Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold510
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: 29735
ACGTcount: A:0.32, C:0.20, G:0.18, T:0.30
Found at i:2116 original size:40 final size:39
Alignment explanation
Indices: 2018--2240 Score: 209
Period size: 40 Copynumber: 5.6 Consensus size: 39
2008 TCCTCGTTCA
* * * *
2018 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC
1 AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
* *
2057 AATGCCTTCGGGACATAACCCGGATTTAATAACTCGCAC
1 AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
*
2096 GAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCAC
1 -AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
* *
2136 AAAGGCCTTCCGGG-CTTAACCCGGAATTT-GTATCTCGCAC
1 -AATGCCTT-CGGGACTTAACCCGG-ATTTAGTAACTCGCAC
** * * * *
2176 AAATGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCAC
1 -AATGCCTTCGGGA-CTTAACCCGGATTTAGTAAC-TCGCAC
* *
2217 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
2241 CAGCATTCAA
Statistics
Matches: 157, Mismatches: 19, Indels: 15
0.82 0.10 0.08
Matches are distributed among these distances:
38 2 0.01
39 39 0.25
40 100 0.64
41 16 0.10
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.26
Consensus pattern (39 bp):
AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
Found at i:2249 original size:41 final size:41
Alignment explanation
Indices: 2172--2249 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
2162 TTTGTATCTC
* * *
2172 GCACAAATGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
2213 GCACAAA-GCCTTCGGGA-CTTAGCCCGGACAGCATTCA
1 GCACAAATGCCTTC-GGATCTTAGCCCGGACA-CATTCA
2250 ATTAATCATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 17 0.53
41 15 0.47
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (41 bp):
GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
Found at i:9394 original size:79 final size:77
Alignment explanation
Indices: 9263--9486 Score: 250
Period size: 79 Copynumber: 2.8 Consensus size: 77
9253 GCTCCTCGTT
* * * * *
9263 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACACAATGCCTTCGGGACTTAACCCGGA
1 CAAATGCCTTC-GGACTTAGCCCGGATTTAGTACCTCGCACAAAGCCTTCGGGACTTAACCCGGA
9328 TTTAATAACTCGCA
65 TTT-ATAACTCGCA
* * *
9342 CGAATGCCTTCGGACTTAACCCGGATTTAGTACCTCGCACAAAGGCCTTCGGGGCTTAACCCGGA
1 CAAATGCCTTCGGACTTAGCCCGGATTTAGTACCTCGCACAAA-GCCTTCGGGACTTAACCCGG-
* *
9407 ATTTGTATCTCGCA
64 ATTTATAACTCGCA
* * * * * *
9421 CAAATGCCTTCGGATCTTAGTCCGGATATATTCACTTAGCACAAAGCCTTCGGGACTTAGCCCGG
1 CAAATGCCTTCGGA-CTTAGCCCGGATTTAGT-ACCTCGCACAAAGCCTTCGGGACTTAACCCGG
9486 A
64 A
9487 CAGCATTCAA
Statistics
Matches: 122, Mismatches: 19, Indels: 8
0.82 0.13 0.05
Matches are distributed among these distances:
78 26 0.21
79 51 0.42
80 35 0.29
81 10 0.08
ACGTcount: A:0.25, C:0.28, G:0.21, T:0.25
Consensus pattern (77 bp):
CAAATGCCTTCGGACTTAGCCCGGATTTAGTACCTCGCACAAAGCCTTCGGGACTTAACCCGGAT
TTATAACTCGCA
Found at i:9419 original size:40 final size:40
Alignment explanation
Indices: 9263--9486 Score: 233
Period size: 39 Copynumber: 5.7 Consensus size: 40
9253 GCTCCTCGTT
* * * *
9263 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
*
9303 C-AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* *
9342 CGAATGCCTTC-GGACTTAACCCGGATTTAGTACCTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* * *
9381 CAAAGGCCTTCGGGGCTTAACCCGGAATTT-GTATCTCGCA
