Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Cotton_A_17821
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: 2325
ACGTcount: A:0.28, C:0.18, G:0.21, T:0.32
Found at i:2096 original size:846 final size:844
Alignment explanation
Indices: 1--2322 Score: 2547
Period size: 846 Copynumber: 2.7 Consensus size: 844
* *
1 ATGGCTTCTCGGGTTTCACATTATGTTCATTTTGAAACTCCTGCAAAGCCTGATTCTCTGATTGC
1 ATGGCTTCTCGGGTTTCA-ATTATGTTCATTTTGAAACTCCTGAAAAGCCTGATTCTCTGATTAC
* **
66 TTTCCTGGAAAACCATGGGTTCTCCAATACCCAAATAGTAAATCTCATCAAAAGACAGCCACTGT
65 TTTCCTGGAAAACCATGGGTTCTCCAATACCCAAAT-GTAAATCTCAT-TAAAGACAGCCAAAGT
*
131 TGCTTGTTCTTGATGCTGAGAAATCCCTTTCGCCCAAATTAGAGTTTCTTTACTCTATAGGTTTT
128 TGCTTGTTCTTGATGCTGAGAAAACCCTTTCGCCCAAATTAGAGTTTCTTTACTCTATAGGTTTT
* * *
196 TCAAGGCCTGAGCTTGCTAAACTCTTGAGTAACTATCCTCGTCTGTTGACATCTAGTTTAGAGAA
193 TCAAGGCCTGAGCTTGCTAAACTCTTGAGTAGCTATCCTCATCTGTTGAAATCTAGTTTAGAGAA
* * * *
261 ACAAATTATCCCTTCTTTTGATTTACTTAGGAACTTGTTTCAATCTCATGATAAGACTATAAAGG
258 ACAAATTATCCCTTCATTTAATTTACTCAGGAACTTGTTTCAATCTCATGATAAGACTATCAAGG
* * * *
326 CTATAAAACGATATACCGGTGTTCTTGCCTATGATTCTGAGTCGTATTTGTATCCGAATTTGAAT
323 CTATAAAACGATATACTGGTATTCTTGTCTATGATTC-GAGTCGTATTTGTATCCGAATATGAAT
*
391 GTTTTGAGAGGAATTGGAGTCCCCGAATCGAATATCCTTGCGCTGCTTAACTGTCAGCCTAGATC
387 GTTTTGAGAGGAATTGGAGTCCCCGAATCGAATATCCTTACGCTGCTTAACTGTCAGCCTAGA--
456 GCTTTTGTTTAATCCGGTTCGGCTTAAGGAGATTGTGGAGGAAGTCAAAAGAATGGGGATTGATT
450 GCTTTTGTTTAATCCGGTTCGGCTTAAGGAGATTGTGGAGGAAGTCAAAAGAATGGGGATTGATT
* * * ** * * *
521 CTTCGAGGAAGAAGTTTCTTGTTGCGGTTTACGCTTTCAGATCAATGAGTAAATCCACATTAGAG
515 CTTCGACGAAGAAGCTTCCTCATGCGGTTT-TGCTTTGAGATCAATGAGCAAATCCACATTAGAG
* **
586 AAGAAGATTGACGTTTATAGGAGATGGGGTTGGTCTGACCAAGAGATTAACGAAGCTTTCCGGAG
579 AAGAAGATTGATGTTTATAGGAGATGGGGTTGGTCTGACCAAGAGATTAACGAAGCTTTCCAAAG
* * ** * *
651 GTATCCATTGTGTATGACGGTTTCAGAGGATAAGATCATGTTTACAATGGATTTTCTGGTGAACA
644 GTATCCATCGTGTATGACGGCTTCAGAGGATAAGATCATGGCTACAATGGACTTTCTCGTGAACA
* * **
716 AAATGGGCTACAGCTCGACTCACATTGCCAAACAACCGAGTTTCTTAACACGGAGCTTAGAGAAG
709 AAATGGGCTACAGCTCGAATCACATTGCCAAACAACCGAGATTCTTAACACAAAGCTTAGAGAAG
* * *
781 AGGATTATGCCAAGGGCATTGTTTGCTCGAGAATTGATATCACAAGGTTTGGTTAATGAATTTAA
774 AGGATTATCCCAAGGGCATTGTTTGCTCGAGAATTGATATCAC-A----TAG-TAA-GAATGTAA
* ** *
846 ATTGTCTGCATTGT
832 ATTCTCCCCA-TGA
* * * * * * * *
860 TTGAC-ACATCGGAAAAGGTGTTC-ATTAGGATGC-TTGTTG-ACCGTTTCGTAAACAAAGCACC
1 ATGGCTTC-TC-G----GGT-TTCAATTATG-TTCATT-TTGAAAC---TCCT-GA-AAAG--CC
