAATATAATCTGCCTTC-CATTTTGCTGATAATTCA
1 CTTTCACTATTCATAAATATAATCTACCTTCTC-TTTTGCTGACAATTCA
114500 CTTTCACTATTCATAAATATAATCTACCTTCTCTTTTGCTGACAATTCA
1 CTTTCACTATTCATAAATATAATCTACCTTCTCTTTTGCTGACAATTCA
114549 CT
1 CT
114551 GTAATTTAAC
Statistics
Matches: 48, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
49 47 0.98
50 1 0.02
ACGTcount: A:0.28, C:0.24, G:0.05, T:0.43
Consensus pattern (49 bp):
CTTTCACTATTCATAAATATAATCTACCTTCTCTTTTGCTGACAATTCA
Found at i:118779 original size:20 final size:19
Alignment explanation
Indices: 118754--118803 Score: 54
Period size: 15 Copynumber: 2.7 Consensus size: 19
118744 TCTCATTTTC
118754 TACCTTCTTCTTTACTCACT
1 TACCTTCTT-TTTACTCACT
118774 TA-C--C-TTTTACTCACT
1 TACCTTCTTTTTACTCACT
118789 TACCTTCTTTCTTAC
1 TACCTTCTTT-TTAC
118804 CTGACCTTTC
Statistics
Matches: 25, Mismatches: 0, Indels: 10
0.71 0.00 0.29
Matches are distributed among these distances:
15 12 0.48
16 2 0.08
17 1 0.04
18 1 0.04
19 3 0.12
20 6 0.24
ACGTcount: A:0.16, C:0.34, G:0.00, T:0.50
Consensus pattern (19 bp):
TACCTTCTTTTTACTCACT
Found at i:118784 original size:15 final size:15
Alignment explanation
Indices: 118764--118794 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
118754 TACCTTCTTC
118764 TTTACTCACTTACCT
1 TTTACTCACTTACCT
118779 TTTACTCACTTACCT
1 TTTACTCACTTACCT
118794 T
1 T
118795 CTTTCTTACC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.19, C:0.32, G:0.00, T:0.48
Consensus pattern (15 bp):
TTTACTCACTTACCT
Done.