Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1507
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: 42256
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Found at i:528 original size:18 final size:17
Alignment explanation
Indices: 505--563 Score: 57
Period size: 16 Copynumber: 3.4 Consensus size: 17
495 TCTTGTAAAG
505 AGAAAACAAAGAAAAGAA
1 AGAAAA-AAAGAAAAGAA
* *
523 AGAAAAAGA-AAAAGCA
1 AGAAAAAAAGAAAAGAA
*
539 AGAGAAAAAGAAAATGAA
1 AGAAAAAAAGAAAA-GAA
*
557 ATAAAAA
1 AGAAAAA
564 GAAAAGAGAG
Statistics
Matches: 32, Mismatches: 7, Indels: 4
0.74 0.16 0.09
Matches are distributed among these distances:
16 13 0.41
17 6 0.19
18 13 0.41
ACGTcount: A:0.76, C:0.03, G:0.17, T:0.03
Consensus pattern (17 bp):
AGAAAAAAAGAAAAGAA
Found at i:535 original size:16 final size:16
Alignment explanation
Indices: 512--568 Score: 71
Period size: 16 Copynumber: 3.5 Consensus size: 16
502 AAGAGAAAAC
512 AAAG-AAAAGAAAGAA
1 AAAGAAAAAGAAAGAA
527 AAAGAAAAAGCAAGAGAA
1 AAAGAAAAAG-AA-AGAA
* *
545 AAAGAAAATGAAATAA
1 AAAGAAAAAGAAAGAA
561 AAAGAAAA
1 AAAGAAAA
569 GAGAGGCAAG
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
15 4 0.11
16 16 0.43
17 4 0.11
18 13 0.35
ACGTcount: A:0.77, C:0.02, G:0.18, T:0.04
Consensus pattern (16 bp):
AAAGAAAAAGAAAGAA
Found at i:557 original size:12 final size:11
Alignment explanation
Indices: 512--568 Score: 55
Period size: 12 Copynumber: 5.2 Consensus size: 11
502 AAGAGAAAAC
512 AAAGAAAAGAA
1 AAAGAAAAGAA
*
523 AGA-AAAAGAA
1 AAAGAAAAGAA
*
533 AAAGCAAGAGAA
1 AAAG-AAAAGAA
545 AAAGAAAATGAA
1 AAAGAAAA-GAA
*
557 ATA-AAAAGAA
1 AAAGAAAAGAA
567 AA
1 AA
569 GAGAGGCAAG
Statistics
Matches: 37, Mismatches: 6, Indels: 7
0.74 0.12 0.14
Matches are distributed among these distances:
10 13 0.35
11 9 0.24
12 15 0.41
ACGTcount: A:0.77, C:0.02, G:0.18, T:0.04
Consensus pattern (11 bp):
AAAGAAAAGAA
Found at i:636 original size:12 final size:12
Alignment explanation
Indices: 619--648 Score: 53
Period size: 11 Copynumber: 2.6 Consensus size: 12
609 TTGAGAGAAC
619 TTGAAAAAGCCT
1 TTGAAAAAGCCT
631 TTG-AAAAGCCT
1 TTGAAAAAGCCT
642 TTGAAAA
1 TTGAAAA
649 GCAAAAAGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
11 11 0.65
12 6 0.35
ACGTcount: A:0.43, C:0.13, G:0.17, T:0.27
Consensus pattern (12 bp):
TTGAAAAAGCCT
Found at i:639 original size:11 final size:11
Alignment explanation
Indices: 623--650 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
613 GAGAACTTGA
623 AAAAGCCTTTG
1 AAAAGCCTTTG
634 AAAAGCCTTTG
1 AAAAGCCTTTG
645 AAAAGC
1 AAAAGC
651 AAAAAGAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.43, C:0.18, G:0.18, T:0.21
Consensus pattern (11 bp):
AAAAGCCTTTG
Found at i:2853 original size:30 final size:30
Alignment explanation
Indices: 2819--2915 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
2809 AGCTCACTCC
2819 TAGCTCATA-TTTAGCTCACGAGCTAAACCT
