Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Cotton_A_11741
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: 1701
ACGTcount: A:0.33, C:0.16, G:0.24, T:0.27
Found at i:1620 original size:612 final size:612
Alignment explanation
Indices: 427--1650 Score: 1817
Period size: 612 Copynumber: 2.0 Consensus size: 612
417 GAGCTTGAAA
* *
427 AATATGAATCCAGCAGTGATTGCTAGCGTTGAGACGATGTTGGAGAAGTGGAAAGGTCGAGAAGG
1 AATATGAATCCAGCAGTGATTGCTAGCGTGGAGACGATGTTGGAGAAGTGGAAAGGCCGAGAAGG
* *
492 CGAAGAGATCGAAGTGTTTAACGAGTTCAGGTTGTTGACTTCAGAAGTTATATCGAGAACGGCTT
66 CGAAGAGATCGAAGTGTTTAACGAGTTCAGGTTGTTGACTGCAGAAGTGATATCGAGAACGGCTT
* * *
557 TCGGTAGTAATTACTTGGAAGGGAAGAAGATTTTCGACATGTTGACGAAATTGGCGATACTAGTT
131 TCGGTAGCAATTACTTGGAAGGGAAGAAGATTTTCGACATGTTGACGAAATTAGCGATACTAGTC
* * * ***
622 AGTCGAAATTATTTCAAAACTCCTATTCCTGGCATCAGCAAGATATGGAAAACCGCGGATGAAAT
196 AGTCAAAATTACTACAAAACTAAGATTCCTGGCATCAGCAAGATATGGAAAACCGCGGATGAAAT
* * **
687 AGAATCAGAGAAACTTGCTAATGGAATTCATGATTGTGTGATGGAAATGGTTAAGAGAAGGGAAA
261 AGAATCAGAGAAACTTGCTAAAGGAATACATGACCGTGTGATGGAAATGGTTAAGAGAAGGGAAA
* ** *
752 AGAAAGTAGAGACAGGAGAAGCTGACGGTTTTGGCAATGATTTTCTAGGATTACTAATAAATGCT
326 AGAAAGTAGAGACAGGAGAAGCCGACAATTTCGGCAATGATTTTCTAGGATTACTAATAAATGCT
*
817 TATCGTGATTCCGACGAGAAAAACCGATTTTCCATCGAGGATCTAGTGGATGAGTGCAAAACATT
391 CATCGTGATTCCGACGAGAAAAACCGATTTTCCATCGAGGATCTAGTGGATGAGTGCAAAACATT
*
882 CTACTTTGCCGGTCAAGAAACAACCAACTCCTTGCTTGCGTGGACGATCCTTGTTTTAGCAATTC
456 CTACTTTGCCGGTCAAGAAACAACCAACTCCTTGCTTGCATGGACGATCCTTGTTTTAGCAATTC
* * *
947 ATACTAAATGGCAAGAAAAAACAAGGCAAGAGGTGTTTGAGGTATTTGGGGACCAAAATCCTAAT
521 ATACTAAATGGCAAGAAAAAACAAGACAAGAGGTGTTTGAGGCATTCGGGGACCAAAATCCTAAT
* *
1012 TCTGAAGGCATTGCCAAATTAAAAATT
586 TCCGAAGGCATTGCCAAACTAAAAATT
*
1039 AATATGAATCCAGCAGTGATTGCTAGTGTGGAGACGATGTTGGAGAAGTGGAAAGGCCGAGAAGG
1 AATATGAATCCAGCAGTGATTGCTAGCGTGGAGACGATGTTGGAGAAGTGGAAAGGCCGAGAAGG
* * * * * *
1104 TGAAGAGATGGAAGTGTTTGAGGAGTTTAGGTTGTTGACTGCGGAAGTGATATCGAGAACGGCTT
66 CGAAGAGATCGAAGTGTTTAACGAGTTCAGGTTGTTGACTGCAGAAGTGATATCGAGAACGGCTT
