Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Cotton_D_gene_10010133
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, 810
Length: 1350
ACGTcount: A:0.22, C:0.37, G:0.17, T:0.24
Found at i:163 original size:15 final size:15
Alignment explanation
Indices: 118--218 Score: 80
Period size: 15 Copynumber: 6.7 Consensus size: 15
108 CCATGTAAAA
*
118 CCACCAGTTACAGTC
1 CCACCAGTGACAGTC
* * * *
133 CCTCCGGTCACTGTC
1 CCACCAGTGACAGTC
148 CCACCAGTGACAGTC
1 CCACCAGTGACAGTC
163 CCACCAGTGACAGTC
1 CCACCAGTGACAGTC
* * **
178 CCTCCAATAGTA-A-AA
1 CCACCAGT-G-ACAGTC
*
193 CCACCAGTTACAGTC
1 CCACCAGTGACAGTC
208 CCACCAGTGAC
1 CCACCAGTGAC
219 TGTTCCTCCT
Statistics
Matches: 64, Mismatches: 18, Indels: 8
0.71 0.20 0.09
Matches are distributed among these distances:
13 1 0.02
14 1 0.02
15 59 0.92
16 2 0.03
17 1 0.02
ACGTcount: A:0.27, C:0.40, G:0.16, T:0.18
Consensus pattern (15 bp):
CCACCAGTGACAGTC
Found at i:276 original size:72 final size:72
Alignment explanation
Indices: 114--376 Score: 271
Period size: 72 Copynumber: 3.6 Consensus size: 72
104 CAATCCATGT
* * * * *
114 AAAACCACCAGTTACAGTCCCTCCGGTCACTGTCCCACCAGTGACAGTCCCACCAG-TGACAGTC
1 AAAACCACCAGTTACAGTCCCACCAGTGACTGTCCCTCCAGTGA-AG--CCACCAGTTGA-ACTC
* *
178 CCTCCAATAGT
62 CCTCCAATTGC
* *
189 AAAACCACCAGTTACAGTCCCACCAGTGACTGTTCCTCCTGTGAAGCCACCAGTTGAACTCCCTC
1 AAAACCACCAGTTACAGTCCCACCAGTGACTGTCCCTCCAGTGAAGCCACCAGTTGAACTCCCTC
*
254 CGATTGC
66 CAATTGC
* * * * *
261 AAAACCACCCA-TTACAGTCCCACCAGTGACTGTTCCTCCTGTAAAGCCACCTGTTGATCTCCCT
1 AAAACCA-CCAGTTACAGTCCCACCAGTGACTGTCCCTCCAGTGAAGCCACCAGTTGAACTCCCT
325 CCAATTGC
65 CCAATTGC
* * * * *
333 TAAGCCACCCA-TTACGGTTCCACCAGTGACAGTCCCTCCAGTGA
1 AAAACCA-CCAGTTACAGTCCCACCAGTGACTGTCCCTCCAGTGA
377 CTGTTCCTCC
Statistics
Matches: 164, Mismatches: 22, Indels: 7
0.85 0.11 0.04
Matches are distributed among these distances:
72 118 0.72
73 6 0.04
74 2 0.01
75 38 0.23
ACGTcount: A:0.25, C:0.37, G:0.16, T:0.22
Consensus pattern (72 bp):
AAAACCACCAGTTACAGTCCCACCAGTGACTGTCCCTCCAGTGAAGCCACCAGTTGAACTCCCTC
CAATTGC
Found at i:285 original size:87 final size:85
Alignment explanation
Indices: 193--463 Score: 253
Period size: 87 Copynumber: 3.3 Consensus size: 85
183 AATAGTAAAA
* * *
193 CCACCAGTTACAGTCCCACCAGTGACTGTTCCTCCTGTGAAGCCACCAGTTGAACTCCCTCCGAT
1 CCACCAGTGACAGTCCCTCCAGTGACTGTTCCTCCTGT-AAGCCACCAGTTG-ACTCCCTCCAAT
* *
258 TGCAAAACCACCCATTACAGTC
64 TGCAAAGCCACCCATTACAGTT
* * * ** * *
280 CCACCAGTGACTGTTCCTCCTGT-AAAG--CCACCTGT-TG-----A--T--CTCCCTCCAATTG
1 CCACCAGTGACAGTCCCTCCAGTGACTGTTCCTCCTGTAAGCCACCAGTTGACTCCCTCCAATTG
