Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold986
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: 21484
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Found at i:2168 original size:52 final size:53
Alignment explanation
Indices: 2075--2195 Score: 201
Period size: 52 Copynumber: 2.3 Consensus size: 53
2065 TACTAGGGCA
*
2075 ATTCTTGTTGATGTTCCTGTTTACTAGGACAATTTGTATGACTTAGTTC-TTT
1 ATTCTTGTTGATGTTCCTGTTTACTAGGACAATTTATATGACTTAGTTCTTTT
*
2127 ATTTCTTGTTGATGTTCCTG-TTACTAGGGCAATTTATATGACTTAGTTCTTTT
1 A-TTCTTGTTGATGTTCCTGTTTACTAGGACAATTTATATGACTTAGTTCTTTT
2180 ATTCTTGTTGATGTTC
1 ATTCTTGTTGATGTTC
2196 TTGAACTTTT
Statistics
Matches: 65, Mismatches: 2, Indels: 4
0.92 0.03 0.06
Matches are distributed among these distances:
52 43 0.66
53 22 0.34
ACGTcount: A:0.18, C:0.13, G:0.17, T:0.51
Consensus pattern (53 bp):
ATTCTTGTTGATGTTCCTGTTTACTAGGACAATTTATATGACTTAGTTCTTTT
Found at i:2290 original size:22 final size:22
Alignment explanation
Indices: 2263--2334 Score: 67
Period size: 22 Copynumber: 3.3 Consensus size: 22
2253 TTACAATTAA
2263 ACATGTTTCTTGTGTTTATGTT
1 ACATGTTTCTTGTGTTTATGTT
* * ** *
2285 ACATGTGTTATTCT-TGCAT-TAA
1 ACATGT-TTCTTGTGTTTATGT-T
2307 ACATGTTTCTTGTGTTTATGTT
1 ACATGTTTCTTGTGTTTATGTT
2329 ACATGT
1 ACATGT
2335 ATTATTTCTT
Statistics
Matches: 36, Mismatches: 10, Indels: 8
0.67 0.19 0.15
Matches are distributed among these distances:
21 6 0.17
22 24 0.67
23 6 0.17
ACGTcount: A:0.19, C:0.11, G:0.17, T:0.53
Consensus pattern (22 bp):
ACATGTTTCTTGTGTTTATGTT
Found at i:2321 original size:44 final size:45
Alignment explanation
Indices: 2221--2355 Score: 218
Period size: 44 Copynumber: 3.0 Consensus size: 45
2211 CTTTATTATT
* *
2221 TTTCTTGTGCTTATGTTACATGTATTATTTTCTTACAATTAAACATG
1 TTTCTTGTGTTTATGTTACATGTATTA-TTTCTTGC-ATTAAACATG
*
2268 TTTCTTGTGTTTATGTTACATGTGTTA-TTCTTGCATTAAACATG
1 TTTCTTGTGTTTATGTTACATGTATTATTTCTTGCATTAAACATG
2312 TTTCTTGTGTTTATGTTACATGTATTATTTCTTGCATTAAACAT
1 TTTCTTGTGTTTATGTTACATGTATTATTTCTTGCATTAAACAT
2356 ATAGAGACAA
Statistics
Matches: 83, Mismatches: 4, Indels: 4
0.91 0.04 0.04
Matches are distributed among these distances:
44 36 0.43
45 22 0.27
47 25 0.30
ACGTcount: A:0.23, C:0.12, G:0.13, T:0.53
Consensus pattern (45 bp):
TTTCTTGTGTTTATGTTACATGTATTATTTCTTGCATTAAACATG
Found at i:6402 original size:32 final size:32
Alignment explanation
Indices: 6352--6415 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 32
