Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr11
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: 102024878
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 3234766 characters in sequence are not A, C, G, or T
File 310 of 310
Found at i:102017598 original size:40 final size:40
Alignment explanation
Indices: 102017414--102017598 Score: 207
Period size: 40 Copynumber: 4.7 Consensus size: 40
102017404 GCTCCTCGTT
* *
102017414 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
* * *
102017454 CAAATGCCTTTGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
* * *
102017494 CAAATGCTTTCGGG-CTTAGCCCGGA-ATTAGTATCTCTCA
1 CAAATGCCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCA
* * * *
102017533 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATATAGTAAC-TCGCA
102017574 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
102017599 CATCATTCAA
Statistics
Matches: 120, Mismatches: 19, Indels: 12
0.79 0.13 0.08
Matches are distributed among these distances:
38 2 0.02
39 30 0.25
40 77 0.64
41 11 0.09
ACGTcount: A:0.25, C:0.26, G:0.22, T:0.26
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
Found at i:102019742 original size:325 final size:325
Alignment explanation
Indices: 102019148--102019785 Score: 1159
Period size: 325 Copynumber: 2.0 Consensus size: 325
102019138 GGGCTGTCAC
*
102019148 AACTCTCCCCCACTTAAGAAATTTTCGTCCCCGAAAATCTTACCGGTAAATAAGTTTGGGTATCA
1 AACTCTCCCCCACTTAAGAAATTTTCGTCCCCGAAAATCTTACCGGTAAATAAGTTTGGATATCA
102019213 TTCTTTCATCGAGCTCTCGGTTTCCCAAGTAGCTTCCTCGATCCCGTGTTTGAGCCATAACACCT
66 TTCTTTCATCGAGCTCTCGGTTTCCCAAGTAGCTTCCTCGATCCCGTGTTTGAGCCATAACACCT
*
102019278 TCACTAACGGAACCCTTTTGTTTCGCAACTCCTTCACTTCATGAGCTAGGATACGCATCGGTTCT
131 TCACTAACGGAACCCTTTTGTTTCGCAACTCCTTCACTTCACGAGCTAGGATACGCATCGGTTCT
*
102019343 TCTTCATAACTCATATCGGCTTGAATTTCTACCTCTGATGGGCTAATTATGTGCGATGGATCAGA
196 TCTTCATAACTCATATCGGCTTGAATTTCAACCTCTGATGGGCTAATTATGTGCGATGGATCAGA
*
102019408 TCGATAGCGTCGAAGCATCAAAACATGAAAGACGTCGTGAATCTTTTCAAGCTTGAGTATTCTAT
261 TCGATAGCGTCGAAGCATCAAAACATGAAAGACGTCATGAATCTTTTCAAGCTTGAGTATTCTAT
* *
102019473 AACTCTCCCCCACTTAAGAAATTTTCGTCCCCGAAAATCTTACCGGTAAATAGGTTTGGATATCG
1 AACTCTCCCCCACTTAAGAAATTTTCGTCCCCGAAAATCTTACCGGTAAATAAGTTTGGATATCA
102019538 TTCTTTCATCGAGCTCTCGGTTTCCCAAGTAGCTTCCTCGATCCCGTGTTTGAGCCATAACACCT
66 TTCTTTCATCGAGCTCTCGGTTTCCCAAGTAGCTTCCTCGATCCCGTGTTTGAGCCATAACACCT
* * * *
102019603 TTACTAGCGGAACTCTTTTGTTTCGTAACTCCTTCACTTCACGAGCTAGGATACGCATCGGTTCT
131 TCACTAACGGAACCCTTTTGTTTCGCAACTCCTTCACTTCACGAGCTAGGATACGCATCGGTTCT
102019668 TCTTCATAACTCATATCGGCTTGAATTTCAACCTCTGATGGGCTAATTATGTGCGATGGATCAGA
196 TCTTCATAACTCATATCGGCTTGAATTTCAACCTCTGATGGGCTAATTATGTGCGATGGATCAGA
* * *
102019733 TCTATAGCGTCGAAGCATCGAAACATGAAAGACGTCATGGATCTTTTCAAGCT
261 TCGATAGCGTCGAAGCATCAAAACATGAAAGACGTCATGAATCTTTTCAAGCT
102019786 CAGGGAGCAA
Statistics
Matches: 300, Mismatches: 13, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
325 300 1.00
ACGTcount: A:0.25, C:0.25, G:0.18, T:0.32
Consensus pattern (325 bp):
AACTCTCCCCCACTTAAGAAATTTTCGTCCCCGAAAATCTTACCGGTAAATAAGTTTGGATATCA
TTCTTTCATCGAGCTCTCGGTTTCCCAAGTAGCTTCCTCGATCCCGTGTTTGAGCCATAACACCT
TCACTAACGGAACCCTTTTGTTTCGCAACTCCTTCACTTCACGAGCTAGGATACGCATCGGTTCT
TCTTCATAACTCATATCGGCTTGAATTTCAACCTCTGATGGGCTAATTATGTGCGATGGATCAGA
TCGATAGCGTCGAAGCATCAAAACATGAAAGACGTCATGAATCTTTTCAAGCTTGAGTATTCTAT
Done.