Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2514
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: 39722
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31
Found at i:5908 original size:40 final size:40
Alignment explanation
Indices: 5824--6048 Score: 287
Period size: 40 Copynumber: 5.7 Consensus size: 40
5814 TTGAATGATG
* * * *
5824 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
* * *
5864 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
* *
5904 TCCGGGCTAAG-CCCGAAGGCATTGGCGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
5943 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
5983 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
*
6024 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
6049 AACGAGGAGC
Statistics
Matches: 163, Mismatches: 17, Indels: 10
0.86 0.09 0.05
Matches are distributed among these distances:
39 33 0.20
40 120 0.74
41 10 0.06
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:5960 original size:79 final size:80
Alignment explanation
Indices: 5824--6048 Score: 269
Period size: 79 Copynumber: 2.8 Consensus size: 80
5814 TTGAATGATG
* ** * * * *
5824 TCCGGGCTAAGTCCCGAAGGCTTTGTGC-TAAGTGACCATATCCGGACTAAGAT-CCGAAGGCAT
1 TCCGGGCTAAGTCCCGAAGGCATTG-GCGCGAGTTACTATAACCGGGCTAAG-TCCCGAAGGCAT
*
5887 TTGTGCGAGATACTAAT
64 TTGTGCGAGATACTAAA
*
5904 TCCGGGCTAAG-CCCGAAGGCATTGGCGCGAGTTACTA-AATCCGGGTTAAGTCCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTGGCGCGAGTTACTATAA-CCGGGCTAAGTCCCGAAGGCATT
*
5967 TGTGCGAGTTACTAAA
65 TGTGCGAGATACTAAA
* * * *
5983 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAACCGGGCTATGTCCCGAAGGCATTT
1 TCCGGGCTAAGTCCCGAAGGCATTGGCGCGAGTTACTATAACCGGGCTAAGTCCCGAAGGCATTT
6048 G
66 G
6049 AACGAGGAGC
Statistics
Matches: 125, Mismatches: 15, Indels: 10
0.83 0.10 0.07
Matches are distributed among these distances:
78 4 0.03
79 61 0.49
80 58 0.46
81 2 0.02
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (80 bp):
TCCGGGCTAAGTCCCGAAGGCATTGGCGCGAGTTACTATAACCGGGCTAAGTCCCGAAGGCATTT
GTGCGAGATACTAAA
Found at i:6070 original size:119 final size:119
Alignment explanation
Indices: 5824--6081 Score: 283
Period size: 119 Copynumber: 2.2 Consensus size: 119
5814 TTGAATGATG
* *
5824 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATTT
1 TCCGGGTTAAGTCCCGAAGGCTTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATTT
* ** *
5889 GTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTGGCGCGAGTTACTAAA
66 GTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTGGAACGAGTGACTAAA
* * * **
5943 TCCGGGTTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCAT
1 TCCGGGTTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCAT
* * * *
6006 TTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-GAGCTATA
64 TTGTGCGAGATACTAAT-ACCGGGCTAAG-CCCGAAGGCATTGGAACGAGTGA-CTAAA
* *
6063 TCC-GGTTAAATTCCGAAGG
1 TCCGGGTTAAGTCCCGAAGG
6082 TACGTGATTT
Statistics
Matches: 117, Mismatches: 17, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
118 3 0.03
119 83 0.71
120 31 0.26
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.24
Consensus pattern (119 bp):
TCCGGGTTAAGTCCCGAAGGCTTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATTT
GTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTGGAACGAGTGACTAAA
Found at i:14598 original size:50 final size:52
Alignment explanation
Indices: 14486--14606 Score: 183
Period size: 50 Copynumber: 2.4 Consensus size: 52
