Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Cotton_A_22270
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: 4632
ACGTcount: A:0.32, C:0.17, G:0.22, T:0.29
Found at i:4543 original size:762 final size:762
Alignment explanation
Indices: 3075--4597 Score: 2492
Period size: 762 Copynumber: 2.0 Consensus size: 762
3065 AGATAAAAGC
* * *
3075 ATTGGAGTTCTCGGAGATGACAGAAAAGAAGCAAATAAGCAACGTGACAGTCCCTGAAAGGAGAG
1 ATTGAAGTTCTCGAAGATGACAGAAAAGAAGCAAATAAGCAACGTGACAGTCCCTGAAAGAAGAG
3140 GAAGAACATCAACATGTAAGGAATATTTAACAATTTCCAATTTTGAAGAGTTATTTGAATATTCT
66 GAAGAACATCAACATGTAAGGAATATTTAACAATTTCCAATTTTGAAGAGTTATTTGAATATTCT
*
3205 GGATATAATCTTTCAACTCTGACGATCCTACACTTGTCCAAACTAACTGAATTGCGGGTGATATG
131 GGATATAATCTTTCAACTCTGAAGATCCTACACTTGTCCAAACTAACTGAATTGCGGGTGATATG
* *
3270 GAGTGGTCTCATCCAAGTTGAATACTTTCAAAATCTCGCTCATTTGACAGTCAAAGATTGCAGAA
196 GAGTGGTCCCATCCAAGTTGAACACTTTCAAAATCTCGCTCATTTGACAGTCAAAGATTGCAGAA
* * *
3335 GGTTAAGATACATCTTCTCGCCTACCATCGCTCGAAATTTGCCACATTTGGGCAAGTTGGATATA
261 GGTTAAGATACATCTTCCCACCTACCATCGCTCGAAATTTGCCACAATTGGGCAAGTTGGATATA
3400 TCTAACTGTGAGGAATTGGAGCAAATAATTGAGAAGGATCAAACTCCATCACAACATCATCTCCA
326 TCTAACTGTGAGGAATTGGAGCAAATAATTGAGAAGGATCAAACTCCATCACAACATCATCTCCA
* ** * ** *
3465 ACCTATTTGCTTCCCTATTTTGAGTTGGATTACAATCGAGATGTGTGAAAACTTGAAATGTTTGT
391 ACCTAATTGCTTCCCTAAATTGAGTTGGATTACAATAGAGAACTGTGAAAACTTGAAATCTTTGT
3530 TCCCAATTACTCTTGCTCATGGCGGCCTTCCAAACCTAGAGCAATTAGACCTTATAAGGCTATCC
456 TCCCAATTACTCTTGCTCATGGCGGCCTTCCAAACCTAGAGCAATTAGACCTTATAAGGCTATCC
3595 AAATTAGAGCAGGTGTTTGAAGGAGATGAGTCAAATGTGAGTAAGGACGAAGAGAAAGTGATACA
521 AAATTAGAGCAGGTGTTTGAAGGAGATGAGTCAAATGTGAGTAAGGACGAAGAGAAAGTGATACA
3660 CCTACCTGAATTAACCGACTTAGTGCTTGATAACCTACCAAACCTCGTGAGCTTCAGCCCTGTGG
586 CCTACCTGAATTAACCGACTTAGTGCTTGATAACCTACCAAACCTCGTGAGCTTCAGCCCTGTGG
* * ** *
3725 ATTATCATTTTGTTTTCCCATCTTTGACAGATTTACGAGTTGAAGGTTGTCCCAACGTAACCACA
651 ATTATCATTTTATTTTCCAATCTTTGACAGATTTAAAAGTAGAAGGTTGTCCCAACGTAACCACA
*
3790 AGATTTAGTTTTGATTCAAAGGAATCAGTGCATGCCAAAACACAGGA
716 AGATTTAGTGTTGATTCAAAGGAATCAGTGCATGCCAAAACACAGGA
3837 ATTGAAGTTCTCGAAGATGACAGAAAAGAAGCAAATAAGCAACGTGACAGTCCCTGAAAGAAGA-
1 ATTGAAGTTCTCGAAGATGACAGAAAAGAAGCAAATAAGCAACGTGACAGTCCCTGAAAGAAGAG
* *
3901 GAAGGAACATCAGCATGTACGGAATATTTAACAATTTCCAATTTTGAAGAGTTATTTGAATATTC
66 GAA-GAACATCAACATGTAAGGAATATTTAACAATTTCCAATTTTGAAGAGTTATTTGAATATTC
* * *
3966 TGGATATAATCTTTCAACTCTGAAGTTCCTACGCTTGTCCAAACTAACTGAATTGGGGGTGATAT
