Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3431
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: 60347
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31
Found at i:18678 original size:93 final size:93
Alignment explanation
Indices: 18568--18738 Score: 297
Period size: 93 Copynumber: 1.8 Consensus size: 93
18558 GCCCCTAAGT
* *
18568 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAATGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAATGAACTCGGACTCAACTCAA
18633 CGAGTTCGGATGCCTAGTTACATCTCAC
66 CGAGTTCGGATGCCTAGTTACATCTCAC
* * *
18661 GAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAATGAACTCGGACTCAACTCAA
18726 CGAGTTCGGATGC
66 CGAGTTCGGATGC
18739 TCAACCATCC
Statistics
Matches: 73, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
93 73 1.00
ACGTcount: A:0.29, C:0.29, G:0.21, T:0.22
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAATGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATCTCAC
Found at i:18735 original size:46 final size:46
Alignment explanation
Indices: 18563--18735 Score: 208
Period size: 46 Copynumber: 3.7 Consensus size: 46
18553 AACCCGCCCC
* * * *
18563 TAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCA
* * *
18609 TAAATGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACAT-C-
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA---C-ATTTGCATCCA
* *
18657 TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCA
18702 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
18736 TGCTCAACCA
Statistics
Matches: 107, Mismatches: 13, Indels: 14
0.80 0.10 0.10
Matches are distributed among these distances:
43 6 0.06
44 2 0.02
45 2 0.02
46 60 0.56
47 29 0.27
48 2 0.02
49 2 0.02
50 4 0.04
ACGTcount: A:0.29, C:0.28, G:0.21, T:0.22
Consensus pattern (46 bp):
TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCA
Found at i:33595 original size:28 final size:28
Alignment explanation
Indices: 33555--33648 Score: 152
Period size: 28 Copynumber: 3.4 Consensus size: 28
33545 GGCTTGACGA
33555 GCCATATGAATGTGATTGGGCCTGATGG
1 GCCATATGAATGTGATTGGGCCTGATGG
*
33583 GCCATGTGAATGTGATTGGGCCTGATGG
1 GCCATATGAATGTGATTGGGCCTGATGG
* *
33611 GCCGTATGAATGTGATTGGGCCTGAAGG
1 GCCATATGAATGTGATTGGGCCTGATGG
*
33639 GCCATGTGAA
1 GCCATATGAA
33649 CAAGATTGGG
Statistics
Matches: 60, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 60 1.00
ACGTcount: A:0.21, C:0.15, G:0.37, T:0.27
Consensus pattern (28 bp):
GCCATATGAATGTGATTGGGCCTGATGG
Found at i:33655 original size:28 final size:28
Alignment explanation
Indices: 33555--33667 Score: 145
Period size: 28 Copynumber: 4.0 Consensus size: 28
33545 GGCTTGACGA
* *
33555 GCCATATGAATGTGATTGGGCCTGATGG
1 GCCATGTGAATGTGATTGGGCCTGAAGG
*
33583 GCCATGTGAATGTGATTGGGCCTGATGG
1 GCCATGTGAATGTGATTGGGCCTGAAGG
* *
33611 GCCGTATGAATGTGATTGGGCCTGAAGG
1 GCCATGTGAATGTGATTGGGCCTGAAGG
*** *
33639 GCCATGTGAACAAGATTGGGCCTAAAGG
