Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold5294.1
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: 27046
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.33
Warning! 134 characters in sequence are not A, C, G, or T
Found at i:5115 original size:23 final size:21
Alignment explanation
Indices: 5065--5115 Score: 54
Period size: 20 Copynumber: 2.4 Consensus size: 21
5055 TAGAATATAG
5065 TTAA-ATTTATTGTTTAAAAA
1 TTAATATTTATTGTTTAAAAA
5085 -T-ATCATTTATTGTTTAACAAAA
1 TTAAT-ATTTATTGTTT-A-AAAA
5107 TTAATATTT
1 TTAATATTT
5116 TTAAATGAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 9
0.74 0.00 0.26
Matches are distributed among these distances:
18 1 0.04
19 1 0.04
20 11 0.44
21 1 0.04
22 4 0.16
23 5 0.20
24 2 0.08
ACGTcount: A:0.41, C:0.04, G:0.04, T:0.51
Consensus pattern (21 bp):
TTAATATTTATTGTTTAAAAA
Found at i:10512 original size:30 final size:31
Alignment explanation
Indices: 10448--10520 Score: 78
Period size: 31 Copynumber: 2.4 Consensus size: 31
10438 TTTAGGGATC
* *
10448 TAATTAAAATTTTCAAAAACTTTTAAGCGTT
1 TAATTAAAATTTTCAAAAACTTTGAAGCGCT
* * *
10479 TAATTAAATTTTTTAAAAA-TTTGAAGGGCT
1 TAATTAAAATTTTCAAAAACTTTGAAGCGCT
10509 TAA-TAAGAATTT
1 TAATTAA-AATTT
10521 CTAAAATTTA
Statistics
Matches: 35, Mismatches: 6, Indels: 3
0.80 0.14 0.07
Matches are distributed among these distances:
29 3 0.09
30 15 0.43
31 17 0.49
ACGTcount: A:0.42, C:0.05, G:0.10, T:0.42
Consensus pattern (31 bp):
TAATTAAAATTTTCAAAAACTTTGAAGCGCT
Found at i:12515 original size:17 final size:18
Alignment explanation
Indices: 12493--12536 Score: 63
Period size: 17 Copynumber: 2.5 Consensus size: 18
12483 GTTTGGTTAG
12493 AAAGAAAATAAAAGAA-A
1 AAAGAAAATAAAAGAAGA
* *
12510 AAAGAAAAGAAAAGAAGG
1 AAAGAAAATAAAAGAAGA
12528 AAAGAAAAT
1 AAAGAAAAT
12537 GAAGAAAATA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
17 15 0.65
18 8 0.35
ACGTcount: A:0.77, C:0.00, G:0.18, T:0.05
Consensus pattern (18 bp):
AAAGAAAATAAAAGAAGA
Found at i:12540 original size:14 final size:13
Alignment explanation
Indices: 12502--12554 Score: 63
Period size: 13 Copynumber: 4.0 Consensus size: 13
12492 GAAAGAAAAT
12502 AAAAGAAAA-AAG
1 AAAAGAAAAGAAG
12514 AAAAGAAAAGAAG
1 AAAAGAAAAGAAG
*
12527 GAAAGAAAATGAAG
1 AAAAGAAAA-GAAG
*
12541 AAAATAAAAAGAAG
1 AAAA-GAAAAGAAG
12555 TGATTCAAAG
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
12 9 0.26
13 11 0.31
14 11 0.31
15 4 0.11
ACGTcount: A:0.75, C:0.00, G:0.21, T:0.04
Consensus pattern (13 bp):
AAAAGAAAAGAAG
Found at i:21350 original size:31 final size:31
Alignment explanation
Indices: 21315--21380 Score: 89
Period size: 31 Copynumber: 2.1 Consensus size: 31
21305 AAAAAAAAGA
* *
21315 TTCAAGCTCTAATT-TGAGAACAGTTGCCTAG
1 TTCAAG-TCTAATTGTGAGAACAATTGCCAAG
*
21346 TTCAAGTCTCATTGTGAGAACAATTGCCAAG
1 TTCAAGTCTAATTGTGAGAACAATTGCCAAG
21377 TTCA
1 TTCA
21381 GAACTTAACT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
30 6 0.19
31 25 0.81
ACGTcount: A:0.30, C:0.20, G:0.18, T:0.32
Consensus pattern (31 bp):
TTCAAGTCTAATTGTGAGAACAATTGCCAAG
Found at i:23615 original size:91 final size:91
Alignment explanation
Indices: 23485--23667 Score: 341
Period size: 91 Copynumber: 2.0 Consensus size: 91
23475 GAAGTTTTGC
*
23485 ACAAATTTTAGGTTAACATCAATCAAAATTTTTGAAATTAAAATTACCCATAATGATTCTTATTC
1 ACAAATGTTAGGTTAACATCAATCAAAATTTTTGAAATTAAAATTACCCATAATGATTCTTATTC
23550 ACATTGCTTAAACCTATAACAACCCT
66 ACATTGCTTAAACCTATAACAACCCT
23576 ACAAATGTTAGGTTAACATCACA-CAAAATTTTTGAAATTAAAATTACCCATAATGATTCTTATT
1 ACAAATGTTAGGTTAACATCA-ATCAAAATTTTTGAAATTAAAATTACCCATAATGATTCTTATT
23640 CACATTGCTTAAACCTATAACAACCCT
65 CACATTGCTTAAACCTATAACAACCCT
23667 A
1 A
23668 AACATTATAA
Statistics
Matches: 90, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
91 89 0.99
92 1 0.01
ACGTcount: A:0.41, C:0.19, G:0.06, T:0.34
Consensus pattern (91 bp):
ACAAATGTTAGGTTAACATCAATCAAAATTTTTGAAATTAAAATTACCCATAATGATTCTTATTC
ACATTGCTTAAACCTATAACAACCCT
Found at i:24190 original size:22 final size:23
Alignment explanation
Indices: 24145--24190 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 23
24135 ATTTAGTTTT
24145 TTATTATTATTTTCAGGAATTTAA
1 TTATTATTATTTTCA-GAATTTAA
24169 TTATT-TTACTTTTCA-AATTTAA
1 TTATTATTA-TTTTCAGAATTTAA
24191 AAACTCATGA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
22 7 0.33
23 3 0.14
24 11 0.52
ACGTcount: A:0.33, C:0.07, G:0.04, T:0.57
Consensus pattern (23 bp):
TTATTATTATTTTCAGAATTTAA
Done.