Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1264
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: 33806
ACGTcount: A:0.31, C:0.21, G:0.17, T:0.31
Found at i:539 original size:39 final size:39
Alignment explanation
Indices: 487--614 Score: 154
Period size: 40 Copynumber: 3.3 Consensus size: 39
477 TAACTCATTC
* *
487 AATG-CTTCGGGACTTAACCCGGATTTAAAACTCGCCACG
1 AATGCCTTCGGGACTTAACCCGGAATTAAAACTCG-CACA
* *
526 AATGCCTTC-GGACTTAA-CCGGAATTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGAATTA-AAACTCGCACA
*
564 AAGGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
1 AATGCCTTCGGGACTTAACCCGGAATTAA-AACTCGCACA
*
604 AATACCTTCGG
1 AATGCCTTCGG
615 ATCTTAGTCG
Statistics
Matches: 75, Mismatches: 9, Indels: 9
0.81 0.10 0.10
Matches are distributed among these distances:
38 19 0.25
39 25 0.33
40 31 0.41
ACGTcount: A:0.30, C:0.27, G:0.20, T:0.23
Consensus pattern (39 bp):
AATGCCTTCGGGACTTAACCCGGAATTAAAACTCGCACA
Found at i:665 original size:79 final size:78
Alignment explanation
Indices: 491--666 Score: 216
Period size: 78 Copynumber: 2.2 Consensus size: 78
481 TCATTCAATG
* * *
491 CTTCGGGACTTAACCCGGATTTAAAACTCGCCACGAATGCCTTCGGACTTAACCGGAATTAGTAT
1 CTTCGGGACTTAACCCGGAATTAAAACTCGCCACAAATACCTTCGGACTTAACCGGAATTAGTAT
*
556 CTCGCACAAAGGC
66 CTAGCACAAAGGC
**
569 CTTCGGGACTTAACCCGGAATTAATAACTCG-CACAAATACCTTCGGATCTTAGTCGG-ATATAG
1 CTTCGGGACTTAACCCGGAATTAA-AACTCGCCACAAATACCTTCGGA-CTTAACCGGAAT-TAG
632 TCA-CTTAGCACAAA-GC
63 T-ATC-TAGCACAAAGGC
*
648 CTTCGGGACTTAGCCCGGA
1 CTTCGGGACTTAACCCGGA
667 CAGCATTCAA
Statistics
Matches: 86, Mismatches: 7, Indels: 9
0.84 0.07 0.09
Matches are distributed among these distances:
78 39 0.45
79 38 0.44
80 9 0.10
ACGTcount: A:0.28, C:0.27, G:0.20, T:0.24
Consensus pattern (78 bp):
CTTCGGGACTTAACCCGGAATTAAAACTCGCCACAAATACCTTCGGACTTAACCGGAATTAGTAT
CTAGCACAAAGGC
Found at i:8395 original size:79 final size:80
Alignment explanation
Indices: 8296--8516 Score: 202
Period size: 80 Copynumber: 2.8 Consensus size: 80
8286 CTCGTTCAAG
* * ** * *
8296 TGCCTTCGGGACATAGCCCGGTCA-TAGTAACTCATTC-AATGCCTTCGGGACTTAACCCGGATT
1 TGCCTTCGGGACATAACCCGG-AATTAGTAACTCACACAAAGGCCTTCGGGACTTAACCCGGA-A
*
8359 TTAA-AACTCGCACGAA
64 TTAATAACTCGCACAAA
* * *
8375 TGCCTTCGGGACTTAACCCGGAATTAGTATCTCGCACAAAGGCCTTCGGGACTTAACCCGGAATT
1 TGCCTTCGGGACATAACCCGGAATTAGTAACTCACACAAAGGCCTTCGGGACTTAACCCGGAATT
8440 AATAACTCGCACAAA
66 AATAACTCGCACAAA
* * ** * * *
8455 TACCTTC-GGATCTTAGTCCGG-ATATAGTCACTTAGCACAAA-GCCTTCGGGACTTAGCCCGGA
1 TGCCTTCGGGA-CATAACCCGGAAT-TAGTAACTCA-CACAAAGGCCTTCGGGACTTAACCCGGA
8517 CAGCATTCAA
Statistics
Matches: 118, Mismatches: 18, Indels: 11
0.80 0.12 0.07
Matches are distributed among these distances:
78 1 0.01
79 37 0.31
80 74 0.63
81 6 0.05
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (80 bp):
