Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Cotton_A_15166
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, 756
Length: 1260
ACGTcount: A:0.32, C:0.26, G:0.18, T:0.25
Found at i:210 original size:51 final size:51
Alignment explanation
Indices: 155--778 Score: 492
Period size: 51 Copynumber: 12.4 Consensus size: 51
145 TCTGTTGATC
* * *
155 TTCAACAACAGCATCGGCCTCCTCGGGAAACTTCTAAGAGTTCCGATCGTA
1 TTCAACAACAGCATCAGCCTCCTCGGGAAACTTATAAGAGTTCCGATCATA
** * * *
206 TTCAACAACAGCATCCA-CCTCCTCTAGATATTTATCAA-AGTTCCGATCATC
1 TTCAACAACAGCAT-CAGCCTCCTCGGGAAACTTAT-AAGAGTTCCGATCATA
* * *
257 TTCAACAACAGCATCGGCCTCCTCGGGAAACTTATAAGAGCTCAGATCATA
1 TTCAACAACAGCATCAGCCTCCTCGGGAAACTTATAAGAGTTCCGATCATA
* * * *
308 TTCAACAACAGCATCCA-CCTCCTCGAGATATTTATCAA-AGTTCCGATCATC
1 TTCAACAACAGCAT-CAGCCTCCTCGGGAAACTTAT-AAGAGTTCCGATCATA
* * * **
359 TTCAACAACAGTATCAG---CCTCGAGAAACTTATAAGAGCTCAAATCATA
1 TTCAACAACAGCATCAGCCTCCTCGGGAAACTTATAAGAGTTCCGATCATA
* * * * * *
407 TTCAACAAGAGCTTC-GTCCTCCTCGAGAAAGTTATCAGAG-TCCAAATCATA
1 TTCAACAACAGCATCAG-CCTCCTCGGGAAACTTATAAGAGTTCC-GATCATA
* * * *
458 TTAAACAACAGCATCAG---CCTCGGGAAACTTCTAAGAGCTCAGATCATA
1 TTCAACAACAGCATCAGCCTCCTCGGGAAACTTATAAGAGTTCCGATCATA
* *
506 TTCAACAACAGCATCAG---CCTCGGGAAACTTATAAGAGCTCAGATCATA
1 TTCAACAACAGCATCAGCCTCCTCGGGAAACTTATAAGAGTTCCGATCATA
* * * * * *
554 TTCAACAACAGCATCAGCCTCATCGGGAGAGTTGTCAGAGTTCCGATCATCT
1 TTCAACAACAGCATCAGCCTCCTCGGGAAACTTATAAGAGTTCCGATCAT-A
* * * *
606 TCATCAACAACAGCGTCAGCCTCCTCGGGAAAGTTATCAGAGTTCCGATCATT
1 T--TCAACAACAGCATCAGCCTCCTCGGGAAACTTATAAGAGTTCCGATCATA
* ** * * * * *
659 TTCAACAACAGCAAT-ATCAGCCTCGAGAAAGTTATCAGGAG-TCGGGA-CATC
1 TTCAACAACAGC-ATCAGCCTCCTCGGGAAACTTAT-AAGAGTTC-CGATCATA
* * * * * * *
710 TTCAACAACTGCATCGGCCTCCTCTGGAAAGTTATCAGAGTTCCAATCATG
1 TTCAACAACAGCATCAGCCTCCTCGGGAAACTTATAAGAGTTCCGATCATA
*
761 TTCAACAACAGCAACAGC
1 TTCAACAACAGCATCAGC
779 TTTCGGAAAG
Statistics
Matches: 463, Mismatches: 83, Indels: 54
0.77 0.14 0.09
Matches are distributed among these distances:
47 3 0.01
48 119 0.26
49 2 0.00
50 13 0.03
51 265 0.57
52 14 0.03
53 2 0.00
54 45 0.10
ACGTcount: A:0.33, C:0.27, G:0.16, T:0.24
Consensus pattern (51 bp):
TTCAACAACAGCATCAGCCTCCTCGGGAAACTTATAAGAGTTCCGATCATA
Found at i:288 original size:102 final size:102
