Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01001541.1 Corchorus capsularis cultivar CVL-1 contig01541, 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: 5641
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Found at i:3675 original size:30 final size:31
Alignment explanation
Indices: 3613--3677 Score: 87
Period size: 30 Copynumber: 2.1 Consensus size: 31
3603 AACTTTATAT
* * * *
3613 TTTCCGATTGTACCCTTATTTTTAAAATATA
1 TTTCCAATTGTACCATTATTTCTAAAACATA
3644 TTTCCAATTGTACCATT-TTTCTAAAACATA
1 TTTCCAATTGTACCATTATTTCTAAAACATA
3674 TTTC
1 TTTC
3678 TAAATTGTCA
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
30 15 0.50
31 15 0.50
ACGTcount: A:0.29, C:0.18, G:0.05, T:0.48
Consensus pattern (31 bp):
TTTCCAATTGTACCATTATTTCTAAAACATA
Found at i:3684 original size:31 final size:31
Alignment explanation
Indices: 3619--3685 Score: 82
Period size: 31 Copynumber: 2.2 Consensus size: 31
3609 ATATTTTCCG
* * * *
3619 ATTGTACCCTTATTTTTAAAATATATTTCCA
1 ATTGTACCATTATTTCTAAAACATATTTCAA
3650 ATTGTACCATT-TTTCTAAAACATATTTCTAA
1 ATTGTACCATTATTTCTAAAACATATTTC-AA
3681 ATTGT
1 ATTGT
3686 CATTACCATT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
30 15 0.48
31 16 0.52
ACGTcount: A:0.33, C:0.15, G:0.04, T:0.48
Consensus pattern (31 bp):
ATTGTACCATTATTTCTAAAACATATTTCAA
Found at i:4858 original size:22 final size:22
Alignment explanation
Indices: 4830--5018 Score: 116
Period size: 22 Copynumber: 8.3 Consensus size: 22
4820 TATCTCTATG
* *
4830 TGGTTATTAAAATTTCATAAGA
1 TGGTTATCAAAATTTCATAGGA
* *
4852 TGGTTATTATAATTTCATGAGGA
1 TGGTTATCAAAATTTCAT-AGGA
*
4875 -GGTTATCAAAATTCCATAGTG-
1 TGGTTATCAAAATTTCATAG-GA
*
4896 TGGTTACCAAAATTTCATATGGA
1 TGGTTATCAAAATTTCATA-GGA
*
4919 -AGTTATCAAAATTTCATATAGTG-
1 TGGTTATCAAAATTTC--ATAG-GA
* *
4942 TGATTACCAAAATTTCATAGGA
1 TGGTTATCAAAATTTCATAGGA
* * *
4964 TCAAGTTATTAAAATTTCTTATTAGGT
1 T--GGTTATCAAAATTTC--A-TAGGA
** *
4991 TGGTTATTGAAATTTCATAGGG
1 TGGTTATCAAAATTTCATAGGA
5013 TGGTTA
1 TGGTTA
5019 ATTATCGCAA
Statistics
Matches: 132, Mismatches: 20, Indels: 30
0.73 0.11 0.16
Matches are distributed among these distances:
21 3 0.02
22 77 0.58
23 6 0.05
24 27 0.20
25 13 0.10
26 1 0.01
27 5 0.04
ACGTcount: A:0.34, C:0.08, G:0.17, T:0.40
Consensus pattern (22 bp):
TGGTTATCAAAATTTCATAGGA
Found at i:4956 original size:46 final size:43
Alignment explanation
Indices: 4862--4963 Score: 141
Period size: 46 Copynumber: 2.3 Consensus size: 43
4852 TGGTTATTAT
* *
4862 AATTTCATGAGGAGGTTATCAAAATTCCATAGTGTGGTTACCAA
1 AATTTCAT-AGGAAGTTATCAAAATTCCATAGTGTGATTACCAA
*
4906 AATTTCATATGGAAGTTATCAAAATTTCATATAGTGTGATTACCAA
1 AATTTCATA-GGAAGTTATCAAAA-TTC-CATAGTGTGATTACCAA
4952 AATTTCATAGGA
1 AATTTCATAGGA
4964 TCAAGTTATT
Statistics
Matches: 52, Mismatches: 3, Indels: 5
0.87 0.05 0.08
Matches are distributed among these distances:
43 1 0.02
44 21 0.40