* *
332 CTAAGCCACCCATTACGGTT
66 CAAAGCCACCCATTACAGTT
*
352 CCACCAGTGACAGTCCCTCCAGTGACTGTTCCTCCTGTAAAGCCACCTGTTGATCTCCCTCCAAT
1 CCACCAGTGACAGTCCCTCCAGTGACTGTTCCTCCTGT-AAGCCACCAGTTGA-CTCCCTCCAAT
417 TGCAAAGCCACCCATTACAGTT
64 TGCAAAGCCACCCATTACAGTT
* * *
439 CCACCAGTGACTGTTCCTCCTGTGA
1 CCACCAGTGACAGTCCCTCCAGTGA
464 AGCCACCAGT
Statistics
Matches: 142, Mismatches: 27, Indels: 30
0.71 0.14 0.15
Matches are distributed among these distances:
72 48 0.34
73 2 0.01
75 8 0.06
77 2 0.01
82 1 0.01
84 8 0.06
86 2 0.01
87 71 0.50
ACGTcount: A:0.23, C:0.37, G:0.15, T:0.25
Consensus pattern (85 bp):
CCACCAGTGACAGTCCCTCCAGTGACTGTTCCTCCTGTAAGCCACCAGTTGACTCCCTCCAATTG
CAAAGCCACCCATTACAGTT
Found at i:491 original size:42 final size:42
Alignment explanation
Indices: 445--569 Score: 241
Period size: 42 Copynumber: 3.0 Consensus size: 42
435 AGTTCCACCA
445 GTGACTGTTCCTCCTGTGAAGCCACCAGTTGATCTCCCTCCG
1 GTGACTGTTCCTCCTGTGAAGCCACCAGTTGATCTCCCTCCG
487 GTGACTGTTCCTCCTGTGAAGCCACCAGTTGATCTCCCTCCG
1 GTGACTGTTCCTCCTGTGAAGCCACCAGTTGATCTCCCTCCG
*
529 GTGACTGTTCCTCCTGTGAAGCCACCAGTTGAGCTCCCTCC
1 GTGACTGTTCCTCCTGTGAAGCCACCAGTTGATCTCCCTCC
570 AATTGCAAAG
Statistics
Matches: 82, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
42 82 1.00
ACGTcount: A:0.14, C:0.36, G:0.22, T:0.28
Consensus pattern (42 bp):
GTGACTGTTCCTCCTGTGAAGCCACCAGTTGATCTCCCTCCG
Found at i:622 original size:72 final size:72
Alignment explanation
Indices: 529--677 Score: 244
Period size: 72 Copynumber: 2.1 Consensus size: 72
519 TCTCCCTCCG
* * * *
529 GTGACTGTTCCTCCTGTGAAGCCACCAGTTGAGCTCCCTCCAATTGCAAAGCCACCCATTACAGT
1 GTGACTGTTCCTCCTGTGAAGCCACCAGTTGACCTCCCCCCAATTGCAAAACCACCCATCACAGT
594 CCCACCA
66 CCCACCA
*
601 GTGACTGTTCCTCCTGTGAAGCCACCAGTTGACCTCCCCCCAATTGCAAAACCGCCCATCACAGT
1 GTGACTGTTCCTCCTGTGAAGCCACCAGTTGACCTCCCCCCAATTGCAAAACCACCCATCACAGT
*
666 CCCTCCA
66 CCCACCA
673 GTGAC
1 GTGAC
678 CCTCCCAGTC
Statistics
Matches: 71, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
72 71 1.00
ACGTcount: A:0.23, C:0.39, G:0.17, T:0.21
Consensus pattern (72 bp):
GTGACTGTTCCTCCTGTGAAGCCACCAGTTGACCTCCCCCCAATTGCAAAACCACCCATCACAGT
CCCACCA
Found at i:705 original size:15 final size:15
Alignment explanation
Indices: 685--722 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
675 GACCCTCCCA
*
685 GTCCCTCCAGTTACT
1 GTCCCTCCAGTGACT
700 GTCCCTCCAGTGACT
1 GTCCCTCCAGTGACT
*
715 GTTCCTCC
1 GTCCCTCC
723 TGTAAAGCCA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.11, C:0.42, G:0.16, T:0.32
Consensus pattern (15 bp):
GTCCCTCCAGTGACT