6342 GCATTCGTAA
6352 GCCTTTGTACTCACGTGCATT-CTCATTTATGT
1 GCCTTTGTACTCACGTGCATTCCT-ATTTATGT
* *
6384 GCCTTTGTGCTCATGTGCATTCCTATTTATGT
1 GCCTTTGTACTCACGTGCATTCCTATTTATGT
6416 CTATTTGCAC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 27 0.93
33 2 0.07
ACGTcount: A:0.14, C:0.23, G:0.17, T:0.45
Consensus pattern (32 bp):
GCCTTTGTACTCACGTGCATTCCTATTTATGT
Found at i:6538 original size:16 final size:16
Alignment explanation
Indices: 6500--6540 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
6490 TCATGAGTAT
6500 TTGCACTCATGTGC-A
1 TTGCACTCATGTGCTA
6515 TTGCCACTCATGT-CTA
1 TTG-CACTCATGTGCTA
6531 TTAGCACTCA
1 TT-GCACTCA
6541 CAAACATCAA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
15 4 0.17
16 18 0.78
17 1 0.04
ACGTcount: A:0.22, C:0.29, G:0.15, T:0.34
Consensus pattern (16 bp):
TTGCACTCATGTGCTA
Found at i:7396 original size:46 final size:47
Alignment explanation
Indices: 7287--7399 Score: 133
Period size: 46 Copynumber: 2.4 Consensus size: 47
7277 TTAGCAATAT
* * *
7287 TCCAAGTATGGACTCTTAACTCTAAAAGTCCCAAATTCGAAAAGAAC
1 TCCAAGTATAGACTCTTGACTCTAAAAGTCCCAAACTCGAAAAGAAC
* * *
7334 TCTAGGTATATACTCTTGACTCT-AAAGTCCCAAACTC-AAAAGAAAC
1 TCCAAGTATAGACTCTTGACTCTAAAAGTCCCAAACTCGAAAAG-AAC
7380 TCCAAGTA-AGAGCTCTTGAC
1 TCCAAGTATAGA-CTCTTGAC
7400 CATGTAAGCT
Statistics
Matches: 55, Mismatches: 9, Indels: 5
0.80 0.13 0.07
Matches are distributed among these distances:
45 7 0.13
46 30 0.55
47 18 0.33
ACGTcount: A:0.38, C:0.24, G:0.13, T:0.25
Consensus pattern (47 bp):
TCCAAGTATAGACTCTTGACTCTAAAAGTCCCAAACTCGAAAAGAAC
Found at i:8647 original size:155 final size:155
Alignment explanation
Indices: 8315--9010 Score: 477
Period size: 155 Copynumber: 4.5 Consensus size: 155
8305 ACGAATATAC
* ** ** * * *
8315 TCCT-AATGCACACCTTTGACATAAAAGTGACTTAGTGATTACATCAA-ACTTGGTTCTAAAAAA
1 TCCTAAATGCACACCTTTGGCATAAAAGTGACCCAGTGACCAC-TTAAGACTTGATTCTAAAGAA
* * * * * * ** *
8378 ATTATCGAAATACCTATAAG-TATACTTTTGATAT-AAAAGTATC-CCGATAA-CCTAACAGGAC
65 ATTACCAAAATACCAATAGGATATACCTTTAAGGTGAAAA-TATCTCAG-TAATCCTAA-AGGAC
* * * *
8439 ATG-AAAAGATAATAAAAAGATGGATCTA
127 ATGAAAAAGATAAGAAAAAGACGAACCTA
* * * ** * *
8467 TCCTAAATGCACAGCTTTGGGATAAAAGTGACCCATTGATGACTTAGGACTTGATTCTAAATAAA
1 TCCTAAATGCACACCTTTGGCATAAAAGTGACCCAGTGACCACTTAAGACTTGATTCTAAAGAAA
* ** * * *
8532 TTACCAAAATGCCCTTAGGATATA-CTTTCAATGTGAAAGTATCGT-AGTACTCCTAAAGGACAT