130 TGGATATAATCTTTCAACTCTGAAGATCCTACACTTGTCCAAACTAACTGAATTGCGGGTGATAT
* *
4031 GGAGTGGTCCCATCCAAGTTGAACACTTTCAAAATCTCTG-TACA-TTGACAGTTAAAGATTGTA
195 GGAGTGGTCCCATCCAAGTTGAACACTTTCAAAATCTC-GCT-CATTTGACAGTCAAAGATTGCA
* * **
4094 GAAGGTTAAGATACATCTTCCCATCTACCATCGCTCGAAATTTGCCACAATTGTGCTCGTTGGAT
258 GAAGGTTAAGATACATCTTCCCACCTACCATCGCTCGAAATTTGCCACAATTGGGCAAGTTGGAT
*
4159 ATATCTGACTGTGAGGAATTGGAGCAAATAATTGAGAAGGATCAAACTCCATCACAACATCATCT
323 ATATCTAACTGTGAGGAATTGGAGCAAATAATTGAGAAGGATCAAACTCCATCACAACATCATCT
4224 CCAACCTAATTGCTTCCCTAAATTGAGTTGGATTACAATA-AGGAACTGTGAAAACTTGAAATCT
388 CCAACCTAATTGCTTCCCTAAATTGAGTTGGATTACAATAGA-GAACTGTGAAAACTTGAAATCT
* ** *
4288 TTGTTCCC-ATTAACTCTTGCTCATGGCGGCGTTCCAAACCTAG-GTGGATTATACCTTGA-AAG
452 TTGTTCCCAATT-ACTCTTGCTCATGGCGGCCTTCCAAACCTAGAG-CAATTAGACCTT-ATAAG
*
4350 GGTCA-CCAAATTAGAGCAGGTGTTTGAAGGAGATGAGTCAAATGTGAGTAAGGACGAAGAGAAA
514 GCT-ATCCAAATTAGAGCAGGTGTTTGAAGGAGATGAGTCAAATGTGAGTAAGGACGAAGAGAAA
*
4414 GTGATACACCTACCTGAATTAACCGACTTAGTGCTTGATAACCTACCAAACCTCGTGAGCTTTAG
578 GTGATACACCTACCTGAATTAACCGACTTAGTGCTTGATAACCTACCAAACCTCGTGAGCTTCAG
*
4479 CCCTGTTGG-TTATCATTTTATTTTCCAAAT-TTTGA-GGTATTTAAAAGTAGAAGGTTGTCCCA
643 CCCTG-TGGATTATCATTTTATTTTCC-AATCTTTGACAG-ATTTAAAAGTAGAAGGTTGTCCCA
*
4541 ACGTAACCACAAGATTTAGTGTTGATTCAAAGGAATCAGTTCATGCCAAAACACAGG
705 ACGTAACCACAAGATTTAGTGTTGATTCAAAGGAATCAGTGCATGCCAAAACACAGG
4598 TACACTACTC
Statistics
Matches: 708, Mismatches: 42, Indels: 22
0.92 0.05 0.03
Matches are distributed among these distances:
761 9 0.01
762 689 0.97
763 10 0.01
ACGTcount: A:0.33, C:0.19, G:0.20, T:0.28
Consensus pattern (762 bp):
ATTGAAGTTCTCGAAGATGACAGAAAAGAAGCAAATAAGCAACGTGACAGTCCCTGAAAGAAGAG
GAAGAACATCAACATGTAAGGAATATTTAACAATTTCCAATTTTGAAGAGTTATTTGAATATTCT
GGATATAATCTTTCAACTCTGAAGATCCTACACTTGTCCAAACTAACTGAATTGCGGGTGATATG
GAGTGGTCCCATCCAAGTTGAACACTTTCAAAATCTCGCTCATTTGACAGTCAAAGATTGCAGAA
GGTTAAGATACATCTTCCCACCTACCATCGCTCGAAATTTGCCACAATTGGGCAAGTTGGATATA
TCTAACTGTGAGGAATTGGAGCAAATAATTGAGAAGGATCAAACTCCATCACAACATCATCTCCA
ACCTAATTGCTTCCCTAAATTGAGTTGGATTACAATAGAGAACTGTGAAAACTTGAAATCTTTGT
TCCCAATTACTCTTGCTCATGGCGGCCTTCCAAACCTAGAGCAATTAGACCTTATAAGGCTATCC
AAATTAGAGCAGGTGTTTGAAGGAGATGAGTCAAATGTGAGTAAGGACGAAGAGAAAGTGATACA
CCTACCTGAATTAACCGACTTAGTGCTTGATAACCTACCAAACCTCGTGAGCTTCAGCCCTGTGG
ATTATCATTTTATTTTCCAATCTTTGACAGATTTAAAAGTAGAAGGTTGTCCCAACGTAACCACA
AGATTTAGTGTTGATTCAAAGGAATCAGTGCATGCCAAAACACAGGA
Done.