Found at i:733 original size:180 final size:180
Alignment explanation
Indices: 521--965 Score: 782
Period size: 180 Copynumber: 2.5 Consensus size: 180
511 CCAGTTGATC
* * * *
521 TCCCTCCGGTGACTGTTCCTCCTGTGAAGCCACCAGTTGAGCTCCCTCCAATTGCAAAGCCACCC
1 TCCCTCCAGTGACTGTTCCTCCTGTAAAGCCACCAGTTGACCTCCCTCCAATTGCAAAACCACCC
*
586 ATTACAGTCCCACCAGTGACTGTTCCTCCTGTGAAGCCACCAGTTGACCTCCCCCCAATTGCAAA
66 ATCACAGTCCCACCAGTGACTGTTCCTCCTGTGAAGCCACCAGTTGACCTCCCCCCAATTGCAAA
* *
651 ACCGCCCATCACAGTCCCTCCAGTGACCCTCCCAGTCCCTCCAGTTACTG
131 ACCACCCATCACAGTCCCTCCAGTGACACTCCCAGTCCCTCCAGTTACTG
701 TCCCTCCAGTGACTGTTCCTCCTGTAAAGCCACCAGTTGACCTCCCTCCAATTGCAAAACCACCC
1 TCCCTCCAGTGACTGTTCCTCCTGTAAAGCCACCAGTTGACCTCCCTCCAATTGCAAAACCACCC
* *
766 ATCACAGTCCCACCAGTGACTGTTCCTCCTGTGAAGCCACCAGTTGACCTCCCTCCAATTGCGAA
66 ATCACAGTCCCACCAGTGACTGTTCCTCCTGTGAAGCCACCAGTTGACCTCCCCCCAATTGCAAA
* *
831 ACCACCCATCACAGTCCCTCCGGTGACAGTCCCAGTCCCTCCAGTTACTG
131 ACCACCCATCACAGTCCCTCCAGTGACACTCCCAGTCCCTCCAGTTACTG
*
881 TCCCTCCAGTGACTGTTCCTCCCGTAAAGCCACCAGTTGACCTCCCTCCAATTGCAAAACCACCC
1 TCCCTCCAGTGACTGTTCCTCCTGTAAAGCCACCAGTTGACCTCCCTCCAATTGCAAAACCACCC
946 ATCACAGTCCCACCAGTGAC
66 ATCACAGTCCCACCAGTGAC
966 CGTCCCAGTC
Statistics
Matches: 253, Mismatches: 12, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
180 253 1.00
ACGTcount: A:0.22, C:0.41, G:0.15, T:0.22
Consensus pattern (180 bp):
TCCCTCCAGTGACTGTTCCTCCTGTAAAGCCACCAGTTGACCTCCCTCCAATTGCAAAACCACCC
ATCACAGTCCCACCAGTGACTGTTCCTCCTGTGAAGCCACCAGTTGACCTCCCCCCAATTGCAAA
ACCACCCATCACAGTCCCTCCAGTGACACTCCCAGTCCCTCCAGTTACTG
Found at i:738 original size:108 final size:108
Alignment explanation
Indices: 587--785 Score: 344
Period size: 108 Copynumber: 1.8 Consensus size: 108
577 AAGCCACCCA
*
587 TTACAGTCCCACCAGTGACTGTTCCTCCTGTGAAGCCACCAGTTGACCTCCCCCCAATTGCAAAA
1 TTACAGTCCCACCAGTGACTGTTCCTCCTGTAAAGCCACCAGTTGACCTCCCCCCAATTGCAAAA
* *
652 CCGCCCATCACAGTCCCTCCAGTGACCCTCCCAGTCCCTCCAG
66 CCACCCATCACAGTCCCACCAGTGACCCTCCCAGTCCCTCCAG
* * *
695 TTACTGTCCCTCCAGTGACTGTTCCTCCTGTAAAGCCACCAGTTGACCTCCCTCCAATTGCAAAA
1 TTACAGTCCCACCAGTGACTGTTCCTCCTGTAAAGCCACCAGTTGACCTCCCCCCAATTGCAAAA
760 CCACCCATCACAGTCCCACCAGTGAC
66 CCACCCATCACAGTCCCACCAGTGAC
786 TGTTCCTCCT
Statistics
Matches: 85, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
108 85 1.00
ACGTcount: A:0.23, C:0.42, G:0.14, T:0.22
Consensus pattern (108 bp):
TTACAGTCCCACCAGTGACTGTTCCTCCTGTAAAGCCACCAGTTGACCTCCCCCCAATTGCAAAA
CCACCCATCACAGTCCCACCAGTGACCCTCCCAGTCCCTCCAG
Found at i:786 original size:72 final size:72
Alignment explanation
