Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3305
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: 25963
ACGTcount: A:0.29, C:0.16, G:0.19, T:0.37
Found at i:460 original size:9 final size:9
Alignment explanation
Indices: 444--490 Score: 51
Period size: 9 Copynumber: 5.2 Consensus size: 9
434 AACAAAAAGC
444 AAAA-AAAA
1 AAAAGAAAA
452 AAAAGAAAA
1 AAAAGAAAA
* *
461 GAAAGAAAG
1 AAAAGAAAA
470 AAAAGAAAA
1 AAAAGAAAA
*
479 ATAAGAAGAA
1 AAAAGAA-AA
489 AA
1 AA
491 TATAAAATAT
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
8 4 0.13
9 24 0.77
10 3 0.10
ACGTcount: A:0.83, C:0.00, G:0.15, T:0.02
Consensus pattern (9 bp):
AAAAGAAAA
Found at i:460 original size:13 final size:13
Alignment explanation
Indices: 437--490 Score: 54
Period size: 14 Copynumber: 3.9 Consensus size: 13
427 GCAGAGAAAC
437 AAAAAGCAAAAAAA
1 AAAAAG-AAAAAAA
*
451 AAAAAGAAAAGAA
1 AAAAAGAAAAAAA
*
464 AGAAAGAAAAGAAA
1 AAAAAGAAAA-AAA
*
478 AATAAGAAGAAAA
1 AAAAAGAA-AAAA
491 TATAAAATAT
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
13 15 0.45
14 16 0.48
15 2 0.06
ACGTcount: A:0.81, C:0.02, G:0.15, T:0.02
Consensus pattern (13 bp):
AAAAAGAAAAAAA
Found at i:475 original size:18 final size:18
Alignment explanation
Indices: 438--490 Score: 56
Period size: 18 Copynumber: 2.9 Consensus size: 18
428 CAGAGAAACA
* *
438 AAAAGCAAAAAAAAAAAAG
1 AAAAG-AAAGAAAGAAAAG
457 AAAAGAAAGAAAGAAAAG
1 AAAAGAAAGAAAGAAAAG
475 AAAA-ATAAG-AAGAAAA
1 AAAAGA-AAGAAAGAAAA
491 TATAAAATAT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
17 8 0.26
18 18 0.58
19 5 0.16
ACGTcount: A:0.81, C:0.02, G:0.15, T:0.02
Consensus pattern (18 bp):
AAAAGAAAGAAAGAAAAG
Found at i:2465 original size:190 final size:189
Alignment explanation
Indices: 2142--2516 Score: 669
Period size: 190 Copynumber: 2.0 Consensus size: 189
2132 ACAAGATCTC
* *
2142 TAAAGAAATATCTGAAATAAAAATTAGATAGAATATTTCTTTAATTTCATTTATGTGACGGGCTT
1 TAAAGAAATATCTGAAATAAAAATTAGATAGAATATTGCTTTAATTTCATTTATGTGAAGGGCTT
*
2207 CTACCAACATTTTGCTTTATCTCTATTTCTCTCATTTTTCTTTAGGTTATATAAGGGCATTGATA
66 CTACCAACATTTTGCTTTATCTCTATTTCTCTCATTTTTCTTAAGGTTATATAAGGGCATTGATA
2272 CTGTCTGGTTTCTTTTGTCATAAGAGGCGGATATAAGCTTATTGTACAGGGATTCTAAAA
131 CTGTCTGGTTTCTTTTGTCATAAGA-GCGGATATAAGCTTATTGTACAGGGATTCTAAAA
**
2332 TAAAGAAATATCTGAAATAAAAATTAGATAGAATATTGCTTTAATTTCATTTATGTGAAGGTTTT
1 TAAAGAAATATCTGAAATAAAAATTAGATAGAATATTGCTTTAATTTCATTTATGTGAAGGGCTT
*
2397 TTACCAACATTTTGCTTTATCTCTATTTCTCTCATTTTTCTTAAGGTTATATAAGGGCATTGATA
66 CTACCAACATTTTGCTTTATCTCTATTTCTCTCATTTTTCTTAAGGTTATATAAGGGCATTGATA
* *
2462 CTGTCTGGTTTCTTTTGTCATAAGAGCGTATCTAAGCTTATTGTACAGGGATTCT
131 CTGTCTGGTTTCTTTTGTCATAAGAGCGGATATAAGCTTATTGTACAGGGATTCT
