Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1476
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: 39590
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Found at i:4128 original size:55 final size:55
Alignment explanation
Indices: 4044--4180 Score: 267
Period size: 55 Copynumber: 2.5 Consensus size: 55
4034 AGCAGCAAGG
4044 GAGATGTTCCCATGCATGGAACGGCATTTAAAGGAAGCAAAGACATGGATTTAAT
1 GAGATGTTCCCATGCATGGAACGGCATTTAAAGGAAGCAAAGACATGGATTTAAT
4099 GAGATGTTCCCATGCATGGAACGGCATTTAAAGGAAGCAAAGACATGGATTTAAT
1 GAGATGTTCCCATGCATGGAACGGCATTTAAAGGAAGCAAAGACATGGATTTAAT
4154 GAGATGTTCCCATGCATGG-ACGGCATT
1 GAGATGTTCCCATGCATGGAACGGCATT
4181 AATGAAAGCA
Statistics
Matches: 82, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
54 8 0.10
55 74 0.90
ACGTcount: A:0.34, C:0.16, G:0.26, T:0.24
Consensus pattern (55 bp):
GAGATGTTCCCATGCATGGAACGGCATTTAAAGGAAGCAAAGACATGGATTTAAT
Found at i:8792 original size:62 final size:63
Alignment explanation
Indices: 8669--8793 Score: 162
Period size: 62 Copynumber: 2.0 Consensus size: 63
8659 ACTAAATCGA
* *
8669 CACTACCTAAATTCGATCGAGAACATAATACGACTCATCACATCATCCGAATCGAGCTCGTAT
1 CACTACCTAAATTCGATCGAGAACATAATACGACTCATCACATCATACGAAACGAGCTCGTAT
* * * * * **
8732 CACTACCTAATTTCGATCGGGAA-ATATTACGACTCGTTATTTCATACGAAACGAGCTCGTAT
1 CACTACCTAAATTCGATCGAGAACATAATACGACTCATCACATCATACGAAACGAGCTCGTAT
8794 TAGTTGGTAT
Statistics
Matches: 53, Mismatches: 9, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
62 32 0.60
63 21 0.40
ACGTcount: A:0.33, C:0.26, G:0.14, T:0.27
Consensus pattern (63 bp):
CACTACCTAAATTCGATCGAGAACATAATACGACTCATCACATCATACGAAACGAGCTCGTAT
Found at i:8859 original size:13 final size:13
Alignment explanation
Indices: 8841--8886 Score: 74
Period size: 13 Copynumber: 3.5 Consensus size: 13
8831 TTGTAGATTC
8841 AAAAAAAAATCGA
1 AAAAAAAAATCGA
8854 AAAAAAAAATCGA
1 AAAAAAAAATCGA
*
8867 GAAAAAAAAATTGA
1 -AAAAAAAAATCGA
8881 AAAAAA
1 AAAAAA
8887 TTTTTTTGAA
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
13 19 0.61
14 12 0.39
ACGTcount: A:0.78, C:0.04, G:0.09, T:0.09
Consensus pattern (13 bp):
AAAAAAAAATCGA
Found at i:14887 original size:20 final size:20
Alignment explanation
Indices: 14864--14909 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
14854 CCAGCTCGAA
*
14864 TTAGCTCACATGAGCTTAAT
1 TTAGCTCACATGAGCTCAAT
***
14884 TTAGCTCGTTTGAGCTCAAT
1 TTAGCTCACATGAGCTCAAT
14904 TTAGCT
1 TTAGCT
14910 TACTTTAGCT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.24, C:0.20, G:0.17, T:0.39
Consensus pattern (20 bp):
TTAGCTCACATGAGCTCAAT
Found at i:14891 original size:30 final size:30
Alignment explanation
Indices: 14856--14929 Score: 80
Period size: 30 Copynumber: 2.5 Consensus size: 30
14846 AGTTTTTCCC
14856 AGCTCGAATT-AGCTCACA-TGAGCTTAATTT
1 AGCTCG-ATTGAGCTCA-ATTGAGCTTAATTT
* * *
14886 AGCTCGTTTGAGCTCAATTTAGCTTACTTT
1 AGCTCGATTGAGCTCAATTGAGCTTAATTT
*
14916 AGCTCGTTTGAGCT
1 AGCTCGATTGAGCT
14930 TGGCTTAAGT
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
29 3 0.08
30 36 0.92
ACGTcount: A:0.23, C:0.20, G:0.19, T:0.38
Consensus pattern (30 bp):
AGCTCGATTGAGCTCAATTGAGCTTAATTT
