Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold461
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: 88335
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33
Found at i:900 original size:20 final size:20
Alignment explanation
Indices: 877--930 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
867 AGTTTTTCCC
*
877 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTCACATG
* ***
897 AGCTTAATTTAGCTCGTTTG
1 AGCTCAATTTAGCTCACATG
917 AGCTCAATTTAGCT
1 AGCTCAATTTAGCT
931 TACTTTAGCT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.24, C:0.20, G:0.19, T:0.37
Consensus pattern (20 bp):
AGCTCAATTTAGCTCACATG
Found at i:912 original size:30 final size:30
Alignment explanation
Indices: 877--950 Score: 98
Period size: 30 Copynumber: 2.5 Consensus size: 30
867 AGTTTTTCCC
877 AGCTCGATTT-AGCTCACA-TGAGCTTAATTT
1 AGCTCG-TTTGAGCTCA-ATTGAGCTTAATTT
* *
907 AGCTCGTTTGAGCTCAATTTAGCTTACTTT
1 AGCTCGTTTGAGCTCAATTGAGCTTAATTT
937 AGCTCGTTTGAGCT
1 AGCTCGTTTGAGCT
951 TGGCTTAAGT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
29 4 0.10
30 36 0.90
ACGTcount: A:0.22, C:0.20, G:0.19, T:0.39
Consensus pattern (30 bp):
AGCTCGTTTGAGCTCAATTGAGCTTAATTT
Found at i:940 original size:20 final size:20
Alignment explanation
Indices: 877--941 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
867 AGTTTTTCCC
* * * *
877 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTTACTTT
*
897 AGCTTAATTTAGC-T-CGTTT
1 AGCTCAATTTAGCTTAC-TTT
916 GAGCTCAATTTAGCTTACTTT
1 -AGCTCAATTTAGCTTACTTT
937 AGCTC
1 AGCTC
942 GTTTGAGCTT
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 28 0.80
21 4 0.11
22 1 0.03
ACGTcount: A:0.23, C:0.22, G:0.17, T:0.38
Consensus pattern (20 bp):
AGCTCAATTTAGCTTACTTT
Found at i:13643 original size:22 final size:21
Alignment explanation
Indices: 13612--13662 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 21
13602 ACCTCTTTGA
13612 ACCATTACCAATTCGTACCAAAT
1 ACCA-TACCAATTCGTACC-AAT
*
13635 ACCATACCATTTCGTACCAAT
1 ACCATACCAATTCGTACCAAT
*
13656 TCCATAC
1 ACCATAC
13663 TATTTTGAAC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
21 9 0.35
22 13 0.50
23 4 0.15
ACGTcount: A:0.35, C:0.33, G:0.04, T:0.27
Consensus pattern (21 bp):
ACCATACCAATTCGTACCAAT
Found at i:13662 original size:21 final size:21
Alignment explanation
Indices: 13617--13679 Score: 72
Period size: 21 Copynumber: 3.0 Consensus size: 21
13607 TTTGAACCAT
* *
13617 TACCAATTCGTACCAAATACCA
1 TACCATTTCGTACC-AATTCCA
13639 TACCATTTCGTACCAATTCCA
1 TACCATTTCGTACCAATTCCA
* * *
13660 TACTATTTTGAACCAATTCC
1 TACCATTTCGTACCAATTCC
13680 CAAATACCAA
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
21 23 0.64
22 13 0.36
ACGTcount: A:0.33, C:0.30, G:0.05, T:0.32
Consensus pattern (21 bp):
TACCATTTCGTACCAATTCCA
Found at i:20714 original size:17 final size:18
Alignment explanation
Indices: 20692--20728 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