1 TAGCTCA-ACTTTAGCTCACGAGCTAAACCT
* * * * * *
2849 TAGCTCAACTTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
* *
2879 CAGCTCAACTTTAGCTCACGAGCTAAAGCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
2909 TAGCTCA
1 TAGCTCA
2916 TTTTAGTTTA
Statistics
Matches: 51, Mismatches: 15, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
29 1 0.02
30 50 0.98
ACGTcount: A:0.28, C:0.27, G:0.16, T:0.29
Consensus pattern (30 bp):
TAGCTCAACTTTAGCTCACGAGCTAAACCT
Found at i:7585 original size:14 final size:14
Alignment explanation
Indices: 7568--7607 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
7558 CAAATGGAAT
*
7568 GGTAGGAACGAAAG
1 GGTAGGAACAAAAG
7582 GGTAGGAACAAAAG
1 GGTAGGAACAAAAG
* *
7596 GATATGAACAAA
1 GGTAGGAACAAA
7608 TTGGTCGGTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.50, C:0.07, G:0.33, T:0.10
Consensus pattern (14 bp):
GGTAGGAACAAAAG
Found at i:10562 original size:23 final size:22
Alignment explanation
Indices: 10510--10562 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
10500 TCCACGTCTT
*
10510 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
10532 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
10555 TTTCTTTT
1 TTTCTTTT
10563 TCACTCTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:15378 original size:11 final size:12
Alignment explanation
Indices: 15346--15378 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
15336 GAGCTACAGC
15346 AAACTTAATTAT
1 AAACTTAATTAT
*
15358 AAACTGAATTA-
1 AAACTTAATTAT
15369 AAACTTAATT
1 AAACTTAATT
15379 TATTAGAATG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
11 9 0.47
12 10 0.53
ACGTcount: A:0.52, C:0.09, G:0.03, T:0.36
Consensus pattern (12 bp):
AAACTTAATTAT
Found at i:15446 original size:20 final size:21
Alignment explanation
Indices: 15410--15448 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
15400 AGCTGAATCA
*
15410 AGCTGAATTCTAGCTCAAACG
1 AGCTGAATTCGAGCTCAAACG
15431 AGCTGAA-TCGAGCTCAAA
1 AGCTGAATTCGAGCTCAAA
15449 TGAACTAATG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.36, C:0.23, G:0.21, T:0.21
Consensus pattern (21 bp):
AGCTGAATTCGAGCTCAAACG
Found at i:17765 original size:26 final size:26
Alignment explanation
Indices: 17745--17894 Score: 255
Period size: 26 Copynumber: 5.8 Consensus size: 26
17735 AAAATTACTA
17745 AAATACCCCTATAGGGTAAATTATCG
1 AAATACCCCTATAGGGTAAATTATCG
*
17771 AAATACCCTTATAGGGTAAATTATCG
1 AAATACCCCTATAGGGTAAATTATCG
17797 AAATACCCCTATAGGGTAAATTATCG
1 AAATACCCCTATAGGGTAAATTATCG
* *
17823 AAATACCCTTATAGTGTAAATTATCG
1 AAATACCCCTATAGGGTAAATTATCG
* *
17849 AAATACCCTTATAGTGTAAATTATCG
1 AAATACCCCTATAGGGTAAATTATCG
17875 AAATACCCCTATAGGGTAAA
1 AAATACCCCTATAGGGTAAA
17895 ATGACTATTT
Statistics
Matches: 118, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 118 1.00
ACGTcount: A:0.39, C:0.17, G:0.14, T:0.29
Consensus pattern (26 bp):