Found at i:20139 original size:30 final size:31
Alignment explanation
Indices: 20045--20141 Score: 101
Period size: 30 Copynumber: 3.2 Consensus size: 31
20035 TAAACCAAAA
*
20045 TGAGCTAAGCTTTAGCTCGTGAGCT-AAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTGAAAGT
* * * * * *
20075 TGAGCTGAGGCTAAACTCCTAAGCTG-AAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTGAAAGT
*
20105 TGAGCTAAGGTTTAGCTCGTGAGTTGAAAG-
1 TGAGCTAAGGTTTAGCTCGTGAGCTGAAAGT
20135 TGAGCTA
1 TGAGCTA
20142 GGAGTGAGCT
Statistics
Matches: 51, Mismatches: 14, Indels: 4
0.74 0.20 0.06
Matches are distributed among these distances:
30 48 0.94
31 3 0.06
ACGTcount: A:0.28, C:0.15, G:0.29, T:0.28
Consensus pattern (31 bp):
TGAGCTAAGGTTTAGCTCGTGAGCTGAAAGT
Found at i:20436 original size:15 final size:15
Alignment explanation
Indices: 20416--20463 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
20406 TCAAAGATGG
20416 GTTTATGGATATGAA
1 GTTTATGGATATGAA
* * *
20431 GTTTATGTAGATG-G
1 GTTTATGGATATGAA
*
20445 GTTTATGGATATAAA
1 GTTTATGGATATGAA
20460 GTTT
1 GTTT
20464 TTGTAGGTTT
Statistics
Matches: 25, Mismatches: 7, Indels: 2
0.74 0.21 0.06
Matches are distributed among these distances:
14 10 0.40
15 15 0.60
ACGTcount: A:0.29, C:0.00, G:0.27, T:0.44
Consensus pattern (15 bp):
GTTTATGGATATGAA
Found at i:20450 original size:14 final size:14
Alignment explanation
Indices: 20410--20453 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
20400 AAGGATTCAA
20410 AGATGGGTTTATGG
1 AGATGGGTTTATGG
* * *
20424 ATATGAAGTTTATGT
1 AGATG-GGTTTATGG
20439 AGATGGGTTTATGG
1 AGATGGGTTTATGG
20453 A
1 A
20454 TATAAAGTTT
Statistics
Matches: 23, Mismatches: 6, Indels: 2
0.74 0.19 0.06
Matches are distributed among these distances:
14 12 0.52
15 11 0.48
ACGTcount: A:0.27, C:0.00, G:0.34, T:0.39
Consensus pattern (14 bp):
AGATGGGTTTATGG
Found at i:20479 original size:29 final size:29
Alignment explanation
Indices: 20410--20469 Score: 102
Period size: 29 Copynumber: 2.1 Consensus size: 29
20400 AAGGATTCAA
*
20410 AGATGGGTTTATGGATATGAAGTTTATGT
1 AGATGGGTTTATGGATATAAAGTTTATGT
*
20439 AGATGGGTTTATGGATATAAAGTTTTTGT
1 AGATGGGTTTATGGATATAAAGTTTATGT
20468 AG
1 AG
20470 GTTTGGTTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.28, C:0.00, G:0.30, T:0.42
Consensus pattern (29 bp):
AGATGGGTTTATGGATATAAAGTTTATGT
Found at i:21227 original size:14 final size:14
Alignment explanation
Indices: 21185--21229 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
21175 TTAAAGAAGC
21185 AACTCATTAAATTA
1 AACTCATTAAATTA
* *
21199 AATTCATCAAA-TA
1 AACTCATTAAATTA
*
21212 AACTCATTTAATTA
1 AACTCATTAAATTA
21226 AACT
1 AACT
21230 AAGATGAGTT
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
13 10 0.40
14 15 0.60
ACGTcount: A:0.49, C:0.16, G:0.00, T:0.36
Consensus pattern (14 bp):
AACTCATTAAATTA
Found at i:23729 original size:18 final size:18
Alignment explanation
Indices: 23708--23757 Score: 73
Period size: 18 Copynumber: 2.8 Consensus size: 18
23698 AAACTCTTTT
23708 TCATTCTCTTTTTCAATC
1 TCATTCTCTTTTTCAATC
* *
23726 TCATTTTCTTTTTCACTC
1 TCATTCTCTTTTTCAATC
*
23744 TCAATCTCTTTTTC
1 TCATTCTCTTTTTC
