Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006969.1 Corchorus capsularis cultivar CVL-1 contig06990, 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: 10872
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.35
Found at i:1689 original size:10 final size:9
Alignment explanation
Indices: 1673--1697 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
1663 TCTGGTCGAA
1673 ATTTTTTTT
1 ATTTTTTTT
1682 ATTTTTTTT
1 ATTTTTTTT
1691 ATTTTTT
1 ATTTTTT
1698 ATATATTTCG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (9 bp):
ATTTTTTTT
Found at i:1806 original size:8 final size:8
Alignment explanation
Indices: 1778--1811 Score: 50
Period size: 8 Copynumber: 4.1 Consensus size: 8
1768 GAATCGGTTA
1778 TGAATTTT
1 TGAATTTT
*
1786 TGAAGTTTC
1 TGAA-TTTT
1795 TGAATTTT
1 TGAATTTT
1803 TGAATTTT
1 TGAATTTT
1811 T
1 T
1812 CAAGAAGGTG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
8 16 0.70
9 7 0.30
ACGTcount: A:0.24, C:0.03, G:0.15, T:0.59
Consensus pattern (8 bp):
TGAATTTT
Found at i:2743 original size:20 final size:22
Alignment explanation
Indices: 2718--2759 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
2708 AAAGGATCAT
2718 ATGGCCGA-T-TGTGGCCGGGC
1 ATGGCCGAGTATGTGGCCGGGC
2738 ATGGCCGAGTCATGTGGCCGGG
1 ATGGCCGAGT-ATGTGGCCGGG
2760 TGTGGCCGGG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 8 0.42
21 1 0.05
23 10 0.53
ACGTcount: A:0.12, C:0.24, G:0.45, T:0.19
Consensus pattern (22 bp):
ATGGCCGAGTATGTGGCCGGGC
Found at i:2764 original size:33 final size:32
Alignment explanation
Indices: 2727--2838 Score: 104
Period size: 33 Copynumber: 3.4 Consensus size: 32
2717 TATGGCCGAT
2727 TGTGGCCGGGCATGGCCGA-GTC-ATGTGGCCGGG
1 TGTGGCCGGGCATGGCC-ATGTCGA-GTGGCC-GG
*
2760 TGTGGCCGGGCTTGGCCATGTCGAGTGGCCGG
1 TGTGGCCGGGCATGGCCATGTCGAGTGGCCGG
** *
2792 TGATGGCCGGGCATCTCCATGTCGCA-TGGCTGG
1 TG-TGGCCGGGCATGGCCATGTCG-AGTGGCCGG
*
2825 TGTTGCGCGGGCAT
1 TGTGGC-CGGGCAT
2839 CTCCAAATCG
Statistics
Matches: 68, Mismatches: 6, Indels: 10
0.81 0.07 0.12
Matches are distributed among these distances:
32 8 0.12
33 58 0.85
34 2 0.03
ACGTcount: A:0.09, C:0.25, G:0.44, T:0.22
Consensus pattern (32 bp):
TGTGGCCGGGCATGGCCATGTCGAGTGGCCGG
Found at i:2870 original size:21 final size:21
Alignment explanation
Indices: 2837--2878 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
2827 TTGCGCGGGC
*
2837 ATCTCCAAATCGCGTGGCCGG
1 ATCTCCAAATCGCATGGCCGG
* *
2858 ATCTCTAAGTCGCATGGCCGG
1 ATCTCCAAATCGCATGGCCGG
2879 TCACTTGTGC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.19, C:0.31, G:0.29, T:0.21
Consensus pattern (21 bp):
ATCTCCAAATCGCATGGCCGG
Found at i:3476 original size:32 final size:32
Alignment explanation
Indices: 3431--3501 Score: 106
Period size: 32 Copynumber: 2.2 Consensus size: 32
3421 TAAAGTCAGG
**
3431 TCGGGTTGAATTTGGGTCAAGTTAATTCGGGT
1 TCGGGTTTTATTTGGGTCAAGTTAATTCGGGT
* *
3463 TTGGGTTTTATTTGGGTCAGGTTAATTCGGGT
1 TCGGGTTTTATTTGGGTCAAGTTAATTCGGGT
3495 TCGGGTT
1 TCGGGTT
3502 CAGTTTGGGT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.14, C:0.08, G:0.35, T:0.42
Consensus pattern (32 bp):
TCGGGTTTTATTTGGGTCAAGTTAATTCGGGT
