Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2494
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: 24032
ACGTcount: A:0.30, C:0.18, G:0.20, T:0.31
Found at i:5306 original size:46 final size:46
Alignment explanation
Indices: 5256--5428 Score: 219
Period size: 46 Copynumber: 3.7 Consensus size: 46
5246 TGGTTGAGCA
5256 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
5302 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
*
5347 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* *
5395 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTA
5429 GGGCGGGTTA
Statistics
Matches: 109, Mismatches: 9, 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 61 0.56
47 29 0.27
48 3 0.03
50 4 0.04
51 2 0.02
ACGTcount: A:0.21, C:0.21, G:0.28, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:5412 original size:93 final size:93
Alignment explanation
Indices: 5253--5423 Score: 315
Period size: 93 Copynumber: 1.8 Consensus size: 93
5243 GGATGGTTGA
* *
5253 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
5318 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
*
5346 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
5411 TGAGTCCGAGTTC
66 TGAGTCCGAGTTC
5424 ACTTAGGGCG
Statistics
Matches: 75, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.21, C:0.22, G:0.29, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:10252 original size:39 final size:39
Alignment explanation
Indices: 10209--10379 Score: 261
Period size: 39 Copynumber: 4.4 Consensus size: 39
10199 CATGGTATTT
* * * *
10209 GAAATATATCCGGCCATGAGGTCCACAAGATATATGCTG
1 GAAATATATCCGGACATGAGGTCCGCAGGCTATATGCTG
*
10248 GAAATATATTCGGACATGAGGTCCGCAGGCTATATGCTG
1 GAAATATATCCGGACATGAGGTCCGCAGGCTATATGCTG
* * *
10287 GAAATATATCCGAACATGAAGTCCGTAGGCTATATGCTG
1 GAAATATATCCGGACATGAGGTCCGCAGGCTATATGCTG
*
10326 GGAATATATCCGGACATGAGGTCCGCAGGCTATATGCTG
1 GAAATATATCCGGACATGAGGTCCGCAGGCTATATGCTG
10365 GAAATATATCCGGAC
1 GAAATATATCCGGAC
10380 TAGAAGTCCG
Statistics
Matches: 118, Mismatches: 14, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
39 118 1.00
ACGTcount: A:0.31, C:0.19, G:0.26, T:0.24
Consensus pattern (39 bp):
GAAATATATCCGGACATGAGGTCCGCAGGCTATATGCTG
Found at i:10403 original size:78 final size:78
Alignment explanation
Indices: 10209--10406 Score: 245
Period size: 78 Copynumber: 2.5 Consensus size: 78
10199 CATGGTATTT
** * * ** * *
10209 GAAATATATCCGGCCATGAGGTCCACAAGATATATGCTGGAAATATATTCGGACATGAGGTCCGC
1 GAAATATATCCGAACATGAAGTCCGCAAGCCACATGCTGGAAATATATCCGGACATGAGGTCCGC
10274 AGGCTATATGCTG
66 AGGCTATATGCTG
* * * * *
10287 GAAATATATCCGAACATGAAGTCCGTAGGCTATATGCTGGGAATATATCCGGACATGAGGTCCGC
1 GAAATATATCCGAACATGAAGTCCGCAAGCCACATGCTGGAAATATATCCGGACATGAGGTCCGC
10352 AGGCTATATGCTG
66 AGGCTATATGCTG
* *
10365 GAAATATATCCGGAC-TAGAAGTCCGCAAGCCACGTGCTGGAA
1 GAAATATATCCGAACAT-GAAGTCCGCAAGCCACATGCTGGAA
10407 TGGTATACGG
Statistics
Matches: 103, Mismatches: 16, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
77 1 0.01
78 102 0.99
ACGTcount: A:0.31, C:0.20, G:0.26, T:0.23
Consensus pattern (78 bp):
GAAATATATCCGAACATGAAGTCCGCAAGCCACATGCTGGAAATATATCCGGACATGAGGTCCGC
AGGCTATATGCTG
Found at i:15575 original size:39 final size:40
Alignment explanation
Indices: 15530--15753 Score: 224
Period size: 40 Copynumber: 5.7 Consensus size: 40
15520 GCTCCTCGTT
* * * *
15530 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* *
15570 C-AATGCCTTCGGGACTTAACCCGGATTTAATGACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* *
15609 CGAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* * *
15649 CAAAGGCCTTCGGG-CTTAACCCGGAACTT-GTATCTCGCA
1 CAAATGCCTTCGGGACTTAACCCGG-ATTTAGTAACTCGCA
** * * * *
15688 CAAATGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAACCCGGATTTAGTAAC-TCGCA
*
15729 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAACCCGGA
15754 CAGCATTCAA
Statistics
Matches: 155, Mismatches: 22, Indels: 14
0.81 0.12 0.07
Matches are distributed among these distances:
38 2 0.01
39 65 0.42
40 77 0.50
41 11 0.07
ACGTcount: A:0.25, C:0.28, G:0.21, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
Found at i:15623 original size:40 final size:38
Alignment explanation
Indices: 15497--15753 Score: 200
Period size: 40 Copynumber: 6.5 Consensus size: 38
15487 CAAATCACTA
* * *
