Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Cotton_A_28898
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, 629
Length: 1049
ACGTcount: A:0.23, C:0.36, G:0.16, T:0.24
Found at i:276 original size:72 final size:72
Alignment explanation
Indices: 187--380 Score: 217
Period size: 72 Copynumber: 2.8 Consensus size: 72
177 GGTCACTGTC
* *
187 CCACCAGTGACAGTCCCTCCAATAGTAAAACCA-CCAGTTACAGTCCCACCAGTGACTGTTCCTC
1 CCACCAGTGACACTCCCTCCAATAGCAAAACCACCCA-TTACAGTCCCACCAGTGACTGTTCCTC
251 CTGTGAAG
65 CTGTGAAG
* *
259 CCACCAGTTGA-ACTCCCTCCGATTGCAAAACCACCCATTACAGTCCCACCAGTGACTGTTCCTC
1 CCACCAG-TGACACTCCCTCCAATAGCAAAACCACCCATTACAGTCCCACCAGTGACTGTTCCTC
323 C--T----
65 CTGTGAAG
* * * * *
325 CCACCAGTTGAC-CTCCCTCCAATTGCAAAACCGCCCATCACAGTTCCTCCAGTGAC
1 CCACCAG-TGACACTCCCTCCAATAGCAAAACCACCCATTACAGTCCCACCAGTGAC
381 CCTCCCAGTC
Statistics
Matches: 110, Mismatches: 9, Indels: 12
0.84 0.07 0.09
Matches are distributed among these distances:
66 50 0.45
70 1 0.01
72 53 0.48
73 6 0.05
ACGTcount: A:0.26, C:0.39, G:0.14, T:0.21
Consensus pattern (72 bp):
CCACCAGTGACACTCCCTCCAATAGCAAAACCACCCATTACAGTCCCACCAGTGACTGTTCCTCC
TGTGAAG
Found at i:399 original size:66 final size:66
Alignment explanation
Indices: 259--386 Score: 175
Period size: 66 Copynumber: 1.9 Consensus size: 66
249 TCCTGTGAAG
* * ** *
259 CCACCAGTTGAACTCCCTCCGATTGCAAAACCACCCATTACAGTCCCACCAGTGACTGTTCCTCC
1 CCACCAGTTGAACTCCCTCCAATTGCAAAACCACCCATCACAGTCCCACCAGTGACCCTCCCTCC
324 T
66 T
* * * *
325 CCACCAGTTGACCTCCCTCCAATTGCAAAACCGCCCATCACAGTTCCTCCAGTGACCCTCCC
1 CCACCAGTTGAACTCCCTCCAATTGCAAAACCACCCATCACAGTCCCACCAGTGACCCTCCC
387 AGTCCCTCCA
Statistics
Matches: 53, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
66 53 1.00
ACGTcount: A:0.23, C:0.44, G:0.12, T:0.21
Consensus pattern (66 bp):
CCACCAGTTGAACTCCCTCCAATTGCAAAACCACCCATCACAGTCCCACCAGTGACCCTCCCTCC
T
Found at i:408 original size:15 final size:15
Alignment explanation
Indices: 388--425 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
378 GACCCTCCCA
*
388 GTCCCTCCAGTTACT
1 GTCCCTCCAGTGACT
403 GTCCCTCCAGTGACT
1 GTCCCTCCAGTGACT
*
418 GTTCCTCC
1 GTCCCTCC
426 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:485 original size:72 final size:72
Alignment explanation
Indices: 403--560 Score: 289
Period size: 72 Copynumber: 2.2 Consensus size: 72
393 TCCAGTTACT
403 GTCCCTCCAGTGACTGTTCCTCCTGTAAAGCCACCAGTTGACCTCCCTCCAATTGCAAAACCACC
1 GTCCCTCCAGTGACTGTTCCTCCTGTAAAGCCACCAGTTGACCTCCCTCCAATTGCAAAACCACC
*
468 CATCACA
66 AATCACA
* *
475 GTCCCACCAGTGACTGTTCCTCCTGTGAAGCCACCAGTTGACCTCCCTCCAATTGCAAAACCACC
1 GTCCCTCCAGTGACTGTTCCTCCTGTAAAGCCACCAGTTGACCTCCCTCCAATTGCAAAACCACC
540 AATCACA
66 AATCACA
547 GTCCCTCCAGTGAC
1 GTCCCTCCAGTGAC
561 CGTCCCAGTC
Statistics
Matches: 82, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
72 82 1.00
ACGTcount: A:0.25, C:0.40, G:0.14, T:0.22
Consensus pattern (72 bp):
GTCCCTCCAGTGACTGTTCCTCCTGTAAAGCCACCAGTTGACCTCCCTCCAATTGCAAAACCACC
AATCACA
Found at i:571 original size:21 final size:21
Alignment explanation
Indices: 545--587 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
535 CCACCAATCA
*
545 CAGTCCCTCCAGTGACCGTCC
1 CAGTCCCTCCAGTAACCGTCC
*
566 CAGTCCCTCCAGTAACTGTCC
