Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013841.1 Corchorus capsularis cultivar CVL-1 contig13862, 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: 29348
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.35
Found at i:3426 original size:18 final size:18
Alignment explanation
Indices: 3403--3443 Score: 82
Period size: 18 Copynumber: 2.3 Consensus size: 18
3393 CAAATAGCAG
3403 AAGTCGCAGTCCAATTTA
1 AAGTCGCAGTCCAATTTA
3421 AAGTCGCAGTCCAATTTA
1 AAGTCGCAGTCCAATTTA
3439 AAGTC
1 AAGTC
3444 ACAAGAAGGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.34, C:0.22, G:0.17, T:0.27
Consensus pattern (18 bp):
AAGTCGCAGTCCAATTTA
Found at i:5020 original size:17 final size:16
Alignment explanation
Indices: 4981--5031 Score: 68
Period size: 18 Copynumber: 3.1 Consensus size: 16
4971 ATTTAAATAG
4981 ATAAAAAAATATTAAAA
1 ATAAAAAAATATT-AAA
4998 ATTAAAAGAAATATTAAA
1 A-TAAAA-AAATATTAAA
5016 ATAAAAAAA-ATTAAA
1 ATAAAAAAATATTAAA
5031 A
1 A
5032 AATAAGAAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
15 7 0.22
16 3 0.09
17 6 0.19
18 9 0.28
19 7 0.22
ACGTcount: A:0.75, C:0.00, G:0.02, T:0.24
Consensus pattern (16 bp):
ATAAAAAAATATTAAA
Found at i:5033 original size:17 final size:18
Alignment explanation
Indices: 4981--5042 Score: 76
Period size: 17 Copynumber: 3.6 Consensus size: 18
4971 ATTTAAATAG
4981 ATAAAAAAATATTAAAAA
1 ATAAAAAAATATTAAAAA
*
4999 TTAAAAGAAATATT--AAA
1 ATAAAA-AAATATTAAAAA
5016 ATAAAAAAA-ATTAAAAA
1 ATAAAAAAATATTAAAAA
*
5033 ATAAGAAAAT
1 ATAAAAAAAT
5043 TTATTTTGAA
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
15 3 0.08
16 3 0.08
17 19 0.51
18 5 0.14
19 7 0.19
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.23
Consensus pattern (18 bp):
ATAAAAAAATATTAAAAA
Found at i:5903 original size:12 final size:12
Alignment explanation
Indices: 5886--5921 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
5876 ATTTTCTTAT
5886 TTTTAATTTTTA
1 TTTTAATTTTTA
* *
5898 TTTTAATATTTC
1 TTTTAATTTTTA
5910 TTTTAATTTTTA
1 TTTTAATTTTTA
5922 ATATATTTTT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.25, C:0.03, G:0.00, T:0.72
Consensus pattern (12 bp):
TTTTAATTTTTA
Found at i:7418 original size:78 final size:76
Alignment explanation
Indices: 7256--7484 Score: 335
Period size: 78 Copynumber: 3.1 Consensus size: 76
7246 TTCTATATAG
* * * *
7256 TTTTACTTAACTAAAAACTCTATTTTTATTTAATTAAATATAATATCTTTATAAC---TATTTT-
1 TTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATCTAATATCCTTATAACTTATATTTTA
7317 --ATTTTACTA
66 CCATTTTACTA
7326 TTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATCTAATATCCTTATAACTATTATATTT
1 TTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATCTAATATCCTTATAAC--TTATATTT
* *
7391 TATCATTTTAGTA
64 TACCATTTTACTA
*
7404 TTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATCTAATATCCTTATTACTTATATTTTA
1 TTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATCTAATATCCTTATAACTTATATTTTA
7469 CCATTTTACTA
66 CCATTTTACTA
7480 TTTTA
1 TTTTA
7485 ATTAAAAAAT
Statistics
Matches: 143, Mismatches: 8, Indels: 10
0.89 0.05 0.06
Matches are distributed among these distances:
70 51 0.36
75 6 0.04
76 24 0.17
78 62 0.43
ACGTcount: A:0.36, C:0.13, G:0.00, T:0.51