* *** * * * * **
921 CGA-TCTCTTGA--AGCTTTACAAAGAAAAACTTAAGATT-T-CAGA-A---AAA---AAA-AAC
50 TGATTCTC-TGATTA-CTTT-CCTGGAAAACCAT-GGGTTCTCCA-ATACCCAAATGTAAATCTC
* ** * * * *
973 A-T--AGA-A-CCTACTTTGCTTCTT-TCTGATACTGAGAAAACCCTTTTGCCCAAATTGGAGTT
110 ATTAAAGACAGCCAAAGTTGCTTGTTCT-TGATGCTGAGAAAACCCTTTCGCCCAAATTAGAGTT
* * * * **
1032 TCTTTACTCTATAGGCTTTTCAAGGCCTGAGCTTGCCAAACTCTTGAGTAGCTACCCTCTTCTAC
174 TCTTTACTCTATAGGTTTTTCAAGGCCTGAGCTTGCTAAACTCTTGAGTAGCTATCCTCATCTGT
* * *
1097 TGAAATCTAGTTTAAAGAAACAAATTATCCCTTCATTTAATTTACTGAGGGACTTGTTTCAATC-
239 TGAAATCTAGTTTAGAGAAACAAATTATCCCTTCATTTAATTTACTCAGGAACTTGTTTCAATCT
* * * *
1161 CAATGATAAGACTATCAAGGCTATAAAACGATTTGCTGGAATTCTTGTGTATGA-T---G-CGTA
304 C-ATGATAAGACTATCAAGGCTATAAAACGATATACTGGTATTCTTGTCTATGATTCGAGTCGTA
* * * * * * *
1221 TGTGTTTTCGAATATAAAGGTTTTGAGAGGAATTGGAGTCCCTGAATCGAATATCCTTACGATG-
368 TTTGTATCCGAATATGAATGTTTTGAGAGGAATTGGAGTCCCCGAATCGAATATCCTTACGCTGC
* * * * ** *
1285 TTTA-T-TAATCCTCGAGCATTGTTGCGTAATCCGGTTCGGTTTAAGGAGATTGTGGAGGAAG-C
433 TTAACTGTCAGCCTAGAGC-TT-TTGTTTAATCCGGTTCGGCTTAAGGAGATTGTGGAGGAAGTC
* * * *
1347 TAAAAGAATGGGG-TTCGATTCTTTGACGAAGAAG-TTCGCCCATGTGGTTATTTCTTTGA-ATT
496 -AAAAGAATGGGGATT-GATTCTTCGACGAAGAAGCTTC-CTCATGCGGTT-TTGCTTTGAGA-T
* * * *
1409 CAATGAGCAAATCCACACTAGAGAAGAA-ATTTGATGTATATAGGAGATGGTGTTGGTCGGACCA
556 CAATGAGCAAATCCACATTAGAGAAGAAGA-TTGATGTTTATAGGAGATGGGGTTGGTCTGACCA
*** * * * *
1473 AGAGATTCGTGAAGCTTTTCAAAGGTATCCGTCGTGTATTACTGCTTCAGAGGATAAGATCATGG
620 AGAGATTAACGAAGCTTTCCAAAGGTATCCATCGTGTATGACGGCTTCAGAGGATAAGATCATGG
* * * * *
1538 CTATAATGGACTTTCTCGTGAACAAAATGGGCTATC-GTTCGAATCTCGTTGCTAAACAACCGAG
685 CTACAATGGACTTTCTCGTGAACAAAATGGGCTA-CAGCTCGAATCACATTGCCAAACAACCGAG
* ** * * * *
1602 CATT-TTGAGGCAAAGCTTTGAGAAGAGGATTGTCCCGAGGGC-TCTGTTTGCTCGAGAATTGTT
749 -ATTCTTAACACAAAGCTTAGAGAAGAGGATTATCCCAAGGGCAT-TGTTTGCTCGAGAATTGAT
***
1665 ATCAC-TAG-ACA-AATGTGGGTTCTCCCCA-GAA
812 ATCACATAGTA-AGAATGTAAATTCTCCCCATG-A
1696 ATGGCTTCTCGGGTTTCAAATTATGTTCATTTTGAAACTCCTGAAAAGCCTGATTCTCTGATTAC
1 ATGGCTTCTCGGGTTTC-AATTATGTTCATTTTGAAACTCCTGAAAAGCCTGATTCTCTGATTAC
1761 TTTCCTGGAAAACCATGGGTTCTCCAATACCCAAATCGTAAATCTCATTAGAAGACAGCCAAAGT
65 TTTCCTGGAAAACCATGGGTTCTCCAATACCCAAAT-GTAAATCTCATTA-AAGACAGCCAAAGT
1826 TGCTTGTTCTTGATGCTGAGAAAACCCTTTCGCCCAAATTAGAGTTTCTTTACTCTATAGGTTTT
128 TGCTTGTTCTTGATGCTGAGAAAACCCTTTCGCCCAAATTAGAGTTTCTTTACTCTATAGGTTTT
* *
1891 TCAAGGCCTGAGCTTGCTAAAATCTTGAGTAGCTATCCTCATCTGTTGAAATATAGTTTAGAGAA