Indices: 700--857 Score: 280
Period size: 72 Copynumber: 2.2 Consensus size: 72
690 TCCAGTTACT
700 GTCCCTCCAGTGACTGTTCCTCCTGTAAAGCCACCAGTTGACCTCCCTCCAATTGCAAAACCACC
1 GTCCCTCCAGTGACTGTTCCTCCTGTAAAGCCACCAGTTGACCTCCCTCCAATTGCAAAACCACC
765 CATCACA
66 CATCACA
* * *
772 GTCCCACCAGTGACTGTTCCTCCTGTGAAGCCACCAGTTGACCTCCCTCCAATTGCGAAACCACC
1 GTCCCTCCAGTGACTGTTCCTCCTGTAAAGCCACCAGTTGACCTCCCTCCAATTGCAAAACCACC
837 CATCACA
66 CATCACA
*
844 GTCCCTCCGGTGAC
1 GTCCCTCCAGTGAC
858 AGTCCCAGTC
Statistics
Matches: 81, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
72 81 1.00
ACGTcount: A:0.23, C:0.41, G:0.15, T:0.22
Consensus pattern (72 bp):
GTCCCTCCAGTGACTGTTCCTCCTGTAAAGCCACCAGTTGACCTCCCTCCAATTGCAAAACCACC
CATCACA
Found at i:883 original size:21 final size:21
Alignment explanation
Indices: 842--884 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
832 CCACCCATCA
*
842 CAGTCCCTCCGGTGACAGTCC
1 CAGTCCCTCCAGTGACAGTCC
* *
863 CAGTCCCTCCAGTTACTGTCC
1 CAGTCCCTCCAGTGACAGTCC
884 C
1 C
885 TCCAGTGACT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.14, C:0.44, G:0.19, T:0.23
Consensus pattern (21 bp):
CAGTCCCTCCAGTGACAGTCC
Found at i:891 original size:108 final size:108
Alignment explanation
Indices: 772--1000 Score: 359
Period size: 108 Copynumber: 2.1 Consensus size: 108
762 ACCCATCACA
* * * *
772 GTCCCACCAGTGACTGTTCCTCCTGTGAAGCCACCAGTTGACCTCCCTCCAATTGCGAAACCACC
1 GTCCCTCCAGTGACTGTTCCTCCCGTAAAGCCACCAGTTGACCTCCCTCCAATTGCAAAACCACC
* * * *
837 CATCACAGTCCCTCCGGTGACAGTCCCAGTCCCTCCAGTTACT
66 CATCACAGTCCCACCAGTGACAGTCCCAGTCCCACCAGTGACT
880 GTCCCTCCAGTGACTGTTCCTCCCGTAAAGCCACCAGTTGACCTCCCTCCAATTGCAAAACCACC
1 GTCCCTCCAGTGACTGTTCCTCCCGTAAAGCCACCAGTTGACCTCCCTCCAATTGCAAAACCACC
*
945 CATCACAGTCCCACCAGTGACCGTCCCAGTCCCACCAGTGACT
66 CATCACAGTCCCACCAGTGACAGTCCCAGTCCCACCAGTGACT
* *
988 GTTCCTCCTGTGA
1 GTCCCTCCAGTGA
1001 AACCACCTAT
Statistics
Matches: 110, Mismatches: 11, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
108 110 1.00
ACGTcount: A:0.21, C:0.41, G:0.16, T:0.22
Consensus pattern (108 bp):
GTCCCTCCAGTGACTGTTCCTCCCGTAAAGCCACCAGTTGACCTCCCTCCAATTGCAAAACCACC
CATCACAGTCCCACCAGTGACAGTCCCAGTCCCACCAGTGACT
Found at i:895 original size:15 final size:15
Alignment explanation
Indices: 865--902 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
855 GACAGTCCCA
*
865 GTCCCTCCAGTTACT
1 GTCCCTCCAGTGACT
880 GTCCCTCCAGTGACT
1 GTCCCTCCAGTGACT
*
895 GTTCCTCC
1 GTCCCTCC
903 CGTAAAGCCA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.11, C:0.42, G:0.16, T:0.32
Consensus pattern (15 bp):
GTCCCTCCAGTGACT
Done.