23758 TTTTTCTTTC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.14, C:0.28, G:0.00, T:0.58
Consensus pattern (18 bp):
TCATTCTCTTTTTCAATC
Found at i:23763 original size:24 final size:24
Alignment explanation
Indices: 23683--23760 Score: 93
Period size: 24 Copynumber: 3.2 Consensus size: 24
23673 CTTGTTCACA
*
23683 TTCTTTCTCTCTCTCAAACTCTTT
1 TTCTTTCTCTCTCTCAATCTCTTT
* * * *
23707 TTCATTCTCTTTTTCAATCTCATT
1 TTCTTTCTCTCTCTCAATCTCTTT
* *
23731 TTCTTTTTCACTCTCAATCTCTTT
1 TTCTTTCTCTCTCTCAATCTCTTT
23755 TTCTTT
1 TTCTTT
23761 TTCTTTCATT
Statistics
Matches: 43, Mismatches: 11, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
24 43 1.00
ACGTcount: A:0.13, C:0.28, G:0.00, T:0.59
Consensus pattern (24 bp):
TTCTTTCTCTCTCTCAATCTCTTT
Found at i:30301 original size:23 final size:22
Alignment explanation
Indices: 30250--30301 Score: 54
Period size: 23 Copynumber: 2.3 Consensus size: 22
30240 CCTCGTCTTT
*
30250 TTCTTTTGTTTCTTTTTCTAAC
1 TTCTTTTCTTTCTTTTTCTAAC
30272 -TCATTTTCTCTTCTTTCTTC-AAC
1 TTC-TTTTCT-TTCTTT-TTCTAAC
30295 TTCTTTT
1 TTCTTTT
30302 TCAATTTTCT
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 2 0.08
22 5 0.20
23 13 0.52
24 5 0.20
ACGTcount: A:0.10, C:0.23, G:0.02, T:0.65
Consensus pattern (22 bp):
TTCTTTTCTTTCTTTTTCTAAC
Found at i:31683 original size:6 final size:6
Alignment explanation
Indices: 31672--31703 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
31662 ATAAATAAAT
31672 AAATAA AAATAA AAATAA AAATAA AAATAA AA
1 AAATAA AAATAA AAATAA AAATAA AAATAA AA
31704 CTTTACAACT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (6 bp):
AAATAA
Found at i:36784 original size:49 final size:49
Alignment explanation
Indices: 36721--37053 Score: 279
Period size: 51 Copynumber: 6.5 Consensus size: 49
36711 CTGGTATGTA
* * * *
36721 TAGTAGCCTGCACTTAGTACTACACATGCGACCAACTGTCTGGTACATG
1 TAGTAGCCTGCACTTAGTACTACACACGTGACCAACTATCTGGTACACG
* * * **
36770 TAGTAGCCTCCACTTAGTACTTCGTATTACACACGTGACCTCACCATCTAATACACG
1 TAGTAGCCTGCACTTAGTA---C----TACACACGTGACC-AACTATCTGGTACACG
** * * * *
36827 TAGTAGCCTGCACTTAGTACTACACACGTGATCACAGTTTTCGGGTACGCA
1 TAGTAGCCTGCACTTAGTACTACACACGTGA-C-CAACTATCTGGTACACG
* * * *
36878 TAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCCGGTACACG
1 TAGTAGCCTGCACTTAGTACTACACACGTGACCAACTATCTGGTACACG
* * *
36927 TAATAGCCTGCACTTAGTACTACACACGTGACCTAACCATCTGATACACG
1 TAGTAGCCTGCACTTAGTACTACACACGTGACC-AACTATCTGGTACACG
* * * * * * *
36977 TAGTAGCCTACACTTAGTACTACACACGTGATCATAGTTTTCGGGTACGCA
1 TAGTAGCCTGCACTTAGTACTACACACGTGACCA-A-CTATCTGGTACACG
*
37028 TAGTAGCCTGCACTTAGAACTACACA
1 TAGTAGCCTGCACTTAGTACTACACA
37054 TGCGACCTCA
Statistics
Matches: 225, Mismatches: 46, Indels: 24
0.76 0.16 0.08
Matches are distributed among these distances:
49 61 0.27
50 55 0.24
51 67 0.30
52 2 0.01
54 1 0.00
56 11 0.05
57 28 0.12
ACGTcount: A:0.29, C:0.28, G:0.17, T:0.26
Consensus pattern (49 bp):
TAGTAGCCTGCACTTAGTACTACACACGTGACCAACTATCTGGTACACG
Found at i:36996 original size:50 final size:49
Alignment explanation
Indices: 36788--37007 Score: 224
Period size: 50 Copynumber: 4.4 Consensus size: 49
36778 TCCACTTAGT
* * * *
36788 ACTTCGTATTACACACGTGACCTCACCATCTAATACACGTAGTAGCCTGC
