Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold632
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: 52786
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.31
Found at i:448 original size:1 final size:1
Alignment explanation
Indices: 444--562 Score: 85
Period size: 1 Copynumber: 119.0 Consensus size: 1
434 CGTCCTTCGC
* * * * * * * * *
444 AAAAAAAAAACAAAAACAAAACAAAACAAACAAACAAAAAAAAACAAAAAAAAAACAAAAAACAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* * * * * * * *
509 ATAAAACAAAACAAAAAACAAACAAAAAACAAACAAAAAAAAAAAAAACAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
563 CGAAAAGGGT
Statistics
Matches: 84, Mismatches: 34, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
1 84 1.00
ACGTcount: A:0.86, C:0.13, G:0.00, T:0.01
Consensus pattern (1 bp):
A
Found at i:459 original size:11 final size:11
Alignment explanation
Indices: 443--568 Score: 141
Period size: 11 Copynumber: 11.5 Consensus size: 11
433 GCGTCCTTCG
443 CAAAAAAAAAA
1 CAAAAAAAAAA
*
454 CAAAAACAAAA
1 CAAAAAAAAAA
465 CAAAACAAACAAA
1 CAAAA-AAA-AAA
478 C-AAAAAAAAA
1 CAAAAAAAAAA
488 CAAAAAAAAAA
1 CAAAAAAAAAA
*
499 CAAAAAACAAA
1 CAAAAAAAAAA
* *
510 -TAAAACAAAA
1 CAAAAAAAAAA
*
520 CAAAAAACAAA
1 CAAAAAAAAAA
*
531 CAAAAAACAAA
1 CAAAAAAAAAA
542 CAAAAAAAAAA
1 CAAAAAAAAAA
*
553 -AAAACAAAAA
1 CAAAAAAAAAA
563 CGAAAA
1 C-AAAA
569 GGGTCCGAAT
Statistics
Matches: 98, Mismatches: 11, Indels: 11
0.82 0.09 0.09
Matches are distributed among these distances:
10 20 0.20
11 65 0.66
12 9 0.09
13 4 0.04
ACGTcount: A:0.84, C:0.14, G:0.01, T:0.01
Consensus pattern (11 bp):
CAAAAAAAAAA
Found at i:507 original size:32 final size:32
Alignment explanation
Indices: 445--568 Score: 169
Period size: 32 Copynumber: 3.8 Consensus size: 32
435 GTCCTTCGCA
*
445 AAAAAAAAACAAAAACAAAACAAAACAAACAAAC
1 AAAAAAAAACAAAAAAAAAAC-AAA-AAACAAAC
*
479 AAAAAAAAACAAAAAAAAAACAAAAAACAAAT
1 AAAAAAAAACAAAAAAAAAACAAAAAACAAAC
* *
511 AAAACAAAACAAAAAACAAACAAAAAACAAAC
1 AAAAAAAAACAAAAAAAAAACAAAAAACAAAC
*
543 AAAAAAAAA-AAAAACAAAAACGAAAA
1 AAAAAAAAACAAAAA-AAAAACAAAAA
569 GGGTCCGAAT
Statistics
Matches: 81, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
31 5 0.06
32 53 0.65
33 3 0.04
34 20 0.25
ACGTcount: A:0.85, C:0.14, G:0.01, T:0.01
Consensus pattern (32 bp):
AAAAAAAAACAAAAAAAAAACAAAAAACAAAC
Found at i:568 original size:7 final size:6
Alignment explanation
Indices: 443--568 Score: 95
Period size: 6 Copynumber: 21.0 Consensus size: 6
433 GCGTCCTTCG
443 CAAAAA -AAAAA CAAAAA C-AAAA C-AAAA CAAACAA -ACAAAA -AAAAA
1 CAAAAA CAAAAA CAAAAA CAAAAA CAAAAA CAAA-AA CA-AAAA CAAAAA
* *
488 CAAAAA -AAAAA CAAAAAA CAAATAA AACAAAA CAAAAA -ACAAA CAAAAAA
1 CAAAAA CAAAAA C-AAAAA CAAA-AA CA-AAAA CAAAAA CAAAAA C-AAAAA
* * *
538 CAAACAA AAAAAA AAAAAA CAAAAA CGAAAA
1 CAAA-AA CAAAAA CAAAAA CAAAAA CAAAAA
569 GGGTCCGAAT
Statistics
Matches: 101, Mismatches: 7, Indels: 24
0.77 0.05 0.18
Matches are distributed among these distances:
5 28 0.28
6 45 0.45
7 26 0.26
8 2 0.02
ACGTcount: A:0.84, C:0.14, G:0.01, T:0.01
Consensus pattern (6 bp):
CAAAAA
Found at i:4334 original size:33 final size:33
Alignment explanation
Indices: 4288--4423 Score: 254
Period size: 33 Copynumber: 4.1 Consensus size: 33
4278 TACATTGTAA
*
4288 AATGTATCAATACAATGAGCAATGTATCGATAC
