Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01016510.1 Corchorus capsularis cultivar CVL-1 contig16531, 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: 59695
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:597 original size:21 final size:21
Alignment explanation
Indices: 571--614 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 21
561 AAATTTCTTG
571 ATTGTTCTCTTAG-TTAATTTT
1 ATTGTT-TCTTAGATTAATTTT
*
592 ATTGTTTGTTAGATTTAATTTT
1 ATTGTTTCTTAGA-TTAATTTT
614 A
1 A
615 AACTCTTCTT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
20 5 0.25
21 6 0.30
22 9 0.45
ACGTcount: A:0.23, C:0.05, G:0.11, T:0.61
Consensus pattern (21 bp):
ATTGTTTCTTAGATTAATTTT
Found at i:10327 original size:21 final size:21
Alignment explanation
Indices: 10301--10344 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 21
10291 AATTTTCTTG
10301 ATTGTTCTCTTAG-TTAATTTT
1 ATTGTT-TCTTAGATTAATTTT
*
10322 ATTGTTTTTTAGATTTAATTTT
1 ATTGTTTCTTAGA-TTAATTTT
10344 A
1 A
10345 AACTCTTCTT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
20 5 0.25
21 6 0.30
22 9 0.45
ACGTcount: A:0.23, C:0.05, G:0.09, T:0.64
Consensus pattern (21 bp):
ATTGTTTCTTAGATTAATTTT
Found at i:11505 original size:27 final size:28
Alignment explanation
Indices: 11458--11514 Score: 73
Period size: 27 Copynumber: 2.1 Consensus size: 28
11448 TTAATTTTAC
11458 TTGCTCTTAATTGATTGAATTTTT-TTT
1 TTGCTCTTAATTGATTGAATTTTTGTTT
* *
11485 TTGCTCTTAATT-TTCTTAATTTTTGTTT
1 TTGCTCTTAATTGAT-TGAATTTTTGTTT
11513 TT
1 TT
11515 TTATTACAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
26 1 0.04
27 20 0.77
28 5 0.19
ACGTcount: A:0.16, C:0.09, G:0.09, T:0.67
Consensus pattern (28 bp):
TTGCTCTTAATTGATTGAATTTTTGTTT
Found at i:20561 original size:53 final size:53
Alignment explanation
Indices: 20478--20585 Score: 207
Period size: 53 Copynumber: 2.0 Consensus size: 53
20468 TAGCTTGCTC
20478 ATACTCCGAACCACTCCCTATGTCAGTAGATGCTGTGGTGAGAACATGTAACT
1 ATACTCCGAACCACTCCCTATGTCAGTAGATGCTGTGGTGAGAACATGTAACT
*
20531 ATACTCCGAACCACTCCCTATGTCATTAGATGCTGTGGTGAGAACATGTAACT
1 ATACTCCGAACCACTCCCTATGTCAGTAGATGCTGTGGTGAGAACATGTAACT
20584 AT
1 AT
20586 CTCTATTTCA
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
53 54 1.00
ACGTcount: A:0.29, C:0.24, G:0.19, T:0.28
Consensus pattern (53 bp):
ATACTCCGAACCACTCCCTATGTCAGTAGATGCTGTGGTGAGAACATGTAACT
Found at i:24715 original size:28 final size:29
Alignment explanation
Indices: 24675--24733 Score: 93
Period size: 28 Copynumber: 2.1 Consensus size: 29
24665 CCTAATGGTC
24675 CAATGACAAGATCCAGA-CCCAAGAAGTT
1 CAATGACAAGATCCAGATCCCAAGAAGTT
**
24703 CAATGACAAGATCCAGATCCCTCGAAGTT
1 CAATGACAAGATCCAGATCCCAAGAAGTT
24732 CA
1 CA
24734 CTTGAAGACA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
28 17 0.61
29 11 0.39
ACGTcount: A:0.39, C:0.27, G:0.17, T:0.17
Consensus pattern (29 bp):
CAATGACAAGATCCAGATCCCAAGAAGTT
Found at i:26481 original size:20 final size:20
Alignment explanation
Indices: 26448--26486 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
26438 CGTAGATGAA
*
26448 ATTTTCAGAAATTATTATTT
1 ATTTTCAGAAATTAGTATTT
26468 ATTTTCA-AATATTAGTATT
1 ATTTTCAGAA-ATTAGTATT
26487 GAATTCAGGT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 2 0.12
20 15 0.88
ACGTcount: A:0.36, C:0.05, G:0.05, T:0.54
Consensus pattern (20 bp):
ATTTTCAGAAATTAGTATTT
Found at i:26526 original size:16 final size:16
Alignment explanation
Indices: 26505--26586 Score: 76
Period size: 16 Copynumber: 5.1 Consensus size: 16
26495 GTTTTTCAGG
26505 TTCGGGTTCGGGTTTT
1 TTCGGGTTCGGGTTTT
* *
26521 TTCGGGTTTC-AGATTT
1 TTCGGG-TTCGGGTTTT