TGCCTTCGGGACATAACCCGGAATTAGTAACTCACACAAAGGCCTTCGGGACTTAACCCGGAATT
AATAACTCGCACAAA
Found at i:8447 original size:80 final size:80
Alignment explanation
Indices: 8336--8516 Score: 219
Period size: 80 Copynumber: 2.3 Consensus size: 80
8326 CTCATTCAAT
* * *
8336 GCCTTCGGGACTTAACCCGGATTTTAAAACTCGCACGAATGCCTTCGGGA-CTTAACCCGGA-AT
1 GCCTTCGGGACTTAACCCGGATATTAAAACTCGCACAAATACCTTC-GGATCTTAACCCGGATA-
*
8399 TAGT-A-TCTCGCACAAA
64 TAGTCACT-TAGCACAAA
**
8415 GGCCTTCGGGACTTAACCCGGA-ATTAATAACTCGCACAAATACCTTCGGATCTTAGTCCGGATA
1 -GCCTTCGGGACTTAACCCGGATATTAA-AACTCGCACAAATACCTTCGGATCTTAACCCGGATA
8479 TAGTCACTTAGCACAAA
64 TAGTCACTTAGCACAAA
*
8496 GCCTTCGGGACTTAGCCCGGA
1 GCCTTCGGGACTTAACCCGGA
8517 CAGCATTCAA
Statistics
Matches: 89, Mismatches: 7, Indels: 10
0.84 0.07 0.09
Matches are distributed among these distances:
79 7 0.08
80 71 0.80
81 10 0.11
82 1 0.01
ACGTcount: A:0.28, C:0.28, G:0.21, T:0.24
Consensus pattern (80 bp):
GCCTTCGGGACTTAACCCGGATATTAAAACTCGCACAAATACCTTCGGATCTTAACCCGGATATA
GTCACTTAGCACAAA
Found at i:8476 original size:40 final size:40
Alignment explanation
Indices: 8333--8516 Score: 196
Period size: 40 Copynumber: 4.6 Consensus size: 40
8323 TAACTCATTC
* *
8333 AATGCCTTCGGGACTTAACCCGGATTTTAA-AACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGA-ATTAATAACTCGCACA
* *
8373 AATGCCTTCGGGACTTAACCCGGAATTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
*
8413 AAGGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
1 AATGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
* ** * * *
8453 AATACCTTC-GGATCTTAGTCCGG-ATATAGTCACTTAGCACA
1 AATGCCTTCGGGA-CTTAACCCGGAAT-TAATAAC-TCGCACA
*
8494 AA-GCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
8517 CAGCATTCAA
Statistics
Matches: 122, Mismatches: 16, Indels: 11
0.82 0.11 0.07
Matches are distributed among these distances:
39 8 0.07
40 103 0.84
41 11 0.09
ACGTcount: A:0.28, C:0.27, G:0.21, T:0.24
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
Found at i:25364 original size:40 final size:40
Alignment explanation
Indices: 25274--25534 Score: 235
Period size: 40 Copynumber: 6.5 Consensus size: 40
25264 CTCAAGAAAT
* * * *
25274 CTTCGGGATTTAG-CCGGATATA-ACTACTTGCAC-AAGGC
1 CTTCGGGACTTAGCCCGGATATAGTC-ACTAGCACAAATGC
* * * *
25312 CTTCGGGTCTTAGCCCGGATGTGGTCACTAGCATAAATGC
1 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
* *
25352 CTTTGGGACTTAGCCCGGATATAGTCGCTAGCACAAATGC
1 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
* ** * *
25392 CTTCAGGTTTTAGCCCGGATATAATCGCTAGCACAAATGC
1 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
* * *
25432 CTTCGGGTCTTAGCCCGGATATAG-CAACTCGCACGAATGC
1 CTTCGGGACTTAGCCCGGATATAGTC-ACTAGCACAAATGC
* * * * *
25472 CTT-TGGATCTTAGTCCGGTTATAGTCACCTAGCATAAAAGC