2517 GAGATGACTC
Statistics
Matches: 177, Mismatches: 8, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
189 28 0.16
190 149 0.84
ACGTcount: A:0.30, C:0.13, G:0.15, T:0.42
Consensus pattern (189 bp):
TAAAGAAATATCTGAAATAAAAATTAGATAGAATATTGCTTTAATTTCATTTATGTGAAGGGCTT
CTACCAACATTTTGCTTTATCTCTATTTCTCTCATTTTTCTTAAGGTTATATAAGGGCATTGATA
CTGTCTGGTTTCTTTTGTCATAAGAGCGGATATAAGCTTATTGTACAGGGATTCTAAAA
Found at i:3535 original size:6 final size:6
Alignment explanation
Indices: 3526--3557 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
3516 AAAAAGAGAC
3526 AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AA
1 AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AA
3558 TCTTAATAGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:3652 original size:115 final size:115
Alignment explanation
Indices: 3450--3660 Score: 361
Period size: 115 Copynumber: 1.8 Consensus size: 115
3440 ACTTTGTAAG
* * * *
3450 AGTCATATGCATTTCTTTTGAAATCTCGAGGTTGACCGAGCAATATAACTCTGGTTATACACGAA
1 AGTCATATGCAGTTCTTTTAAAATCTCGAAGTTGACAGAGCAATATAACTCTGGTTATACACGAA
*
3515 GAAAAAGAGACAAAAAGAAAAAGAAAAAGAAAAAGAAAAAGAATCTTAAT
66 GAAAAAGAGAAAAAAAGAAAAAGAAAAAGAAAAAGAAAAAGAATCTTAAT
3565 AGTCATATGCAGTTCTTTTAAAATCTCGAAGTTGACAGAGCAATATAACTCTGGTTATACAC-AG
1 AGTCATATGCAGTTCTTTTAAAATCTCGAAGTTGACAGAGCAATATAACTCTGGTTATACACGA-
3629 AGAAAAAGAGAAAAAAAGAAAAAGAAAAAGAA
65 AGAAAAAGAGAAAAAAAGAAAAAGAAAAAGAA
3661 TCTTATGCCA
Statistics
Matches: 90, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
114 1 0.01
115 89 0.99
ACGTcount: A:0.49, C:0.12, G:0.18, T:0.21
Consensus pattern (115 bp):
AGTCATATGCAGTTCTTTTAAAATCTCGAAGTTGACAGAGCAATATAACTCTGGTTATACACGAA
GAAAAAGAGAAAAAAAGAAAAAGAAAAAGAAAAAGAAAAAGAATCTTAAT
Found at i:22978 original size:17 final size:16
Alignment explanation
Indices: 22956--22987 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
22946 CTGTTGTGTT
22956 TTATTATTGGTTATTTA
1 TTATTATT-GTTATTTA
22973 TTATTATTGTTATTT
1 TTATTATTGTTATTT
22988 TGTTCATATG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.22, C:0.00, G:0.09, T:0.69
Consensus pattern (16 bp):
TTATTATTGTTATTTA
Found at i:25404 original size:32 final size:31
Alignment explanation
Indices: 25353--25413 Score: 95
Period size: 32 Copynumber: 1.9 Consensus size: 31
25343 TCGTGTGGCT
*
25353 TCTACGCTTGCTCCAATGATTTGATTTTCAC
1 TCTACGCTTACTCCAATGATTTGATTTTCAC
*
25384 TCTACAGCTTACTCCGATGATTTGATTTTC
1 TCTAC-GCTTACTCCAATGATTTGATTTTC
25414 CCTCCCCAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
31 5 0.19
32 22 0.81
ACGTcount: A:0.20, C:0.25, G:0.13, T:0.43
Consensus pattern (31 bp):
TCTACGCTTACTCCAATGATTTGATTTTCAC
Done.