1 ACTTAGTACTACACACGTGACC-AACCATCTGATACACGTAGTAGCCTGC
**** * * * *
36838 ACTTAGTACTACACACGTGATCACAGTTTTCGGGTACGCATAGTAGCCTGC
1 ACTTAGTACTACACACGTGA-C-CAACCATCTGATACACGTAGTAGCCTGC
* * ** * * *
36889 ACTTAGTACTACACATGCGACCAATTATCCGGTACACGTAATAGCCTGC
1 ACTTAGTACTACACACGTGACCAACCATCTGATACACGTAGTAGCCTGC
*
36938 ACTTAGTACTACACACGTGACCTAACCATCTGATACACGTAGTAGCCTAC
1 ACTTAGTACTACACACGTGACC-AACCATCTGATACACGTAGTAGCCTGC
36988 ACTTAGTACTACACACGTGA
1 ACTTAGTACTACACACGTGA
37008 TCATAGTTTT
Statistics
Matches: 139, Mismatches: 28, Indels: 6
0.80 0.16 0.03
Matches are distributed among these distances:
49 42 0.30
50 60 0.43
51 36 0.26
52 1 0.01
ACGTcount: A:0.30, C:0.29, G:0.16, T:0.25
Consensus pattern (49 bp):
ACTTAGTACTACACACGTGACCAACCATCTGATACACGTAGTAGCCTGC
Found at i:37008 original size:150 final size:152
Alignment explanation
Indices: 36720--37060 Score: 524
Period size: 150 Copynumber: 2.2 Consensus size: 152
36710 TCTGGTATGT
* * * *
36720 ATAGTAGCCTGCACTTAGTACTACACATGCGACCAACTGTCTGGTACATGTAGTAGCCTCCACTT
1 ATAGTAGCCTGCACTTAGTACTACACATGCGACCAACTATCCGGTACACGTAATAGCCTCCACTT
* *
36785 AGTACTTCGTATTACACACGTGACCTCACCATCTAATACACGTAGTAGCCTGCACTTAGTACTAC
66 AGTA--TC---TTACACACGTGACCTAACCATCTAATACACGTAGTAGCCTACACTTAGTACTAC
36850 ACACGTGATCACAGTTTTCGGGTACGC
126 ACACGTGATCACAGTTTTCGGGTACGC
* *
36877 ATAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCCGGTACACGTAATAGCCTGCACTT
1 ATAGTAGCCTGCACTTAGTACTACACATGCGACCAACTATCCGGTACACGTAATAGCCTCCACTT
*
36942 AGTA-C-TACACACGTGACCTAACCATCTGATACACGTAGTAGCCTACACTTAGTACTACACACG
66 AGTATCTTACACACGTGACCTAACCATCTAATACACGTAGTAGCCTACACTTAGTACTACACACG
*
37005 TGATCATAGTTTTCGGGTACGC
131 TGATCACAGTTTTCGGGTACGC
*
37027 ATAGTAGCCTGCACTTAGAACTACACATGCGACC
1 ATAGTAGCCTGCACTTAGTACTACACATGCGACC
37061 TCACAATAGA
Statistics
Matches: 173, Mismatches: 11, Indels: 7
0.91 0.06 0.04
Matches are distributed among these distances:
150 109 0.63
154 1 0.01
157 63 0.36
ACGTcount: A:0.28, C:0.28, G:0.18, T:0.26
Consensus pattern (152 bp):
ATAGTAGCCTGCACTTAGTACTACACATGCGACCAACTATCCGGTACACGTAATAGCCTCCACTT
AGTATCTTACACACGTGACCTAACCATCTAATACACGTAGTAGCCTACACTTAGTACTACACACG
TGATCACAGTTTTCGGGTACGC
Found at i:37061 original size:101 final size:99
Alignment explanation
Indices: 36878--37061 Score: 242
Period size: 101 Copynumber: 1.8 Consensus size: 99
36868 CGGGTACGCA
* * *
36878 TAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCCGGTACACGTAATAGCCTGCACTTA
1 TAGTAGCCTACACTTAGTACTACACACGCGACCAATTATCCGGTACACATAATAGCCTGCACTTA
* *
36943 GTACTACACACGTGACCTAACCATCTGATACACG
66 GAACTACACACGCGACCTAACCATCTGATACACG
* * * * * *
36977 TAGTAGCCTACACTTAGTACTACACACGTGATCATAGTTTTCGGGTACGCATAGTAGCCTGCACT
1 TAGTAGCCTACACTTAGTACTACACACGCGACCA-A-TTATCCGGTACACATAATAGCCTGCACT
*
37042 TAGAACTACACATGCGACCT
64 TAGAACTACACACGCGACCT
37062 CACAATAGAT
Statistics
Matches: 71, Mismatches: 12, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
99 30 0.42
100 1 0.01
101 40 0.56
ACGTcount: A:0.29, C:0.28, G:0.17, T:0.26
Consensus pattern (99 bp):
TAGTAGCCTACACTTAGTACTACACACGCGACCAATTATCCGGTACACATAATAGCCTGCACTTA
GAACTACACACGCGACCTAACCATCTGATACACG
Done.