1 GCCATGTGAATGTGATTGGGCCTGAAGG
33667 G
1 G
33668 GCCAAATGAA
Statistics
Matches: 75, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 75 1.00
ACGTcount: A:0.23, C:0.15, G:0.37, T:0.25
Consensus pattern (28 bp):
GCCATGTGAATGTGATTGGGCCTGAAGG
Found at i:34008 original size:27 final size:27
Alignment explanation
Indices: 33987--34477 Score: 514
Period size: 27 Copynumber: 18.3 Consensus size: 27
33977 GAAATTATTA
* *
33987 AAATACCCTCGATTTGTAAAATTATCA
1 AAATACCCTCGATTTGTAAAATTACCG
*
34014 AAATACCAC-CGATTTGTAAAATTATCG
1 AAATACC-CTCGATTTGTAAAATTACCG
* **
34041 AAATACCCTCGA-TTGTGAAATTATTG
1 AAATACCCTCGATTTGTAAAATTACCG
* *
34067 AAATACCCT-AATTTGTGAAATTACCG
1 AAATACCCTCGATTTGTAAAATTACCG
* *
34093 AAATACCCTCGA-TTGTGAAATTATCG
1 AAATACCCTCGATTTGTAAAATTACCG
*
34119 AAATACCCTCGATTTGTAAAATTACCA
1 AAATACCCTCGATTTGTAAAATTACCG
* *
34146 AAATACCCTCGATTTGTGAAATTACCA
1 AAATACCCTCGATTTGTAAAATTACCG
* *
34173 AAACACCCTCGATTTGTAAAATTATCG
1 AAATACCCTCGATTTGTAAAATTACCG
* *
34200 AAATACCCCCGATTTGTAAAATTGCC-
1 AAATACCCTCGATTTGTAAAATTACCG
* * *
34226 AAACTAACCTCGA-TTGTGAAATTACCA
1 AAA-TACCCTCGATTTGTAAAATTACCG
* * *
34253 AAATACCCTTGATTTGTAAAATAACTG
1 AAATACCCTCGATTTGTAAAATTACCG
* *
34280 AAATATCCC-CGATTTATGAAATTACCG
1 AAATA-CCCTCGATTTGTAAAATTACCG
* * * *
34307 AAACACCCTTGATTTGTAAAATTATCA
1 AAATACCCTCGATTTGTAAAATTACCG
* *
34334 AAACACCCTCGATTTGTAAAATTATCG
1 AAATACCCTCGATTTGTAAAATTACCG
* *
34361 AAACACCCTCGATTTGTAAAATTACCA
1 AAATACCCTCGATTTGTAAAATTACCG
*
34388 AAATACCCTCAATTTGTAAAATTACCG
1 AAATACCCTCGATTTGTAAAATTACCG
* * *
34415 AAACA-TCTCCGATTTGTAAAATTATCG
1 AAATACCCT-CGATTTGTAAAATTACCG
* * *
34442 AAATACCCTTG-TAGTGTAAAATTACTG
1 AAATACCCTCGAT-TTGTAAAATTACCG
34469 AAATACCCT
1 AAATACCCT
34478 TGTAGTGTAA
Statistics
Matches: 393, Mismatches: 58, Indels: 26
0.82 0.12 0.05
Matches are distributed among these distances:
25 1 0.00
26 95 0.24
27 291 0.74
28 6 0.02
ACGTcount: A:0.38, C:0.21, G:0.11, T:0.30
Consensus pattern (27 bp):
AAATACCCTCGATTTGTAAAATTACCG
Found at i:34216 original size:81 final size:81
Alignment explanation
Indices: 33986--34477 Score: 570
Period size: 81 Copynumber: 6.1 Consensus size: 81
33976 AGAAATTATT
* *
33986 AAAATACCCTCGATTTGTAAAATTATCAAAATACCAC-CGATTTGTAAAATTATCGAAATACCCT
1 AAAATACCCTCGATTTGTAAAATTACCAAAACACC-CTCGATTTGTAAAATTATCGAAATACCCT
* **
34050 CGA-TTGTGAAATTATT
65 CGATTTGTAAAATTACC
* * * * * *
34066 GAAATACCCT-AATTTGTGAAATTACCGAAATACCCTCGA-TTGTGAAATTATCGAAATACCCTC
1 AAAATACCCTCGATTTGTAAAATTACCAAAACACCCTCGATTTGTAAAATTATCGAAATACCCTC
34129 GATTTGTAAAATTACC
66 GATTTGTAAAATTACC
* *
34145 AAAATACCCTCGATTTGTGAAATTACCAAAACACCCTCGATTTGTAAAATTATCGAAATACCCCC
1 AAAATACCCTCGATTTGTAAAATTACCAAAACACCCTCGATTTGTAAAATTATCGAAATACCCTC
*
34210 GATTTGTAAAATTGCC
66 GATTTGTAAAATTACC
* * * * * *
34226 AAACTAACCTCGA-TTGTGAAATTACCAAAATACCCTTGATTTGTAAAA-TAACTGAAATATCCC
1 AAAATACCCTCGATTTGTAAAATTACCAAAACACCCTCGATTTGTAAAATTATC-GAAATA-CCC