* *
26537 TTCGGGTTCTGATTTT
1 TTCGGGTTCGGGTTTT
* * * *
26553 TTTGGGTTTGAGCTTT
1 TTCGGGTTCGGGTTTT
26569 TTCGGGTTCGGGTTTT
1 TTCGGGTTCGGGTTTT
26585 TT
1 TT
26587 TTGGGTTCGA
Statistics
Matches: 49, Mismatches: 15, Indels: 4
0.72 0.22 0.06
Matches are distributed among these distances:
15 3 0.06
16 43 0.88
17 3 0.06
ACGTcount: A:0.05, C:0.11, G:0.30, T:0.54
Consensus pattern (16 bp):
TTCGGGTTCGGGTTTT
Found at i:26587 original size:32 final size:32
Alignment explanation
Indices: 26505--26593 Score: 124
Period size: 32 Copynumber: 2.8 Consensus size: 32
26495 GTTTTTCAGG
*
26505 TTCGGGTTCGGGTTTTTTCGGGTTTCAGATTT
1 TTCGGGTTCGGGTTTTTTTGGGTTTCAGATTT
* * * *
26537 TTCGGGTTCTGATTTTTTTGGGTTTGAGCTTT
1 TTCGGGTTCGGGTTTTTTTGGGTTTCAGATTT
26569 TTCGGGTTCGGGTTTTTTTTGGGTT
1 TTCGGGTTCGGG-TTTTTTTGGGTT
26594 CGAGTTCAGG
Statistics
Matches: 49, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
32 37 0.76
33 12 0.24
ACGTcount: A:0.04, C:0.10, G:0.31, T:0.54
Consensus pattern (32 bp):
TTCGGGTTCGGGTTTTTTTGGGTTTCAGATTT
Found at i:27050 original size:33 final size:33
Alignment explanation
Indices: 26976--27052 Score: 86
Period size: 33 Copynumber: 2.3 Consensus size: 33
26966 GCTGATGACC
** *
26976 GTGCCGCCCCAGGAGGGCGGCAGGTCGTGGTAT
1 GTGCCGCCCCAGGAGGGCGGCAGACCATGGTAT
*
27009 GTGGCGCCCCAGGAGGGCGGCATGAACCATGGT-T
1 GTGCCGCCCCAGGAGGGCGGCA-G-ACCATGGTAT
27043 -TGCCGCCCCA
1 GTGCCGCCCCA
27053 AATGCCACGG
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
33 30 0.81
34 2 0.05
35 5 0.14
ACGTcount: A:0.14, C:0.31, G:0.40, T:0.14
Consensus pattern (33 bp):
GTGCCGCCCCAGGAGGGCGGCAGACCATGGTAT
Found at i:27234 original size:20 final size:19
Alignment explanation
Indices: 27209--27246 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
27199 AATATTTTTT
27209 TGTAACATTATTATGTATTA
1 TGTAACATTATTA-GTATTA
*
27229 TGTAACATTGTTAGTATT
1 TGTAACATTATTAGTATT
27247 GGGTCAATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.32, C:0.05, G:0.13, T:0.50
Consensus pattern (19 bp):
TGTAACATTATTAGTATTA
Found at i:27767 original size:32 final size:32
Alignment explanation
Indices: 27730--27806 Score: 145
Period size: 32 Copynumber: 2.4 Consensus size: 32
27720 AGTGAAGAAT
27730 TGAAGATTTGAAGTTCATGTTTGAAGATAATC
1 TGAAGATTTGAAGTTCATGTTTGAAGATAATC
*
27762 TGAAGATTTGAAGTTCGTGTTTGAAGATAATC
1 TGAAGATTTGAAGTTCATGTTTGAAGATAATC
27794 TGAAGATTTGAAG
1 TGAAGATTTGAAG
27807 ATCCTTGAAA
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
32 44 1.00
ACGTcount: A:0.34, C:0.05, G:0.25, T:0.36
Consensus pattern (32 bp):
TGAAGATTTGAAGTTCATGTTTGAAGATAATC
Found at i:27773 original size:19 final size:19
Alignment explanation
Indices: 27749--27808 Score: 69
Period size: 19 Copynumber: 3.5 Consensus size: 19
27739 GAAGTTCATG
27749 TTTGAAGATAATCTGAAGA
1 TTTGAAGATAATCTGAAGA
*
27768 TTTGAAG-T--TC-G-TG-
1 TTTGAAGATAATCTGAAGA
27781 TTTGAAGATAATCTGAAGA
1 TTTGAAGATAATCTGAAGA
27800 TTTGAAGAT
1 TTTGAAGAT
27809 CCTTGAAAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 12
0.70 0.04 0.26
Matches are distributed among these distances:
13 7 0.21
14 2 0.06
15 1 0.03
16 4 0.12
17 1 0.03
18 2 0.06
19 16 0.48
ACGTcount: A:0.35, C:0.05, G:0.23, T:0.37
Consensus pattern (19 bp):
TTTGAAGATAATCTGAAGA
Found at i:50903 original size:1 final size:1
Alignment explanation
Indices: 50897--50921 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
50887 GCTGGATGAG
50897 CCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCC
50922 TCTCCTCCGC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:1.00, G:0.00, T:0.00
Consensus pattern (1 bp):
C
Done.