Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2946
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: 411495
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
File 2 of 2
Found at i:378617 original size:17 final size:18
Alignment explanation
Indices: 378578--378619 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
378568 AAGAAGAAAA
378578 ACAAAA-AGATGAGTGAT
1 ACAAAAGAGATGAGTGAT
*
378595 AAAAAAGAGA-GAGTGAT
1 ACAAAAGAGATGAGTGAT
*
378612 TCAAAAGA
1 ACAAAAGA
378620 AAAAGAAATG
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 18 0.86
18 3 0.14
ACGTcount: A:0.57, C:0.05, G:0.24, T:0.14
Consensus pattern (18 bp):
ACAAAAGAGATGAGTGAT
Found at i:385922 original size:20 final size:20
Alignment explanation
Indices: 385876--385922 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
385866 AGCTCGTTTC
*
385876 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* *
385896 CAACTCACTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
385916 CAGCTCA
1 CAGCTCA
385923 ATCTTAACCC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.30, C:0.36, G:0.13, T:0.21
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:387512 original size:27 final size:26
Alignment explanation
Indices: 387458--387521 Score: 85
Period size: 26 Copynumber: 2.4 Consensus size: 26
387448 AAAAAAAGTG
*
387458 AAAAAAA-TCGAGCAAAAAAAAGAAAA
1 AAAAAAAGT-GAGCAAAAAAAACAAAA
*
387484 AAAAAAAGTGAGCAAAAAAATCAAGAA
1 AAAAAAAGTGAGCAAAAAAAACAA-AA
387511 AAAAAAAGTGA
1 AAAAAAAGTGA
387522 AAAGTCTTGC
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
26 20 0.59
27 14 0.41
ACGTcount: A:0.73, C:0.06, G:0.14, T:0.06
Consensus pattern (26 bp):
AAAAAAAGTGAGCAAAAAAAACAAAA
Found at i:388612 original size:48 final size:47
Alignment explanation
Indices: 388533--388638 Score: 135
Period size: 48 Copynumber: 2.2 Consensus size: 47
388523 GAGTGTCATG
*
388533 GAAAAAGAAATTGAGATTGAAAAAGGATGTGA-AAAAGAGAAAGAAATC
1 GAAAAAGAAATTGAGATTGAAAAAAGATGTGAGAAAA-AGAAA-AAATC
* *
388581 GAAAAAGAAATTGAGATTGAACAAAAG-TGTGAGGAAAAAGAGAAAATT
1 GAAAAAGAAATTGAGATTGAA-AAAAGATGTGA-GAAAAAGAAAAAATC
388629 GAAAAAGAAA
1 GAAAAAGAAA
388639 GAAAAGACAA
Statistics
Matches: 52, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
48 40 0.77
49 8 0.15
50 4 0.08
ACGTcount: A:0.59, C:0.02, G:0.25, T:0.14
Consensus pattern (47 bp):
GAAAAAGAAATTGAGATTGAAAAAAGATGTGAGAAAAAGAAAAAATC
Found at i:390354 original size:20 final size:20
Alignment explanation
Indices: 390308--390354 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
390298 AGCTCGTTTC
*
390308 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* *
390328 CAACTCACTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
390348 CAGCTCA
1 CAGCTCA
390355 ATCTTAACCC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.30, C:0.36, G:0.13, T:0.21
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:395283 original size:23 final size:22
Alignment explanation
Indices: 395232--395283 Score: 54
Period size: 23 Copynumber: 2.3 Consensus size: 22
395222 CCTCGTCTTT
*