AAATACCCCTATAGGGTAAATTATCG
Found at i:19705 original size:30 final size:30
Alignment explanation
Indices: 19658--19751 Score: 163
Period size: 30 Copynumber: 3.2 Consensus size: 30
19648 CAAGTAGCCG
19658 AAGCTAG-TTAAATCGCACACTTAGTGCCA
1 AAGCTAGTTTAAATCGCACACTTAGTGCCA
*
19687 AAGCTAGTTTAGATCGCACACTTAGTGCCA
1 AAGCTAGTTTAAATCGCACACTTAGTGCCA
*
19717 AAGCTAGTTTAAATCGCACACTAAGTGCCA
1 AAGCTAGTTTAAATCGCACACTTAGTGCCA
19747 AAGCT
1 AAGCT
19752 TCCGATTCAT
Statistics
Matches: 61, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
29 7 0.11
30 54 0.89
ACGTcount: A:0.34, C:0.23, G:0.18, T:0.24
Consensus pattern (30 bp):
AAGCTAGTTTAAATCGCACACTTAGTGCCA
Found at i:23883 original size:13 final size:12
Alignment explanation
Indices: 23853--23908 Score: 53
Period size: 12 Copynumber: 4.7 Consensus size: 12
23843 AATGTGAAAC
*
23853 AAAAAGAAATTG
1 AAAAAGAAGTTG
23865 AAAAAGAAGTTG
1 AAAAAGAAGTTG
*
23877 AAGAAAGAAG-AG
1 AA-AAAGAAGTTG
*
23889 AAAATG-AGTTAG
1 AAAAAGAAGTT-G
23901 AAAAAGAA
1 AAAAAGAA
23909 ACAAAAGAAA
Statistics
Matches: 35, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
10 2 0.06
11 3 0.09
12 22 0.63
13 8 0.23
ACGTcount: A:0.64, C:0.00, G:0.23, T:0.12
Consensus pattern (12 bp):
AAAAAGAAGTTG
Found at i:25708 original size:4 final size:4
Alignment explanation
Indices: 25701--25728 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
25691 TTTTTTTATT
25701 TTTA TTTA TTTA TTTA TTTA TTTA TTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA
25729 CTTAGTTTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (4 bp):
TTTA
Found at i:31237 original size:11 final size:11
Alignment explanation
Indices: 31221--31269 Score: 82
Period size: 11 Copynumber: 4.5 Consensus size: 11
31211 TAAATCACTC
31221 TTTTTTT-ATT
1 TTTTTTTGATT
31231 TTTTTTTGATT
1 TTTTTTTGATT
*
31242 TTTTTTTGAAT
1 TTTTTTTGATT
31253 TTTTTTTGATT
1 TTTTTTTGATT
31264 TTTTTT
1 TTTTTT
31270 AACTTGTATA
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
10 7 0.19
11 29 0.81
ACGTcount: A:0.10, C:0.00, G:0.06, T:0.84
Consensus pattern (11 bp):
TTTTTTTGATT
Found at i:40963 original size:431 final size:431
Alignment explanation
Indices: 40160--41024 Score: 1628
Period size: 431 Copynumber: 2.0 Consensus size: 431
40150 GATCGTGTTG
40160 ATGAACACTTAGATCGAAACGTGCTTGACTGTCCTATTTTATTTATGATGATCATCTGTTTTGAT
1 ATGAACACTTAGATCGAAACGTGCTTGACTGTCCTATTTTATTTATGATGATCATCTGTTTTGAT
40225 GGTTGATAAAAAGATTCTTGTTTTTGATAATGCATGTGTGAGTGAATCTATAGACCGTCGATTAA
66 GGTTGATAAAAAGATTCTTGTTTTTGATAATGCATGTGTGAGTGAATCTATAGACCGTCGATTAA
40290 TGCATGGTATGATTATGCAACTCTGTGAACCATGTAAATCTTTTCAAATACCTACTTGTGACGAT
131 TGCATGGTATGATTATGCAACTCTGTGAACCATGTAAATCTTTTCAAATACCTACTTGTGACGAT
*
40355 TATGTTTACCATTTGATTTATTACTTGCAATTTATTCATGGTTTGTGGGAACAATGTGAGACGAC
196 TATGTTTACCATTTGATTTATTACTCGCAATTTATTCATGGTTTGTGGGAACAATGTGAGACGAC
*