1 AATGTATCGATACAATGAGCAATGTATCGATAC
4321 AATGTATCGATACAATGAGCAATGTATCGATAC
1 AATGTATCGATACAATGAGCAATGTATCGATAC
*
4354 AATGTATAGATACAATGAGCAATGTATCGATAC
1 AATGTATCGATACAATGAGCAATGTATCGATAC
4387 AATGTATCGATACAATGAGCAATGTATCGATAC
1 AATGTATCGATACAATGAGCAATGTATCGATAC
4420 AATG
1 AATG
4424 AACAATGTAT
Statistics
Matches: 100, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 100 1.00
ACGTcount: A:0.41, C:0.14, G:0.18, T:0.27
Consensus pattern (33 bp):
AATGTATCGATACAATGAGCAATGTATCGATAC
Found at i:4343 original size:20 final size:19
Alignment explanation
Indices: 4268--4441 Score: 132
Period size: 20 Copynumber: 9.8 Consensus size: 19
4258 AAAATGCCTG
* *
4268 AATGTATCGATACATTGTAA
1 AATGTATCGATACAATG-AC
*
4288 AATGTATCAATACAATGAGC
1 AATGTATCGATACAATGA-C
4308 AATGTATCG-----AT-AC
1 AATGTATCGATACAATGAC
4321 AATGTATCGATACAATGAGC
1 AATGTATCGATACAATGA-C
4341 AATGTATCG-----AT-AC
1 AATGTATCGATACAATGAC
*
4354 AATGTATAGATACAATGAGC
1 AATGTATCGATACAATGA-C
4374 AATGTATCG-----AT-AC
1 AATGTATCGATACAATGAC
4387 AATGTATCGATACAATGAGC
1 AATGTATCGATACAATGA-C
4407 AATGTATCGATACAATGAAC
1 AATGTATCGATACAATG-AC
4427 AATGTATCGATACAA
1 AATGTATCGATACAA
4442 ATTGTGAAAA
Statistics
Matches: 125, Mismatches: 6, Indels: 46
0.71 0.03 0.26
Matches are distributed among these distances:
13 29 0.23
14 3 0.02
15 6 0.05
18 6 0.05
19 4 0.03
20 76 0.61
21 1 0.01
ACGTcount: A:0.42, C:0.14, G:0.17, T:0.28
Consensus pattern (19 bp):
AATGTATCGATACAATGAC
Found at i:4377 original size:53 final size:53
Alignment explanation
Indices: 4319--4441 Score: 153
Period size: 53 Copynumber: 2.3 Consensus size: 53
4309 ATGTATCGAT
*
4319 ACAATGTATCGATACAATG-AGCAATGTATCGAT-A-CAATGTATAGATACAATGA
1 ACAATGTATCGATACAATGTAGCAA--TA-CAATGAGCAATGTATAGATACAATGA
* * * *
4372 GCAATGTATCGATACAATGTATCGATACAATGAGCAATGTATCGATACAATGA
1 ACAATGTATCGATACAATGTAGCAATACAATGAGCAATGTATAGATACAATGA
4425 ACAATGTATCGATACAA
1 ACAATGTATCGATACAA
4442 ATTGTGAAAA
Statistics
Matches: 61, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
51 3 0.05
52 3 0.05
53 52 0.85
54 3 0.05
ACGTcount: A:0.42, C:0.15, G:0.17, T:0.26
Consensus pattern (53 bp):
ACAATGTATCGATACAATGTAGCAATACAATGAGCAATGTATAGATACAATGA
Found at i:4422 original size:13 final size:13
Alignment explanation
Indices: 4307--4403 Score: 101
Period size: 13 Copynumber: 8.4 Consensus size: 13
4297 ATACAATGAG
4307 CAATGTATCGATA
1 CAATGTATCGATA
4320 CAATGTATCGATA
1 CAATGTATCGATA
4333 CAATG-A--G---
1 CAATGTATCGATA
4340 CAATGTATCGATA
1 CAATGTATCGATA
*
4353 CAATGTATAGATA
1 CAATGTATCGATA
4366 CAATG-A--G---
1 CAATGTATCGATA
4373 CAATGTATCGATA
1 CAATGTATCGATA
4386 CAATGTATCGATA
1 CAATGTATCGATA
4399 CAATG
1 CAATG
4404 AGCAATGTAT
Statistics
Matches: 71, Mismatches: 1, Indels: 24
0.74 0.01 0.25
Matches are distributed among these distances:
7 10 0.14
8 2 0.03
10 4 0.06
12 2 0.03
13 53 0.75
ACGTcount: A:0.40, C:0.14, G:0.18, T:0.28
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:7309 original size:7 final size:7
Alignment explanation
Indices: 7297--7328 Score: 64
Period size: 7 Copynumber: 4.6 Consensus size: 7
7287 AGGATTTTTC
7297 TTAATTT
1 TTAATTT
7304 TTAATTT
1 TTAATTT
7311 TTAATTT
1 TTAATTT
7318 TTAATTT
1 TTAATTT
7325 TTAA
1 TTAA
7329 AATTTATCAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (7 bp):
