Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: LOC111313163
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: 8714
ACGTcount: A:0.30, C:0.17, G:0.21, T:0.32
Found at i:2181 original size:21 final size:21
Alignment explanation
Indices: 2157--2196 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
2147 CCTTCTTGTT
2157 CTCTG-TTATGGCTTCCTCTTC
1 CTCTGCTTAT-GCTTCCTCTTC
*
2178 CTCTGCTTCTGCTTCCTCT
1 CTCTGCTTATGCTTCCTCT
2197 ACTCAAGCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 14 0.82
22 3 0.18
ACGTcount: A:0.03, C:0.38, G:0.12, T:0.47
Consensus pattern (21 bp):
CTCTGCTTATGCTTCCTCTTC
Found at i:4866 original size:474 final size:474
Alignment explanation
Indices: 3965--4900 Score: 1531
Period size: 474 Copynumber: 2.0 Consensus size: 474
3955 TTTGAACAAC
* *
3965 TTTGGAATGGAGATCAGAATCTTGAGAATTTAAGAGTGCTTGATCTTTCGTTTTGCAAGAATTTA
1 TTTGGAATGGAGACCAGAATCTTGAGAATTTAAGAGTGCTAGATCTTTCGTTTTGCAAGAATTTA
4030 ACCAGGATCCCAAGTTTGTCAGCATCCAAAAATATTGAACAACTGGAAATTAGTTGGTGCGAAAG
66 ACCAGGATCCCAAGTTTGTCAGCATCCAAAAATATTGAACAACTGGAAATTAGTTGGTGCGAAAG
* * * *
4095 CTTGGTTGAACTCCCATCCATGGTTCATTTGAAATCTCTTTGCTTTAGCCTAAGCGGTTGTGGTT
131 CTTGGTTGAACTCCCATCCATGGTTCATTTGAAATCTCTTTGCTCTAGCCTAAGAGGTTGAGGGT
4160 TAAAAAATTTGAAGAAATTTCCTGAGCTCCCACAGCATACTAAAAGGTTGATTTTAACAGACACT
196 TAAAAAATTTGAAGAAATTTCCTGAGCTCCCACAGCATACTAAAAGGTTGATTTTAACAGACACT
*
4225 GCAATAGAAGAAATTCCGGAGTCAATCGGGTTTCTCCATCAACTTGCTTTTTTGGATATGAGTGG
261 GCAATAGAAGAAATTCCGGAGTCAATCGGGTTTCTCCATCAACTTGCATTTTTGGATATGAGTGG
* *
4290 TGGCCGAATTCATAATCTTCCAAGCACTATTATTCAGTTGCATGCCCTTAAAGACATCCGACTCT
326 TGGCCGAATTCATAATATTCCAAGCACTATTATTCAGTTGCATGCCCTTAAAGACATCCGACTCC
* * * * * *
4355 GTGATTGCCCAAACATCACAAATTTTCCGATTGTTCCGGCGAAGATAGAGGTCTTATATTTGGAT
391 GTGATTGCCCAAACATAAAAAATTTTCCGATTGTTCCGGAGAACATAGAGATCTTAGATTTGGAT
4420 AACACTCCAGTAGAAGAAT
456 AACACTCCAGTAGAAGAAT
*
4439 TTTGGACTGGAGACCAGAATCTTGAGAATTTAAGAGTGCTAGATC-TTCGGTTTTGCAAGAATTT
1 TTTGGAATGGAGACCAGAATCTTGAGAATTTAAGAGTGCTAGATCTTTC-GTTTTGCAAGAATTT
* * *
4503 AACGAGGATCCCAAGTTTGTCAGCGTCCAAAAATATTGAACAACTGGAAATTAG-TGGATGCGAG
65 AACCAGGATCCCAAGTTTGTCAGCATCCAAAAATATTGAACAACTGGAAATTAGTTGG-TGCGAA
*
4567 AGCTTGGTTGAACTCCCATCCATGGTTCATTTGAAATCTCTTCT-CTCTCGCCTAAGAGG-TGAA
129 AGCTTGGTTGAACTCCCATCCATGGTTCATTTGAAATCTCTT-TGCTCTAGCCTAAGAGGTTG-A
* **
4630 GGGTTAACAAATTTGAAGAAATTTCCTGAGCTCCCACAGCATA-TTGAAGAGTTGATTTTAACAG
192 GGGTTAAAAAATTTGAAGAAATTTCCTGAGCTCCCACAGCATACTAAAAG-GTTGATTTTAACAG
* *
4694 GCACTGCAATAGAAGAAATTCCGGAGTCAATCGGGTTTCTCCATCAATTTGCATTTTTGGATATG
256 ACACTGCAATAGAAGAAATTCCGGAGTCAATCGGGTTTCTCCATCAACTTGCATTTTTGGATATG
* *
4759 ATTGGTGGCCGAATTCGTAATATTCCAAGCACTATTATTCAGTTGCATGCCCTTAAAGACATCCG
321 AGTGGTGGCCGAATTCATAATATTCCAAGCACTATTATTCAGTTGCATGCCCTTAAAGACATCCG
* *
4824 GCTCCGTGATTGCCCAAACATAAAAAATTTTCCGATTGTTCCGGAGAACATAGAGATGTTAGATT
386 ACTCCGTGATTGCCCAAACATAAAAAATTTTCCGATTGTTCCGGAGAACATAGAGATCTTAGATT
4889 TGGATAACACTC
451 TGGATAACACTC
4901 GAATAAAAAA
Statistics
Matches: 428, Mismatches: 29, Indels: 10
0.92 0.06 0.02
Matches are distributed among these distances:
473 12 0.03
474 415 0.97
475 1 0.00
ACGTcount: A:0.30, C:0.19, G:0.21, T:0.31
Consensus pattern (474 bp):
TTTGGAATGGAGACCAGAATCTTGAGAATTTAAGAGTGCTAGATCTTTCGTTTTGCAAGAATTTA
ACCAGGATCCCAAGTTTGTCAGCATCCAAAAATATTGAACAACTGGAAATTAGTTGGTGCGAAAG
CTTGGTTGAACTCCCATCCATGGTTCATTTGAAATCTCTTTGCTCTAGCCTAAGAGGTTGAGGGT
TAAAAAATTTGAAGAAATTTCCTGAGCTCCCACAGCATACTAAAAGGTTGATTTTAACAGACACT
GCAATAGAAGAAATTCCGGAGTCAATCGGGTTTCTCCATCAACTTGCATTTTTGGATATGAGTGG
TGGCCGAATTCATAATATTCCAAGCACTATTATTCAGTTGCATGCCCTTAAAGACATCCGACTCC
GTGATTGCCCAAACATAAAAAATTTTCCGATTGTTCCGGAGAACATAGAGATCTTAGATTTGGAT
AACACTCCAGTAGAAGAAT
Found at i:7141 original size:29 final size:29
Alignment explanation
Indices: 7091--7150 Score: 93
Period size: 29 Copynumber: 2.1 Consensus size: 29
7081 TAATTCCATC
*
7091 ATAGTTTTGAATTATAGTTTTTGGGGTTT
1 ATAGTTTTGAATTATAGATTTTGGGGTTT
* *
7120 ATAGTTTTGAATTGTAGATTTTTGGGTTT
1 ATAGTTTTGAATTATAGATTTTGGGGTTT
7149 AT
1 AT
7151 GTAGTAGAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.22, C:0.00, G:0.23, T:0.55
Consensus pattern (29 bp):
ATAGTTTTGAATTATAGATTTTGGGGTTT
Done.