45 6 0.12
46 24 0.46
ACGTcount: A:0.37, C:0.12, G:0.17, T:0.34
Consensus pattern (43 bp):
AATTTCATAGGAAGTTATCAAAATTCCATAGTGTGATTACCAA
Found at i:4957 original size:24 final size:24
Alignment explanation
Indices: 4890--4960 Score: 85
Period size: 24 Copynumber: 3.0 Consensus size: 24
4880 TCAAAATTCC
*
4890 ATAGTGTGGTTACCAAAATTTCAT
1 ATAGTGTGATTACCAAAATTTCAT
* *
4914 AT-G-G-AAGTTATCAAAATTTCAT
1 ATAGTGTGA-TTACCAAAATTTCAT
4936 ATAGTGTGATTACCAAAATTTCAT
1 ATAGTGTGATTACCAAAATTTCAT
4960 A
1 A
4961 GGATCAAGTT
Statistics
Matches: 38, Mismatches: 5, Indels: 8
0.75 0.10 0.16
Matches are distributed among these distances:
22 17 0.45
23 2 0.05
24 18 0.47
25 1 0.03
ACGTcount: A:0.38, C:0.11, G:0.14, T:0.37
Consensus pattern (24 bp):
ATAGTGTGATTACCAAAATTTCAT
Found at i:5079 original size:22 final size:21
Alignment explanation
Indices: 5054--5448 Score: 165
Period size: 22 Copynumber: 17.7 Consensus size: 21
5044 ATCAAAGAGA
*
5054 TTATCAAAATGTCATAGCGAGG
1 TTATCAAAATTTCATAG-GAGG
*
5076 TTAT-AAGAATTTCATAGTGTGG
1 TTATCAA-AATTTCATAG-GAGG
*
5098 TTAACAAAATTTCATTAGGAGG
1 TTATCAAAATTTCA-TAGGAGG
* *
5120 TTA-CTAATATTTCATGGGGAGG
1 TTATC-AAAATTTCAT-AGGAGG
* *
5142 TTAATTATCAAAATTTTATAGTGTGG
1 ----TTATCAAAATTTCATAG-GAGG
*
5168 TTATCAAAATTTCATATGAAGG
1 TTATCAAAATTTCATA-GGAGG
* *
5190 TTAT-AAAAGTCTCAATTTCATGAGG
1 TTATCAAAA-TTTC-A--T-AGGAGG
* * * *
5215 AGTACCAAAATTTGATAGAAGG
1 -TTATCAAAATTTCATAGGAGG
*
5237 TTATC-AAATCTCATA-GAGTG
1 TTATCAAAATTTCATAGGAG-G
* *
5257 ATTATCGAAATTTCATAGAGATCAGA
1 -TTATCAAAATTTCATAG-G---AGG
*
5283 TTATCAAAATTT-ATAGGAAGA
1 TTATCAAAATTTCATAGG-AGG
**
5304 TTATC-AAATTTCATAGTGTTG
1 TTATCAAAATTTCATAG-GAGG
*
5325 TTATCAAAATTTCAAAGCGAGG
1 TTATCAAAATTTCATAG-GAGG
* * * *
5347 TTATCAAAATTACATAATGTGA
1 TTATCAAAATTTCAT-AGGAGG
* *
5369 TTATCAGAATTTCATAGAGGGG
1 TTATCAAAATTTCATAG-GAGG
* * *
5391 TTAACAAAATTTTATAAAGAGG
1 TTATCAAAATTTCAT-AGGAGG
**
5413 TTATCAAAATTTCATAAATAGG
1 TTATCAAAATTTCAT-AGGAGG
*
5435 TTATCAAATTTTCA
1 TTATCAAAATTTCA
5449 AAATGCGATT
Statistics
Matches: 282, Mismatches: 58, Indels: 66
0.69 0.14 0.16
Matches are distributed among these distances:
19 2 0.01
20 15 0.05
21 34 0.12
22 172 0.61
23 11 0.04
24 5 0.02
25 17 0.06
26 19 0.07
27 7 0.02
ACGTcount: A:0.39, C:0.09, G:0.17, T:0.35
Consensus pattern (21 bp):
TTATCAAAATTTCATAGGAGG
Found at i:5603 original size:22 final size:22
Alignment explanation
Indices: 5573--5634 Score: 81
Period size: 22 Copynumber: 2.8 Consensus size: 22
5563 TCAGGGAGGA
**
5573 TATCAAAATTTCATAGTTTAGT
1 TATCAAAATTTCATAGTAGAGT
*
5595 TTTCAAAATTTCATAAG-AGAGT
1 TATCAAAATTTCAT-AGTAGAGT
5617 TATCAAAATTTCATAGTA
1 TATCAAAATTTCATAGTA
5635 TGTAGAT
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
21 2 0.06
22 30 0.88
23 2 0.06
ACGTcount: A:0.40, C:0.10, G:0.10, T:0.40
Consensus pattern (22 bp):
TATCAAAATTTCATAGTAGAGT
Done.