TTAATTT
Found at i:7717 original size:168 final size:168
Alignment explanation
Indices: 7315--7759 Score: 469
Period size: 167 Copynumber: 2.7 Consensus size: 168
7305 TAATTTTTAA
* * * * * * * *
7315 TTTTTAATTTTTAAAATTTATCAAATATTATTATTTATTTCAT-GTAATTAAGTTTTCAAAAGTT
1 TTTTCAATTTTTAAAATTCATCAAATATCATCATTTATTTCATATTAATTCAGTTTTAAAAAATT
* * **
7379 CATTCACTTTCATCAGTTTTTGATTTTTTTCCTTGAAATTCCCTTTTTTTCCCAAATACGGTGTT
66 CATTCACTTTCATCAGTTTTTGATCTTTTTCCTTGAAACTCCCTTTTTTTCCCAAATACAATGTT
* *
7444 TTCTACTTCGTAAATTTTTTTGAGAAAATTTTTCTTGG
131 TTCTACTTCGTAAATTTTTCTGAGAAAATTTCTCTTGG
* * * *
7482 TTTTTAATTTTTAAAATTCTTCAAATATTATCATTTATTTCATATTAATTCAGTTTTCAAAAATT
1 TTTTCAATTTTTAAAATTCATCAAATATCATCATTTATTTCATATTAATTCAGTTTTAAAAAATT
* *
7547 CATTCA-TTTGCATGAGTTTTTGATCTTTTTCCTTGAAACT-CCTTTTTTT-CGAAATACAATGT
66 CATTCACTTT-CATCAGTTTTTGATCTTTTTCCTTGAAACTCCCTTTTTTTCCCAAATACAATGT
* * *
7609 TTTCTACTTTGTAAATTTTTCCTG-G-AGATTTCTGTTGG
130 TTTCTACTTCGTAAATTTTT-CTGAGAAAATTTCTCTTGG
* * * * * *
7647 TTTTCCATTTTTAAAATTGATCAAA-ATCATTATTTGA-TTCATATTAATTCATTTTTTAAAAAG
1 TTTTCAATTTTTAAAATTCATCAAATATCATCATTT-ATTTCATATTAATTCAGTTTTAAAAAAT
* * ** * *
7710 TAATTCATTTTCAT-AAATTTTG-TATTTTTCTTTGAAATCTCCCTTTTTTT
65 TCATTCACTTTCATCAGTTTTTGATCTTTTTCCTTGAAA-CTCCCTTTTTTT
7760 GAAAAATCGA
Statistics
Matches: 240, Mismatches: 31, Indels: 17
0.83 0.11 0.06
Matches are distributed among these distances:
162 13 0.05
163 8 0.03
164 49 0.20
165 35 0.15
166 30 0.12
167 54 0.22
168 51 0.21
ACGTcount: A:0.27, C:0.13, G:0.08, T:0.53
Consensus pattern (168 bp):
TTTTCAATTTTTAAAATTCATCAAATATCATCATTTATTTCATATTAATTCAGTTTTAAAAAATT
CATTCACTTTCATCAGTTTTTGATCTTTTTCCTTGAAACTCCCTTTTTTTCCCAAATACAATGTT
TTCTACTTCGTAAATTTTTCTGAGAAAATTTCTCTTGG
Found at i:7757 original size:164 final size:168
Alignment explanation
Indices: 7315--7763 Score: 490
Period size: 164 Copynumber: 2.7 Consensus size: 168
7305 TAATTTTTAA
* * * * *
7315 TTTTTAATTTTTAAAATTTATCAAATATTATTATTTATTTCAT-GTAATT-AAGTTTTCAAAAGT
1 TTTTCAATTTTTAAAATTCATCAAATATTATTATTTATTTCATATTAATTCAATTTTTAAAAAG-
* * * **
7378 TCATTCACTTTCATCAGTTTTTGATTTTTTTCCTTGAAAT-TCCCTTTTTTTCCCAAATACGGTG
65 TCATTCATTTTCATCAGTTTTTGATATTTTTCCTTGAAATCTCCCTTTTTTT-CGAAATACAATG
* *
7442 TTTTCTACTTCGTAAATTTTTTTGAGAAAATTTTTCTTGG
129 TTTTCTACTTCGTAAATTTTTCTGAGAAAATTTCTCTTGG
* * * * * *
7482 TTTTTAATTTTTAAAATTCTTCAAATATTATCATTTATTTCATATTAATTCAGTTTTCAAAAATT
1 TTTTCAATTTTTAAAATTCATCAAATATTATTATTTATTTCATATTAATTCAATTTTTAAAAAGT
* * *
7547 CATTCATTTGCATGAGTTTTTGATCTTTTTCCTTGAAA-CT-CCTTTTTTTCGAAATACAATGTT
66 CATTCATTTTCATCAGTTTTTGATATTTTTCCTTGAAATCTCCCTTTTTTTCGAAATACAATGTT
* * *
7610 TTCTACTTTGTAAATTTTTCCTG-G-AGATTTCTGTTGG
131 TTCTACTTCGTAAATTTTT-CTGAGAAAATTTCTCTTGG
* * * *
7647 TTTTCCATTTTTAAAATTGATCAAA-ATCATTATTTGA-TTCATATTAATTCATTTTTTAAAAAG
1 TTTTCAATTTTTAAAATTCATCAAATATTATTATTT-ATTTCATATTAATTCAATTTTTAAAAAG
* ** *
7710 TAATTCATTTTCAT-AAATTTTG-TATTTTTCTTTGAAATCTCCCTTTTTTT-GAAA
65 TCATTCATTTTCATCAGTTTTTGATATTTTTCCTTGAAATCTCCCTTTTTTTCGAAA
7764 AATCGAGTTT
Statistics
Matches: 239, Mismatches: 36, Indels: 18
0.82 0.12 0.06
Matches are distributed among these distances:
162 13 0.05
163 12 0.05
164 52 0.22
165 32 0.13
166 30 0.13
167 51 0.21
168 41 0.17
169 8 0.03
ACGTcount: A:0.28, C:0.12, G:0.08, T:0.52
Consensus pattern (168 bp):