14476 ATGAACAAAT
* * *
14486 GAGTTACTTAATGCATGACTTAATTTAATGATGCAAACTTTAACTAACATGG
1 GAGTTACATAATGCATGACATAATTTAATGATGCAAACTTTAACTAACATGA
* *
14538 GAGTTGCATAATGCATGTCATAATTT-ATGATGCAAAC-TTAACTAACATGA
1 GAGTTACATAATGCATGACATAATTTAATGATGCAAACTTTAACTAACATGA
14588 GAGTTACATAATGCATGAC
1 GAGTTACATAATGCATGAC
14607 TTTATTAAAT
Statistics
Matches: 62, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
50 29 0.47
51 11 0.18
52 22 0.35
ACGTcount: A:0.37, C:0.14, G:0.17, T:0.32
Consensus pattern (52 bp):
GAGTTACATAATGCATGACATAATTTAATGATGCAAACTTTAACTAACATGA
Found at i:14709 original size:30 final size:32
Alignment explanation
Indices: 14637--14725 Score: 92
Period size: 33 Copynumber: 2.7 Consensus size: 32
14627 TAGTGCTTGT
*
14637 CATAATTAGAAGATGTAGATTAATAATGCAAGA
1 CATAATTA-AAGATGTAGATTAATAATACAAGA
* *
14670 CATTAATTAAAGATGTATA-TAATAA-ACAAGG
1 CA-TAATTAAAGATGTAGATTAATAATACAAGA
*
14701 CATAATTAAAAGCTGTAGAATTAAT
1 CATAATT-AAAGATGTAG-ATTAAT
14726 TAAACTAAAC
Statistics
Matches: 47, Mismatches: 5, Indels: 8
0.78 0.08 0.13
Matches are distributed among these distances:
30 5 0.11
31 14 0.30
32 7 0.15
33 15 0.32
34 6 0.13
ACGTcount: A:0.49, C:0.07, G:0.15, T:0.29
Consensus pattern (32 bp):
CATAATTAAAGATGTAGATTAATAATACAAGA
Found at i:16701 original size:104 final size:105
Alignment explanation
Indices: 16521--16788 Score: 450
Period size: 104 Copynumber: 2.6 Consensus size: 105
16511 TAACCGTTAT
* **
16521 TGGTGGATCTCGCACTTAGCACCACCGCTGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGG
1 TGGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGG
16586 AATCAGCACATAGCAACCCCC-TTTCACATTTCAAAGATA
66 AATCAGCACATAGCAACCCCCTTTTCACATTTCAAAGATA
*
16625 TGGTGGATATCGCACTTAGCACCACCAATGAACCGGGGAATCAGCACTTAGCAACCCCTCGGGGG
1 TGGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGG
16690 AATCAGCACATAGCAACCCCCTTTTCACATTTCAAAGATA
66 AATCAGCACATAGCAACCCCCTTTTCACATTTCAAAGATA
* **
16730 TGGTGGATCA-CGCACATAGCACCACCAATGAATCGGGGAATCAGCACACAGCAACCCCT
1 TGGTGGAT-ATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCT
16789 TTATATACAA
Statistics
Matches: 154, Mismatches: 8, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
104 82 0.53
105 71 0.46
106 1 0.01
ACGTcount: A:0.30, C:0.31, G:0.21, T:0.19
Consensus pattern (105 bp):
TGGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGG
AATCAGCACATAGCAACCCCCTTTTCACATTTCAAAGATA
Found at i:17149 original size:29 final size:29
Alignment explanation
Indices: 17116--17179 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 29
17106 TAATCCACCA
17116 CCCAACTTTTTG-AAAATTACAATTTTGCC
1 CCCAAC-TTTTGCAAAATTACAATTTTGCC
* * *
17145 CCCAAACTTTTGCATAATTACACTTTTGTC
1 CCC-AACTTTTGCAAAATTACAATTTTGCC
17175 CCCAA
1 CCCAA
17180 GCTCGGAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
29 10 0.33
30 20 0.67
ACGTcount: A:0.30, C:0.28, G:0.06, T:0.36
Consensus pattern (29 bp):
CCCAACTTTTGCAAAATTACAATTTTGCC
Found at i:17153 original size:30 final size:30
Alignment explanation
Indices: 17123--17179 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
17113 CCACCCAACT
17123 TTTTG-AAAATTACAATTTTGCCCCCAAAC
1 TTTTGCAAAATTACAATTTTGCCCCCAAAC
* * *
17152 TTTTGCATAATTACACTTTTGTCCCCAA
1 TTTTGCAAAATTACAATTTTGCCCCCAA
17180 GCTCGGAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 5 0.21
30 19 0.79
ACGTcount: A:0.30, C:0.25, G:0.07, T:0.39
Consensus pattern (30 bp):
TTTTGCAAAATTACAATTTTGCCCCCAAAC
Found at i:18166 original size:25 final size:25