1 CAAATGCCTTCGGGACTTAACCCGG-ATTTAGTAACTCGCA
** * * * *
9421 CAAATGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAACCCGGATTTAGTAAC-TCGCA
*
9462 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAACCCGGA
9487 CAGCATTCAA
Statistics
Matches: 156, Mismatches: 21, Indels: 14
0.82 0.11 0.07
Matches are distributed among these distances:
39 74 0.47
40 67 0.43
41 15 0.10
ACGTcount: A:0.25, C:0.28, G:0.21, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
Found at i:9495 original size:41 final size:41
Alignment explanation
Indices: 9418--9495 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
9408 TTTGTATCTC
* * *
9418 GCACAAATGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
9459 GCACAAA-GCCTTCGGGA-CTTAGCCCGGACAGCATTCA
1 GCACAAATGCCTTC-GGATCTTAGCCCGGACA-CATTCA
9496 ATTAATCATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 17 0.53
41 15 0.47
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (41 bp):
GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
Found at i:13808 original size:41 final size:41
Alignment explanation
Indices: 13746--13831 Score: 136
Period size: 41 Copynumber: 2.1 Consensus size: 41
13736 TTTAATTAGG
* *
13746 TGTTTTAAATATGCCTGGACGAATTTAATGCCGCCACTACA
1 TGTTATAAATATGCCTGGACGAATTTAATGCCACCACTACA
* *
13787 TGTTATAAATATGCCTGGACGAATTTAATGCTACTACTACA
1 TGTTATAAATATGCCTGGACGAATTTAATGCCACCACTACA
13828 TGTT
1 TGTT
13832 TGGCCGAATT
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.30, C:0.19, G:0.16, T:0.35
Consensus pattern (41 bp):
TGTTATAAATATGCCTGGACGAATTTAATGCCACCACTACA
Found at i:18637 original size:13 final size:13
Alignment explanation
Indices: 18634--18658 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
18624 AAATTCAAAA
18634 AAAAAAAAAATTC
1 AAAAAAAAAATTC
18647 AAAAAAAAAATT
1 AAAAAAAAAATT
18659 TGGTTTCCAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.80, C:0.04, G:0.00, T:0.16
Consensus pattern (13 bp):
AAAAAAAAAATTC
Found at i:18641 original size:17 final size:17
Alignment explanation
Indices: 18619--18656 Score: 76
Period size: 17 Copynumber: 2.2 Consensus size: 17
18609 TAGTTTCTTC
18619 AAAAAAAATTCAAAAAA
1 AAAAAAAATTCAAAAAA
18636 AAAAAAAATTCAAAAAA
1 AAAAAAAATTCAAAAAA
18653 AAAA
1 AAAA
18657 TTTGGTTTCC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.84, C:0.05, G:0.00, T:0.11
Consensus pattern (17 bp):
AAAAAAAATTCAAAAAA
Found at i:18716 original size:15 final size:15
Alignment explanation
Indices: 18696--18750 Score: 92
Period size: 15 Copynumber: 3.5 Consensus size: 15
18686 GATATCAAGT
18696 TGAAAAAAAAATTCG
1 TGAAAAAAAAATTCG
18711 TGAAAAAAAAATTCG
1 TGAAAAAAAAATTCG
18726 TGAAAAAAAAATTTTCG
1 TGAAAAAAAAA--TTCG
18743 TGAAAAAA
1 TGAAAAAA
18751 GAAGAAGAAG
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
15 26 0.68
17 12 0.32
ACGTcount: A:0.60, C:0.05, G:0.13, T:0.22
Consensus pattern (15 bp):
TGAAAAAAAAATTCG
Found at i:18720 original size:17 final size:17
Alignment explanation
Indices: 18698--18750 Score: 74
Period size: 17 Copynumber: 3.2 Consensus size: 17
18688 TATCAAGTTG
18698 AAAAAAAAATTCGTG--
1 AAAAAAAAATTCGTGAA
18713 AAAAAAAAATTCGTGAA
1 AAAAAAAAATTCGTGAA
**
18730 AAAAAAATTTTCGTGAA
1 AAAAAAAAATTCGTGAA
18747 AAAA
1 AAAA
18751 GAAGAAGAAG
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
15 15 0.44
17 19 0.56
ACGTcount: A:0.62, C:0.06, G:0.11, T:0.21
Consensus pattern (17 bp):
AAAAAAAAATTCGTGAA
