Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: evm.model.Scaffold263.98
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, 979
Length: 1632
ACGTcount: A:0.33, C:0.14, G:0.30, T:0.23
Found at i:539 original size:12 final size:11
Alignment explanation
Indices: 522--599 Score: 88
Period size: 12 Copynumber: 6.8 Consensus size: 11
512 TTGGTGAAAG
522 TGATGATGA-T
1 TGATGATGATT
532 T-ATGATGAGTT
1 TGATGATGA-TT
*
543 TGGTGATGAGTT
1 TGATGATGA-TT
555 TGATGATGAATT
1 TGATGATG-ATT
567 TGATGATGAGTT
1 TGATGATGA-TT
579 TGATGATGAATT
1 TGATGATG-ATT
591 TGATGATGA
1 TGATGATGA
600 GGAGGAATTT
Statistics
Matches: 60, Mismatches: 2, Indels: 11
0.82 0.03 0.15
Matches are distributed among these distances:
9 7 0.12
10 1 0.02
11 4 0.07
12 46 0.77
13 2 0.03
ACGTcount: A:0.28, C:0.00, G:0.31, T:0.41
Consensus pattern (11 bp):
TGATGATGATT
Found at i:560 original size:24 final size:24
Alignment explanation
Indices: 522--600 Score: 119
Period size: 24 Copynumber: 3.4 Consensus size: 24
512 TTGGTGAAAG
*
522 TGATGATGA--TT-ATGATGAGTT
1 TGATGATGAGTTTGATGATGAATT
*
543 TGGTGATGAGTTTGATGATGAATT
1 TGATGATGAGTTTGATGATGAATT
567 TGATGATGAGTTTGATGATGAATT
1 TGATGATGAGTTTGATGATGAATT
591 TGATGATGAG
1 TGATGATGAG
601 GAGGAATTTG
Statistics
Matches: 52, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
21 8 0.15
23 2 0.04
24 42 0.81
ACGTcount: A:0.28, C:0.00, G:0.32, T:0.41
Consensus pattern (24 bp):
TGATGATGAGTTTGATGATGAATT
Found at i:573 original size:36 final size:34
Alignment explanation
Indices: 522--599 Score: 113
Period size: 36 Copynumber: 2.3 Consensus size: 34
512 TTGGTGAAAG
* *
522 TGATGATG-ATTATGATGAGTTTGGTGATGAGTT
1 TGATGATGAATTATGATGAGTTTGATGATGAATT
555 TGATGATGAATTTGATGATGAGTTTGATGATGAATT
1 TGATGATGAA-TT-ATGATGAGTTTGATGATGAATT
591 TGATGATGA
1 TGATGATGA
600 GGAGGAATTT
Statistics
Matches: 40, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
33 8 0.20
34 1 0.03
35 2 0.05
36 29 0.73
ACGTcount: A:0.28, C:0.00, G:0.31, T:0.41
Consensus pattern (34 bp):
TGATGATGAATTATGATGAGTTTGATGATGAATT
Found at i:620 original size:6 final size:6
Alignment explanation
Indices: 609--647 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
599 AGGAGGAATT
* * *
609 TGGTCA TGGTCA TGGTCA TGGTCA GGGACA TGGCCA TGG
1 TGGTCA TGGTCA TGGTCA TGGTCA TGGTCA TGGTCA TGG
648 GCATCAAATG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.18, C:0.18, G:0.38, T:0.26
Consensus pattern (6 bp):
TGGTCA
Found at i:1229 original size:21 final size:21
Alignment explanation
Indices: 1204--1254 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 21
1194 GAATATGGGG
*
1204 CAGATGGGTCAAATGGGTGGT
1 CAGATGGGTCAAATGGGTCGT
*
1225 CAGATGGGTCACATGGGTCGT
1 CAGATGGGTCAAATGGGTCGT
*
1246 CAAATGGGT
1 CAGATGGGT
1255 GGTCAGATGG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.24, C:0.14, G:0.39, T:0.24
Consensus pattern (21 bp):
CAGATGGGTCAAATGGGTCGT
Found at i:1231 original size:12 final size:12
Alignment explanation
Indices: 1210--1266 Score: 57
Period size: 12 Copynumber: 5.0 Consensus size: 12
1200 GGGGCAGATG
1210 GGTCAAATGGGT
1 GGTCAAATGGGT
*
1222 GGTCAGAT--G-
1 GGTCAAATGGGT
*
1231 GGTCACATGGGT
1 GGTCAAATGGGT
*
1243 CGTCAAATGGGT
1 GGTCAAATGGGT
*
1255 GGTCAGATGGGT
1 GGTCAAATGGGT
1267 TACAATATGG
Statistics
Matches: 36, Mismatches: 6, Indels: 6
0.75 0.12 0.12
Matches are distributed among these distances:
9 7 0.19
10 1 0.03
11 1 0.03
12 27 0.75
ACGTcount: A:0.21, C:0.12, G:0.42, T:0.25
Consensus pattern (12 bp):
GGTCAAATGGGT
Found at i:1286 original size:33 final size:30
Alignment explanation
Indices: 1198--1266 Score: 84
Period size: 33 Copynumber: 2.2 Consensus size: 30
1188 TGGTAAGAAT
* * *
1198 ATGGGGCAGATGGGTCAAATGGGTGGTCAG
1 ATGGGTCACATGGGCCAAATGGGTGGTCAG
1228 ATGGGTCACATGGGTCGTCAAATGGGTGGTCAG
1 ATGGGTCACATGGG-C--CAAATGGGTGGTCAG
1261 ATGGGT
1 ATGGGT
1267 TACAATATGG
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
30 12 0.36
33 21 0.64
ACGTcount: A:0.22, C:0.12, G:0.43, T:0.23
Consensus pattern (30 bp):
ATGGGTCACATGGGCCAAATGGGTGGTCAG
Done.