Alignment explanation
Indices: 112--778 Score: 574
Period size: 102 Copynumber: 6.6 Consensus size: 102
102 GAGCCAGCAG
* * * * * * *
112 CAGCATCGACCTCCTCGAGAAAGTTATCAGAGCTCTGTTGATCTTCAACAACAGCATCGGCCTCC
1 CAGCATCCACCTCCTCGAGAAAGTTATCAAAGTTCCGATCATCTTCAACAACAGCATCAGCCTCC
* * * *
177 TCGGGAAACTTCTAAGAGTTCCGATCGTATTCAACAA
66 TCGGGAAACTTATAAGAGCTCAGATCATATTCAACAA
* * * *
214 CAGCATCCACCTCCTCTAGATATTTATCAAAGTTCCGATCATCTTCAACAACAGCATCGGCCTCC
1 CAGCATCCACCTCCTCGAGAAAGTTATCAAAGTTCCGATCATCTTCAACAACAGCATCAGCCTCC
279 TCGGGAAACTTATAAGAGCTCAGATCATATTCAACAA
66 TCGGGAAACTTATAAGAGCTCAGATCATATTCAACAA
* * *
316 CAGCATCCACCTCCTCGAGATATTTATCAAAGTTCCGATCATCTTCAACAACAGTATCAG---CC
1 CAGCATCCACCTCCTCGAGAAAGTTATCAAAGTTCCGATCATCTTCAACAACAGCATCAGCCTCC
* *
378 TCGAGAAACTTATAAGAGCTCAAATCATATTCAACAA
66 TCGGGAAACTTATAAGAGCTCAGATCATATTCAACAA
* * ** * * * *
415 GAGCTTCGTCCTCCTCGAGAAAGTTATCAGAG-TCCAAATCATATTAAACAACAGCATCAG---C
1 CAGCATCCACCTCCTCGAGAAAGTTATCAAAGTTCC-GATCATCTTCAACAACAGCATCAGCCTC
*
476 CTCGGGAAACTTCTAAGAGCTCAGATCATATTCAACAA
65 CTCGGGAAACTTATAAGAGCTCAGATCATATTCAACAA
* * * * * *
514 CAGCAT-CA--GCCTCGGGAAACTTAT-AAGAGCTCAGATCATATTCAACAACAGCATCAGCCTC
1 CAGCATCCACCTCCTCGAGAAAGTTATCAA-AGTTCCGATCATCTTCAACAACAGCATCAGCCTC
* * * * * * * *
575 ATCGGGAGAGTTGTCAGAGTTCCGATCATCTTCATCAACAA
65 CTCGGGAAACTTATAAGAGCTCAGATCAT-AT--TCAACAA
* * * * * **
616 CAGCGT-CAGCCTCCTCGGGAAAGTTATCAGAGTTCCGATCATTTTCAACAACAGCAAT-ATCAG
1 CAGCATCCA-CCTCCTCGAGAAAGTTATCAAAGTTCCGATCATCTTCAACAACAGC-ATCAGCCT
* * * * *
679 CCTCGAGAAAGTTATCAGGAG-TCGGGA-CATCTTCAACAA
64 CCTCGGGAAACTTAT-AAGAGCTC-AGATCATATTCAACAA
* ** * * * *
718 CTGCATCGGCCTCCTCTG-GAAAGTTATCAGAGTTCCAATCATGTTCAACAACAGCAACAGC
1 CAGCATCCACCTCCTC-GAGAAAGTTATCAAAGTTCCGATCATCTTCAACAACAGCATCAGC
779 TTTCGGAAAG
Statistics
Matches: 469, Mismatches: 77, Indels: 38
0.80 0.13 0.07
Matches are distributed among these distances:
95 1 0.00
96 37 0.08
97 2 0.00
98 3 0.01
99 145 0.31
100 1 0.00
101 1 0.00
102 215 0.46
103 1 0.00
104 1 0.00
105 54 0.12
106 8 0.02
ACGTcount: A:0.32, C:0.27, G:0.16, T:0.24
Consensus pattern (102 bp):
CAGCATCCACCTCCTCGAGAAAGTTATCAAAGTTCCGATCATCTTCAACAACAGCATCAGCCTCC
TCGGGAAACTTATAAGAGCTCAGATCATATTCAACAA
Found at i:626 original size:54 final size:51
Alignment explanation
Indices: 112--861 Score: 434