1 CTTCGGGA-CTTAGCCCGGATATAGTCA-CTAGCACAAATGC
*
25513 CTTTGGGACTTAGCCCGGATAT
1 CTTCGGGACTTAGCCCGGATAT
25535 CATTCGAATA
Statistics
Matches: 179, Mismatches: 36, Indels: 13
0.79 0.16 0.06
Matches are distributed among these distances:
38 11 0.06
39 16 0.09
40 124 0.69
41 25 0.14
42 3 0.02
ACGTcount: A:0.24, C:0.25, G:0.24, T:0.27
Consensus pattern (40 bp):
CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
Found at i:25423 original size:80 final size:80
Alignment explanation
Indices: 25278--25534 Score: 270
Period size: 80 Copynumber: 3.2 Consensus size: 80
25268 AGAAATCTTC
* * * * * * * *
25278 GGGATTTAG-CCGGATATAACTACTTGCAC-AAGGCCTTCGGGTCTTAGCCCGGATGTGGTCACT
1 GGGACTTAGCCCGGATATAGCAACTAGCACAAATGCCTTCAGGTCTTAGCCCGGATATAGTCACT
25341 AGCATAAATGCCTTT
66 AGCATAAATGCCTTT
* * * *
25356 GGGACTTAGCCCGGATATAGTC-GCTAGCACAAATGCCTTCAGGTTTTAGCCCGGATATAATCGC
1 GGGACTTAGCCCGGATATAG-CAACTAGCACAAATGCCTTCAGGTCTTAGCCCGGATATAGTCAC
* *
25420 TAGCACAAATGCCTTC
65 TAGCATAAATGCCTTT
* * * * * *
25436 GGGTCTTAGCCCGGATATAGCAACTCGCACGAATGCCTT-TGGATCTTAGTCCGGTTATAGTCAC
1 GGGACTTAGCCCGGATATAGCAACTAGCACAAATGCCTTCAGG-TCTTAGCCCGGATATAGTCA-
*
25500 CTAGCATAAAAGCCTTT
64 CTAGCATAAATGCCTTT
25517 GGGACTTAGCCCGGATAT
1 GGGACTTAGCCCGGATAT
25535 CATTCGAATA
Statistics
Matches: 146, Mismatches: 27, Indels: 9
0.80 0.15 0.05
Matches are distributed among these distances:
78 8 0.05
79 18 0.12
80 89 0.61
81 31 0.21
ACGTcount: A:0.25, C:0.25, G:0.24, T:0.27
Consensus pattern (80 bp):
GGGACTTAGCCCGGATATAGCAACTAGCACAAATGCCTTCAGGTCTTAGCCCGGATATAGTCACT
AGCATAAATGCCTTT
Found at i:26765 original size:15 final size:15
Alignment explanation
Indices: 26745--26773 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
26735 AACTTTCAAA
26745 GCAACATTAAACATT
1 GCAACATTAAACATT
26760 GCAACATTAAACAT
1 GCAACATTAAACAT
26774 ACCTTAATCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.48, C:0.21, G:0.07, T:0.24
Consensus pattern (15 bp):
GCAACATTAAACATT
Found at i:32509 original size:40 final size:40
Alignment explanation
Indices: 32431--32573 Score: 155
Period size: 40 Copynumber: 3.6 Consensus size: 40
32421 GTGCGAGTTG
*
32431 CTATATCGCGGGCTAAGACCCGAAGGCATTTGTGCTAGCGA
1 CTATATC-CGGGCTAAAACCCGAAGGCATTTGTGCTAGCGA
* *
32472 TTATATCC-GGCTAAAACCTGAAGGCTATTTGTGCTAGCGA
1 CTATATCCGGGCTAAAACCCGAAGGC-ATTTGTGCTAGCGA
** * * *
32512 CTA-ATCCGGGCTAAGTCCCAAAGGCATTTATGCTAGTGA
1 CTATATCCGGGCTAAAACCCGAAGGCATTTGTGCTAGCGA
* * *
32551 CCACATCCGGGCTAAGACCCGAA
1 CTATATCCGGGCTAAAACCCGAA
32574 AGGCCTGTGC
Statistics
Matches: 86, Mismatches: 13, Indels: 7
0.81 0.12 0.07
Matches are distributed among these distances:
39 33 0.38
40 47 0.55
41 6 0.07
ACGTcount: A:0.27, C:0.25, G:0.24, T:0.23
Consensus pattern (40 bp):
CTATATCCGGGCTAAAACCCGAAGGCATTTGTGCTAGCGA
Done.