* *
34289 -CGATTTATGAAATTACC
64 TCGATTTGTAAAATTACC
* * * * *
34306 GAAACACCCTTGATTTGTAAAATTATCAAAACACCCTCGATTTGTAAAATTATCGAAACACCCTC
1 AAAATACCCTCGATTTGTAAAATTACCAAAACACCCTCGATTTGTAAAATTATCGAAATACCCTC
34371 GATTTGTAAAATTACC
66 GATTTGTAAAATTACC
* * *
34387 AAAATACCCTCAATTTGTAAAATTACCGAAACA-TCTCCGATTTGTAAAATTATCGAAATACCCT
1 AAAATACCCTCGATTTGTAAAATTACCAAAACACCCT-CGATTTGTAAAATTATCGAAATACCCT
* * *
34451 TG-TAGTGTAAAATTACT
65 CGAT-TTGTAAAATTACC
*
34468 GAAATACCCT
1 AAAATACCCT
34478 TGTAGTGTAA
Statistics
Matches: 352, Mismatches: 49, Indels: 21
0.83 0.12 0.05
Matches are distributed among these distances:
78 26 0.07
79 45 0.13
80 102 0.29
81 176 0.50
82 3 0.01
ACGTcount: A:0.39, C:0.21, G:0.11, T:0.30
Consensus pattern (81 bp):
AAAATACCCTCGATTTGTAAAATTACCAAAACACCCTCGATTTGTAAAATTATCGAAATACCCTC
GATTTGTAAAATTACC
Found at i:34478 original size:27 final size:27
Alignment explanation
Indices: 34441--34523 Score: 123
Period size: 27 Copynumber: 3.1 Consensus size: 27
34431 TAAAATTATC
*
34441 GAAATACCCTTGTAGTGTAAAATTACT
1 GAAATACCCTTGTAGTGTAAAATGACT
34468 GAAATACCCTTGTAGTGTAAAATGACT
1 GAAATACCCTTGTAGTGTAAAATGACT
* *
34495 -AACATACCATTGTAGGGTAAAATGACT
1 GAA-ATACCCTTGTAGTGTAAAATGACT
34522 GA
1 GA
34524 CTTAGACTTC
Statistics
Matches: 51, Mismatches: 3, Indels: 3
0.89 0.05 0.05
Matches are distributed among these distances:
26 2 0.04
27 48 0.94
28 1 0.02
ACGTcount: A:0.39, C:0.14, G:0.18, T:0.29
Consensus pattern (27 bp):
GAAATACCCTTGTAGTGTAAAATGACT
Found at i:44076 original size:30 final size:30
Alignment explanation
Indices: 44040--44099 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
44030 TAAAAAGGAA
44040 GTAAATACTAGTACTCGTAGTTCCTTTGAG
1 GTAAATACTAGTACTCGTAGTTCCTTTGAG
44070 GTAAATACTAGTACTCGTAGTTCCTTTGAG
1 GTAAATACTAGTACTCGTAGTTCCTTTGAG
44100 TTCGACAATT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.27, C:0.17, G:0.20, T:0.37
Consensus pattern (30 bp):
GTAAATACTAGTACTCGTAGTTCCTTTGAG
Found at i:53453 original size:32 final size:32
Alignment explanation
Indices: 53412--53473 Score: 115
Period size: 32 Copynumber: 1.9 Consensus size: 32
53402 CATCTATTTT
53412 CATTGTTCAACTCTTTGACAACACGAAAAATC
1 CATTGTTCAACTCTTTGACAACACGAAAAATC
*
53444 CATTGTTCAACTCTTTGACAACATGAAAAA
1 CATTGTTCAACTCTTTGACAACACGAAAAA
53474 ACCAAAAGCT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.39, C:0.23, G:0.10, T:0.29
Consensus pattern (32 bp):
CATTGTTCAACTCTTTGACAACACGAAAAATC
Found at i:57110 original size:19 final size:20
Alignment explanation
Indices: 57086--57123 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
57076 GGTACCACCA
57086 AAACAT-ATATCA-CATCTTT
1 AAACATCAT-TCATCATCTTT
57105 AAACATCATTCATCATCTT
1 AAACATCATTCATCATCTT
57124 ACCACCTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.39, C:0.24, G:0.00, T:0.37
Consensus pattern (20 bp):
AAACATCATTCATCATCTTT
Done.