Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2388
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: 23007
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31
Found at i:3130 original size:40 final size:40
Alignment explanation
Indices: 3041--3302 Score: 291
Period size: 40 Copynumber: 6.6 Consensus size: 40
3031 TCCTCGTTCA
* * * *
3041 AATGCCTTC-GGACATAGCCCGGTTTTAGTAACTCA-CAC-
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACT-AGCACG
* *
3079 AATGCCTTCGGGACATAACCCGGATTTAACAACTAGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTAGCACG
*
3119 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTAGCACG
*
3159 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTAGCACG
* * * *
3199 AATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTAGCACG
* * * * *
3239 AAGGCCTTC-GGATCTTAATCCGGATATATTCACTTAGCAC-
1 AATGCCTTCGGGA-CTTAACCCGGATTTAATAAC-TAGCACG
* *
3279 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
3303 CAGCATTCAA
Statistics
Matches: 198, Mismatches: 20, Indels: 10
0.87 0.09 0.04
Matches are distributed among these distances:
38 10 0.05
39 26 0.13
40 154 0.78
41 8 0.04
ACGTcount: A:0.27, C:0.27, G:0.20, T:0.25
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGATTTAATAACTAGCACG
Found at i:6143 original size:57 final size:57
Alignment explanation
Indices: 6044--6158 Score: 158
Period size: 57 Copynumber: 2.0 Consensus size: 57
6034 ATGGGAGCAC
* * ** *
6044 CCCAAGGCGAAAAACTCGATCTTGCAAATATTTTATCGGTTAATTCTTGCAACTGAG
1 CCCAAGGCGAAAAACTCGATCATGCAAATACTCGATCAGTTAATTCTTGCAACTGAG
* * *
6101 CCCAAGGTGAAAAACTCGATCATGCAAATCCTCGATCAGTTAATTGTTGCAACTGAG
1 CCCAAGGCGAAAAACTCGATCATGCAAATACTCGATCAGTTAATTCTTGCAACTGAG
6158 C
1 C
6159 TTTTAGTTCT
Statistics
Matches: 50, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
57 50 1.00
ACGTcount: A:0.32, C:0.23, G:0.18, T:0.27
Consensus pattern (57 bp):
CCCAAGGCGAAAAACTCGATCATGCAAATACTCGATCAGTTAATTCTTGCAACTGAG
Found at i:7455 original size:6 final size:6
Alignment explanation
Indices: 7443--7477 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
7433 AAGAAATATT
* *
7443 ATCAGA ATTAGA ATCAGA ATCAGA ATCAGT ATCAG
1 ATCAGA ATCAGA ATCAGA ATCAGA ATCAGA ATCAG
7478 GTAATAGAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.46, C:0.14, G:0.17, T:0.23
Consensus pattern (6 bp):
ATCAGA
Found at i:7679 original size:27 final size:26
Alignment explanation
Indices: 7635--7695 Score: 77
Period size: 27 Copynumber: 2.3 Consensus size: 26
7625 CTACTCAGTT
*
7635 ATCAGATATTATGACAGAGTCACCAA
1 ATCAGATATTATGACAGAGCCACCAA
* * *
7661 ATACAGATATTGTGGCAGAGCCACCAG
1 AT-CAGATATTATGACAGAGCCACCAA
7688 ATCAGATA
1 ATCAGATA
7696 ATGTAGGAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
26 8 0.27
27 22 0.73
ACGTcount: A:0.39, C:0.20, G:0.20, T:0.21
Consensus pattern (26 bp):
ATCAGATATTATGACAGAGCCACCAA
Found at i:8444 original size:27 final size:27
Alignment explanation
Indices: 8360--8472 Score: 97
Period size: 27 Copynumber: 4.3 Consensus size: 27
8350 GGGGCAAAAT
* * * *
8360 GGTAATTTTACCCCACA-AAGTATCTC
1 GGTAATTCTACCCTACAGAGGTATTTC
* * *
8386 AGTAATTCTACCCTACAGGGGTATTTT
1 GGTAATTCTACCCTACAGAGGTATTTC
*
8413 AGTAATTCTACCCTACAGAGGTATTTC
1 GGTAATTCTACCCTACAGAGGTATTTC
* **
8440 GGTAATTTTACAAT-C-GATGGTATTTC
1 GGTAATTCTACCCTACAGA-GGTATTTC
8466 GGTAATT
1 GGTAATT
8473 TTATAAACCG
Statistics
Matches: 72, Mismatches: 13, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
25 2 0.03
26 30 0.42
27 40 0.56
ACGTcount: A:0.28, C:0.19, G:0.17, T:0.36
Consensus pattern (27 bp):
GGTAATTCTACCCTACAGAGGTATTTC
Found at i:8524 original size:26 final size:26
Alignment explanation
Indices: 8432--8526 Score: 77
Period size: 26 Copynumber: 3.6 Consensus size: 26
8422 ACCCTACAGA
* **
8432 GGTATTTCGGTAATTTTACAA-TCGAT
1 GGTATTTCAGTAATTTTACAACT-GGG
* * *
8458 GGTATTTCGGTAATTTTATAAACCGGG
1 GGTATTTCAGTAATTTTA-CAACTGGG
* *
8485 GGCACTTTGA-TAATTTTACAACTGGG
1 GGTA-TTTCAGTAATTTTACAACTGGG
8511 GGTATTTCAGTAATTT
1 GGTATTTCAGTAATTT
8527 GGTAAACTAA
Statistics
Matches: 54, Mismatches: 11, Indels: 8
0.74 0.15 0.11
Matches are distributed among these distances:
25 4 0.07
26 33 0.61
27 14 0.26
28 3 0.06
ACGTcount: A:0.26, C:0.12, G:0.22, T:0.40
Consensus pattern (26 bp):
GGTATTTCAGTAATTTTACAACTGGG
Found at i:14847 original size:47 final size:48
Alignment explanation
Indices: 14781--14912 Score: 230
Period size: 49 Copynumber: 2.7 Consensus size: 48
14771 GAAATGATAG
14781 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG-TATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGATATATATGTGA
14828 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG-ATATATATGTGA
*
14877 TAGGGCCTAATGGCCGATGTGATGAATGTGATAAGT
1 TAAGGCCTAATGGCCGATGTGATGAATGTGA-AAGT
14913 CTCGAAGGGC
Statistics
Matches: 81, Mismatches: 1, Indels: 3
0.95 0.01 0.04
Matches are distributed among these distances:
47 36 0.44
49 41 0.51
50 4 0.05
ACGTcount: A:0.31, C:0.09, G:0.30, T:0.30
Consensus pattern (48 bp):
TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGATATATATGTGA
Found at i:15085 original size:36 final size:37
Alignment explanation
Indices: 15030--15107 Score: 122
Period size: 36 Copynumber: 2.1 Consensus size: 37
15020 CCGAGCTCTA
* *
15030 AAGACCCGATGACTACGTGTGGGGATT-TGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
*
15066 AAGACCCGATAACTTCGTGTGGAGATTATGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
15103 AAGAC
1 AAGAC
15108 TTCGTAATAA
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
36 24 0.63
37 14 0.37
ACGTcount: A:0.24, C:0.19, G:0.32, T:0.24
Consensus pattern (37 bp):
AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
Found at i:17052 original size:29 final size:30
Alignment explanation
Indices: 17012--17091 Score: 110
Period size: 29 Copynumber: 2.7 Consensus size: 30
17002 GTTGTGAGAT
*
17012 TGGCACTAAGTGTGCGGGGTTGAAA-TGCA
1 TGGCACTAAGTGTGCGGGGTTGAAAGTACA
* *
17041 TGGCACTAAGTGTGC-GAGTTTAAAGTACA
1 TGGCACTAAGTGTGCGGGGTTGAAAGTACA
*
17070 TGGCACTAAGTGTGCGTGGTTG
1 TGGCACTAAGTGTGCGGGGTTG
17092 TTTATTAAGC
Statistics
Matches: 43, Mismatches: 6, Indels: 3
0.83 0.12 0.06
Matches are distributed among these distances:
28 7 0.16
29 33 0.77
30 3 0.07
ACGTcount: A:0.24, C:0.14, G:0.35, T:0.28
Consensus pattern (30 bp):
TGGCACTAAGTGTGCGGGGTTGAAAGTACA
Found at i:17521 original size:40 final size:40
Alignment explanation
Indices: 17398--17620 Score: 227
Period size: 40 Copynumber: 5.6 Consensus size: 40
17388 TCGAATGATG
* *
17398 TCCGGGCTAAGTCCCGAAG-GC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGAGCATTCGTGCT-AGTGA-TATA
* * * * * *
17438 TCCGGACTAAGACCCGAAG-GCATTGGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGA-TATA
* *
17478 TCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGTA
1 TCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATATA
*
17518 TCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATATA
1 TCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATATA
** ** * * *
17558 TCCATGCTAAACCCCGAAGAGCATTCGTGCTGGTGTTATG
1 TCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATATA
*
17598 TCCGGGCTAGGTCCCGAAGAGCA
1 TCCGGGCTAAGTCCCGAAGAGCA
17621 ATCATGCTGG
Statistics
Matches: 150, Mismatches: 31, Indels: 4
0.81 0.17 0.02
Matches are distributed among these distances:
40 132 0.88
41 18 0.12
ACGTcount: A:0.25, C:0.24, G:0.28, T:0.24
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATATA
Found at i:21156 original size:47 final size:47
Alignment explanation
Indices: 21090--21500 Score: 774
Period size: 47 Copynumber: 8.7 Consensus size: 47
21080 GAAATGATAG
21090 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
21137 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
21184 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
21231 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
21278 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
21325 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
21372 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
21419 T-AGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TATATATGTGA
21467 T-AGG-CTAATGGCCGATGTGATGAATGTGATAAGT
1 TAAGGCCTAATGGCCGATGTGATGAATGTGA-AAGT
21501 CGAAGGGCAT
Statistics
Matches: 361, Mismatches: 0, Indels: 5
0.99 0.00 0.01
Matches are distributed among these distances:
46 34 0.09
47 308 0.85
48 19 0.05
ACGTcount: A:0.32, C:0.09, G:0.30, T:0.30
Consensus pattern (47 bp):
TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
Found at i:21671 original size:36 final size:37
Alignment explanation
Indices: 21616--21693 Score: 122
Period size: 36 Copynumber: 2.1 Consensus size: 37
21606 CCGAGCTCTA
* *
21616 AAGACCCGATGACTACGTGTGGGGATT-TGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
*
21652 AAGACCCGATAACTTCGTGTGGAGATTATGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
21689 AAGAC
1 AAGAC
21694 TTCGTAATAA
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
36 24 0.63
37 14 0.37
ACGTcount: A:0.24, C:0.19, G:0.32, T:0.24
Consensus pattern (37 bp):
AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
Done.