15497 CCTTCGGGATTTAA-CCGGATATAGCTCCTCGTTCA-AATG
1 CCTTCGGGACTTAACCCGGATTTAG-TACTCG--CACAATG
* * * *
15536 CCTTCGGGACATAGCCCGGTTTTAGTAACTCACACAATG
1 CCTTCGGGACTTAACCCGGATTTAGT-ACTCGCACAATG
*
15575 CCTTCGGGACTTAACCCGGATTTAATGACTCGCACGAATG
1 CCTTCGGGACTTAACCCGGATTTAGT-ACTCGCAC-AATG
*
15615 CCTTCGGGACTTAACCCGGATTTAGTATCTCGCACAAAGG
1 CCTTCGGGACTTAACCCGGATTTAGTA-CTCGCAC-AATG
*
15655 CCTTCGGG-CTTAACCCGGAACTT-GTATCTCGCACAAATG
1 CCTTCGGGACTTAACCCGG-ATTTAGTA-CTCGCAC-AATG
** * * * *
15694 CCTTC-GGATCTTAGTCCGGATATATTCACTTAGCACAAAG
1 CCTTCGGGA-CTTAACCCGGATTTAGT-AC-TCGCACAATG
*
15734 CCTTCGGGACTTAGCCCGGA
1 CCTTCGGGACTTAACCCGGA
15754 CAGCATTCAA
Statistics
Matches: 180, Mismatches: 26, Indels: 23
0.79 0.11 0.10
Matches are distributed among these distances:
38 4 0.02
39 78 0.43
40 89 0.49
41 9 0.05
ACGTcount: A:0.24, C:0.28, G:0.21, T:0.26
Consensus pattern (38 bp):
CCTTCGGGACTTAACCCGGATTTAGTACTCGCACAATG
Found at i:15686 original size:79 final size:78
Alignment explanation
Indices: 15530--15753 Score: 213
Period size: 79 Copynumber: 2.8 Consensus size: 78
15520 GCTCCTCGTT
* * *
15530 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACACAATGCCTTCGGGACTTAACCCGGA
1 CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCACACAAGGCCTTCGGGACTTAACCCGGA
15595 TTTAATGACTCGCA
66 TTTAAT-ACTCGCA
* * * *
15609 CGAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACAAAGGCCTTCGGG-CTTAACCCGG
1 CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCACAC-AAGGCCTTCGGGACTTAACCCGG
15673 AACTTGT-AT-CTCGCA
65 -A-TT-TAATACTCGCA
* ** * * * * * *
15688 CAAATGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCACAAAGCCTTCGGGACTTAGCCCG
1 CAAATGCCTTCGGGA-CATAACCCGGATTTAGTAACTCA-CACAAGGCCTTCGGGACTTAACCCG
15752 GA
64 GA
15754 CAGCATTCAA
Statistics
Matches: 120, Mismatches: 18, Indels: 14
0.79 0.12 0.09
Matches are distributed among these distances:
78 3 0.03
79 88 0.73
80 24 0.20
81 4 0.03
82 1 0.01
ACGTcount: A:0.25, C:0.28, G:0.21, T:0.25
Consensus pattern (78 bp):
CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCACACAAGGCCTTCGGGACTTAACCCGGA
TTTAATACTCGCA
Found at i:15762 original size:41 final size:41
Alignment explanation
Indices: 15685--15762 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
15675 CTTGTATCTC
* * *
15685 GCACAAATGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
15726 GCACAAA-GCCTTCGGGA-CTTAGCCCGGACAGCATTCA
1 GCACAAATGCCTTC-GGATCTTAGCCCGGACA-CATTCA
15763 ATTAATCATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 17 0.53
41 15 0.47
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (41 bp):
GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
Found at i:23559 original size:40 final size:39
Alignment explanation
Indices: 23399--23655 Score: 236
Period size: 40 Copynumber: 6.5 Consensus size: 39
23389 CAAATCACTA
* * * **
23399 CCTTCGGGATTTAA-CCGGATATAGCTCCTCGTTCAAATG
1 CCTTCGGGACTTAACCCGGATTTAG-TACTCGCACAAATG
* * * *
23438 CCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-AATG
1 CCTTCGGGACTTAACCCGGATTTAGT-ACTCGCACAAATG
* *
23477 CCTTCGGGACTTAACCCGGATTTAATACTCGCACGAATG
1 CCTTCGGGACTTAACCCGGATTTAGTACTCGCACAAATG
*
23516 CCTTCGGGACTTAACCCGGATTTAGTATCTCGCACAAAGG
1 CCTTCGGGACTTAACCCGGATTTAGTA-CTCGCACAAATG
*
23556 CCTTCGGGGCTTAACCCGGAATTT-GTATCTCGCACAAATG
1 CCTTCGGGACTTAACCCGG-ATTTAGTA-CTCGCACAAATG
** * * *
23596 CCTTC-GGATCTTAGTCCGGATATATTCACTTAGCACAAA-G
1 CCTTCGGGA-CTTAACCCGGATTTAGT-AC-TCGCACAAATG
*
23636 CCTTCGGGACTTAGCCCGGA
1 CCTTCGGGACTTAACCCGGA
23656 CAGCATTCAA
Statistics
Matches: 182, Mismatches: 26, Indels: 19
0.80 0.11 0.08
Matches are distributed among these distances:
38 7 0.04
39 73 0.40
40 86 0.47
41 16 0.09
ACGTcount: A:0.24, C:0.28, G:0.21, T:0.27
Consensus pattern (39 bp):
CCTTCGGGACTTAACCCGGATTTAGTACTCGCACAAATG
Found at i:23664 original size:41 final size:41
Alignment explanation
Indices: 23587--23664 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
23577 TTTGTATCTC
* * *
23587 GCACAAATGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
23628 GCACAAA-GCCTTCGGGA-CTTAGCCCGGACAGCATTCA
1 GCACAAATGCCTTC-GGATCTTAGCCCGGACA-CATTCA
23665 ATTAATCATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 17 0.53
41 15 0.47
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (41 bp):
GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
Done.