Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2447
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: 48617
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32
Found at i:7780 original size:22 final size:21
Alignment explanation
Indices: 7746--7788 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
7736 GGGCTGTTAA
*
7746 AAAAGGAGCTTAAAGATCATT
1 AAAAGGAGCTTAAAGAGCATT
*
7767 AAAAGGAGTTTTAAAGAGCATT
1 AAAAGGAG-CTTAAAGAGCATT
7789 TTATGCCCTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 8 0.42
22 11 0.58
ACGTcount: A:0.47, C:0.07, G:0.21, T:0.26
Consensus pattern (21 bp):
AAAAGGAGCTTAAAGAGCATT
Found at i:8626 original size:13 final size:12
Alignment explanation
Indices: 8608--8667 Score: 93
Period size: 12 Copynumber: 4.8 Consensus size: 12
8598 GTAGTTTCTC
*
8608 AAAAAAAACTCGA
1 AAAAAAAATTC-A
8621 AAAAAAAATTCA
1 AAAAAAAATTCA
8633 AAAAAAAATTCAA
1 AAAAAAAATTC-A
8646 AAAAAAAATTCA
1 AAAAAAAATTCA
8658 AAAAAAAATT
1 AAAAAAAATT
8668 TGGTTTCCAT
Statistics
Matches: 45, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
12 23 0.51
13 22 0.49
ACGTcount: A:0.75, C:0.08, G:0.02, T:0.15
Consensus pattern (12 bp):
AAAAAAAATTCA
Found at i:8648 original size:25 final size:25
Alignment explanation
Indices: 8608--8667 Score: 102
Period size: 25 Copynumber: 2.4 Consensus size: 25
8598 GTAGTTTCTC
* *
8608 AAAAAAAACTCGAAAAAAAAATTCA
1 AAAAAAAATTCAAAAAAAAAATTCA
8633 AAAAAAAATTCAAAAAAAAAATTCA
1 AAAAAAAATTCAAAAAAAAAATTCA
8658 AAAAAAAATT
1 AAAAAAAATT
8668 TGGTTTCCAT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
25 33 1.00
ACGTcount: A:0.75, C:0.08, G:0.02, T:0.15
Consensus pattern (25 bp):
AAAAAAAATTCAAAAAAAAAATTCA
Found at i:8667 original size:12 final size:13
Alignment explanation
Indices: 8608--8665 Score: 91
Period size: 13 Copynumber: 4.5 Consensus size: 13
8598 GTAGTTTCTC
* *
8608 AAAAAAAACTCGA
1 AAAAAAAATTCAA
8621 AAAAAAAATTC-A
1 AAAAAAAATTCAA
8633 AAAAAAAATTCAA
1 AAAAAAAATTCAA
8646 AAAAAAAATTCAA
1 AAAAAAAATTCAA
8659 AAAAAAA
1 AAAAAAA
8666 TTTGGTTTCC
Statistics
Matches: 43, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
12 12 0.28
13 31 0.72
ACGTcount: A:0.78, C:0.09, G:0.02, T:0.12
Consensus pattern (13 bp):
AAAAAAAATTCAA
Found at i:14355 original size:11 final size:12
Alignment explanation
Indices: 14323--14355 Score: 59
Period size: 11 Copynumber: 2.8 Consensus size: 12
14313 ATGGAAGCCA
14323 AATTTTTTTTGG
1 AATTTTTTTTGG
14335 AATTTTTTTT-G
1 AATTTTTTTTGG
14346 AATTTTTTTT
1 AATTTTTTTT
14356 TCGAGTTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 11 0.52
12 10 0.48
ACGTcount: A:0.18, C:0.00, G:0.09, T:0.73
Consensus pattern (12 bp):
AATTTTTTTTGG
Found at i:14356 original size:12 final size:13
Alignment explanation
Indices: 14325--14385 Score: 81
Period size: 13 Copynumber: 4.8 Consensus size: 13
14315 GGAAGCCAAA
*
14325 TTTTTTTTGGAA-
1 TTTTTTTTCGAAT
14337 TTTTTTTT-GAAT
1 TTTTTTTTCGAAT
*
14349 TTTTTTTTCGAGT
1 TTTTTTTTCGAAT
*
14362 TTTTTTTTCGAGT
1 TTTTTTTTCGAAT
14375 TTTTTTTTCGA
1 TTTTTTTTCGA
14386 GAAACTACTA
Statistics