66 TTACCAAAATACCAATAGGATATACCTTT-AAGGTGAAAATATC-TCAGTAATCCTAAAGGACAT
*
8595 GAAAAAGATCAGAAAAAGGACGAACCTA
129 GAAAAAGATAAGAAAAA-GACGAACCTA
* * * * *
8623 TCCTAAATGCA-ACCTTTGGTATAAAAGTGAGCTAGTGACCACTTAAGACTTGATTTTAAGGAAA
1 TCCTAAATGCACACCTTTGGCATAAAAGTGACCCAGTGACCACTTAAGACTTGATTCTAAAGAAA
* * * *
8687 TTACCAAAATATCAATAGGATATACCTTTGAGGTGAAAATATCTCGGTAATCCTAAAGAACATGA
66 TTACCAAAATACCAATAGGATATACCTTTAAGGTGAAAATATCTCAGTAATCCTAAAGGACATGA
* * *
8752 AAAAGATAAGGAAAATGACTAACTTA
131 AAAAGATAA-GAAAAAGACGAACCTA
* * ** * * * * * *
8778 TCCTAAATACACACCTTTGGCATAAAAATGATTCGGTGACTATTTTAGACTT-ATATTTAGAGAA
1 TCCTAAATGCACACCTTTGGCATAAAAGTGACCCAGTGACCACTTAAGACTTGAT-TCTAAAGAA
*** * * * * * * *
8842 ATTACCAAAA-AGCCCCGAGGTTATAGCTTTGATGTGAAAGTATTTCAATAA-CCTTAAAGGACA
65 ATTACCAAAATA-CCAATAGGATATACCTTTAAGGTGAAAATATCTCAGTAATCC-TAAAGGACA
* * * *
8905 TGAAAATGATAAGTAAAGGATGAACCTA
128 TGAAAAAGATAAGAAAAAGACGAACCTA
* * * * *
8933 TCCTAAATGCACA-CTTTGGCATAAAAGTGATCTAGTGACTACCTAAGACTT-AGTTCTAAGAAA
1 TCCTAAATGCACACCTTTGGCATAAAAGTGACCCAGTGACCACTTAAGACTTGA-TTCTAA-AGA
*
8996 AATTATCAAAATACC
64 AATTACCAAAATACC
9011 TCTAGGTATT
Statistics
Matches: 429, Mismatches: 95, Indels: 37
0.76 0.17 0.07
Matches are distributed among these distances:
152 6 0.01
153 62 0.14
154 57 0.13
155 181 0.42
156 123 0.29
ACGTcount: A:0.41, C:0.16, G:0.16, T:0.28
Consensus pattern (155 bp):
TCCTAAATGCACACCTTTGGCATAAAAGTGACCCAGTGACCACTTAAGACTTGATTCTAAAGAAA
TTACCAAAATACCAATAGGATATACCTTTAAGGTGAAAATATCTCAGTAATCCTAAAGGACATGA
AAAAGATAAGAAAAAGACGAACCTA
Found at i:12535 original size:93 final size:93
Alignment explanation
Indices: 12429--12613 Score: 298
Period size: 93 Copynumber: 2.0 Consensus size: 93
12419 GAAAATGGAG
* * * *
12429 AGTAGCTAGGAAGAAAAAGAAGGCACGGGCAACTCACAGCAACAAGGAATGAAGAAAAAGGAAGC
1 AGTAGCTAGGAAGAAAAAGAAAGCACGGGCAACTCACAGCAACAAAGAATGAAGAAAAAGAAAAC
*
12494 ATGTGTAACATGAAAAGGAGTAGCCAGT
66 ATGTGCAACATGAAAAGGAGTAGCCAGT
* * *
12522 AGTAGCTAGGAAGAAAAAGAAAGCGCGGGCAGCTCGCAGCAACAAAGAATGAAGAAAAAGAAAAC
1 AGTAGCTAGGAAGAAAAAGAAAGCACGGGCAACTCACAGCAACAAAGAATGAAGAAAAAGAAAAC
12587 ATGTGCAACATGAAAAGGAGTAGCCAG
66 ATGTGCAACATGAAAAGGAGTAGCCAG
12614 CAGCAGCGTG
Statistics
Matches: 84, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
93 84 1.00
ACGTcount: A:0.47, C:0.15, G:0.29, T:0.10
Consensus pattern (93 bp):
AGTAGCTAGGAAGAAAAAGAAAGCACGGGCAACTCACAGCAACAAAGAATGAAGAAAAAGAAAAC
ATGTGCAACATGAAAAGGAGTAGCCAGT