20682 TGGAATAAAC
20692 TTAGTTAA-TTAAATAAG
1 TTAGTTAATTTAAATAAG
*
20709 TTAGTTAATTTAATTAAG
1 TTAGTTAATTTAAATAAG
20727 TT
1 TT
20729 TAGCTCAACA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 8 0.44
18 10 0.56
ACGTcount: A:0.41, C:0.00, G:0.11, T:0.49
Consensus pattern (18 bp):
TTAGTTAATTTAAATAAG
Found at i:36186 original size:30 final size:29
Alignment explanation
Indices: 36087--36188 Score: 89
Period size: 30 Copynumber: 3.4 Consensus size: 29
36077 CGAGTTTAAA
* *
36087 CTAAAATGAGCTAAGTTTTAGCTCGTGA-
1 CTAAATTGAGCTAAGGTTTAGCTCGTGAG
* * * * * *
36115 CTAAAGTTGAGCTGAGGCTAAACTCCTAAG
1 CTAAA-TTGAGCTAAGGTTTAGCTCGTGAG
*
36145 CTGAAGTTGAGCTAAGGTTTAGCTCGTGAG
1 CT-AAATTGAGCTAAGGTTTAGCTCGTGAG
36175 CTAAATATGAGCTA
1 CTAAAT-TGAGCTA
36189 GGAGTGAGCT
Statistics
Matches: 54, Mismatches: 16, Indels: 6
0.71 0.21 0.08
Matches are distributed among these distances:
28 5 0.09
29 18 0.33
30 29 0.54
31 2 0.04
ACGTcount: A:0.31, C:0.16, G:0.25, T:0.28
Consensus pattern (29 bp):
CTAAATTGAGCTAAGGTTTAGCTCGTGAG
Found at i:40154 original size:15 final size:15
Alignment explanation
Indices: 40132--40171 Score: 73
Period size: 14 Copynumber: 2.7 Consensus size: 15
40122 GATATCAAGT
40132 TGAAAAAAAAATT-G
1 TGAAAAAAAAATTCG
40146 TGAAAAAAAAATTCG
1 TGAAAAAAAAATTCG
40161 TGAAAAAAAAA
1 TGAAAAAAAAA
40172 GAAGAAGCTA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
14 13 0.52
15 12 0.48
ACGTcount: A:0.68, C:0.03, G:0.12, T:0.17
Consensus pattern (15 bp):
TGAAAAAAAAATTCG
Found at i:41142 original size:21 final size:23
Alignment explanation
Indices: 41097--41143 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
41087 TCACCTGCAA
* *
41097 TAAACACATTAAAATGAGTTTAT
1 TAAACACATTAAAATCAGCTTAT
41120 TAAACACATTAAAA-CA-CTTAT
1 TAAACACATTAAAATCAGCTTAT
41141 TAA
1 TAA
41144 TCATAACACA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 7 0.32
22 1 0.05
23 14 0.64
ACGTcount: A:0.51, C:0.13, G:0.04, T:0.32
Consensus pattern (23 bp):
TAAACACATTAAAATCAGCTTAT
Found at i:46783 original size:30 final size:29
Alignment explanation
Indices: 46681--46783 Score: 89
Period size: 30 Copynumber: 3.4 Consensus size: 29
46671 CGAGGTTAAA
* *
46681 CTAAAATGAGCTAAGTTTTAGCTCGTGAG
1 CTAAATTGAGCTAAGGTTTAGCTCGTGAG
* * * * * * *
46710 CTAAAGTTGAGTTGAGGCTAAACTCCTAAG
1 CTAAA-TTGAGCTAAGGTTTAGCTCGTGAG
*
46740 CTGAAGTTGAGCTAAGGTTTAGCTCGTGAG
1 CT-AAATTGAGCTAAGGTTTAGCTCGTGAG
46770 CTAAATATGAGCTA
1 CTAAAT-TGAGCTA
46784 GGAGTGAGCT
Statistics
Matches: 53, Mismatches: 18, Indels: 5
0.70 0.24 0.07
Matches are distributed among these distances:
29 8 0.15
30 43 0.81
31 2 0.04
ACGTcount: A:0.31, C:0.15, G:0.25, T:0.29
Consensus pattern (29 bp):
CTAAATTGAGCTAAGGTTTAGCTCGTGAG
Found at i:53208 original size:15 final size:16
Alignment explanation
Indices: 53188--53244 Score: 71
Period size: 16 Copynumber: 3.6 Consensus size: 16
