Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Cotton_D_gene_10023079
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: 3438
ACGTcount: A:0.28, C:0.19, G:0.20, T:0.33
Found at i:1682 original size:720 final size:720
Alignment explanation
Indices: 82--2198 Score: 3095
Period size: 720 Copynumber: 2.9 Consensus size: 720
72 TGTAGCTAAG
* * * * ** * * * *
82 TGCTCAAGGTGTCGCGACAAGGTGTCAACTCCATGTTTTGGCTGTGCCGAGGATTGTGGGTTTTA
1 TGCTCGAGGTGTGGGGAGAAGGTGTCTGCTCCATGTTTTTGCTGTGCAGAGCACTGTGGGTTTTA
* * * * *
147 CCTTCACAAGGTATGCGCTGAGGCACCTTTGGAGCTTCATCACCCTTTTCATCCTGATCATCC-T
66 TCTTCATAAGGTATGTGCCGAGGCACCTTTGGAGCTTAATCACCCTTTTCAT-C---TCATCCAT
* *
211 CTTCTTCTTATGCAAAATGCACTTTATTCATCTGGAATGTACATTTGCAATTTTTGCAATAAATC
127 CCTCTTCTTATGCAAAATGCACCTTATTCATCTGGAATGTACATTTGCAATTTTTGCAATAAATC
*
276 TGGTCGCAAGTCTGTTTATCGCTGCTCTACTTGTGAATTGGACTTTCATATTAAATGTGCTTTGT
192 TGGTCACAAGTCTGTTTATCGCTGCTCTACTTGTGAATTGGACTTTCATATTAAATGTGCTTTGT
*
341 TTACATTTAATATTGCTGAGAATAATTTGAAAGAGCTTGACCATGTTGCCCTTCAAGTTGAAGA-
257 TTACATTTAATATTGCTGAGAATAATTTGAAAGAGCTTGACCATGTTGCCCTTCAAGATGAA-AC
*
405 ACTTGAAGATGATAGTAAGTGCTTCGGGTGTCGGGAACCATTAGCAAAGTATACACACTTTTCTC
321 ACTTGAAGATGATAGTAAGTGCTTTGGGTGTCGGGAACCATTAGCAAAGTATACACACTTTTCTC
* * *
470 CTAACTGTGGATTTAATTTACATGAGAAATGCGCTGAGCTTCCCTTCAAACTGAATCTTGTGTGC
386 CTGACTGTGGATTTAATTTACATGAGAAATGCGCTGAGCTTCCTTTCAAACTGAATCTTGAGTGC
* * *
535 CATCGCGAACATCCTCTTGTTCTACAATTTAATAGCCAACGGCTCTCTTGCAAGATATGCAG--A
451 CATCGCGAACATCCTCTTGTTCTACAATTTTATAGCGAACGGCTCTCTTGCAAGATATGCTGCCA
* * *
598 -GAAATCAATGTAGAAGCTATAGGATTTGTTTATGGTTGTTCTCCTTGTACGTTTGTTGTTCACA
516 GGAAA-CAA-G--G-CG-AATAGGATTTGTTTATGGTTGTTCTCCTTGTAAGTTTGTTGTTCACA
* *
662 TTGAATGTGCATCGCAATCACCATTGCAAGTTATTAAGAGTACAAATCATGAACATCCATTTACC
575 TTGAATGTGCATCACAATCACCATTACAAGTTATTAAGAGTACAAATCATGAACATCCATTTACC
*
727 TTGTTTAACGGTCACCAACATCCCCTGTTTCTTATGTTAAATCAAGAGCAGCTGATGGACAATCA
640 TTGTTTAACGGGCACCAACATCCCCTGTTTCTTATGTTAAATCAAGAGCAGCTGATGGACAATCA
792 AAGGGGTGTAACTGAT
705 AAGGGGTGTAACTGAT
*
808 TGCTCGAGGTGTGGGGAGAAGGTGTCTGCTCCATGTTTTTGCTGTGCGGAGCACTGTGGGTTTTA