TTTTCAATTTTTAAAATTCATCAAATATTATTATTTATTTCATATTAATTCAATTTTTAAAAAGT
CATTCATTTTCATCAGTTTTTGATATTTTTCCTTGAAATCTCCCTTTTTTTCGAAATACAATGTT
TTCTACTTCGTAAATTTTTCTGAGAAAATTTCTCTTGG
Found at i:9539 original size:131 final size:130
Alignment explanation
Indices: 9349--9602 Score: 357
Period size: 131 Copynumber: 1.9 Consensus size: 130
9339 CCCCGTTAAT
* * *
9349 TTAAACAAATATTAATTATTTTTAATCTTTTACATTCCTATGGGTATCTATAGGGGTATAAAAAA
1 TTAAACAAATATTAATCATTTTTAATCTTTTACATTCCTATGGGTATCTATAAGAGTATAAAAAA
* * * *
9414 TTTCAAAAACTTTTCGTATTTTTTCGGGTATCCATTAAGGTACGAAATGATTATTTTTCCAAACA
66 TTTAAAAAACTTTTCGTATCTTTTCGGGTATACATTAAGGTACAAAATGATTATTTTTCCAAACA
* * *
9479 TTAAA-AAATATTAATCATTTTTTAATTTTTTTATATTCCTATGGGTATCTGTAAGAGTATAAAA
1 TTAAACAAATATTAATCA-TTTTTAA-TCTTTTACATTCCTATGGGTATCTATAAGAGTATAAAA
* * * *
9543 GATTTAAAAAATTTTTTGTATCTTTTCGGGTATACATTAAGGTACAAAATGATTTTTTTT
64 AATTTAAAAAACTTTTCGTATCTTTTCGGGTATACATTAAGGTACAAAATGATTATTTTT
9603 AGAAATAATT
Statistics
Matches: 108, Mismatches: 14, Indels: 3
0.86 0.11 0.02
Matches are distributed among these distances:
129 11 0.10
130 12 0.11
131 85 0.79
ACGTcount: A:0.35, C:0.09, G:0.11, T:0.44
Consensus pattern (130 bp):
TTAAACAAATATTAATCATTTTTAATCTTTTACATTCCTATGGGTATCTATAAGAGTATAAAAAA
TTTAAAAAACTTTTCGTATCTTTTCGGGTATACATTAAGGTACAAAATGATTATTTTTCCAAACA
Found at i:10460 original size:32 final size:30
Alignment explanation
Indices: 10424--10482 Score: 75
Period size: 32 Copynumber: 1.9 Consensus size: 30
10414 GAAATCAAAT
10424 ACAAAGAGCT-TAGAAAAATAATAACAATATGA
1 ACAAA-AGCTCTAGAAAAAT-ATAA-AATATGA
*
10456 ACAAAAGCTCTTGAAAAATATAAAATA
1 ACAAAAGCTCTAGAAAAATATAAAATA
10483 CTTTGATCTA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
30 4 0.16
31 8 0.32
32 13 0.52
ACGTcount: A:0.59, C:0.10, G:0.10, T:0.20
Consensus pattern (30 bp):
ACAAAAGCTCTAGAAAAATATAAAATATGA
Found at i:10715 original size:20 final size:20
Alignment explanation
Indices: 10673--10711 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
10663 CGTGTGAATG
* *
10673 TATCGATACAATTTTTGATA
1 TATCGATACAATATTTGAAA
10693 TATCGATAC-ATATTTGAAA
1 TATCGATACAATATTTGAAA
10712 ATATAGCCGT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.38, C:0.10, G:0.10, T:0.41
Consensus pattern (20 bp):
TATCGATACAATATTTGAAA
Found at i:10781 original size:13 final size:13
Alignment explanation
Indices: 10763--10788 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
10753 AATTTTTTTG
10763 TGTATCGATACAT
1 TGTATCGATACAT
10776 TGTATCGATACAT
1 TGTATCGATACAT
10789 ACTTTGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:11547 original size:59 final size:59
Alignment explanation
Indices: 11455--11595 Score: 264
Period size: 59 Copynumber: 2.4 Consensus size: 59
11445 ATTCGTACAT
11455 TCTCCCCCTTAATAAGATAATTTTAGCAAATTTACGCATTCTCCCATTTTATTAAAAAA
1 TCTCCCCCTTAATAAGATAATTTTAGCAAATTTACGCATTCTCCCATTTTATTAAAAAA
*
11514 TCTCCCCCTTAATAAGATAATTTTAGCAAATTTACGCATTCTCCCCTTTTATTAAAAAA
1 TCTCCCCCTTAATAAGATAATTTTAGCAAATTTACGCATTCTCCCATTTTATTAAAAAA
*
11573 TCTCCCCCTTAATAAGGTAATTT
1 TCTCCCCCTTAATAAGATAATTT
11596 ATACACATAT
Statistics
Matches: 80, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
59 80 1.00
ACGTcount: A:0.33, C:0.23, G:0.06, T:0.38
Consensus pattern (59 bp):
TCTCCCCCTTAATAAGATAATTTTAGCAAATTTACGCATTCTCCCATTTTATTAAAAAA