Alignment explanation
Indices: 18102--18170 Score: 86
Period size: 25 Copynumber: 2.8 Consensus size: 25
18092 CAAGCCCATT
*
18102 TTCACAACTCATGTGAGCAATCTAA
1 TTCACATCTCATGTGAGCAATCTAA
* *
18127 TTCATATCTCATGTGAGCAATCTGA
1 TTCACATCTCATGTGAGCAATCTAA
*
18152 TTCACAGT-TCGTGTGAGCA
1 TTCACA-TCTCATGTGAGCA
18171 TACATGTGCA
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
25 37 0.97
26 1 0.03
ACGTcount: A:0.29, C:0.22, G:0.17, T:0.32
Consensus pattern (25 bp):
TTCACATCTCATGTGAGCAATCTAA
Found at i:21377 original size:47 final size:47
Alignment explanation
Indices: 21290--21558 Score: 403
Period size: 47 Copynumber: 5.6 Consensus size: 47
21280 GTATATTTGA
21290 ATGAATGTGAAAGTGTATATATATATGTGATAAGGCCTAATGGCCGATGTG
1 ATGAATGTGAAAGTG----TATATATGTGATAAGGCCTAATGGCCGATGTG
21341 ATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTG
1 ATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTG
*
21388 ATGAATGTGAAAGCGTATATATGTGATAAGGCCTAATGGCCGATGTG
1 ATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTG
*
21435 ATGAATGTGAAAGCGTATATATGTGATAAGGCCTAATGGCCGATGTG
1 ATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTG
* * * * * * *
21482 ATGAATGTGAAAGTGTATTTATGTGACAGGGCCGAGTGGCCAACGTG
1 ATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTG
* *
21529 ATGGATGTGAAAGTGTATAAATGTGATAAG
1 ATGAATGTGAAAGTGTATATATGTGATAAG
21559 TCCCGAAGGG
Statistics
Matches: 204, Mismatches: 14, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
47 189 0.93
51 15 0.07
ACGTcount: A:0.32, C:0.09, G:0.30, T:0.29
Consensus pattern (47 bp):
ATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTG
Found at i:21735 original size:37 final size:37
Alignment explanation
Indices: 21677--21755 Score: 106
Period size: 37 Copynumber: 2.1 Consensus size: 37
21667 CCGAGCTCTA
* * *
21677 AAGACCCGATGACTACGTGTGG-GAATTTTGTCCGGGT
1 AAGACCCGATAACTACATGTGGAG-ATTATGTCCGGGT
*
21714 AAGACCCGATAACTTCATGTGGAGATTATGTCCGGGT
1 AAGACCCGATAACTACATGTGGAGATTATGTCCGGGT
21751 AAGAC
1 AAGAC
21756 TTCGTAATAA
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
37 36 0.97
38 1 0.03
ACGTcount: A:0.27, C:0.19, G:0.29, T:0.25
Consensus pattern (37 bp):
AAGACCCGATAACTACATGTGGAGATTATGTCCGGGT
Found at i:31904 original size:29 final size:27
Alignment explanation
Indices: 31886--31955 Score: 113
Period size: 27 Copynumber: 2.6 Consensus size: 27
31876 ATATTAAGTC
31886 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTCAGTGCTATATAATCAACT
*
31913 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTCAGTGCTATATAATC-AACT
*
31941 CGCACACTTAGTGCT
1 CGCACACTCAGTGCT
31956 GTACAATTTA
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
27 22 0.54
28 19 0.46
ACGTcount: A:0.31, C:0.29, G:0.13, T:0.27
Consensus pattern (27 bp):
CGCACACTCAGTGCTATATAATCAACT
Found at i:31949 original size:28 final size:28
Alignment explanation
Indices: 31886--31983 Score: 135
Period size: 28 Copynumber: 3.5 Consensus size: 28
31876 ATATTAAGTC
*
31886 CGCACACTCAGTGCTATATAATC-AACT
1 CGCACACTTAGTGCTATATAATCAAACT
31913 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* * * *
31941 CGCACACTTAGTGCTGTACAATTTAAACC
1 CGCACACTTAGTGCTATATAA-TCAAACT
31970 CGCACACTTAGTGC
1 CGCACACTTAGTGC
31984 CAATCTCATG
Statistics
Matches: 64, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
27 22 0.34
28 23 0.36
29 19 0.30
ACGTcount: A:0.32, C:0.29, G:0.13, T:0.27
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Done.