Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold334
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: 36676
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.32
Found at i:1412 original size:41 final size:40
Alignment explanation
Indices: 1274--1441 Score: 268
Period size: 40 Copynumber: 4.2 Consensus size: 40
1264 TCAGGATTTA
* *
1274 CCGGATATAG-CAACTCGCACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAGTCAA-TAGCACAAATGCCTTCGGGACTTAGC
1314 CCGGATATAGTCAATAGCACAAA-GCCTTCGGGACTTAGC
1 CCGGATATAGTCAATAGCACAAATGCCTTCGGGACTTAGC
* *
1353 TCGGATATAGTCACTAGCACAAATGCCTTCGGGACTTATGC
1 CCGGATATAGTCAATAGCACAAATGCCTTCGGGACTTA-GC
1394 CCGGATATAGTCAATAGCACAAATGCCTTCGGGACTTAGC
1 CCGGATATAGTCAATAGCACAAATGCCTTCGGGACTTAGC
1434 CCGGATAT
1 CCGGATAT
1442 CATTCGAATA
Statistics
Matches: 119, Mismatches: 6, Indels: 6
0.91 0.05 0.05
Matches are distributed among these distances:
39 36 0.30
40 42 0.35
41 41 0.34
ACGTcount: A:0.28, C:0.26, G:0.23, T:0.23
Consensus pattern (40 bp):
CCGGATATAGTCAATAGCACAAATGCCTTCGGGACTTAGC
Found at i:10379 original size:29 final size:28
Alignment explanation
Indices: 10344--10421 Score: 104
Period size: 29 Copynumber: 2.7 Consensus size: 28
10334 TCATGAGATT
10344 GGCACTAAGTGTGCGGGTTTAAATTGTACA
1 GGCACTAAGTGTGCGGGTTTAAA--GTACA
*
10374 -GCACTAAGTGTGCGAGTTTAAAGTACA
1 GGCACTAAGTGTGCGGGTTTAAAGTACA
10401 TGGCACTAAGTGTGCGCGGTT
1 -GGCACTAAGTGTGCG-GGTT
10422 GATTATTAAG
Statistics
Matches: 43, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
27 5 0.12
29 35 0.81
30 3 0.07
ACGTcount: A:0.26, C:0.15, G:0.31, T:0.28
Consensus pattern (28 bp):
GGCACTAAGTGTGCGGGTTTAAAGTACA
Found at i:12355 original size:40 final size:40
Alignment explanation
Indices: 12295--12516 Score: 351
Period size: 40 Copynumber: 5.6 Consensus size: 40
12285 TATTCGAATG
12295 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTATTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTATTGACT
*
12335 ATATTCGGGCTAAGTCCCGAAGGCATTTGTGCTATTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTATTGACT
*
12375 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTATTGACT
*
12415 ATATCCGGGCTAAGTCCCGAAGGCTTTTGTGCTATTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTATTGACT
**
12455 ATATCCGGGCTAACACCCGAAGGCATTTGTG-TGAGTTG-CT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCT-A-TTGACT
*
12495 ATATCC-GGCTAAATCCCGAAGG
1 ATATCCGGGCTAAGTCCCGAAGG
12517 TACTTGGGTT
Statistics
Matches: 170, Mismatches: 10, Indels: 5
0.92 0.05 0.03
Matches are distributed among these distances:
39 15 0.09
40 152 0.89
41 3 0.02
ACGTcount: A:0.23, C:0.23, G:0.26, T:0.29
Consensus pattern (40 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTATTGACT
Found at i:14194 original size:248 final size:248
Alignment explanation
Indices: 13756--14251 Score: 965
Period size: 248 Copynumber: 2.0 Consensus size: 248
13746 GGAACTCGAG
13756 ATATGATTTTTAAAGTAACTGTGATGCAGTTAGCCAACTTGTCTGGAAATTTTAAAATGAACTGT
1 ATATGATTTTTAAAGTAACTGTGATGCAGTTAGCCAACTTGTCTGGAAATTTTAAAATGAACTGT
*
13821 GTAATTAAATGAATTAAGTCCGTTAACACCTCGTGTTCGACTCCGGCAACGGTCTCGGGTACGGG
66 GTAAGTAAATGAATTAAGTCCGTTAACACCTCGTGTTCGACTCCGGCAACGGTCTCGGGTACGGG
*
13886 GCGTTATACATTCAACCTGTTGTAAAACATCTCTATTTGAGCCTAGTGTTGGAATCCATGCATCA
131 GCGTTACACATTCAACCTGTTGTAAAACATCTCTATTTGAGCCTAGTGTTGGAATCCATGCATCA
*
13951 GACATTTTCTAATTAAGTCTTTAAATCGTTCCCAAGCTTCATATAGGGTCTCA
196 GACATTTTCTAATTAAGTCTTTAAATCGTTCCCAAGCTTCATATAGCGTCTCA
14004 ATATGATTTTTAAAGTAACTGTGATGCAGTTAGCCAACTTGTCTGGAAATTTTAAAATGAACTGT
1 ATATGATTTTTAAAGTAACTGTGATGCAGTTAGCCAACTTGTCTGGAAATTTTAAAATGAACTGT
14069 GTAAGTAAATGAATTAAGTCCGTTAACACCTCGTGTTCGACTCCGGCAACGGTCTCGGGTACGGG