Found at i:12953 original size:21 final size:20
Alignment explanation
Indices: 12924--12966 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
12914 GACTAGTGTG
* *
12924 GGGACTGCCCGGTTGTGACCT
1 GGGACTG-CCGGTCGCGACCT
*
12945 GGGAGTGCCGGTCGCGACCT
1 GGGACTGCCGGTCGCGACCT
12965 GG
1 GG
12967 TGGTGCTGCC
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 13 0.68
21 6 0.32
ACGTcount: A:0.09, C:0.28, G:0.44, T:0.19
Consensus pattern (20 bp):
GGGACTGCCGGTCGCGACCT
Found at i:13423 original size:13 final size:13
Alignment explanation
Indices: 13405--13442 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
13395 ATAATCCCCC
13405 TGTATCGATACAG
1 TGTATCGATACAG
*
13418 TGTATCGATACAT
1 TGTATCGATACAG
13431 TGTATCGATACA
1 TGTATCGATACA
13443 AAGAAAAATG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Consensus pattern (13 bp):
TGTATCGATACAG
Found at i:17341 original size:21 final size:21
Alignment explanation
Indices: 17312--17356 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
17302 AAGTTTTTAT
*
17312 TTTTCTTAGCTAAC-TCATTA
1 TTTTCTTAGCCAACTTCATTA
*
17332 TTTTCATTAGCCAACTTCTTTA
1 TTTTC-TTAGCCAACTTCATTA
17354 TTT
1 TTT
17357 CAACTTGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 8 0.38
22 8 0.38
ACGTcount: A:0.22, C:0.20, G:0.04, T:0.53
Consensus pattern (21 bp):
TTTTCTTAGCCAACTTCATTA
Found at i:19596 original size:13 final size:13
Alignment explanation
Indices: 19578--19603 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
19568 AATTTTTTTG
19578 TGTATCGATACAT
1 TGTATCGATACAT
19591 TGTATCGATACAT
1 TGTATCGATACAT
19604 ACTTTGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:29115 original size:20 final size:19
Alignment explanation
Indices: 29087--29161 Score: 87
Period size: 20 Copynumber: 3.8 Consensus size: 19
29077 TTTTACCCTG
*
29087 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTAT-A
* *
29107 ATATATCGATACATGTATGA
1 ATGTATCGATACATTTAT-A
*
29127 ATGTATCGATATATTCTATA
1 ATGTATCGATACATT-TATA
29147 ATGTATCGATACATT
1 ATGTATCGATACATT
29162 ATGTCTTTTT
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
20 43 0.93
21 3 0.07
ACGTcount: A:0.35, C:0.12, G:0.12, T:0.41
Consensus pattern (19 bp):
ATGTATCGATACATTTATA
Found at i:29154 original size:40 final size:39
Alignment explanation
Indices: 29087--29164 Score: 104
Period size: 40 Copynumber: 2.0 Consensus size: 39
29077 TTTTACCCTG
*
29087 ATGTATCGATACATTTTTCAATATATCGATACATGTATGA
1 ATGTATCGATACATTTATCAATATATCGATACAT-TATGA
* *
29127 ATGTATCGATATATTCTAT-AATGTATCGATACATTATG
1 ATGTATCGATACATT-TATCAATATATCGATACATTATG
29165 TCTTTTTACC
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
39 4 0.12
40 28 0.82
41 2 0.06
ACGTcount: A:0.35, C:0.12, G:0.13, T:0.41
Consensus pattern (39 bp):
ATGTATCGATACATTTATCAATATATCGATACATTATGA
Found at i:30104 original size:22 final size:22
Alignment explanation
Indices: 30074--30127 Score: 92
Period size: 21 Copynumber: 2.5 Consensus size: 22
30064 AGCCTTTGAC
*
30074 CATGTATTTTTTTATTATGTTT
1 CATGCATTTTTTTATTATGTTT
30096 CATGCA-TTTTTTATTATGTTT
1 CATGCATTTTTTTATTATGTTT
30117 CATGCATTTTT
1 CATGCATTTTT
30128 AACATGTCCA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
21 21 0.70
22 9 0.30
ACGTcount: A:0.19, C:0.09, G:0.09, T:0.63
Consensus pattern (22 bp):
