Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022648.1 Corchorus olitorius cultivar O-4 contig22681, 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: 19442
ACGTcount: A:0.30, C:0.19, G:0.17, T:0.34
Found at i:2666 original size:15 final size:15
Alignment explanation
Indices: 2632--2666 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
2622 GCTGAAATGG
*
2632 CATGCATGGAAAAGC
1 CATGGATGGAAAAGC
2647 CATGGATGGAAAAGC
1 CATGGATGGAAAAGC
2662 CATGG
1 CATGG
2667 GTTGGTATGG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.37, C:0.17, G:0.31, T:0.14
Consensus pattern (15 bp):
CATGGATGGAAAAGC
Found at i:4206 original size:13 final size:13
Alignment explanation
Indices: 4173--4225 Score: 60
Period size: 12 Copynumber: 4.4 Consensus size: 13
4163 GCACCCAAAA
*
4173 CATTTAT-TAAAA
1 CATTTATATAAAG
4185 CATTT-TATAAAG
1 CATTTATATAAAG
4197 CATTTATATAAAG
1 CATTTATATAAAG
*
4210 CAGTTATA-AAA-
1 CATTTATATAAAG
4221 CATTT
1 CATTT
4226 CCTCAACGGG
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
11 5 0.14
12 17 0.47
13 14 0.39
ACGTcount: A:0.45, C:0.09, G:0.06, T:0.40
Consensus pattern (13 bp):
CATTTATATAAAG
Found at i:4653 original size:27 final size:28
Alignment explanation
Indices: 4623--4686 Score: 85
Period size: 28 Copynumber: 2.3 Consensus size: 28
4613 TCTGACGTTT
* *
4623 AAGGGCAAAATTGTAA-TTTAGTCAACC
1 AAGGGCAAAATGGTAATTTTAGCCAACC
* *
4650 AAGGGTAAAATGGTAATTTTAGCCGACC
1 AAGGGCAAAATGGTAATTTTAGCCAACC
4678 AAGGGCAAA
1 AAGGGCAAA
4687 TACGTAATTC
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
27 14 0.45
28 17 0.55
ACGTcount: A:0.41, C:0.14, G:0.23, T:0.22
Consensus pattern (28 bp):
AAGGGCAAAATGGTAATTTTAGCCAACC
Found at i:4687 original size:27 final size:26
Alignment explanation
Indices: 4623--4687 Score: 67
Period size: 27 Copynumber: 2.4 Consensus size: 26
4613 TCTGACGTTT
* *
4623 AAGGGCAAAATTGTAATTTAGTCAACC
1 AAGGGC-AAATGGTAATTTAGCCAACC
* *
4650 AAGGGTAAAATGGTAATTTTAGCCGACC
1 AAGGG-CAAATGGTAA-TTTAGCCAACC
4678 AAGGGCAAAT
1 AAGGGCAAAT
4688 ACGTAATTCT
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
27 17 0.55
28 14 0.45
ACGTcount: A:0.40, C:0.14, G:0.23, T:0.23
Consensus pattern (26 bp):
AAGGGCAAATGGTAATTTAGCCAACC
Found at i:5510 original size:17 final size:15
Alignment explanation
Indices: 5466--5514 Score: 53
Period size: 16 Copynumber: 3.1 Consensus size: 15
5456 CCTTATTTCC
*
5466 TTTCTTCTTCTTTTTT
1 TTTCTTCAT-TTTTTT
*
5482 TTTCTTCCTTTTTCTT
1 TTTCTTCATTTTT-TT
5498 TTTCATTCATTTTTTT
1 TTTC-TTCATTTTTTT
5514 T
1 T
5515 CCTTTTTTCC
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
15 4 0.14
16 17 0.59
17 8 0.28
ACGTcount: A:0.04, C:0.18, G:0.00, T:0.78
Consensus pattern (15 bp):
TTTCTTCATTTTTTT
Found at i:5529 original size:30 final size:27
Alignment explanation
Indices: 5451--5531 Score: 81
Period size: 30 Copynumber: 2.8 Consensus size: 27
5441 TATTCCCAAA
*
5451 TTTTTCCTTATTTCCTTTCTTCTTCTTT
1 TTTTTCCTTTTTTCCTTT-TTCTTCTTT
* *
5479 TTTTTTCTTCCTTTTTCTTTTTCATTCATTT
1 TTTTTCCTT--TTTTCCTTTTTC-TTC-TTT
5510 TTTTTCCTTTTTTCCCTTTTTC
1 TTTTTCCTTTTTT-CCTTTTTC
5532 CTTTTTCCTC
Statistics
Matches: 43, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
28 8 0.19
29 7 0.16
30 17 0.40
31 11 0.26
ACGTcount: A:0.04, C:0.23, G:0.00, T:0.73
Consensus pattern (27 bp):
TTTTTCCTTTTTTCCTTTTTCTTCTTT
Found at i:6688 original size:8 final size:9
Alignment explanation
Indices: 6664--6697 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
6654 TCTTTCATTT
*
6664 TCTTTTCTT
1 TCTTTTCTC
6673 TCTTTTCTC
1 TCTTTTCTC
6682 T-TTTTCTC
1 TCTTTTCTC
6690 TCTTTTCT
1 TCTTTTCT
6698 TCACCATTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
8 8 0.35
9 15 0.65
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (9 bp):
TCTTTTCTC
Found at i:14722 original size:21 final size:21
Alignment explanation
Indices: 14698--14752 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 21
14688 CGCCCATTCA
* *
14698 CCGTGCGACCACCGGTTAAGC
1 CCGTGCCACCACCGGCTAAGC
*
14719 CCGTGCCACCACCGGCTATGC
1 CCGTGCCACCACCGGCTAAGC
*
14740 CCGTGCCATCACC
1 CCGTGCCACCACC
14753 ATTCCAAGCC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.16, C:0.45, G:0.24, T:0.15
Consensus pattern (21 bp):
CCGTGCCACCACCGGCTAAGC
Found at i:15124 original size:15 final size:14
Alignment explanation
Indices: 15104--15133 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
15094 ATTTTTTTAA
15104 TTTTCCTTGCATTAT
1 TTTTCCTTG-ATTAT
15119 TTTTCCTTGATTAT
1 TTTTCCTTGATTAT
15133 T
1 T
15134 GCTTTGATTG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.40
15 9 0.60
ACGTcount: A:0.13, C:0.17, G:0.07, T:0.63
Consensus pattern (14 bp):
TTTTCCTTGATTAT
Found at i:19413 original size:2 final size:2
Alignment explanation
Indices: 19408--19437 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
19398 TTTTTATTTG
19408 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
19438 GAATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.