1 TGCTCGAGGTGTGGGGAGAAGGTGTCTGCTCCATGTTTTTGCTGTGCAGAGCACTGTGGGTTTTA
*
873 TCTTCATAAGGTATGTGCCAAGGCACCTTTGGAGCTTAATCACCCTTTTCATCTCATCCATCCTC
66 TCTTCATAAGGTATGTGCCGAGGCACCTTTGGAGCTTAATCACCCTTTTCATCTCATCCATCCTC
938 TTCTTATGCAAAATGCACCTTATTCATCTGGAATGTACATTTGCAATTTTTGCAATAAATCTGGT
131 TTCTTATGCAAAATGCACCTTATTCATCTGGAATGTACATTTGCAATTTTTGCAATAAATCTGGT
*
1003 CACAAGTCTGTTTATCGCTGCTCTACTTGTGAATTGGACTTTCATATTAAATGTGATTTGTTTAC
196 CACAAGTCTGTTTATCGCTGCTCTACTTGTGAATTGGACTTTCATATTAAATGTGCTTTGTTTAC
1068 ATTTAATATTGCTGAGAATAATTTGAAAGAGCTTGACCATGTTGCCCTTCAAGATGAAACACTTG
261 ATTTAATATTGCTGAGAATAATTTGAAAGAGCTTGACCATGTTGCCCTTCAAGATGAAACACTTG
* *
1133 AAGATGATAGTAAGTGCTTTGGGTGTTGGGAACCATTAGCAAAGTATACACACTTTTCTCCGGAC
326 AAGATGATAGTAAGTGCTTTGGGTGTCGGGAACCATTAGCAAAGTATACACACTTTTCTCCTGAC
* * *
1198 TGTGGATTTAATTTACATGACAAATGCGCCGAGCTTTCTTTCAAACTGAATCTTGAGTGCCATCG
391 TGTGGATTTAATTTACATGAGAAATGCGCTGAGCTTCCTTTCAAACTGAATCTTGAGTGCCATCG
**
1263 CGAACATCCTCTTGTTCTACAATTTTATAGCGAACAACTCTCTTGCAAGATATGCTGCCAGGAAA
456 CGAACATCCTCTTGTTCTACAATTTTATAGCGAACGGCTCTCTTGCAAGATATGCTGCCAGGAAA
* * *
1328 CAAGGCGAATAGGATTTTTTTATGGTTGTTCTCCCTGTAAGTCTGTTGTTCACATTGAATGTGCA
521 CAAGGCGAATAGGATTTGTTTATGGTTGTTCTCCTTGTAAGTTTGTTGTTCACATTGAATGTGCA
1393 TCACAATCACCATTACAAGTTATTAAGAGTACAAATCATGAACATCCATTTACCTTGTTTAACGG
586 TCACAATCACCATTACAAGTTATTAAGAGTACAAATCATGAACATCCATTTACCTTGTTTAACGG
* *
1458 GCACCAACATCCCCTGTTTCTTATGTTGAATCAAGAGCAGCTGATGGATAATCAAAGGGGTGTAA
651 GCACCAACATCCCCTGTTTCTTATGTTAAATCAAGAGCAGCTGATGGACAATCAAAGGGGTGTAA
1523 CTGAT
716 CTGAT
*
1528 TGCTCGAGGTGTGGGGAGAAGGTGTCTGCTCCATGTTTTTTCTGTGCAGAGCACTGTGGGTTTTA
1 TGCTCGAGGTGTGGGGAGAAGGTGTCTGCTCCATGTTTTTGCTGTGCAGAGCACTGTGGGTTTTA
*
1593 TCTTCATAAGGTATGTGCCGAGGCACCTTTGGAGCTTAATCATCCC-TTTCATCTCAACCATCCT
66 TCTTCATAAGGTATGTGCCGAGGCACCTTTGGAGCTTAATCA-CCCTTTTCATCTCATCCATCCT
*
1657 CTTCTTATGCAAAATGCACCTTATTCATCTGGAATGTACATTTGCAATTTCTGCAATAAATCTGG
130 CTTCTTATGCAAAATGCACCTTATTCATCTGGAATGTACATTTGCAATTTTTGCAATAAATCTGG
* *
1722 TCACAAGTCTGTTTATCGCTGCTCTTCTTGTGAATTGAACTTTCATATTAAATGTGCTTTGTTTA
195 TCACAAGTCTGTTTATCGCTGCTCTACTTGTGAATTGGACTTTCATATTAAATGTGCTTTGTTTA
* *