CATGCATTTTTTTATTATGTTT
Found at i:30128 original size:20 final size:21
Alignment explanation
Indices: 30081--30127 Score: 94
Period size: 21 Copynumber: 2.2 Consensus size: 21
30071 GACCATGTAT
30081 TTTTTTATTATGTTTCATGCA
1 TTTTTTATTATGTTTCATGCA
30102 TTTTTTATTATGTTTCATGCA
1 TTTTTTATTATGTTTCATGCA
30123 TTTTT
1 TTTTT
30128 AACATGTCCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.17, C:0.09, G:0.09, T:0.66
Consensus pattern (21 bp):
TTTTTTATTATGTTTCATGCA
Found at i:30134 original size:20 final size:21
Alignment explanation
Indices: 30081--30134 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
30071 GACCATGTAT
**
30081 TTTTTTATTATGTTTCATGCA
1 TTTTTTAACATGTTTCATGCA
**
30102 TTTTTTATTATGTTTCATGCA
1 TTTTTTAACATGTTTCATGCA
30123 -TTTTTAACATGT
1 TTTTTTAACATGT
30135 CCAGCATCTC
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
20 10 0.32
21 21 0.68
ACGTcount: A:0.20, C:0.09, G:0.09, T:0.61
Consensus pattern (21 bp):
TTTTTTAACATGTTTCATGCA
Found at i:43207 original size:18 final size:18
Alignment explanation
Indices: 43184--43228 Score: 72
Period size: 18 Copynumber: 2.4 Consensus size: 18
43174 TTTACACCAA
43184 AAAAAAAAAAAAAAAAAC
1 AAAAAAAAAAAAAAAAAC
*
43202 AAAAAAACAAAAAAAAAC
1 AAAAAAAAAAAAAAAAAC
43220 AAGAAAAAA
1 AA-AAAAAA
43229 TAGCAAAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
18 19 0.79
19 5 0.21
ACGTcount: A:0.91, C:0.07, G:0.02, T:0.00
Consensus pattern (18 bp):
AAAAAAAAAAAAAAAAAC
Found at i:43238 original size:1 final size:1
Alignment explanation
Indices: 43182--43228 Score: 58
Period size: 1 Copynumber: 47.0 Consensus size: 1
43172 CCTTTACACC
* * * *
43182 AAAAAAAAAAAAAAAAAAACAAAAAAACAAAAAAAAACAAGAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
43229 TAGCAAAAAA
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
1 38 1.00
ACGTcount: A:0.91, C:0.06, G:0.02, T:0.00
Consensus pattern (1 bp):
A
Found at i:44551 original size:28 final size:29
Alignment explanation
Indices: 44485--45529 Score: 1212
Period size: 28 Copynumber: 36.5 Consensus size: 29
44475 CAGTGGCTCG
44485 CAAGTCAGTGGCACTCTTTTCAAAGCCCA
1 CAAGTCAGTGGCACTCTTTTCAAAGCCCA
* *
44514 CAAATTAGTGGCACTCTTTTC-AAGCCCA
1 CAAGTCAGTGGCACTCTTTTCAAAGCCCA
*
44542 CAAGTCAGTGGCAC-CCTTTCAAAGCCCA
1 CAAGTCAGTGGCACTCTTTTCAAAGCCCA
* *
44570 CAAATAAGTGGCACTCTTTTCAAAGCCCA
1 CAAGTCAGTGGCACTCTTTTCAAAGCCCA
* *
44599 CAAGTCAGTGGCAC-CCTTTCAAAGCGCA
1 CAAGTCAGTGGCACTCTTTTCAAAGCCCA
44627 CAAGTCAGTGGCACTCTTTTCAAAGCCCA
1 CAAGTCAGTGGCACTCTTTTCAAAGCCCA
* * * *
44656 CAAGTTATTGGCAC-CCTTTCAGAGCCCA
1 CAAGTCAGTGGCACTCTTTTCAAAGCCCA
* * *
44684 CAAGTGAGTGGC-C-CCTTTCGAAGCCCA
1 CAAGTCAGTGGCACTCTTTTCAAAGCCCA
* * *
44711 CAAGTCAGTGGCAC-CCTTACGAAGCCCA
1 CAAGTCAGTGGCACTCTTTTCAAAGCCCA
*
44739 CAAGTCAGT-GCACT-TTTTCAAAACCCA
1 CAAGTCAGTGGCACTCTTTTCAAAGCCCA
*
44766 CAAGTCAGTGGCAC-CCTTTCAAAGCCACA
1 CAAGTCAGTGGCACTCTTTTCAAAGCC-CA
*
44795 CAAGTCAGTGGCACTCCTTTTAAAAGCCCA
1 CAAGTCAGTGGCACT-CTTTTCAAAGCCCA
44825 CGCAAGTCAGTGGCACTCTTTTCAAAGCCCA
1 --CAAGTCAGTGGCACTCTTTTCAAAGCCCA
*
44856 CAAGTCAGTGGCAC-C-CTTCAAAGCCCA
1 CAAGTCAGTGGCACTCTTTTCAAAGCCCA
44883 CAAGTCAGTGGCACTCTTTTCAAAGCCCA
1 CAAGTCAGTGGCACTCTTTTCAAAGCCCA
*
44912 CAAATCAGTGGCACTCTTTTCAAAGCCCA
1 CAAGTCAGTGGCACTCTTTTCAAAGCCCA
* *
44941 CAAGTGAGTGGCAC-CCTTTCAAAGCCCA
