Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Cotton_A_33122
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: 1959
ACGTcount: A:0.32, C:0.20, G:0.21, T:0.27
Found at i:1870 original size:408 final size:408
Alignment explanation
Indices: 1111--1926 Score: 1048
Period size: 408 Copynumber: 2.0 Consensus size: 408
1101 ACTCAAAACT
* *
1111 ATGACCATGATCATTAATGAAACTCTAAGATTGTATGGTCCATCAAATGGAATGTTGAGAAGAGT
1 ATGACCATGATCATTAATGAAACTCTAAGATTGTATGGTCCAGCAAATGGAATGTTGAGAAGAGG
* * *
1176 TGGAAGAGATGTTCAAATGGAAAAGGTAGTCCTCCCTGCTAATATAGATCTTCTAATTGCAAATG
66 TGGAAGAGAAGTTCAAATGGAAAAGCTAGTCCTCCCTGCTAATATAGATATTCTAATTGCAAATG
* *
1241 CTGTACTTCACCATGACCCTCAACTGTGGGGAGAAGATGTGCATCTTTTTAAACCAGACAGATTC
131 CTGCACTTCACCATGACCCTCAACTATGGGGAGAAGATGTGCATCTTTTTAAACCAGACAGATTC
* * ** *
1306 GCGGAAGGGATTGCCAAAGCTACCAATTACAACGCGGCTGCATTTTTACCCTTTGGATTGGGACC
196 GCCGAAGGGATTGCCAAAGCTACCAATTACAACACAACAGCATTTTTACCCTTTGGATTGGGACC
** * * **
1371 TCGAACTTGTGTTGGTATGACCTTTGCAGCCACAGAAACCAAGATTGTTCTCTCCATGATCCTAC
261 TCGAACTTGTGTTGGTACAACCTTCGCAACCACAGAAACCAAGATTGCACTCTCCATGATCCTAC
* * * *
1436 AACGCTACGCTATTACACTTTCCCCTGCCTATGTCCACTCACCAATACCTATAATCAGCC-TTAA
326 AACGCTACACCATTACACTCTCCCCTGCCTATGTCCACGCACCAATACCTATAATCA-CCGTTAA
1500 ACCACAACATGGAATTCAA
390 ACCACAACATGGAATTCAA
* * * ** **
1519 ATGACCATGATTATTAATGAACCTCTAAGATTGTTTGGTCCAGCAGTTGGCCTGTTGAGGAA-AG
1 ATGACCATGATCATTAATGAAACTCTAAGATTGTATGGTCCAGCAAATGGAATGTTGA-GAAGAG
* *** * * * * *
1583 GTGGAAGTGAAGTTCTGTTAGG-AAATCTAGTCTTGCCTGCTGATATAGATATTCTTATTGCAAA
65 GTGGAAGAGAAGTTCAAAT-GGAAAAGCTAGTCCTCCCTGCTAATATAGATATTCTAATTGCAAA
* *
1647 TGCTGCACTTCACCATGACCCTCAACTATGGGGAGATA-ATGTGCATCTTTTTAAGCCAGAGAGA
129 TGCTGCACTTCACCATGACCCTCAACTATGGGGAGA-AGATGTGCATCTTTTTAAACCAGACAGA
1711 TTCGCCGAAGGGATTGCCAAAGCTACCAATTACAACACAACAGCATTTTGT-CCCTTTGGATTGG
193 TTCGCCGAAGGGATTGCCAAAGCTACCAATTACAACACAACAGCATTTT-TACCCTTTGGATTGG
* * ** *** * *
1775 GACCTCGGACTTGTGTTGGTACAACCTTCGCAATCATGGAAGTGAAGATTGCAGTCTCCATGATT
257 GACCTCGAACTTGTGTTGGTACAACCTTCGCAACCACAGAAACCAAGATTGCACTCTCCATGATC
* * * * * * *
1840 CTACAACGCTACACCATTTCCCTCTCCCCTGCTTATGTCCACGCGCCAGTATCTATTATCACCGT
322 CTACAACGCTACACCATTACACTCTCCCCTGCCTATGTCCACGCACCAATACCTATAATCACCGT
1905 TAAACCACAACATGGAATTCAA
387 TAAACCACAACATGGAATTCAA
1927 GTAATACTCG
Statistics
Matches: 347, Mismatches: 56, Indels: 10
0.84 0.14 0.02
Matches are distributed among these distances:
407 2 0.01
408 338 0.97
409 7 0.02
ACGTcount: A:0.29, C:0.23, G:0.20, T:0.28
Consensus pattern (408 bp):
ATGACCATGATCATTAATGAAACTCTAAGATTGTATGGTCCAGCAAATGGAATGTTGAGAAGAGG
TGGAAGAGAAGTTCAAATGGAAAAGCTAGTCCTCCCTGCTAATATAGATATTCTAATTGCAAATG
CTGCACTTCACCATGACCCTCAACTATGGGGAGAAGATGTGCATCTTTTTAAACCAGACAGATTC
GCCGAAGGGATTGCCAAAGCTACCAATTACAACACAACAGCATTTTTACCCTTTGGATTGGGACC
TCGAACTTGTGTTGGTACAACCTTCGCAACCACAGAAACCAAGATTGCACTCTCCATGATCCTAC
AACGCTACACCATTACACTCTCCCCTGCCTATGTCCACGCACCAATACCTATAATCACCGTTAAA
CCACAACATGGAATTCAA
Done.