Period size: 51 Copynumber: 14.8 Consensus size: 51
102 GAGCCAGCAG
* * * * * * *
112 CAGCATC-GACCTCCTCGAGAAAGTTATCAGAGCTCTGTTGATCTTCAACAA
1 CAGCATCAG-CCTCATCGGGAAAGTTATCAGAGTTCCGATCATTTTCAACAA
* * * * * * *
163 CAGCATCGGCCTCCTCGGGAAACTTCTAAGAGTTCCGATCGTATTCAACAA
1 CAGCATCAGCCTCATCGGGAAAGTTATCAGAGTTCCGATCATTTTCAACAA
* ** * * * *
214 CAGCATCCA-CCTCCTCTAGATATTTATCAAAGTTCCGATCATCTTCAACAA
1 CAGCAT-CAGCCTCATCGGGAAAGTTATCAGAGTTCCGATCATTTTCAACAA
* * * * * * *
265 CAGCATCGGCCTCCTCGGGAAACTTATAAGAGCTCAGATCATATTCAACAA
1 CAGCATCAGCCTCATCGGGAAAGTTATCAGAGTTCCGATCATTTTCAACAA
* * * * * *
316 CAGCATCCA-CCTCCTCGAGATATTTATCAAAGTTCCGATCATCTTCAACAA
1 CAGCAT-CAGCCTCATCGGGAAAGTTATCAGAGTTCCGATCATTTTCAACAA
* * * * * ** *
367 CAGTATCAG-C-C-TCGAGAAACTTATAAGAGCTCAAATCATATTCAACAA
1 CAGCATCAGCCTCATCGGGAAAGTTATCAGAGTTCCGATCATTTTCAACAA
* * * * * * *
415 GAGCTTC-GTCCTCCTCGAGAAAGTTATCAGAG-TCCAAATCATATTAAACAA
1 CAGCATCAG-CCTCATCGGGAAAGTTATCAGAGTTCC-GATCATTTTCAACAA
* * * * * *
466 CAGCATCAG-C-C-TCGGGAAACTTCTAAGAGCTCAGATCATATTCAACAA
1 CAGCATCAGCCTCATCGGGAAAGTTATCAGAGTTCCGATCATTTTCAACAA
* * * * *
514 CAGCATCAG-C-C-TCGGGAAACTTATAAGAGCTCAGATCATATTCAACAA
1 CAGCATCAGCCTCATCGGGAAAGTTATCAGAGTTCCGATCATTTTCAACAA
* *
562 CAGCATCAGCCTCATCGGGAGAGTTGTCAGAGTTCCGATCATCTTCATCAACAA
1 CAGCATCAGCCTCATCGGGAAAGTTATCAGAGTTCCGATCAT-TT--TCAACAA
* *
616 CAGCGTCAGCCTCCTCGGGAAAGTTATCAGAGTTCCGATCATTTTCAACAA
1 CAGCATCAGCCTCATCGGGAAAGTTATCAGAGTTCCGATCATTTTCAACAA
* * *
667 CAGCAATATCAG-C-C-TCGAGAAAGTTATCAGGAG-TCGGGA-CATCTTCAACAA
1 CAGC---ATCAGCCTCATCGGGAAAGTTATCA-GAGTTC-CGATCATTTTCAACAA
* * * * * *
718 CTGCATCGGCCTCCTCTGGAAAGTTATCAGAGTTCCAATCATGTTCAACAA
1 CAGCATCAGCCTCATCGGGAAAGTTATCAGAGTTCCGATCATTTTCAACAA
* * * * *
769 CAGCAACAG-CT-TTC-GGAAAGTTATCATCAGAGTTTCAATCATCTTCAACAGCA
1 CAGCATCAGCCTCATCGGGAAAG-T-T-ATCAGAGTTCCGATCATTTTCAACA--A
* *
822 GCAGCATGAG-C-C-TCGGGAAAGTTATCAGAGCTCCGATCAT
1 -CAGCATCAGCCTCATCGGGAAAGTTATCAGAGTTCCGATCAT
862 CTTCCTCCTC
Statistics
Matches: 565, Mismatches: 98, Indels: 72
0.77 0.13 0.10
Matches are distributed among these distances:
47 1 0.00
48 126 0.22
49 10 0.02
50 17 0.03
51 329 0.58
52 12 0.02
53 7 0.01
54 63 0.11
ACGTcount: A:0.32, C:0.27, G:0.17, T:0.24
Consensus pattern (51 bp):
CAGCATCAGCCTCATCGGGAAAGTTATCAGAGTTCCGATCATTTTCAACAA