193 TCAAGGCCTGAGCTTGCTAAACTCTTGAGTAGCTATCCTCATCTGTTGAAATCTAGTTTAGAGAA
*
1956 ACAAATTATCCCTTCATTTAATTTACTCAGGAACTTGTTTCAATCTCATGATAAGATTATCAAGG
258 ACAAATTATCCCTTCATTTAATTTACTCAGGAACTTGTTTCAATCTCATGATAAGACTATCAAGG
* *
2021 CTATAAAACGACATACTGGTATTCTTGTCTATGATTCCGAGTCGTATTTGTGTCCGAATATGAAT
323 CTATAAAACGATATACTGGTATTCTTGTCTATGATT-CGAGTCGTATTTGTATCCGAATATGAAT
* *
2086 GTTTTGAGAGGAATTGGAGTCCCCGAATCAAATATCCTTATGCTGCTTAACTGTCAGCCTAGAGC
387 GTTTTGAGAGGAATTGGAGTCCCCGAATCGAATATCCTTACGCTGCTTAACTGTCAGCCTAGA--
*
2151 GCTTTTGTTTAATCCGGTTCGGCTTAAGGAGATTGTGGAGGAAATCAAAAGAATGGGGATTGATT
450 GCTTTTGTTTAATCCGGTTCGGCTTAAGGAGATTGTGGAGGAAGTCAAAAGAATGGGGATTGATT
* *
2216 CTTCGACGAAGAAGCTT-CTCATTGCGGTTCGTGCTTTGAGATCAATGACCAAATCCACATTAGA
515 CTTCGACGAAGAAGCTTCCTCA-TGCGGTT-TTGCTTTGAGATCAATGAGCAAATCCACATTAGA
*
2280 GAAGAAGATTGATGTTTATAGGCGATGGGGTTGGTCTGACCAA
578 GAAGAAGATTGATGTTTATAGGAGATGGGGTTGGTCTGACCAA
2323 TAG
Statistics
Matches: 1188, Mismatches: 195, Indels: 170
0.76 0.13 0.11
Matches are distributed among these distances:
824 3 0.00
825 17 0.01
826 11 0.01
827 5 0.00
828 1 0.00
829 6 0.01
830 3 0.00
831 8 0.01
832 9 0.01
833 3 0.00
834 2 0.00
835 3 0.00
836 5 0.00
837 11 0.01
838 4 0.00
839 2 0.00
840 210 0.18
841 3 0.00
844 2 0.00
845 12 0.01
846 357 0.30
847 8 0.01
848 7 0.01
849 202 0.17
850 10 0.01
851 2 0.00
854 3 0.00
855 202 0.17
856 1 0.00
857 3 0.00
858 1 0.00
859 5 0.00
860 1 0.00
861 2 0.00
862 3 0.00
863 9 0.01
864 8 0.01
865 3 0.00
866 6 0.01
868 4 0.00
869 11 0.01
870 17 0.01
871 3 0.00
ACGTcount: A:0.28, C:0.18, G:0.21, T:0.32
Consensus pattern (844 bp):
ATGGCTTCTCGGGTTTCAATTATGTTCATTTTGAAACTCCTGAAAAGCCTGATTCTCTGATTACT
TTCCTGGAAAACCATGGGTTCTCCAATACCCAAATGTAAATCTCATTAAAGACAGCCAAAGTTGC
TTGTTCTTGATGCTGAGAAAACCCTTTCGCCCAAATTAGAGTTTCTTTACTCTATAGGTTTTTCA
AGGCCTGAGCTTGCTAAACTCTTGAGTAGCTATCCTCATCTGTTGAAATCTAGTTTAGAGAAACA
AATTATCCCTTCATTTAATTTACTCAGGAACTTGTTTCAATCTCATGATAAGACTATCAAGGCTA
TAAAACGATATACTGGTATTCTTGTCTATGATTCGAGTCGTATTTGTATCCGAATATGAATGTTT
TGAGAGGAATTGGAGTCCCCGAATCGAATATCCTTACGCTGCTTAACTGTCAGCCTAGAGCTTTT
GTTTAATCCGGTTCGGCTTAAGGAGATTGTGGAGGAAGTCAAAAGAATGGGGATTGATTCTTCGA
CGAAGAAGCTTCCTCATGCGGTTTTGCTTTGAGATCAATGAGCAAATCCACATTAGAGAAGAAGA
TTGATGTTTATAGGAGATGGGGTTGGTCTGACCAAGAGATTAACGAAGCTTTCCAAAGGTATCCA
TCGTGTATGACGGCTTCAGAGGATAAGATCATGGCTACAATGGACTTTCTCGTGAACAAAATGGG
CTACAGCTCGAATCACATTGCCAAACAACCGAGATTCTTAACACAAAGCTTAGAGAAGAGGATTA
TCCCAAGGGCATTGTTTGCTCGAGAATTGATATCACATAGTAAGAATGTAAATTCTCCCCATGA
Done.