53178 TAGCTTCTTC
53188 TTTTTTTCACGAAAATT
1 TTTTTTTCACGAAAA-T
*
53205 TTTTTTTCACG-AATT
1 TTTTTTTCACGAAAAT
**
53220 TTTTTTTCACGAATTT
1 TTTTTTTCACGAAAAT
53236 TTTTTTTCA
1 TTTTTTTCA
53245 ACTTGATATC
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
15 12 0.32
16 14 0.38
17 11 0.30
ACGTcount: A:0.21, C:0.12, G:0.05, T:0.61
Consensus pattern (16 bp):
TTTTTTTCACGAAAAT
Found at i:53210 original size:17 final size:16
Alignment explanation
Indices: 53188--53244 Score: 89
Period size: 15 Copynumber: 3.6 Consensus size: 16
53178 TAGCTTCTTC
53188 TTTTTTTCACGAAAATT
1 TTTTTTTCACG-AAATT
53205 TTTTTTTCACG-AATT
1 TTTTTTTCACGAAATT
*
53220 TTTTTTTCACGAATTT
1 TTTTTTTCACGAAATT
53236 TTTTTTTCA
1 TTTTTTTCA
53245 ACTTGATATC
Statistics
Matches: 38, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
15 15 0.39
16 12 0.32
17 11 0.29
ACGTcount: A:0.21, C:0.12, G:0.05, T:0.61
Consensus pattern (16 bp):
TTTTTTTCACGAAATT
Found at i:53730 original size:157 final size:157
Alignment explanation
Indices: 53444--53758 Score: 585
Period size: 157 Copynumber: 2.0 Consensus size: 157
53434 TCGTGAATTG
53444 AGTAAGGATGGATTCATTTAGGTTTTAAAATGAAACAAAATAGAGATAATGGCTTCAAACAAAGG
1 AGTAAGGATGGATTCATTTAGGTTTTAAAATGAAACAAAATAGAGATAATGGCTTCAAACAAAGG
*
53509 TAATAAACAAAATAAAGAGGAAACAATAACAAATTAATTGGCTAAGACCGAAAATGAACCAACAA
66 TAATAAACAAAATAAAGAGGAAACAATAACAAATTAATTGGCTAAGACCAAAAATGAACCAACAA
*
53574 TAACGAATTGTTGACCCGAATCTCAAA
131 TAACAAATTGTTGACCCGAATCTCAAA
* * *
53601 AGTAAGGATGGATTCGTTTCGGTTTTAAAATGAAACAAAATAGAGATAATGGCTTCAAGCAAAGG
1 AGTAAGGATGGATTCATTTAGGTTTTAAAATGAAACAAAATAGAGATAATGGCTTCAAACAAAGG
53666 TAATAAACAAAATAAAGAGGAAACAATAACAAATTAATTGGCTAAGACCAAAAATGAACCAACAA
66 TAATAAACAAAATAAAGAGGAAACAATAACAAATTAATTGGCTAAGACCAAAAATGAACCAACAA
53731 TAACAAATTGTTGACCCGAATCTCAAA
131 TAACAAATTGTTGACCCGAATCTCAAA
53758 A
1 A
53759 TGGTCTTTAG
Statistics
Matches: 153, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
157 153 1.00
ACGTcount: A:0.49, C:0.13, G:0.17, T:0.22
Consensus pattern (157 bp):
AGTAAGGATGGATTCATTTAGGTTTTAAAATGAAACAAAATAGAGATAATGGCTTCAAACAAAGG
TAATAAACAAAATAAAGAGGAAACAATAACAAATTAATTGGCTAAGACCAAAAATGAACCAACAA
TAACAAATTGTTGACCCGAATCTCAAA
Found at i:54510 original size:21 final size:23
Alignment explanation
Indices: 54465--54511 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
54455 TCACCTGCAA
* *
54465 TAAACACATTAAAATGAGTTTAT
1 TAAACACATTAAAATCAGCTTAT
54488 TAAACACATTAAAA-CA-CTTAT
1 TAAACACATTAAAATCAGCTTAT
54509 TAA
1 TAA
54512 TCATAACACA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 7 0.32
22 1 0.05
23 14 0.64
ACGTcount: A:0.51, C:0.13, G:0.04, T:0.32
Consensus pattern (23 bp):
TAAACACATTAAAATCAGCTTAT
Found at i:56014 original size:20 final size:20
Alignment explanation
Indices: 55968--56014 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
55958 AGCTCGTTTC
*
55968 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* *