395232 TTCTTTTGTTTCTTTTTCTAAC
1 TTCTTTTCTTTCTTTTTCTAAC
395254 -TCATTTTCTCTTCTTTCTTC-AAC
1 TTC-TTTTCT-TTCTTT-TTCTAAC
395277 TTCTTTT
1 TTCTTTT
395284 TCAATTTCTT
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 2 0.08
22 5 0.20
23 13 0.52
24 5 0.20
ACGTcount: A:0.10, C:0.23, G:0.02, T:0.65
Consensus pattern (22 bp):
TTCTTTTCTTTCTTTTTCTAAC
Found at i:395292 original size:12 final size:12
Alignment explanation
Indices: 395241--395295 Score: 51
Period size: 12 Copynumber: 4.6 Consensus size: 12
395231 TTTCTTTTGT
395241 TTCTTTTTCTAAC
1 TTCTTTTTC-AAC
* *
395254 -TCATTTTC-TC
1 TTCTTTTTCAAC
395264 TTCTTTCTTCAAC
1 TTCTTT-TTCAAC
*
395277 TTCTTTTTCAAT
1 TTCTTTTTCAAC
395289 TTCTTTT
1 TTCTTTT
395296 CTGTTTCACA
Statistics
Matches: 34, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
10 1 0.03
11 4 0.12
12 22 0.65
13 7 0.21
ACGTcount: A:0.13, C:0.24, G:0.00, T:0.64
Consensus pattern (12 bp):
TTCTTTTTCAAC
Found at i:395302 original size:17 final size:18
Alignment explanation
Indices: 395277--395314 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
395267 TTTCTTCAAC
* *
395277 TTCTTTTTCA-ATTTCTT
1 TTCTGTTTCACATTCCTT
395294 TTCTGTTTCACATTCCTT
1 TTCTGTTTCACATTCCTT
395312 TTC
1 TTC
395315 CTCTCAATCT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 9 0.50
18 9 0.50
ACGTcount: A:0.11, C:0.24, G:0.03, T:0.63
Consensus pattern (18 bp):
TTCTGTTTCACATTCCTT
Found at i:400048 original size:21 final size:21
Alignment explanation
Indices: 400009--400065 Score: 87
Period size: 21 Copynumber: 2.7 Consensus size: 21
399999 CCATTACAAA
*
400009 TTCATACCAAATACCATACCAT
1 TTCATACC-AATTCCATACCAT
400031 TTCATACCAATTCCATACCAT
1 TTCATACCAATTCCATACCAT
*
400052 TTCGTACCAATTCC
1 TTCATACCAATTCC
400066 CAAATACCAA
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
21 25 0.76
22 8 0.24
ACGTcount: A:0.33, C:0.33, G:0.02, T:0.32
Consensus pattern (21 bp):
TTCATACCAATTCCATACCAT
Found at i:400049 original size:11 final size:11
Alignment explanation
Indices: 400007--400065 Score: 52
Period size: 10 Copynumber: 5.5 Consensus size: 11
399997 AACCATTACA
400007 AATT-CATACC
1 AATTCCATACC
*
400017 AAATACCATACC
1 -AATTCCATACC
*
400029 -ATTTCATACC
1 AATTCCATACC
400039 AATTCCATACC
1 AATTCCATACC
* *
400050 -ATTTCGTACC
1 AATTCCATACC
400060 AATTCC
1 AATTCC
400066 CAAATACCAA
Statistics
Matches: 38, Mismatches: 7, Indels: 6
0.75 0.14 0.12
Matches are distributed among these distances:
10 16 0.42
11 16 0.42
12 6 0.16
ACGTcount: A:0.36, C:0.32, G:0.02, T:0.31
Consensus pattern (11 bp):
AATTCCATACC
Found at i:410117 original size:26 final size:24
Alignment explanation
Indices: 410090--410137 Score: 69
Period size: 25 Copynumber: 2.0 Consensus size: 24
410080 TAAAACTACT
410090 TTTAAAAAAACTCAAGAGAGAATTC
1 TTTAAAAAAACTCAA-AGAGAATTC
* *
410115 TTTGAGAAAACTCAAAGAGAATT
1 TTTAAAAAAACTCAAAGAGAATT
410138 TTTCACTCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 8 0.38
25 13 0.62
ACGTcount: A:0.50, C:0.10, G:0.15, T:0.25
Consensus pattern (24 bp):
TTTAAAAAAACTCAAAGAGAATTC
Done.