Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Cotton_A_10508
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: 2091
ACGTcount: A:0.38, C:0.13, G:0.27, T:0.22
Found at i:756 original size:225 final size:228
Alignment explanation
Indices: 226--877 Score: 707
Period size: 225 Copynumber: 2.9 Consensus size: 228
216 TAAGACAAGT
* *
226 AAAGATGCAGTTGAAGAGATTCCAATGGAAACTTGTTTGGGTGGAAAAGAGAATGCAGAACAAGA
1 AAAGATG-AGTTGAAGAGATTTCAATGGAAACTTGTTTAGGTGGAAAAGAGAATGCAGAACAAGA
* ** * *
291 AAGTCGCAAGGTGATGAACTTGGAGAACAATGGGGAAGCAAAAAGGGTTAAGAAAGACAAACATA
65 AAGTAGCAAGGTGATGAACTTGGAGAACAATGGGGAAGCAAAAAGGGTTGGGAAAGATAAACACA
* * * ** * * **
356 AGAA-GA-ACAGGGACGAGACCGATGTAGTTGCTACTGTGACTGAAACCCTCAAACATAGTAAAA
130 AGAAGGAGACAAGGATGGGATTGATGCAGTTGGTACTGTGACTGAAACCCTTGAACATAGTAAAA
* *
419 AGGAATCTGAGAAGGCTCATAAAAAGCATGAGAAAAG
195 AGGAATCTCAGAAGGCGCAT--AAAGCA-GAGAAAAG
* * * * * * **
456 TAAAGATGAGGTTAAAGAGATTTCAGTAGAAAATTATTTAGGTGGAAAAAAGAACACAGAACAAG
1 -AAAGATGA-GTTGAAGAGATTTCAATGGAAACTTGTTTAGGTGGAAAAGAGAATGCAGAACAAG
* * *
521 AAAGTAGCAAGGCGATGAACTTGGAGAACAAAGGGGAAGCAAAAAGGGTCGGGAAAGATAAACAC
64 AAAGTAGCAAGGTGATGAACTTGGAGAACAATGGGGAAGCAAAAAGGGTTGGGAAAGATAAACAC
* * * *
586 AAGAAGGACGACAAGGATGGGATTAATGCAGTTGGTATTGTGACCGGAACCCTTGAACATAGTAA
129 AAGAAGGA-GACAAGGATGGGATTGATGCAGTTGGTACTGTGACTGAAACCCTTGAACATAGTAA
*
651 AAAGGAATCTCCA-AAGGCGCGT-AAG-A-A-AAAA-
193 AAAGGAATCT-CAGAAGGCGCATAAAGCAGAGAAAAG
* *
682 AAAGATGTAGTTGAAGAGATTTCAATGGAAACTTGTTTAGGTGGAAAAGATAATGCAGAAAAAGA
1 AAAGATG-AGTTGAAGAGATTTCAATGGAAACTTGTTTAGGTGGAAAAGAGAATGCAGAACAAGA
* * * *
747 AAGTAGCAAGGTGGTGAATTTGGGGAACAATGGGGAAGCAGAAAA-GGTTGGGGAAGATAAACAC
65 AAGTAGCAAGGTGATGAACTTGGAGAACAATGGGGAAGCA-AAAAGGGTTGGGAAAGATAAACAC
* * *
811 AAG-AGGAAGAATAAGG-TCGGAATTGATGCAGTTGCG-ACTGTGACTGAAACCATTGAACATAG
129 AAGAAGG-AG-ACAAGGAT-GGGATTGATGCAGTTG-GTACTGTGACTGAAACCCTTGAACATAG
873 TAAAA
190 TAAAA
878 TGCAAGAGCC
Statistics
Matches: 352, Mismatches: 58, Indels: 28
0.80 0.13 0.06
Matches are distributed among these distances:
224 5 0.01
225 155 0.44
226 6 0.02
227 4 0.01
228 1 0.00
230 2 0.01
231 117 0.33
232 2 0.01
234 59 0.17
235 1 0.00
ACGTcount: A:0.43, C:0.11, G:0.28, T:0.18
Consensus pattern (228 bp):
AAAGATGAGTTGAAGAGATTTCAATGGAAACTTGTTTAGGTGGAAAAGAGAATGCAGAACAAGAA
AGTAGCAAGGTGATGAACTTGGAGAACAATGGGGAAGCAAAAAGGGTTGGGAAAGATAAACACAA
GAAGGAGACAAGGATGGGATTGATGCAGTTGGTACTGTGACTGAAACCCTTGAACATAGTAAAAA
GGAATCTCAGAAGGCGCATAAAGCAGAGAAAAG
Done.