Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold1263
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: 2228
ACGTcount: A:0.35, C:0.19, G:0.18, T:0.28
Found at i:1445 original size:20 final size:20
Alignment explanation
Indices: 1407--1446 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
1397 TTAAGAATGG
*
1407 ACAACGAAATCTACAAATCT
1 ACAACGAAATCCACAAATCT
*
1427 ACAACGAAATCCACGAATCT
1 ACAACGAAATCCACAAATCT
1447 CCAAGTACTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.47, C:0.28, G:0.07, T:0.17
Consensus pattern (20 bp):
ACAACGAAATCCACAAATCT
Found at i:2143 original size:203 final size:197
Alignment explanation
Indices: 1766--2228 Score: 567
Period size: 203 Copynumber: 2.3 Consensus size: 197
1756 AACATAACAC
** * ***
1766 TTAACTTCAAATAACAAAGAA-AGTAGCAGCAACATAGGAAAATCCTTTGGCAC-AGTCATTCTA
1 TTAACTTCTTATAACAAA-AATATTAGCAGCAACATAGGAAAATCCTTTGGCACGA-TCAAAGTA
* *
1829 GGACATATAAGGAATAAGAAAATGCTAATATCTCAGGATATTTTGCGTATTTCTCGAGAAAAGTC
64 GGACACATAAGGAATAAGAAAATGCTAACATCTCAGGATATTTTGCGTATTTCTCGAGAAAAGTC
* * * * *
1894 CATTTGAAGTTGGCAACCTCGAATAAGCCCTATGCTACCCATGTAAAATCCACGTATGCACTTAT
129 CATCTAAAGTTGGCAACCTCGAATAAGCCCTATGCTACCAATGTAAAATCAACG--T-CA---AA
*
1959 TACTCAAA-T
188 TACCCAAACT
*
1968 TTAAAGTTCTTATAA-AAAAATTATTAGCAGCAACATAGGAAAATCCTTTGGCACGATCAAAGTA
1 TT-AACTTCTTATAACAAAAA-TATTAGCAGCAACATAGGAAAATCCTTTGGCACGATCAAAGTA
* * * * *
2032 TGATACCTAAGGAATAAGAAAATGTTAACGTC-CAGGAGTATTTTGCGTATTTCTCGAGAAAAGT
64 GGACACATAAGGAATAAGAAAATGCTAACATCTCAGGA-TATTTTGCGTATTTCTCGAGAAAAGT
* * *
2096 CCATCTAAAGTTGGCAACCTCGAATCAGCCCTATGTTAGCAATGTAAAATCAACGTCAAATACCC
128 CCATCTAAAGTTGGCAACCTCGAATAAGCCCTATGCTACCAATGTAAAATCAACGTCAAATACCC
2161 AAACT
193 AAACT
* *
2166 TTAACTTCTTATAACAAAGATATTAGCAGCAACATAGGAAAACCCTTTGGCACGATCAAAGTA
1 TTAACTTCTTATAACAAAAATATTAGCAGCAACATAGGAAAATCCTTTGGCACGATCAAAGTA
Statistics
Matches: 228, Mismatches: 26, Indels: 19
0.84 0.10 0.07
Matches are distributed among these distances:
197 61 0.27
198 7 0.03
200 2 0.01
201 3 0.01
202 10 0.04
203 144 0.63
204 1 0.00
ACGTcount: A:0.39, C:0.19, G:0.16, T:0.27
Consensus pattern (197 bp):
TTAACTTCTTATAACAAAAATATTAGCAGCAACATAGGAAAATCCTTTGGCACGATCAAAGTAGG
ACACATAAGGAATAAGAAAATGCTAACATCTCAGGATATTTTGCGTATTTCTCGAGAAAAGTCCA
TCTAAAGTTGGCAACCTCGAATAAGCCCTATGCTACCAATGTAAAATCAACGTCAAATACCCAAA
CT
Done.