1787 CATTTAATATTGCTGAGAATAATTTGAAAGAGCTTGAGCATGTTGCCCTTCAACATCCATTGATT
260 CATTTAATATTGCTGAGAATAATTTGAAAGAGCTTGACCATGTTGCCCTTC-A-A--GA-TGA--
** *
1852 CCCAC-TGAAAATAGTGATGAAAAACTAAAAGATGTTTCTAAGTGCTTTGGGTGCCGGGAACCAT
318 AACACTTG---A-A--GATG----A-T-----A-G----TAAGTGCTTTGGGTGTCGGGAACCAT
* * * * * * *
1916 TACCAAATTATACACACTTTTCTCCTTG-CCGTGGATTTAACTTACACGAGAAATGCACTGAGAT
362 TAGCAAAGTATACACACTTTTCTCC-TGACTGTGGATTTAATTTACATGAGAAATGCGCTGAGCT
* * * *
1980 TCCTTTCAAATTGAATCAT-ATGTGGCATCGC-AAGCATCCTCTTGTCCTACAA-TTTAGTAGCG
426 TCCTTTCAAACTGAATCTTGA-GTGCCATCGCGAA-CATCCTCTTGTTCTACAATTTTA-TAGCG
* * * *
2042 AACGGCTCTCTTGCAAGATATGCTGCCAGGTAACAAAGCGAAGAGGATTTGGTTATGGTTGTTCT
488 AACGGCTCTCTTGCAAGATATGCTGCCAGGAAACAAGGCGAATAGGATTTGTTTATGGTTGTTCT
2107 CCTTGTAAGTTTGTTGTTCACATTGAATGTGCATCACAATCACCATTACAAGTTATTAAGAGTAC
553 CCTTGTAAGTTTGTTGTTCACATTGAATGTGCATCACAATCACCATTACAAGTTATTAAGAGTAC
* *
2172 AAATCATGAACATTCATTCACCTTGTT
618 AAATCATGAACATCCATTTACCTTGTT
2199 GTTGAGACAA
Statistics
Matches: 1267, Mismatches: 86, Indels: 55
0.90 0.06 0.04
Matches are distributed among these distances:
720 480 0.38
721 5 0.00
722 9 0.01
723 366 0.29
724 2 0.00
725 8 0.01
726 107 0.08
727 3 0.00
729 1 0.00
730 1 0.00
732 4 0.00
736 1 0.00
737 1 0.00
742 1 0.00
743 1 0.00
746 7 0.01
747 269 0.21
748 1 0.00
ACGTcount: A:0.27, C:0.20, G:0.20, T:0.34
Consensus pattern (720 bp):
TGCTCGAGGTGTGGGGAGAAGGTGTCTGCTCCATGTTTTTGCTGTGCAGAGCACTGTGGGTTTTA
TCTTCATAAGGTATGTGCCGAGGCACCTTTGGAGCTTAATCACCCTTTTCATCTCATCCATCCTC
TTCTTATGCAAAATGCACCTTATTCATCTGGAATGTACATTTGCAATTTTTGCAATAAATCTGGT
CACAAGTCTGTTTATCGCTGCTCTACTTGTGAATTGGACTTTCATATTAAATGTGCTTTGTTTAC
ATTTAATATTGCTGAGAATAATTTGAAAGAGCTTGACCATGTTGCCCTTCAAGATGAAACACTTG
AAGATGATAGTAAGTGCTTTGGGTGTCGGGAACCATTAGCAAAGTATACACACTTTTCTCCTGAC
TGTGGATTTAATTTACATGAGAAATGCGCTGAGCTTCCTTTCAAACTGAATCTTGAGTGCCATCG
CGAACATCCTCTTGTTCTACAATTTTATAGCGAACGGCTCTCTTGCAAGATATGCTGCCAGGAAA
CAAGGCGAATAGGATTTGTTTATGGTTGTTCTCCTTGTAAGTTTGTTGTTCACATTGAATGTGCA
TCACAATCACCATTACAAGTTATTAAGAGTACAAATCATGAACATCCATTTACCTTGTTTAACGG
GCACCAACATCCCCTGTTTCTTATGTTAAATCAAGAGCAGCTGATGGACAATCAAAGGGGTGTAA
CTGAT
Done.