55988 CAACTCACTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
56008 CAGCTCA
1 CAGCTCA
56015 ATCTTAACCC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.30, C:0.36, G:0.13, T:0.21
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:57417 original size:18 final size:17
Alignment explanation
Indices: 57396--57440 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 17
57386 GAGTGACGAG
57396 AGAAAAAGAAACTGAAAA
1 AGAAAAA-AAACTGAAAA
*
57414 AGAAACAAAAATTGAAAA
1 AGAAA-AAAAACTGAAAA
57432 AGAGAAAAA
1 AGA-AAAAA
57441 GATTGGAGAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
18 20 0.83
19 4 0.17
ACGTcount: A:0.73, C:0.04, G:0.16, T:0.07
Consensus pattern (17 bp):
AGAAAAAAAACTGAAAA
Found at i:57445 original size:18 final size:18
Alignment explanation
Indices: 57394--57445 Score: 52
Period size: 18 Copynumber: 2.8 Consensus size: 18
57384 AAGAGTGACG
*
57394 AGAGAAAAAGAAACTGAAAA
1 AGAGAAAAAG--ATTGAAAA
*
57414 AGA-AACAAAAATTGAAAA
1 AGAGAA-AAAGATTGAAAA
57432 AGAGAAAAAGATTG
1 AGAGAAAAAGATTG
57446 GAGAAAGAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 6
0.75 0.08 0.17
Matches are distributed among these distances:
18 17 0.63
19 4 0.15
20 6 0.22
ACGTcount: A:0.67, C:0.04, G:0.19, T:0.10
Consensus pattern (18 bp):
AGAGAAAAAGATTGAAAA
Found at i:59680 original size:20 final size:20
Alignment explanation
Indices: 59657--59703 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
59647 GGGTTAAGAT
*
59657 TGAGCTGAATTGAGCTTGAG
1 TGAGCTGAATTGAGCTCGAG
* *
59677 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAG
59697 TGAGCTG
1 TGAGCTG
59704 GAAACGAGCT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.21, C:0.13, G:0.36, T:0.30
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAG
Found at i:61427 original size:48 final size:48
Alignment explanation
Indices: 61372--61477 Score: 137
Period size: 48 Copynumber: 2.2 Consensus size: 48
61362 TTGTCTTTTC
*
61372 TTTCTTTTTCAATTT-TCTCT-TTTTCCTCACA-CTTTTGTTCAATCTCAA
1 TTTCTTTTTCAATTTCTCTCTCTTTT--TCACATCCTTT-TTCAATCTCAA
* *
61420 TTTCTTTTTCGATTTCTTTCTCTTTTTCACATCCTTTTTCAATCTCAA
1 TTTCTTTTTCAATTTCTCTCTCTTTTTCACATCCTTTTTCAATCTCAA
61468 TTTCTTTTTC
1 TTTCTTTTTC
61478 CATGACACTC
Statistics
Matches: 52, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
48 40 0.77
49 8 0.15
50 4 0.08
ACGTcount: A:0.14, C:0.25, G:0.02, T:0.59
Consensus pattern (48 bp):
TTTCTTTTTCAATTTCTCTCTCTTTTTCACATCCTTTTTCAATCTCAA
Found at i:61474 original size:18 final size:17
Alignment explanation
Indices: 61453--61537 Score: 62
Period size: 18 Copynumber: 4.6 Consensus size: 17
61443 TTTTCACATC
61453 CTTTTTCAATCTCAATTT
1 CTTTTTCAATCTC-ATTT
* *
61471 CTTTTTCCATGACACTCGTTT
1 CTTTTT-CA--A-TCTCATTT
* *
61492 CTTTTACACTCTCATTT
1 CTTTTTCAATCTCATTT
*
61509 CTTTCTTCAATCTCACTCT
1 CTTT-TTCAATCTCA-TTT
61528 CTTTTTCAAT
1 CTTTTTCAAT
61538 TTCTTGTTCC
Statistics