40420 TGAATGCCTTAAAACATTTCCATCTTTGTTTCAAATATTTGACGAGGCAGTGGTGAGTAAATTAG
261 TGAATGCCTTAAAACATGTCCATCTTTGTTTCAAATATTTGACGAGGCAGTGGTGAGTAAATTAG
40485 ATTGTTTGCATGGTAATCTGAATCTGTCACATTCACATGCGTTATACCTGTTCTGTTATGCTTAT
326 ATTGTTTGCATGGTAATCTGAATCTGTCACATTCACATGCGTTATACCTGTTCTGTTATGCTTAT
40550 GATTGGACTACAAGCTTGTTTCCGTTGCTATTTACTATCTC
391 GATTGGACTACAAGCTTGTTTCCGTTGCTATTTACTATCTC
40591 ATGAACACTTAGATCGAAACGTGCTTGACTGTCCTA-TTTATTTATTGATGATCTATCTGTTTTG
1 ATGAACACTTAGATCGAAACGTGCTTGACTGTCCTATTTTATTTA-TGATGATC-ATCTGTTTTG
*
40655 ATGGTTGATAAAAATATTCTTGTTTTTGATAATGCATGTGTGAGTGAATCTATAGACCGTCGATT
64 ATGGTTGATAAAAAGATTCTTGTTTTTGATAATGCATGTGTGAGTGAATCTATAGACCGTCGATT
*
40720 AATGCATGGTATGATTATGCAACTCTGTGAACCATGTGAATCTTTTCAAATACCTACTTGTGACG
129 AATGCATGGTATGATTATGCAACTCTGTGAACCATGTAAATCTTTTCAAATACCTACTTGTGACG
*
40785 ATTATGTTTACCATTTGA-TTATTACTCGCAATTTATTCATGGTTTGTGGGAACAATGTGAGATG
194 ATTATGTTTACCATTTGATTTATTACTCGCAATTTATTCATGGTTTGTGGGAACAATGTGAGACG
40849 ACTGAATGCCTTAAAACATGTCCATCTTTGTTTCAAATATTTGACGAGGCAGTGGTGGAGTAAAT
259 ACTGAATGCCTTAAAACATGTCCATCTTTGTTTCAAATATTTGACGAGGCAGTGGT-GAGTAAAT
*
40914 TAGATTGTTTGCATGGTAATCTGAATCTGTC-CATTCACATGTGTTATACCTGTTCTGTTATGCT
323 TAGATTGTTTGCATGGTAATCTGAATCTGTCACATTCACATGCGTTATACCTGTTCTGTTATGCT
40978 TATGATTGGACTACAAGCTTGTTTCCGTTGCTATTTACTATCTC
388 TATGATTGGACTACAAGCTTGTTTCCGTTGCTATTTACTATCTC
41022 ATG
1 ATG
41025 GCTATTCTTT
Statistics
Matches: 425, Mismatches: 6, Indels: 6
0.97 0.01 0.01
Matches are distributed among these distances:
430 8 0.02
431 222 0.52
432 195 0.46
ACGTcount: A:0.26, C:0.15, G:0.19, T:0.39
Consensus pattern (431 bp):
ATGAACACTTAGATCGAAACGTGCTTGACTGTCCTATTTTATTTATGATGATCATCTGTTTTGAT
GGTTGATAAAAAGATTCTTGTTTTTGATAATGCATGTGTGAGTGAATCTATAGACCGTCGATTAA
TGCATGGTATGATTATGCAACTCTGTGAACCATGTAAATCTTTTCAAATACCTACTTGTGACGAT
TATGTTTACCATTTGATTTATTACTCGCAATTTATTCATGGTTTGTGGGAACAATGTGAGACGAC
TGAATGCCTTAAAACATGTCCATCTTTGTTTCAAATATTTGACGAGGCAGTGGTGAGTAAATTAG
ATTGTTTGCATGGTAATCTGAATCTGTCACATTCACATGCGTTATACCTGTTCTGTTATGCTTAT
GATTGGACTACAAGCTTGTTTCCGTTGCTATTTACTATCTC
Found at i:41272 original size:6 final size:6
Alignment explanation
Indices: 41261--41298 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
41251 AGTTGTAAAG
* *
41261 TTTTTA TTTTTA TTTTTA TTTTT- TTATTA TTATTA TTT
1 TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTT
41299 ACTAGTTTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
5 4 0.14
6 25 0.86
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (6 bp):
TTTTTA
Found at i:41286 original size:20 final size:21
Alignment explanation
Indices: 41261--41299 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
41251 AGTTGTAAAG
*
41261 TTTTTATTTTTATT-TTTATT
1 TTTTTATTATTATTATTTATT
41281 TTTTTATTATTATTATTTA
1 TTTTTATTATTATTATTTA
41300 CTAGTTTAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (21 bp):
TTTTTATTATTATTATTTATT
Done.