1 CAAGTCAGTGGCACTCTTTTCAAAGCCCA
*
44969 CAAGTCAGTGGCACTCCTTTCAAAGCCCA
1 CAAGTCAGTGGCACTCTTTTCAAAGCCCA
* * *
44998 CAAGGCAGAGGCACTCCTTTCAAAGCCCA
1 CAAGTCAGTGGCACTCTTTTCAAAGCCCA
45027 CAAGTCAGTGGCACTCTTTTCAAAGCCCA
1 CAAGTCAGTGGCACTCTTTTCAAAGCCCA
* *
45056 -AAATCAGTGGCACTCTTTTCAAAGCCTA
1 CAAGTCAGTGGCACTCTTTTCAAAGCCCA
*
45084 CAAATCAGTGGCACTCTTTTCAAAGCCCA
1 CAAGTCAGTGGCACTCTTTTCAAAGCCCA
* * *
45113 CAAGTCAGTGGCACCCTTTT-AGAGCCGA
1 CAAGTCAGTGGCACTCTTTTCAAAGCCCA
* *
45141 CAAGTCAGTGGCAC-CCTTTCGAAGCCCA
1 CAAGTCAGTGGCACTCTTTTCAAAGCCCA
* *
45169 CAAGTTAGTGGCAC-CCTTTCAAAGCCCACA
1 CAAGTCAGTGGCACTCTTTTCAAAG-CC-CA
45199 CAAGTCAGTGGCACTCCTTTT-AAAGCCCA
1 CAAGTCAGTGGCACT-CTTTTCAAAGCCCA
* **
45228 CGCAAGTTAGTGGCAC-CTTTGAAAAGCCCA
1 --CAAGTCAGTGGCACTCTTTTCAAAGCCCA
*
45258 CGAGTCAGTGGCACTC-TTTCAAA-CCCA
1 CAAGTCAGTGGCACTCTTTTCAAAGCCCA
*
45285 CAAGTCAGTGGCAC-CATTTC-AAGCCCA
1 CAAGTCAGTGGCACTCTTTTCAAAGCCCA
* *
45312 CGAGTCAGTGGTAC-CTTTTCAAAGCCCA
1 CAAGTCAGTGGCACTCTTTTCAAAGCCCA
*
45340 CGAGTCAGTGGCACTC-TTTCAAAG-CCA
1 CAAGTCAGTGGCACTCTTTTCAAAGCCCA
*
45367 CAAGTCAGTGGCA-TCCTTTCAAAGCCCA
1 CAAGTCAGTGGCACTCTTTTCAAAGCCCA
* * *
45395 CAAGTCAATGGCATTC-TTTCAAATCCCA
1 CAAGTCAGTGGCACTCTTTTCAAAGCCCA
*
45423 CGCAAGTCAGTGGCACCCTTTT-AAAGCCCA
1 --CAAGTCAGTGGCACTCTTTTCAAAGCCCA
* **
45453 CGCAAGTTAGTAACACTCTTTTCAAAGCCCA
1 --CAAGTCAGTGGCACTCTTTTCAAAGCCCA
** * *
45484 CGTGTCAGTGGCAACTTTTTTCGAAGCCTACA
1 CAAGTCAGTGGC-ACTCTTTTCAAAGCC--CA
*
45516 CAAGTTAGTGGCAC
1 CAAGTCAGTGGCAC
45530 ATTTTTTTTA
Statistics
Matches: 885, Mismatches: 92, Indels: 76
0.84 0.09 0.07
Matches are distributed among these distances:
26 5 0.01
27 145 0.16
28 294 0.33
29 280 0.32
30 78 0.09
31 53 0.06
32 30 0.03
ACGTcount: A:0.28, C:0.31, G:0.18, T:0.22
Consensus pattern (29 bp):
CAAGTCAGTGGCACTCTTTTCAAAGCCCA
Found at i:44554 original size:57 final size:57
Alignment explanation
Indices: 44485--45529 Score: 1244
Period size: 57 Copynumber: 18.2 Consensus size: 57
44475 CAGTGGCTCG
* * *
44485 CAAGTCAGTGGCACTCTTTTCAAAGCCCACAAATTAGTGGCACTCTTTTC-AAGCCCA
1 CAAGTCAGTGGCAC-CCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCA
* *
44542 CAAGTCAGTGGCACCCTTTCAAAGCCCACAAATAAGTGGCACTCTTTTCAAAGCCCA
1 CAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCA
*
44599 CAAGTCAGTGGCACCCTTTCAAAGCGCACAAGTCAGTGGCACTCTTTTCAAAGCCCA
1 CAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCA
* * * * * *
44656 CAAGTTATTGGCACCCTTTCAGAGCCCACAAGTGAGTGGC-C-CCTTTCGAAGCCCA
1 CAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCA
* * *
44711 CAAGTCAGTGGCACCCTTACGAAGCCCACAAGTCAGT-GCACT-TTTTCAAAACCCA
1 CAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCA
*
44766 CAAGTCAGTGGCACCCTTTCAAAGCCACACAAGTCAGTGGCACTCCTTTTAAAAGCCCA
1 CAAGTCAGTGGCACCCTTTCAAAGCC-CACAAGTCAGTGGCACT-CTTTTCAAAGCCCA
* *
44825 CGCAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCAC-C-CTTCAAAGCCCA
1 --CAAGTCAGTGGCAC-CCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCA
* *
44883 CAAGTCAGTGGCACTCTTTTCAAAGCCCACAAATCAGTGGCACTCTTTTCAAAGCCCA
1 CAAGTCAGTGGCAC-CCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCA
* *
44941 CAAGTGAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCA
1 CAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCA
* *