Matches: 52, Mismatches: 9, Indels: 12
0.71 0.12 0.16
Matches are distributed among these distances:
17 10 0.19
18 20 0.38
19 8 0.15
20 2 0.04
21 9 0.17
22 3 0.06
ACGTcount: A:0.18, C:0.28, G:0.02, T:0.52
Consensus pattern (17 bp):
CTTTTTCAATCTCATTT
Found at i:64119 original size:20 final size:20
Alignment explanation
Indices: 64096--64142 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
64086 GGGTTAAGAT
*
64096 TGAGCTGAATTGAGCTTGAG
1 TGAGCTGAATTGAGCTCGAG
* *
64116 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAG
64136 TGAGCTG
1 TGAGCTG
64143 GAAACGAGCT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.21, C:0.13, G:0.36, T:0.30
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAG
Found at i:73211 original size:30 final size:30
Alignment explanation
Indices: 73177--73273 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
73167 AGCTCACTCC
73177 TAGCTCATA-TTTAGCTCACGAGCTAAACCT
1 TAGCTCA-ACTTTAGCTCACGAGCTAAACCT
* * * * * *
73207 TAGCTCAACTTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
* *
73237 CAGCTCAACTTTAGCTCACGAGCTAAAACT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
73267 TAGCTCA
1 TAGCTCA
73274 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:0.29, C:0.27, G:0.15, T:0.29
Consensus pattern (30 bp):
TAGCTCAACTTTAGCTCACGAGCTAAACCT
Found at i:74951 original size:21 final size:21
Alignment explanation
Indices: 74906--74968 Score: 83
Period size: 21 Copynumber: 3.0 Consensus size: 21
74896 TTTGAACCAT
* *
74906 TACCAATTCGTACCAAATACCA
1 TACCATTTCGTACC-AATTCCA
74928 TACCATTTCGTACCAATTCCA
1 TACCATTTCGTACCAATTCCA
74949 TACCATTTCG-AGCCAATTCC
1 TACCATTTCGTA-CCAATTCC
74969 TAAATACCAA
Statistics
Matches: 38, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
20 1 0.03
21 24 0.63
22 13 0.34
ACGTcount: A:0.32, C:0.33, G:0.06, T:0.29
Consensus pattern (21 bp):
TACCATTTCGTACCAATTCCA
Found at i:75631 original size:15 final size:16
Alignment explanation
Indices: 75598--75631 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
75588 GGTATAGTGT
*
75598 ATTAAAAAAATTCAGA
1 ATTAAAAAAATTCAAA
75614 ATTAAAAAAA-TCAAA
1 ATTAAAAAAATTCAAA
75629 ATT
1 ATT
75632 CATAGTTGGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.65, C:0.06, G:0.03, T:0.26
Consensus pattern (16 bp):
ATTAAAAAAATTCAAA
Found at i:76347 original size:46 final size:46
Alignment explanation
Indices: 76277--76370 Score: 179
Period size: 46 Copynumber: 2.0 Consensus size: 46
76267 CAAAGAAAAG
76277 ACCTCGACCCACTATCAATAATGATAGGAACCTTGGTATATGATGA
1 ACCTCGACCCACTATCAATAATGATAGGAACCTTGGTATATGATGA
*
76323 ACCTCGACCCACTATCAATGATGATAGGAACCTTGGTATATGATGA
1 ACCTCGACCCACTATCAATAATGATAGGAACCTTGGTATATGATGA
76369 AC
1 AC
76371 GCCACACTAT
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 47 1.00
ACGTcount: A:0.34, C:0.22, G:0.18, T:0.26
Consensus pattern (46 bp):
ACCTCGACCCACTATCAATAATGATAGGAACCTTGGTATATGATGA
Done.