1 CAGTCCCTCCAGTAACCGTCC
587 C
1 C
588 TCCAGTGACT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.16, C:0.47, G:0.16, T:0.21
Consensus pattern (21 bp):
CAGTCCCTCCAGTAACCGTCC
Found at i:588 original size:15 final size:15
Alignment explanation
Indices: 568--610 Score: 59
Period size: 15 Copynumber: 2.9 Consensus size: 15
558 GACCGTCCCA
568 GTCCCTCCAGTAACT
1 GTCCCTCCAGTAACT
*
583 GTCCCTCCAGTGACT
1 GTCCCTCCAGTAACT
* *
598 GTTCCTCCCGTAA
1 GTCCCTCCAGTAA
611 AACCACCAGT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.16, C:0.40, G:0.16, T:0.28
Consensus pattern (15 bp):
GTCCCTCCAGTAACT
Found at i:594 original size:108 final size:108
Alignment explanation
Indices: 475--703 Score: 368
Period size: 108 Copynumber: 2.1 Consensus size: 108
465 ACCCATCACA
* * * *
475 GTCCCACCAGTGACTGTTCCTCCTGTGAAGCCACCAGTTGACCTCCCTCCAATTGCAAAACCACC
1 GTCCCTCCAGTGACTGTTCCTCCCGTAAAACCACCAGTTGACCTCCCTCCAATTGCAAAACCACC
* *
540 AATCACAGTCCCTCCAGTGACCGTCCCAGTCCCTCCAGTAACT
66 AATCACAGTCCCACCAGTGACCGTCCCAGTCCCACCAGTAACT
583 GTCCCTCCAGTGACTGTTCCTCCCGTAAAACCACCAGTTGACCTCCCTCCAATTGCAAAACCACC
1 GTCCCTCCAGTGACTGTTCCTCCCGTAAAACCACCAGTTGACCTCCCTCCAATTGCAAAACCACC
* *
648 CATCACAGTCCCACCAGTGACCGTCCCAGTCCCACCAGTGACT
66 AATCACAGTCCCACCAGTGACCGTCCCAGTCCCACCAGTAACT
* *
691 GTTCCTCCTGTGA
1 GTCCCTCCAGTGA
704 AACCACCTAT
Statistics
Matches: 111, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
108 111 1.00
ACGTcount: A:0.23, C:0.41, G:0.15, T:0.21
Consensus pattern (108 bp):
GTCCCTCCAGTGACTGTTCCTCCCGTAAAACCACCAGTTGACCTCCCTCCAATTGCAAAACCACC
AATCACAGTCCCACCAGTGACCGTCCCAGTCCCACCAGTAACT
Found at i:597 original size:180 final size:174
Alignment explanation
Indices: 220--668 Score: 727
Period size: 180 Copynumber: 2.5 Consensus size: 174
210 AGTAAAACCA
* * * * *
220 CCAGTTACAGTCCCACCAGTGACTGTTCCTCCTGTGAAGCCACCAGTTGAACTCCCTCCGATTGC
1 CCAGTTACTGTCCCTCCAGTGACTGTTCCTCCTGTAAAGCCACCAGTTGACCTCCCTCCAATTGC
*
285 AAAACCACCCATTACAGTCCCACCAGTGACTGTTCCTCCTCCACCAGTTGACCTCCCTCCAATTG
66 AAAACCACCCATCACAGTCCCACCAGTGACTGTTCCTCCTCCACCAGTTGACCTCCCTCCAATTG
* * *
350 CAAAACCGCCCATCACAGTTCCTCCAGTGACCCTCCCAGTCCCT
131 CAAAACCACCAATCACAGTCCCTCCAGTGACCCTCCCAGTCCCT
394 CCAGTTACTGTCCCTCCAGTGACTGTTCCTCCTGTAAAGCCACCAGTTGACCTCCCTCCAATTGC
1 CCAGTTACTGTCCCTCCAGTGACTGTTCCTCCTGTAAAGCCACCAGTTGACCTCCCTCCAATTGC
459 AAAACCACCCATCACAGTCCCACCAGTGACTGTTCCTCCTGTGAAGCCACCAGTTGACCTCCCTC
66 AAAACCACCCATCACAGTCCCACCAGTGACTGTTCCTCC--T----CCACCAGTTGACCTCCCTC
*
524 CAATTGCAAAACCACCAATCACAGTCCCTCCAGTGACCGTCCCAGTCCCT
125 CAATTGCAAAACCACCAATCACAGTCCCTCCAGTGACCCTCCCAGTCCCT
* * *
574 CCAGTAACTGTCCCTCCAGTGACTGTTCCTCCCGTAAAACCACCAGTTGACCTCCCTCCAATTGC
1 CCAGTTACTGTCCCTCCAGTGACTGTTCCTCCTGTAAAGCCACCAGTTGACCTCCCTCCAATTGC
639 AAAACCACCCATCACAGTCCCACCAGTGAC
66 AAAACCACCCATCACAGTCCCACCAGTGAC
669 CGTCCCAGTC
Statistics
Matches: 256, Mismatches: 13, Indels: 6
0.93 0.05 0.02
Matches are distributed among these distances:
174 98 0.38
176 1 0.00
180 157 0.61
ACGTcount: A:0.24, C:0.41, G:0.14, T:0.22
Consensus pattern (174 bp):
CCAGTTACTGTCCCTCCAGTGACTGTTCCTCCTGTAAAGCCACCAGTTGACCTCCCTCCAATTGC
AAAACCACCCATCACAGTCCCACCAGTGACTGTTCCTCCTCCACCAGTTGACCTCCCTCCAATTG
CAAAACCACCAATCACAGTCCCTCCAGTGACCCTCCCAGTCCCT
Done.