Found at i:12720 original size:94 final size:93
Alignment explanation
Indices: 12621--12802 Score: 265
Period size: 94 Copynumber: 1.9 Consensus size: 93
12611 CAGCAGCAGC
* * *
12621 GTGGAATATGGCAGAGCAACGTGCAAACCAAAAGCAACGTAAACAACAAAGAAAAAAATGGATCA
1 GTGGAAGACGGCAGAGCAACGTGCAAACCAAAAGCAACATAAACAACAAAG-AAAAAATGGATCA
* *
12686 AAATAGTAGCAAAATGAAGCAGTAATAGT
65 AAACAGCAGCAAAATGAAGCAGTAATAGT
* * * *
12715 GTGGAAGACGGCAGAGCAACGTGCAAACCAAAAGCAGCATAAATAGCAAAGAAAAAATGGATCGA
1 GTGGAAGACGGCAGAGCAACGTGCAAACCAAAAGCAACATAAACAACAAAGAAAAAATGGATCAA
*
12780 AACAGCAGCAAAATGAAGTAGTA
66 AACAGCAGCAAAATGAAGCAGTA
12803 GCAAGGTGGA
Statistics
Matches: 78, Mismatches: 10, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
93 33 0.42
94 45 0.58
ACGTcount: A:0.50, C:0.15, G:0.23, T:0.12
Consensus pattern (93 bp):
GTGGAAGACGGCAGAGCAACGTGCAAACCAAAAGCAACATAAACAACAAAGAAAAAATGGATCAA
AACAGCAGCAAAATGAAGCAGTAATAGT
Found at i:12984 original size:35 final size:36
Alignment explanation
Indices: 12890--12994 Score: 140
Period size: 36 Copynumber: 2.9 Consensus size: 36
12880 AAAGAACTAG
* * * *
12890 CAGCAAAGACCATCGAAACAACAAGAAAATAAGAGA
1 CAGCAATGACCATCAAAACAGCAAGAAAACAAGAGA
*
12926 CAGCAATGACCATCAAAACAGCAAGAAAACAGGAGA
1 CAGCAATGACCATCAAAACAGCAAGAAAACAAGAGA
* *
12962 CAGCAATG-GCATCAAAATAGCAAGAAAACAAGA
1 CAGCAATGACCATCAAAACAGCAAGAAAACAAGA
12995 AGAAAAATGA
Statistics
Matches: 61, Mismatches: 8, Indels: 1
0.87 0.11 0.01
Matches are distributed among these distances:
35 22 0.36
36 39 0.64
ACGTcount: A:0.55, C:0.20, G:0.18, T:0.07
Consensus pattern (36 bp):
CAGCAATGACCATCAAAACAGCAAGAAAACAAGAGA
Found at i:13013 original size:35 final size:36
Alignment explanation
Indices: 12900--13013 Score: 101
Period size: 36 Copynumber: 3.2 Consensus size: 36
12890 CAGCAAAGAC
* * * * *
12900 CATCGAAACAACAAGAAAATA-AGAGACAGCAATGAC
1 CATCAAAACAGCAAGAAAACAGA-AGACAGAAATGAG
* *
12936 CATCAAAACAGCAAGAAAACAGGAGACAGCAATG-G
1 CATCAAAACAGCAAGAAAACAGAAGACAGAAATGAG
*
12971 CATCAAAATAGCAAGAAAACAAGAAGA-A-AAATGAG
1 CATCAAAACAGCAAGAAAAC-AGAAGACAGAAATGAG
*
13006 CAACAAAA
1 CATCAAAA
13014 AGGGGAAGAA
Statistics
Matches: 66, Mismatches: 9, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
34 4 0.06
35 28 0.42
36 34 0.52
ACGTcount: A:0.58, C:0.18, G:0.18, T:0.07
Consensus pattern (36 bp):
CATCAAAACAGCAAGAAAACAGAAGACAGAAATGAG
Found at i:13048 original size:23 final size:22
