Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012160.1 Corchorus olitorius cultivar O-4 contig12193, 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: 22739
ACGTcount: A:0.34, C:0.19, G:0.16, T:0.32
Found at i:2469 original size:16 final size:17
Alignment explanation
Indices: 2443--2474 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
2433 AGTGCAAATT
2443 AAAATAGAAAAATAAAG
1 AAAATAGAAAAATAAAG
2460 AAAA-AGAAAAATAAA
1 AAAATAGAAAAATAAA
2475 ACGCAATTTC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.81, C:0.00, G:0.09, T:0.09
Consensus pattern (17 bp):
AAAATAGAAAAATAAAG
Found at i:2707 original size:12 final size:13
Alignment explanation
Indices: 2685--2714 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
2675 ACTAGCAATT
2685 AAAATCAATCAAG
1 AAAATCAATCAAG
2698 AAAA-CAATCAAG
1 AAAATCAATCAAG
2710 AAAAT
1 AAAAT
2715 TAAAGAAATC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.67, C:0.13, G:0.07, T:0.13
Consensus pattern (13 bp):
AAAATCAATCAAG
Found at i:5248 original size:21 final size:21
Alignment explanation
Indices: 5215--5263 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
5205 AAGAATTGTA
5215 GCTT-CTTGGAAATCGCTCTT
1 GCTTCCTTGGAAATCGCTCTT
* *
5235 GCTTCCTTTGAAATCTCTCTT
1 GCTTCCTTGGAAATCGCTCTT
5256 GCATTCCT
1 GC-TTCCT
5264 AAAGCATTGA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 4 0.16
21 16 0.64
22 5 0.20
ACGTcount: A:0.14, C:0.29, G:0.14, T:0.43
Consensus pattern (21 bp):
GCTTCCTTGGAAATCGCTCTT
Found at i:6406 original size:6 final size:6
Alignment explanation
Indices: 6395--6436 Score: 61
Period size: 6 Copynumber: 7.3 Consensus size: 6
6385 AATAACTACG
*
6395 AAAAAT AAAAAT AAAAAT AAAAAT --AAAT AAAAAG AAAAAT AA
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AA
6437 CGAAAAAGAA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
4 4 0.12
6 28 0.88
ACGTcount: A:0.83, C:0.00, G:0.02, T:0.14
Consensus pattern (6 bp):
AAAAAT
Found at i:6424 original size:16 final size:16
Alignment explanation
Indices: 6403--6449 Score: 67
Period size: 16 Copynumber: 2.9 Consensus size: 16
6393 CGAAAAATAA
*
6403 AAATAAAAATAAAAAT
1 AAATAAAAAGAAAAAT
6419 AAATAAAAAGAAAAAT
1 AAATAAAAAGAAAAAT
**
6435 AACGAAAAAGAAAAA
1 AAATAAAAAGAAAAA
6450 GATAAAGGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 28 1.00
ACGTcount: A:0.81, C:0.02, G:0.06, T:0.11
Consensus pattern (16 bp):
AAATAAAAAGAAAAAT
Found at i:6448 original size:22 final size:22
Alignment explanation
Indices: 6392--6451 Score: 77
Period size: 22 Copynumber: 2.7 Consensus size: 22
6382 AAAAATAACT
*
6392 ACGAAAAATAAAAATAAAAATA
1 ACGAAAAATAAAAAGAAAAATA
*
6414 A-AAATAAATAAAAAGAAAAATA
1 ACGAA-AAATAAAAAGAAAAATA
*
6436 ACGAAAAAGAAAAAGA
1 ACGAAAAATAAAAAGA
6452 TAAAGGTAAG
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
21 2 0.06
22 28 0.88
23 2 0.06
ACGTcount: A:0.78, C:0.03, G:0.08, T:0.10
Consensus pattern (22 bp):
ACGAAAAATAAAAAGAAAAATA
Found at i:8061 original size:21 final size:21
Alignment explanation
Indices: 8023--8067 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
8013 GGCGCCCGCA
* *
8023 TGGTTTGTCTGAAGACCCATG
1 TGGTTTGTCTGAACACCCAAG
*
8044 TGGTTTGTCTGATCACCCAAG
1 TGGTTTGTCTGAACACCCAAG
8065 TGG
1 TGG
8068 GTAGTGTCAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.18, C:0.20, G:0.29, T:0.33
Consensus pattern (21 bp):
TGGTTTGTCTGAACACCCAAG
Found at i:14801 original size:2 final size:2
Alignment explanation
Indices: 14794--14832 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
14784 CAATTGGCCA
14794 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
14833 CTAATTACAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:16703 original size:18 final size:18
Alignment explanation
Indices: 16680--16717 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
16670 ACCGTTTCTC
*
16680 ATCCCCTTTTGATCTTCG
1 ATCCCCTTTTGATCTCCG
16698 ATCCCCTTTTGATCTCCG
1 ATCCCCTTTTGATCTCCG
16716 AT
1 AT
16718 TATGGTGTGC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.13, C:0.34, G:0.11, T:0.42
Consensus pattern (18 bp):
ATCCCCTTTTGATCTCCG
Found at i:18263 original size:21 final size:21
Alignment explanation
Indices: 18234--18278 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
18224 TAAACAGTTG
* *
18234 GTTGTATTAGTTCAATTTTAT
1 GTTGCATTAGTTAAATTTTAT
*
18255 GTTGCATTAGTTAAATTTTCT
1 GTTGCATTAGTTAAATTTTAT
18276 GTT
1 GTT
18279 TCCCACATTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.22, C:0.07, G:0.16, T:0.56
Consensus pattern (21 bp):
GTTGCATTAGTTAAATTTTAT
Found at i:21529 original size:27 final size:29
Alignment explanation
Indices: 21491--21552 Score: 83
Period size: 27 Copynumber: 2.2 Consensus size: 29
21481 AAGACAACTC
21491 TTGATTCATGAATAAT-T-ACATTATTAA
1 TTGATTCATGAATAATATGACATTATTAA
* *
21518 TTGATTTATGAATAATAATGACATTATTCA
1 TTGATTCATGAATAAT-ATGACATTATTAA
21548 TTGAT
1 TTGAT
21553 GACTTTTCAT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
27 15 0.50
29 1 0.03
30 14 0.47
ACGTcount: A:0.39, C:0.06, G:0.10, T:0.45
Consensus pattern (29 bp):
TTGATTCATGAATAATATGACATTATTAA
Done.