Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020784.1 Corchorus olitorius cultivar O-4 contig20817, whole genome shotgun sequence
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: 28022
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31
Found at i:2457 original size:22 final size:22
Alignment explanation
Indices: 2432--2476 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
2422 TGTTCCAAGA
2432 GAAAATTAAGTTATACTTTATG
1 GAAAATTAAGTTATACTTTATG
2454 GAAAATTAAGTTATACTTTATG
1 GAAAATTAAGTTATACTTTATG
2476 G
1 G
2477 GTTTATATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.40, C:0.04, G:0.16, T:0.40
Consensus pattern (22 bp):
GAAAATTAAGTTATACTTTATG
Found at i:5417 original size:3 final size:3
Alignment explanation
Indices: 5411--5459 Score: 55
Period size: 3 Copynumber: 16.3 Consensus size: 3
5401 TGTTGTTGTA
* * *
5411 GCT GCT GCT GCT GCT GTT GCT GCT GCT GTT GTT G-T GGCT GCT GCT
1 GCT GCT GCT GCT GCT GCT GCT GCT GCT GCT GCT GCT -GCT GCT GCT
5456 GCT G
1 GCT G
5460 TTGATGTTGT
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
2 1 0.02
3 39 0.95
4 1 0.02
ACGTcount: A:0.00, C:0.24, G:0.37, T:0.39
Consensus pattern (3 bp):
GCT
Found at i:5450 original size:24 final size:24
Alignment explanation
Indices: 5423--5469 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
5413 TGCTGCTGCT
* *
5423 GCTGTTGCTGCTGCTGTTGTTGTG
1 GCTGCTGCTGCTGCTGATGTTGTG
*
5447 GCTGCTGCTGCTGTTGATGTTGT
1 GCTGCTGCTGCTGCTGATGTTGT
5470 TGTGACTGCT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.02, C:0.17, G:0.36, T:0.45
Consensus pattern (24 bp):
GCTGCTGCTGCTGCTGATGTTGTG
Found at i:5458 original size:27 final size:27
Alignment explanation
Indices: 5420--5481 Score: 88
Period size: 27 Copynumber: 2.3 Consensus size: 27
5410 AGCTGCTGCT
* *
5420 GCTGCTGTTGCTGCTGCTGTTGTTGTG
1 GCTGCTGCTGCTGCTGATGTTGTTGTG
*
5447 GCTGCTGCTGCTGTTGATGTTGTTGTG
1 GCTGCTGCTGCTGCTGATGTTGTTGTG
*
5474 ACTGCTGC
1 GCTGCTGC
5482 ATTTGAGGAT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.03, C:0.19, G:0.35, T:0.42
Consensus pattern (27 bp):
GCTGCTGCTGCTGCTGATGTTGTTGTG
Found at i:5461 original size:18 final size:18
Alignment explanation
Indices: 5404--5462 Score: 82
Period size: 18 Copynumber: 3.3 Consensus size: 18
5394 TTGAGATTGT
5404 TGTTGTAGCTGCTGCTGC
1 TGTTGTAGCTGCTGCTGC
* * *
5422 TGCTGTTGCTGCTGCTGT
1 TGTTGTAGCTGCTGCTGC
*
5440 TGTTGTGGCTGCTGCTGC
1 TGTTGTAGCTGCTGCTGC
5458 TGTTG
1 TGTTG
5463 ATGTTGTTGT
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 35 1.00
ACGTcount: A:0.02, C:0.20, G:0.36, T:0.42
Consensus pattern (18 bp):
TGTTGTAGCTGCTGCTGC
Found at i:7393 original size:12 final size:12
Alignment explanation
Indices: 7376--7431 Score: 58
Period size: 12 Copynumber: 4.4 Consensus size: 12
7366 ATATGGAGAC
*
7376 TGTTGCTGTTGT
1 TGTTGCTGCTGT
*
7388 TGTTGCTGCTGC
1 TGTTGCTGCTGT
*
7400 TGCTGCTGGCTTTGT
1 TGTTGCT-GC--TGT
7415 TGTTGCTGCTGT
1 TGTTGCTGCTGT
7427 TGTTG
1 TGTTG
7432 GAGTTGGTTA
Statistics
Matches: 36, Mismatches: 5, Indels: 6
0.77 0.11 0.13
Matches are distributed among these distances:
12 24 0.67
13 2 0.06
14 2 0.06
15 8 0.22
ACGTcount: A:0.00, C:0.16, G:0.34, T:0.50
Consensus pattern (12 bp):
TGTTGCTGCTGT
Found at i:21931 original size:24 final size:24
Alignment explanation
Indices: 21887--21932 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
21877 GATTTATATT
* *
21887 CCATGCACTGTCAGTGTATAGAGG
1 CCATACACTGTCAGTGCATAGAGG
21911 CCATACACTGTCAG-GCCATAGA
1 CCATACACTGTCAGTG-CATAGA
21933 ATTATGCCAC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 1 0.05
24 18 0.95
ACGTcount: A:0.28, C:0.26, G:0.24, T:0.22
Consensus pattern (24 bp):
CCATACACTGTCAGTGCATAGAGG
Found at i:24139 original size:49 final size:49
Alignment explanation
Indices: 24075--24179 Score: 192
Period size: 49 Copynumber: 2.1 Consensus size: 49
24065 CCCATGTTGT
*
24075 AGATGAAAACATATGAATCAAAATTAAAGTGCAAACTGTTAACCCAAGA
1 AGATGAAAACATATGAATCAAAATAAAAGTGCAAACTGTTAACCCAAGA
24124 AGATGAAAACATATGAATCAAAATAAAAGTGCAAACTGTTAACCCAAGA
1 AGATGAAAACATATGAATCAAAATAAAAGTGCAAACTGTTAACCCAAGA
*
24173 AGCTGAA
1 AGATGAA
24180 GCTAACAAAA
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
49 54 1.00
ACGTcount: A:0.51, C:0.14, G:0.15, T:0.19
Consensus pattern (49 bp):
AGATGAAAACATATGAATCAAAATAAAAGTGCAAACTGTTAACCCAAGA
Done.