Consensus pattern (76 bp):
TTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATCTAATATCCTTATAACTTATATTTTA
CCATTTTACTA
Found at i:8139 original size:2 final size:2
Alignment explanation
Indices: 8132--8158 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
8122 GTTTAGATCA
8132 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 A
8159 AGATCTAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:10584 original size:13 final size:13
Alignment explanation
Indices: 10566--10596 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
10556 GGAAATTGTT
10566 TTTGACCCTCCAA
1 TTTGACCCTCCAA
10579 TTTGACCCTCCAA
1 TTTGACCCTCCAA
*
10592 CTTGA
1 TTTGA
10597 TCATCTTAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.23, C:0.35, G:0.10, T:0.32
Consensus pattern (13 bp):
TTTGACCCTCCAA
Found at i:11000 original size:108 final size:105
Alignment explanation
Indices: 10781--11043 Score: 379
Period size: 108 Copynumber: 2.5 Consensus size: 105
10771 AATTTTTCTA
* **
10781 ACCCTTAAAATAAAATTTTAATTTTAATTTGGA-CTAAACTTAGTG-AATTAGTTATATATTTTA
1 ACCCTTAAAATAAAAATAAAATTTTAATTTGGAGCTAAACTTAGTGAAATTAGTTATATATTTTA
*
10844 TTTCTAAAACCCTATAACAATATTATTAATTATGGAATTT
66 TTTCTAAAACCCTATAACAATATTATTAATTATGAAATTT
* *
10884 ACCTTTAAAATAAAAATAAAATTTTAATTTGGAGCTAAACTTAGTGAAATTAG-TATTGTATTTT
1 ACCCTTAAAATAAAAATAAAATTTTAATTTGGAGCTAAACTTAGTGAAATTAGTTA-TATA-TTT
*
10948 TATTTCTAAAACCCTATAACAATAAATTATTAATTTTGAAATTT
64 TATTTCTAAAACCCTATAACAAT--ATTATTAATTATGAAATTT
* * *
10992 ACCCTTAAAATAAAAATAAAATTTTAATTTGGGGCTGAACTTGGTGAAATTA
1 ACCCTTAAAATAAAAATAAAATTTTAATTTGGAGCTAAACTTAGTGAAATTA
11044 AGGCTAAACT
Statistics
Matches: 143, Mismatches: 11, Indels: 7
0.89 0.07 0.04
Matches are distributed among these distances:
103 29 0.20
104 14 0.10
105 9 0.06
106 26 0.18
108 65 0.45
ACGTcount: A:0.41, C:0.09, G:0.09, T:0.41
Consensus pattern (105 bp):
ACCCTTAAAATAAAAATAAAATTTTAATTTGGAGCTAAACTTAGTGAAATTAGTTATATATTTTA
TTTCTAAAACCCTATAACAATATTATTAATTATGAAATTT
Found at i:12605 original size:20 final size:20
Alignment explanation
Indices: 12580--12621 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
12570 TAAACTTAAT
* *
12580 AAAAAAATAAAAATAGAAAG
1 AAAAAAAGAAAAAGAGAAAG
*
12600 AAAAAAAGAAACAGAGAAAG
1 AAAAAAAGAAAAAGAGAAAG
12620 AA
1 AA
12622 GACATAGCCT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.79, C:0.02, G:0.14, T:0.05
Consensus pattern (20 bp):
AAAAAAAGAAAAAGAGAAAG
Found at i:27677 original size:25 final size:25
Alignment explanation
Indices: 27643--27696 Score: 99
Period size: 25 Copynumber: 2.2 Consensus size: 25
27633 GGTAAATTTG
27643 AATATCTCCCTTCTTAGATACTCCT
1 AATATCTCCCTTCTTAGATACTCCT
*
27668 AATATCTCCCTTCTTAGATACTCTT
1 AATATCTCCCTTCTTAGATACTCCT
27693 AATA
1 AATA
27697 CTTGTAGTGC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.28, C:0.28, G:0.04, T:0.41
Consensus pattern (25 bp):
AATATCTCCCTTCTTAGATACTCCT
Found at i:29316 original size:2 final size:2
Alignment explanation
Indices: 29309--29345 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
29299 CCATATCTTT
29309 TA TA TA TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
29346 AAT
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Done.