44998 CAAGGCAGAGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCA
1 CAAGTCAGTGGCAC-CCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCA
* * * *
45056 -AAATCAGTGGCACTCTTTTCAAAGCCTACAAATCAGTGGCACTCTTTTCAAAGCCCA
1 CAAGTCAGTGGCAC-CCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCA
* * * * *
45113 CAAGTCAGTGGCACCCTTTTAGAGCCGACAAGTCAGTGGCAC-CCTTTCGAAGCCCA
1 CAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCA
*
45169 CAAGTTAGTGGCACCCTTTCAAAGCCCACACAAGTCAGTGGCACTCCTTTT-AAAGCCCA
1 CAAGTCAGTGGCACCCTTTCAAAG-CC-CACAAGTCAGTGGCACT-CTTTTCAAAGCCCA
* * *
45228 CGCAAGTTAGTGGCA-CCTTTGAAAAGCCCACGAGTCAGTGGCACTC-TTTCAAA-CCCA
1 --CAAGTCAGTGGCACCCTTT-CAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCA
* * *
45285 CAAGTCAGTGGCACCATTTC-AAGCCCACGAGTCAGTGGTAC-CTTTTCAAAGCCCA
1 CAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCA
* * *
45340 CGAGTCAGTGGCACTCTTTCAAAG-CCACAAGTCAGTGGCA-TCCTTTCAAAGCCCA
1 CAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCA
* ** * *
45395 CAAGTCAATGGCATTCTTTCAAATCCCACGCAAGTCAGTGGCACCCTTTT-AAAGCCCA
1 CAAGTCAGTGGCACCCTTTCAAAGCCCA--CAAGTCAGTGGCACTCTTTTCAAAGCCCA
* ** * ** * *
45453 CGCAAGTTAGTAACACTCTTTTCAAAGCCCACGTGTCAGTGGCAACTTTTTTCGAAGCCTACA
1 --CAAGTCAGTGGCAC-CCTTTCAAAGCCCACAAGTCAGTGGC-ACTCTTTTCAAAGCC--CA
*
45516 CAAGTTAGTGGCAC
1 CAAGTCAGTGGCAC
45530 ATTTTTTTTA
Statistics
Matches: 859, Mismatches: 91, Indels: 72
0.84 0.09 0.07
Matches are distributed among these distances:
53 1 0.00
54 29 0.03
55 158 0.18
56 130 0.15
57 250 0.29
58 128 0.15
59 49 0.06
60 26 0.03
61 75 0.09
62 11 0.01
63 2 0.00
ACGTcount: A:0.28, C:0.31, G:0.18, T:0.22
Consensus pattern (57 bp):
CAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCA
Found at i:46118 original size:20 final size:20
Alignment explanation
Indices: 46090--46164 Score: 96
Period size: 20 Copynumber: 3.8 Consensus size: 20
46080 TTTTACCCAG
46090 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
* * * *
46110 ATATATCGATACATGTATGA
1 ATGTATCGATACATTTTTCA
* *
46130 ATGTATCGATATATTCTTCA
1 ATGTATCGATACATTTTTCA
46150 ATGTATCGATACATT
1 ATGTATCGATACATT
46165 ATGTCTTTTA
Statistics
Matches: 44, Mismatches: 11, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.33, C:0.13, G:0.12, T:0.41
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:46150 original size:40 final size:39
Alignment explanation
Indices: 46090--46167 Score: 120
Period size: 40 Copynumber: 2.0 Consensus size: 39
46080 TTTTACCCAG
*
46090 ATGTATCGATACATTTTTCAATATATCGATACATGTATGA
1 ATGTATCGATACATTCTTCAATATATCGATACAT-TATGA
* *
46130 ATGTATCGATATATTCTTCAATGTATCGATACATTATG
1 ATGTATCGATACATTCTTCAATATATCGATACATTATG
46168 TCTTTTACCT
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
39 4 0.11
40 31 0.89
ACGTcount: A:0.33, C:0.13, G:0.13, T:0.41
Consensus pattern (39 bp):
ATGTATCGATACATTCTTCAATATATCGATACATTATGA
Found at i:52130 original size:15 final size:16
Alignment explanation
Indices: 52090--52122 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
52080 AGGGGATCAT
52090 ATCGAAAT-AATGATA
1 ATCGAAATCAATGATA
52105 ATCGAAATCAATG-TA
1 ATCGAAATCAATGATA
52120 ATC
1 ATC
52123 AACATCAAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 13 0.76
16 4 0.24
ACGTcount: A:0.48, C:0.12, G:0.12, T:0.27
Consensus pattern (16 bp):
ATCGAAATCAATGATA
Done.