Alignment explanation
Indices: 12996--13057 Score: 88
Period size: 22 Copynumber: 2.8 Consensus size: 22
12986 AAAACAAGAA
*
12996 GAAAAATGAGCAACAAAAAGGG
1 GAAAAACGAGCAACAAAAAGGG
* *
13018 GAAGAACGAGCAGCAAAAAGGG
1 GAAAAACGAGCAACAAAAAGGG
13040 GAACAAACGAGCAACAAA
1 GAA-AAACGAGCAACAAA
13058 GCAAGCAAGA
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
22 22 0.65
23 12 0.35
ACGTcount: A:0.56, C:0.15, G:0.27, T:0.02
Consensus pattern (22 bp):
GAAAAACGAGCAACAAAAAGGG
Found at i:13217 original size:15 final size:15
Alignment explanation
Indices: 13196--13225 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
13186 GAGTTCAGCT
13196 AAAAAAAAGGAAAAAG
1 AAAAAAAA-GAAAAAG
13212 AAAAAAAAGAAAAA
1 AAAAAAAAGAAAAA
13226 AAGAAAAACT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (15 bp):
AAAAAAAAGAAAAAG
Found at i:13242 original size:17 final size:17
Alignment explanation
Indices: 13196--13233 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
13186 GAGTTCAGCT
*
13196 AAAAAAAAG-GAAAAAG
1 AAAAAAAAGAAAAAAAG
13212 AAAAAAAAGAAAAAAAG
1 AAAAAAAAGAAAAAAAG
13229 AAAAA
1 AAAAA
13234 CTAGGAAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
16 9 0.45
17 11 0.55
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (17 bp):
AAAAAAAAGAAAAAAAG
Found at i:15427 original size:69 final size:69
Alignment explanation
Indices: 15348--15476 Score: 215
Period size: 70 Copynumber: 1.9 Consensus size: 69
15338 CCCCACCATT
15348 TTTTTAAACTCATC-AAATTTAAATCTTATTTTGTCCAAATTATCATTGTCAGGGAATACTCCAA
1 TTTTTAAACTCATCAAAATTTAAATCTTATTTTGTCCAAATTATCATTGTC-GGGAATACTCCAA
15412 CCTTA
65 CCTTA
** *
15417 TTTTTAAACTCATCAAAATTTAGGTCTTATTTTGTCCAAATTATCATTGTCGGGGATACT
1 TTTTTAAACTCATCAAAATTTAAATCTTATTTTGTCCAAATTATCATTGTCGGGAATACT
15477 ACAGCCCCAT
Statistics
Matches: 56, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
69 22 0.39
70 34 0.61
ACGTcount: A:0.31, C:0.17, G:0.10, T:0.42
Consensus pattern (69 bp):
TTTTTAAACTCATCAAAATTTAAATCTTATTTTGTCCAAATTATCATTGTCGGGAATACTCCAAC
CTTA
Found at i:18082 original size:18 final size:17
Alignment explanation
Indices: 18059--18092 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
18049 TTAACTTTTT
18059 GAAAATCAAATAGGAAAA
1 GAAAATCAAAT-GGAAAA
*
18077 GAAAATGAAATGGAAA
1 GAAAATCAAATGGAAA
18093 GAGTCACCAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.65, C:0.03, G:0.21, T:0.12
Consensus pattern (17 bp):
GAAAATCAAATGGAAAA
Done.