Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Cotton_A_32314
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: 1682
ACGTcount: A:0.34, C:0.15, G:0.29, T:0.22
Found at i:542 original size:12 final size:12
Alignment explanation
Indices: 527--580 Score: 72
Period size: 12 Copynumber: 4.5 Consensus size: 12
517 ATTGTGATTT
*
527 TGATGAGTTTGG
1 TGATGAGTTTGA
*
539 TGATGAGTTCGA
1 TGATGAGTTTGA
*
551 TGATGAATTTGA
1 TGATGAGTTTGA
*
563 TGATGAGTTCGA
1 TGATGAGTTTGA
575 TGATGA
1 TGATGA
581 TGATGATGAA
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 36 1.00
ACGTcount: A:0.26, C:0.04, G:0.33, T:0.37
Consensus pattern (12 bp):
TGATGAGTTTGA
Found at i:554 original size:24 final size:24
Alignment explanation
Indices: 527--580 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
517 ATTGTGATTT
* *
527 TGATGAGTTTGGTGATGAGTTCGA
1 TGATGAATTTGATGATGAGTTCGA
551 TGATGAATTTGATGATGAGTTCGA
1 TGATGAATTTGATGATGAGTTCGA
575 TGATGA
1 TGATGA
581 TGATGATGAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.26, C:0.04, G:0.33, T:0.37
Consensus pattern (24 bp):
TGATGAATTTGATGATGAGTTCGA
Found at i:587 original size:24 final size:24
Alignment explanation
Indices: 539--589 Score: 77
Period size: 24 Copynumber: 2.1 Consensus size: 24
529 ATGAGTTTGG
*
539 TGATGAGTTCGATGATGAATTTGA
1 TGATGAGTTCGATGATGAATATGA
563 TGATGAGTTCGATGATG-ATGATGA
1 TGATGAGTTCGATGATGAAT-ATGA
587 TGA
1 TGA
590 AGGGGAATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
23 2 0.08
24 23 0.92
ACGTcount: A:0.29, C:0.04, G:0.31, T:0.35
Consensus pattern (24 bp):
TGATGAGTTCGATGATGAATATGA
Found at i:644 original size:12 final size:12
Alignment explanation
Indices: 603--646 Score: 52
Period size: 12 Copynumber: 3.7 Consensus size: 12
593 GGAATTTGGT
*
603 CATGGTCATGGA
1 CATGGCCATGGA
* *
615 TATGGACATGGA
1 CATGGCCATGGA
*
627 CATGGCCATGGC
1 CATGGCCATGGA
639 CATGGCCA
1 CATGGCCA
647 CCAAATGCAA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
12 27 1.00
ACGTcount: A:0.25, C:0.23, G:0.32, T:0.20
Consensus pattern (12 bp):
CATGGCCATGGA
Found at i:1186 original size:6 final size:6
Alignment explanation
Indices: 1172--1218 Score: 85
Period size: 6 Copynumber: 7.8 Consensus size: 6
1162 GTGGGGGAGG
*
1172 TGGTAC TGGTGC TGGTGC TGGTGC TGGTGC TGGTGC TGGTGC TGGTG
1 TGGTGC TGGTGC TGGTGC TGGTGC TGGTGC TGGTGC TGGTGC TGGTG
1219 GCAGTAAGAA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
6 40 1.00
ACGTcount: A:0.02, C:0.15, G:0.49, T:0.34
Consensus pattern (6 bp):
TGGTGC
Found at i:1265 original size:12 final size:12
Alignment explanation
Indices: 1263--1298 Score: 63
Period size: 12 Copynumber: 3.0 Consensus size: 12
1253 TCGTCAGATG
*
1263 GGTCAAATGGGT
1 GGTCAGATGGGT
1275 GGTCAGATGGGT
1 GGTCAGATGGGT
1287 GGTCAGATGGGT
1 GGTCAGATGGGT
1299 TACAATATGG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.19, C:0.08, G:0.47, T:0.25
Consensus pattern (12 bp):
GGTCAGATGGGT
Found at i:1286 original size:21 final size:21
Alignment explanation
Indices: 1236--1286 Score: 84
Period size: 21 Copynumber: 2.4 Consensus size: 21
1226 GAATATGGGG
*
1236 CAGATGGGCCAAATGGGTCGT
1 CAGATGGGTCAAATGGGTCGT
*
1257 CAGATGGGTCAAATGGGTGGT
1 CAGATGGGTCAAATGGGTCGT
1278 CAGATGGGT
1 CAGATGGGT
1287 GGTCAGATGG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.24, C:0.14, G:0.41, T:0.22
Consensus pattern (21 bp):
CAGATGGGTCAAATGGGTCGT
Found at i:1312 original size:33 final size:32
Alignment explanation
Indices: 1239--1318 Score: 88
Period size: 33 Copynumber: 2.4 Consensus size: 32
1229 TATGGGGCAG
*
1239 ATGGGCCAAATGGGTCGTCAGATGGGTCAAAT
1 ATGGGTCAAATGGGTCGTCAGATGGGTCAAAT
** * * *
1271 GGGTGGTCAGATGGGTGGTCAGATGGGTTACAAT
1 ATG-GGTCAAATGGGTCGTCAGATGGGTCA-AAT
1305 ATGGGTCAAATGGG
1 ATGGGTCAAATGGG
1319 CCAAATGGGG
Statistics
Matches: 37, Mismatches: 9, Indels: 3
0.76 0.18 0.06
Matches are distributed among these distances:
32 1 0.03
33 32 0.86
34 4 0.11
ACGTcount: A:0.25, C:0.11, G:0.40, T:0.24
Consensus pattern (32 bp):
ATGGGTCAAATGGGTCGTCAGATGGGTCAAAT
Done.