Matches: 46, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
11 3 0.07
12 16 0.35
13 27 0.59
ACGTcount: A:0.11, C:0.05, G:0.13, T:0.70
Consensus pattern (13 bp):
TTTTTTTTCGAAT
Found at i:14386 original size:13 final size:13
Alignment explanation
Indices: 14337--14386 Score: 84
Period size: 13 Copynumber: 3.9 Consensus size: 13
14327 TTTTTTGGAA
*
14337 TTTTTTTT-GAAT
1 TTTTTTTTCGAGT
14349 TTTTTTTTCGAGT
1 TTTTTTTTCGAGT
14362 TTTTTTTTCGAGT
1 TTTTTTTTCGAGT
14375 TTTTTTTTCGAG
1 TTTTTTTTCGAG
14387 AAACTACTAT
Statistics
Matches: 36, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
12 8 0.22
13 28 0.78
ACGTcount: A:0.10, C:0.06, G:0.14, T:0.70
Consensus pattern (13 bp):
TTTTTTTTCGAGT
Found at i:15405 original size:21 final size:23
Alignment explanation
Indices: 15360--15406 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
15350 TCACCTACAA
* *
15360 TAAACACATTAAAATGAGTTTAT
1 TAAACACATTAAAATCAGCTTAT
15383 TAAACACATTAAAA-CA-CTTAT
1 TAAACACATTAAAATCAGCTTAT
15404 TAA
1 TAA
15407 TCATAACACA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 7 0.32
22 1 0.05
23 14 0.64
ACGTcount: A:0.51, C:0.13, G:0.04, T:0.32
Consensus pattern (23 bp):
TAAACACATTAAAATCAGCTTAT
Found at i:29512 original size:30 final size:30
Alignment explanation
Indices: 29456--29512 Score: 71
Period size: 30 Copynumber: 1.9 Consensus size: 30
29446 TGGGCTCAAA
* **
29456 TCAAGAAAATCAAGATTCACTTTCTTGTTT
1 TCAAGAAAATCAAGAATCACAATCTTGTTT
29486 TCAAGAAAATCAAGAAATCA-AATCTTG
1 TCAAGAAAATCAAG-AATCACAATCTTG
29513 GCCCAATTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
30 19 0.83
31 4 0.17
ACGTcount: A:0.42, C:0.16, G:0.11, T:0.32
Consensus pattern (30 bp):
TCAAGAAAATCAAGAATCACAATCTTGTTT
Found at i:32220 original size:27 final size:27
Alignment explanation
Indices: 32190--32241 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
32180 ACAAGTGAGG
32190 AAAAAGAAAAAGAGAATGAAAAAGAGC
1 AAAAAGAAAAAGAGAATGAAAAAGAGC
* ** *
32217 AAAAAGAGATTGAGAGTGAAAAAGA
1 AAAAAGAAAAAGAGAATGAAAAAGA
32242 AATTGAAGAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 21 1.00
ACGTcount: A:0.65, C:0.02, G:0.25, T:0.08
Consensus pattern (27 bp):
AAAAAGAAAAAGAGAATGAAAAAGAGC
Found at i:46182 original size:30 final size:28
Alignment explanation
Indices: 46148--46203 Score: 69
Period size: 30 Copynumber: 1.9 Consensus size: 28
46138 GTGATTAAAT
46148 AAAATCGACA-CAAGCAGAATTTAAAAGAAA
1 AAAATCGACAGCAAG-A-AA-TTAAAAGAAA
*
46178 AAAATTGACAGCAAGAAATTAAAAGA
1 AAAATCGACAGCAAGAAATTAAAAGA
46204 TAAGTCCTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
28 8 0.33
29 2 0.08
30 10 0.42
31 4 0.17
ACGTcount: A:0.61, C:0.11, G:0.14, T:0.14
Consensus pattern (28 bp):
AAAATCGACAGCAAGAAATTAAAAGAAA
Found at i:47423 original size:15 final size:15
Alignment explanation
Indices: 47403--47432 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
47393 AATGAATGTC
47403 GATCTTATTCTTGAA
1 GATCTTATTCTTGAA
47418 GATCTTATTCTTGAA
1 GATCTTATTCTTGAA
47433 TCCGTTCTCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.27, C:0.13, G:0.13, T:0.47
Consensus pattern (15 bp):
GATCTTATTCTTGAA
Done.