Found at i:798 original size:102 final size:102
Alignment explanation
Indices: 308--774 Score: 312
Period size: 99 Copynumber: 4.6 Consensus size: 102
298 TCAGATCATA
* * * * * *
308 TTCAACAACAGCATCCA-CCTCCTCGAGATATTTATCAAAGTTCCGATCATCTTCAACAACAG--
1 TTCAACAACAGCAT-CAGCCTCCTCGGGAAAGTTATCAGAGTTCCAATCATGTTCAACAACAGCA
* * ** *
370 -TATCAGCCTCGAGAAACTTAT-AAGAGCTC-AAATCATA
65 ATATCAGCCTCGAGAAAGTTATCAGGAG-TCGGGA-CATC
* * * * *
407 TTCAACAAGAGCTTC-GTCCTCCTCGAGAAAGTTATCAGAG-TCCAAATCATATTAAACAACAGC
1 TTCAACAACAGCATCAG-CCTCCTCGGGAAAGTTATCAGAGTTCC-AATCATGTTCAACAACAGC
* * * * * *
470 ---ATCAGCCTCGGGAAACTTCT-AAGAGCTC-AGATCATA
64 AATATCAGCCTCGAGAAAGTTATCAGGAG-TCGGGA-CATC
* * * *
506 TTCAACAACAGCATCAG---CCTCGGGAAACTTATAAGAGCT-CAGATCATATTCAACAACAGC-
1 TTCAACAACAGCATCAGCCTCCTCGGGAAAGTTATCAGAGTTCCA-ATCATGTTCAACAACAGCA
* * * *
566 --ATCAGCCTCATCGGGAGAGTTGTCA-GAGTTC-CGATCATC
65 ATATCAG-C-C-TCGAGAAAGTTATCAGGAG-TCGGGA-CATC
* * *
605 TTCATCAACAACAGCGTCAGCCTCCTCGGGAAAGTTATCAGAGTTCCGATCATTTTCAACAACAG
1 -T--TCAACAACAGCATCAGCCTCCTCGGGAAAGTTATCAGAGTTCCAATCATGTTCAACAACAG
670 CAATATCAGCCTCGAGAAAGTTATCAGGAGTCGGGACATC
63 CAATATCAGCCTCGAGAAAGTTATCAGGAGTCGGGACATC
* * *
710 TTCAACAACTGCATCGGCCTCCTCTGGAAAGTTATCAGAGTTCCAATCATGTTCAACAACAGCAA
1 TTCAACAACAGCATCAGCCTCCTCGGGAAAGTTATCAGAGTTCCAATCATGTTCAACAACAGCAA
775 CAGCTTTCGG
Statistics
Matches: 306, Mismatches: 39, Indels: 43
0.79 0.10 0.11
Matches are distributed among these distances:
95 1 0.00
96 40 0.13
97 2 0.01
98 5 0.02
99 114 0.37
100 3 0.01
102 73 0.24
104 1 0.00
105 54 0.18
106 7 0.02
107 1 0.00
108 5 0.02
ACGTcount: A:0.34, C:0.26, G:0.16, T:0.24
Consensus pattern (102 bp):
TTCAACAACAGCATCAGCCTCCTCGGGAAAGTTATCAGAGTTCCAATCATGTTCAACAACAGCAA
TATCAGCCTCGAGAAAGTTATCAGGAGTCGGGACATC
Found at i:879 original size:36 final size:36
Alignment explanation
Indices: 832--901 Score: 104
Period size: 36 Copynumber: 1.9 Consensus size: 36
822 GCAGCATGAG
* * *
832 CCTCGGGAAAGTTATCAGAGCTCCGATCATCTTCCT
1 CCTCGAGAAAGTTATCAAAACTCCGATCATCTTCCT
*
868 CCTCGAGAAAGTTATCAAAATTCCGATCATCTTC
1 CCTCGAGAAAGTTATCAAAACTCCGATCATCTTC
902 AGCAACAGCA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 30 1.00
ACGTcount: A:0.27, C:0.29, G:0.16, T:0.29
Consensus pattern (36 bp):
CCTCGAGAAAGTTATCAAAACTCCGATCATCTTCCT
Done.