66 GTAAGTAAATGAATTAAGTCCGTTAACACCTCGTGTTCGACTCCGGCAACGGTCTCGGGTACGGG
14134 GCGTTACACATTCAACCTGTTGTAAAACATCTCTATTTGAGCCTAGTGTTGGAATCCATGCATCA
131 GCGTTACACATTCAACCTGTTGTAAAACATCTCTATTTGAGCCTAGTGTTGGAATCCATGCATCA
14199 GACATTTTCTAATTAAGTCTTTAAATCGTTCCCAAGCTTCATATAGCGTCTCA
196 GACATTTTCTAATTAAGTCTTTAAATCGTTCCCAAGCTTCATATAGCGTCTCA
14252 TCTTTCATTT
Statistics
Matches: 245, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
248 245 1.00
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.33
Consensus pattern (248 bp):
ATATGATTTTTAAAGTAACTGTGATGCAGTTAGCCAACTTGTCTGGAAATTTTAAAATGAACTGT
GTAAGTAAATGAATTAAGTCCGTTAACACCTCGTGTTCGACTCCGGCAACGGTCTCGGGTACGGG
GCGTTACACATTCAACCTGTTGTAAAACATCTCTATTTGAGCCTAGTGTTGGAATCCATGCATCA
GACATTTTCTAATTAAGTCTTTAAATCGTTCCCAAGCTTCATATAGCGTCTCA
Found at i:16324 original size:23 final size:21
Alignment explanation
Indices: 16297--16338 Score: 66
Period size: 23 Copynumber: 1.9 Consensus size: 21
16287 AATGCAATAT
16297 TAAAAATGCTAACTAAAATGTGC
1 TAAAAATGC-AAC-AAAATGTGC
16320 TAAAAATGCAACAAAATGT
1 TAAAAATGCAACAAAATGT
16339 ACTTAAGTAC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 7 0.37
22 3 0.16
23 9 0.47
ACGTcount: A:0.52, C:0.12, G:0.12, T:0.24
Consensus pattern (21 bp):
TAAAAATGCAACAAAATGTGC
Found at i:17237 original size:46 final size:46
Alignment explanation
Indices: 17170--17270 Score: 157
Period size: 46 Copynumber: 2.2 Consensus size: 46
17160 AAAATTATTG
* * *
17170 TTGGGCCTTGAGGTAGTGTGAACCTATTACATCCATGGGTCAATAA
1 TTGGGCCTTGAGGTAGCGTGAACCCATTACATCCATGGGTCAAAAA
* *
17216 TTGGGCTTTGAGGTAGCGTGAACCCATTGCATCCATGGGTCAAAAA
1 TTGGGCCTTGAGGTAGCGTGAACCCATTACATCCATGGGTCAAAAA
17262 TTGGGCCTT
1 TTGGGCCTT
17271 AAGACTCATA
Statistics
Matches: 49, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
46 49 1.00
ACGTcount: A:0.24, C:0.19, G:0.28, T:0.30
Consensus pattern (46 bp):
TTGGGCCTTGAGGTAGCGTGAACCCATTACATCCATGGGTCAAAAA
Found at i:26622 original size:18 final size:18
Alignment explanation
Indices: 26601--26641 Score: 82
Period size: 18 Copynumber: 2.3 Consensus size: 18
26591 CCAGCTCCGG
26601 CTGAAGGAGCAGCGCCGA
1 CTGAAGGAGCAGCGCCGA
26619 CTGAAGGAGCAGCGCCGA
1 CTGAAGGAGCAGCGCCGA
26637 CTGAA
1 CTGAA
26642 AATCCACCTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.29, C:0.27, G:0.37, T:0.07
Consensus pattern (18 bp):
CTGAAGGAGCAGCGCCGA
Found at i:32563 original size:46 final size:46
Alignment explanation
Indices: 32513--32688 Score: 216
Period size: 46 Copynumber: 3.8 Consensus size: 46
32503 TGGTTGAGCA
32513 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
32559 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
*
32604 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
32652 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
32689 GCGGGTTACA
Statistics
Matches: 111, Mismatches: 10, Indels: 18
0.80 0.07 0.13
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
45 3 0.03
46 63 0.57
47 29 0.26
48 3 0.03
50 4 0.04
51 2 0.02
ACGTcount: A:0.20, C:0.21, G:0.30, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:32669 original size:93 final size:93
Alignment explanation
Indices: 32510--32681 Score: 317
Period size: 93 Copynumber: 1.8 Consensus size: 93
32500 GGATGGTTGA
* *
32510 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
32575 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
*
32603 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
32668 TGAGTCCGAGTTCG
66 TGAGTCCGAGTTCG
32682 CTTATGGGCG
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 76 1.00
ACGTcount: A:0.21, C:0.22, G:0.30, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Done.