* * *
1169 TCGGTAGCAATTACTTGGAAGGGAAGAAGATTTTCGAGATGTTGACGAGATTATCGATACTAGTC
131 TCGGTAGCAATTACTTGGAAGGGAAGAAGATTTTCGACATGTTGACGAAATTAGCGATACTAGTC
* *
1234 A-TCAACAATTACTACAAAACTAAGATTCCTGGCATCAGCATGATATGGAAAACTGCGGATGAAA
196 AGTCAA-AATTACTACAAAACTAAGATTCCTGGCATCAGCAAGATATGGAAAACCGCGGATGAAA
*
1298 TAGAATCGGAGAAACTTGCTAAAGGAATACATGACCGTGTGATGGAAATGGTTAAGAGAAGGGAA
260 TAGAATCAGAGAAACTTGCTAAAGGAATACATGACCGTGTGATGGAAATGGTTAAGAGAAGGGAA
* ** *** * * * *
1363 AAGAATGTATCGGTTGGAGAATCCGACAATTTCGGCAATGATTTTCTGGGATTGCTTATAAATGC
325 AAGAAAGTAGAGACAGGAGAAGCCGACAATTTCGGCAATGATTTTCTAGGATTACTAATAAATGC
* * *
1428 TCATCGTGATTCTGACGAGAAAAATCGATTTTCCGTCGAGGATCTAGTGGATGAGTGCAAAACAT
390 TCATCGTGATTCCGACGAGAAAAACCGATTTTCCATCGAGGATCTAGTGGATGAGTGCAAAACAT
* * * *
1493 TCTATTTTGCCGGTCAAGAAACAACTAATTCCTTG-TTGGCATGGACGGT-CTTAGTTTTAGCAA
455 TCTACTTTGCCGGTCAAGAAACAACCAACTCCTTGCTT-GCATGGACGATCCTT-GTTTTAGCAA
* * * *
1556 TTCATACTGAATGGCAAGAAAAAACAAGACGAGAGGT-TTTCGAGGCATTCGGTGACCGAAATCC
518 TTCATACTAAATGGCAAGAAAAAACAAGACAAGAGGTGTTT-GAGGCATTCGGGGACCAAAATCC
*
1620 TAATTCCGAAGGCATTTCCAAACTAAAAATT
582 TAATTCCGAAGGCATTGCCAAACTAAAAATT
1651 GTAAGGAAAT
Statistics
Matches: 545, Mismatches: 63, Indels: 8
0.88 0.10 0.01
Matches are distributed among these distances:
611 11 0.02
612 534 0.98
ACGTcount: A:0.33, C:0.14, G:0.26, T:0.26
Consensus pattern (612 bp):
AATATGAATCCAGCAGTGATTGCTAGCGTGGAGACGATGTTGGAGAAGTGGAAAGGCCGAGAAGG
CGAAGAGATCGAAGTGTTTAACGAGTTCAGGTTGTTGACTGCAGAAGTGATATCGAGAACGGCTT
TCGGTAGCAATTACTTGGAAGGGAAGAAGATTTTCGACATGTTGACGAAATTAGCGATACTAGTC
AGTCAAAATTACTACAAAACTAAGATTCCTGGCATCAGCAAGATATGGAAAACCGCGGATGAAAT
AGAATCAGAGAAACTTGCTAAAGGAATACATGACCGTGTGATGGAAATGGTTAAGAGAAGGGAAA
AGAAAGTAGAGACAGGAGAAGCCGACAATTTCGGCAATGATTTTCTAGGATTACTAATAAATGCT
CATCGTGATTCCGACGAGAAAAACCGATTTTCCATCGAGGATCTAGTGGATGAGTGCAAAACATT
CTACTTTGCCGGTCAAGAAACAACCAACTCCTTGCTTGCATGGACGATCCTTGTTTTAGCAATTC
ATACTAAATGGCAAGAAAAAACAAGACAAGAGGTGTTTGAGGCATTCGGGGACCAAAATCCTAAT
TCCGAAGGCATTGCCAAACTAAAAATT
Done.