Found at i:25892 original size:12 final size:12
Alignment explanation
Indices: 25877--25939 Score: 60
Period size: 12 Copynumber: 5.2 Consensus size: 12
25867 TCAAGCTCGC
25877 TTTCAATTTCTT
1 TTTCAATTTCTT
*
25889 TTTCCACTCTTTCTT
1 TTT-CA--ATTTCTT
25904 TTTC---TTCTT
1 TTTCAATTTCTT
25913 TTTCAATTTCTT
1 TTTCAATTTCTT
*
25925 TTTCAATCTCTT
1 TTTCAATTTCTT
25937 TTT
1 TTT
25940 GCTTTTCACT
Statistics
Matches: 43, Mismatches: 2, Indels: 12
0.75 0.04 0.21
Matches are distributed among these distances:
9 9 0.21
12 22 0.51
13 2 0.05
14 1 0.02
15 9 0.21
ACGTcount: A:0.11, C:0.22, G:0.00, T:0.67
Consensus pattern (12 bp):
TTTCAATTTCTT
Found at i:25996 original size:14 final size:13
Alignment explanation
Indices: 25977--26019 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 13
25967 CTCATTTTCA
25977 TCTTTTTCTTTATT
1 TCTTTTTCTTT-TT
25991 TCTTTTTCTTTTT
1 TCTTTTTCTTTTT
*
26004 CTCTCATTTCTTTTT
1 -TCT-TTTTCTTTTT
26019 T
1 T
26020 TCTTCTCTCA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
13 2 0.08
14 15 0.58
15 9 0.35
ACGTcount: A:0.05, C:0.19, G:0.00, T:0.77
Consensus pattern (13 bp):
TCTTTTTCTTTTT
Found at i:26028 original size:22 final size:21
Alignment explanation
Indices: 25977--26034 Score: 75
Period size: 20 Copynumber: 2.8 Consensus size: 21
25967 CTCATTTTCA
*
25977 TCTTTTTCT-TTATTTCTTTT
1 TCTTTTTCTCTCATTTCTTTT
25997 TCTTTTTCTCTCATTTCTTTT
1 TCTTTTTCTCTCATTTCTTTT
*
26018 T-TTCTTCTCTCAATTTC
1 TCTTTTTCTCTC-ATTTC
26035 ATTCAAGATT
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
20 18 0.53
21 16 0.47
ACGTcount: A:0.07, C:0.22, G:0.00, T:0.71
Consensus pattern (21 bp):
TCTTTTTCTCTCATTTCTTTT
Found at i:26931 original size:11 final size:11
Alignment explanation
Indices: 26917--26962 Score: 60
Period size: 11 Copynumber: 4.3 Consensus size: 11
26907 TTTTTCAAAT
26917 AATTTTTTTTC
1 AATTTTTTTTC
26928 AATTTTTTTTC
1 AATTTTTTTTC
26939 GAA-TTTTTTT-
1 -AATTTTTTTTC
*
26949 AATTTTTTTAC
1 AATTTTTTTTC
26960 AAT
1 AAT
26963 ATCGTAATGA
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
9 2 0.06
10 6 0.19
11 21 0.68
12 2 0.06
ACGTcount: A:0.24, C:0.07, G:0.02, T:0.67
Consensus pattern (11 bp):
AATTTTTTTTC
Found at i:28301 original size:55 final size:56
Alignment explanation
Indices: 28197--28302 Score: 142
Period size: 56 Copynumber: 1.9 Consensus size: 56
28187 ATTAATGCCG
* * * *
28197 TCCATGCATGGGAACATCTCATTAAATCCATGTCTTTGCTTCCCTTTAAATGCTGT
1 TCCATGCATGGGAACATCTCATTAAATCCATGGCTTTGCTGCACATTAAATGCTGT
* * *
28253 TCCATGCATGGGAACATCTCCTT-AATTCGTGGCTTTGCTGCACATTAAAT
1 TCCATGCATGGGAACATCTCATTAAATCCATGGCTTTGCTGCACATTAAAT
28303 CAGCAAGCAG
Statistics
Matches: 43, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
55 21 0.49
56 22 0.51
ACGTcount: A:0.24, C:0.25, G:0.16, T:0.36
Consensus pattern (56 bp):
TCCATGCATGGGAACATCTCATTAAATCCATGGCTTTGCTGCACATTAAATGCTGT
Found at i:28519 original size:23 final size:22
Alignment explanation
Indices: 28485--28548 Score: 101
Period size: 23 Copynumber: 2.8 Consensus size: 22
28475 GACACCATTT
*
28485 AAAACATGCATTAAATTCGGCC
1 AAAACATACATTAAATTCGGCC
28507 AGAAACATACATTAAATTCGGCC
1 A-AAACATACATTAAATTCGGCC
28530 AAAGACATACATTAAATTC
1 AAA-ACATACATTAAATTC
28549 ATCTGGAAAA
Statistics
Matches: 39, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
22 3 0.08
23 36 0.92
ACGTcount: A:0.45, C:0.20, G:0.11, T:0.23
Consensus pattern (22 bp):
AAAACATACATTAAATTCGGCC
Done.