Found at i:3509 original size:32 final size:31
Alignment explanation
Indices: 3431--3511 Score: 99
Period size: 32 Copynumber: 2.5 Consensus size: 31
3421 TAAAGTCAGG
*
3431 TCGGGTTGAATTTGGGTCAAGTTAATTCGGGT
1 TCGGGTT-CATTTGGGTCAAGTTAATTCGGGT
* * *
3463 TTGGGTTTTATTTGGGTCAGGTTAATTCGGGT
1 TCGGG-TTCATTTGGGTCAAGTTAATTCGGGT
3495 TCGGGTTCAGTTTGGGT
1 TCGGGTTCA-TTTGGGT
3512 TTTGGCCAAA
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
31 3 0.07
32 37 0.88
33 2 0.05
ACGTcount: A:0.14, C:0.09, G:0.36, T:0.42
Consensus pattern (31 bp):
TCGGGTTCATTTGGGTCAAGTTAATTCGGGT
Found at i:3683 original size:16 final size:17
Alignment explanation
Indices: 3649--3704 Score: 53
Period size: 16 Copynumber: 3.4 Consensus size: 17
3639 TTTTCTTAAA
* * *
3649 TTTTCGGATTCGGATTT
1 TTTTCGGGTTCTGAGTT
3666 TTTTCGGGTTCTGA-TT
1 TTTTCGGGTTCTGAGTT
* *
3682 TTTTTGGGTT-TGAGCT
1 TTTTCGGGTTCTGAGTT
3698 TTTTCGG
1 TTTTCGG
3705 ATTCGGGTTT
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
15 3 0.09
16 18 0.55
17 12 0.36
ACGTcount: A:0.07, C:0.11, G:0.27, T:0.55
Consensus pattern (17 bp):
TTTTCGGGTTCTGAGTT
Found at i:3700 original size:17 final size:17
Alignment explanation
Indices: 3649--3704 Score: 62
Period size: 17 Copynumber: 3.4 Consensus size: 17
3639 TTTTCTTAAA
* *
3649 TTTTCGGATTCGGATTT
1 TTTTCGGGTTCTGATTT
3666 TTTTCGGGTTCTGATTT
1 TTTTCGGGTTCTGATTT
**
3683 TTTT-GGGTT-TGAGCT
1 TTTTCGGGTTCTGATTT
3698 TTTTCGG
1 TTTTCGG
3705 ATTCGGGTTT
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
15 8 0.24
16 7 0.21
17 19 0.56
ACGTcount: A:0.07, C:0.11, G:0.27, T:0.55
Consensus pattern (17 bp):
TTTTCGGGTTCTGATTT
Found at i:4414 original size:18 final size:18
Alignment explanation
Indices: 4391--4432 Score: 84
Period size: 18 Copynumber: 2.3 Consensus size: 18
4381 TACATTAATC
4391 AAAAGATCAAATTTGCAT
1 AAAAGATCAAATTTGCAT
4409 AAAAGATCAAATTTGCAT
1 AAAAGATCAAATTTGCAT
4427 AAAAGA
1 AAAAGA
4433 AATAAACACT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.55, C:0.10, G:0.12, T:0.24
Consensus pattern (18 bp):
AAAAGATCAAATTTGCAT
Found at i:6429 original size:55 final size:55
Alignment explanation
Indices: 6345--6455 Score: 222
Period size: 55 Copynumber: 2.0 Consensus size: 55
6335 TGTTTAGTAG
6345 CAAATTGTTCTCCACACATCATGGGTTTAGTGGGATTATCAAATCTTATTGAAAC
1 CAAATTGTTCTCCACACATCATGGGTTTAGTGGGATTATCAAATCTTATTGAAAC
6400 CAAATTGTTCTCCACACATCATGGGTTTAGTGGGATTATCAAATCTTATTGAAAC
1 CAAATTGTTCTCCACACATCATGGGTTTAGTGGGATTATCAAATCTTATTGAAAC
6455 C
1 C
6456 TATAGGCCTA
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
55 56 1.00
ACGTcount: A:0.31, C:0.19, G:0.16, T:0.34
Consensus pattern (55 bp):
CAAATTGTTCTCCACACATCATGGGTTTAGTGGGATTATCAAATCTTATTGAAAC
Found at i:9920 original size:15 final size:16
Alignment explanation
Indices: 9900--9932 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
9890 GATTGCTTTC
*
9900 TTAGTTA-ATTTACTT
1 TTAGTTAGATTTAATT
9915 TTAGTTAGATTTAATT
1 TTAGTTAGATTTAATT
9931 TT
1 TT
9933 TAATTCTTCT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.27, C:0.03, G:0.09, T:0.61
Consensus pattern (16 bp):
TTAGTTAGATTTAATT
Done.