Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009753.1 Corchorus capsularis cultivar CVL-1 contig09774, 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: 17123
ACGTcount: A:0.33, C:0.18, G:0.15, T:0.34
Found at i:10687 original size:272 final size:274
Alignment explanation
Indices: 10198--10723 Score: 1002
Period size: 272 Copynumber: 1.9 Consensus size: 274
10188 TTTGGAATTG
10198 CTTAGCCGACTTGGACTATGCATGGACGGTGATTGCAGCTGTAAATTGATGATGCGGAACACTCT
1 CTTAGCCGACTTGGACTATGCATGGACGGTGATTGCAGCTGTAAATTGAT-ATGCGGAACACTCT
*
10263 AATTGGCTATTGAAGATGCTAACTAATGAAGATCTACTTCAACCAATCAAAGCTCATTACTTGGA
65 AATTGGCTATTGAAGATGCTAACTAATGAAGATCTACTTCAACCAATCAAAACTCATTACTTGGA
10328 GACAAAGTTGATGTAATTCATAGTTGTATTAGGACTAGAATTTAGATGTCTATCTTGCCCTTTGT
130 GACAAAGTTGATGTAATTCATAGTTGTATTAGGACTAGAATTTAGATGTCTATCTTGCCCTTTGT
10393 CCCGCCTCATCCAAGGGTTGGTATTGATTGTCATAAGGGTAGGATGTGTCATAGGTTTGCCTATA
195 CCCGCCTCATCCAAGGGTTGGTATTGATTGTCATAAGGGTAGGATGTGTCATAGGTTTGCCTATA
10458 AATACAGAGGATTAT
260 AATACAGAGGATTAT
* *
10473 CTTAGCCGACTTGGACTATGCATGGACGGTGATTGCAGTTGTAAATTGAT-T-TGGAACACTCTA
1 CTTAGCCGACTTGGACTATGCATGGACGGTGATTGCAGCTGTAAATTGATATGCGGAACACTCTA
10536 ATTGGCTATTGAAGATGCTAACTAATGAAGATCTACTTCAACCAATCAAAACTCATTACTTGGAG
66 ATTGGCTATTGAAGATGCTAACTAATGAAGATCTACTTCAACCAATCAAAACTCATTACTTGGAG
10601 ACAAAGTTGATGTAATTCATAGTTGTATTAGGACTAGAATTTAGATGTCTATCTTGCCCTTTGTC
131 ACAAAGTTGATGTAATTCATAGTTGTATTAGGACTAGAATTTAGATGTCTATCTTGCCCTTTGTC
10666 CCGCCTCATCCAAGGGTTGGTATTGATTGTCATAAGGGTAGGATGTGTCATAGGTTTG
196 CCGCCTCATCCAAGGGTTGGTATTGATTGTCATAAGGGTAGGATGTGTCATAGGTTTG
10724 AACGGAGGAT
Statistics
Matches: 248, Mismatches: 3, Indels: 3
0.98 0.01 0.01
Matches are distributed among these distances:
272 198 0.80
273 1 0.00
275 49 0.20
ACGTcount: A:0.28, C:0.17, G:0.22, T:0.33
Consensus pattern (274 bp):
CTTAGCCGACTTGGACTATGCATGGACGGTGATTGCAGCTGTAAATTGATATGCGGAACACTCTA
ATTGGCTATTGAAGATGCTAACTAATGAAGATCTACTTCAACCAATCAAAACTCATTACTTGGAG
ACAAAGTTGATGTAATTCATAGTTGTATTAGGACTAGAATTTAGATGTCTATCTTGCCCTTTGTC
CCGCCTCATCCAAGGGTTGGTATTGATTGTCATAAGGGTAGGATGTGTCATAGGTTTGCCTATAA
ATACAGAGGATTAT
Found at i:11656 original size:14 final size:16
Alignment explanation
Indices: 11632--11665 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
11622 TAATTACTTT
11632 CTTTATAATCTG-TTG
1 CTTTATAATCTGTTTG
11647 CTTT-TAATCTGTTTG
1 CTTTATAATCTGTTTG
11662 CTTT
1 CTTT
11666 CTTAGTTGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 7 0.39
15 11 0.61
ACGTcount: A:0.15, C:0.15, G:0.12, T:0.59
Consensus pattern (16 bp):
CTTTATAATCTGTTTG
Found at i:12832 original size:16 final size:16
Alignment explanation
Indices: 12811--12857 Score: 69
Period size: 16 Copynumber: 3.0 Consensus size: 16
12801 GAATAAGTAC
12811 TATAACCCGAAACCGA
1 TATAACCCGAAACCGA
*
12827 TATAACCCG-AATCGA
1 TATAACCCGAAACCGA
*
12842 GATAACCCGAAACCGA
1 TATAACCCGAAACCGA
12858 CAAAATCCAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
15 13 0.48
16 14 0.52
ACGTcount: A:0.43, C:0.30, G:0.15, T:0.13
Consensus pattern (16 bp):
TATAACCCGAAACCGA
Found at i:12848 original size:15 final size:15
Alignment explanation
Indices: 12812--12857 Score: 56
Period size: 15 Copynumber: 2.9 Consensus size: 15
12802 AATAAGTACT
*
12812 ATAACCCGAAACCGAT
1 ATAACCCG-AACCGAG
*
12828 ATAACCCGAATCGAG
1 ATAACCCGAACCGAG
12843 ATAACCCGAAACCGA
1 ATAACCCG-AACCGA
12858 CAAAATCCAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
15 13 0.50
16 13 0.50
ACGTcount: A:0.43, C:0.30, G:0.15, T:0.11
Consensus pattern (15 bp):
ATAACCCGAACCGAG
Found at i:12963 original size:15 final size:16
Alignment explanation
Indices: 12943--12981 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
12933 TGTGTAAGTG
*
12943 ACCCGAACTT-TATTA
1 ACCCGAACTTGAATTA
12958 ACCCGAA-TTGAATTA
1 ACCCGAACTTGAATTA
12973 ACCCGAACT
1 ACCCGAACT
12982 CAATTTATGG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 2 0.10
15 18 0.86
16 1 0.05
ACGTcount: A:0.36, C:0.28, G:0.10, T:0.26
Consensus pattern (16 bp):
ACCCGAACTTGAATTA
Found at i:12986 original size:15 final size:15
Alignment explanation
Indices: 12943--12986 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
12933 TGTGTAAGTG
**
12943 ACCCGAACTTTATTA
1 ACCCGAACTCAATTA
* *
12958 ACCCGAATTGAATTA
1 ACCCGAACTCAATTA
12973 ACCCGAACTCAATT
1 ACCCGAACTCAATT
12987 TATGGTTTTA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.36, C:0.27, G:0.09, T:0.27
Consensus pattern (15 bp):
ACCCGAACTCAATTA
Found at i:15154 original size:16 final size:16
Alignment explanation
Indices: 15129--15165 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
15119 AAACAAACCG
*
15129 AACCCGAAATGACCCA
1 AACCCAAAATGACCCA
*
15145 AACCCAAAATGACCCG
1 AACCCAAAATGACCCA
15161 AACCC
1 AACCC
15166 GATCAACCCG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.43, C:0.41, G:0.11, T:0.05
Consensus pattern (16 bp):
AACCCAAAATGACCCA
Found at i:16546 original size:15 final size:15
Alignment explanation
Indices: 16492--16548 Score: 53
Period size: 15 Copynumber: 3.6 Consensus size: 15
16482 TCCGAACAGT
*
16492 ATGACCCGAAACCGAAA
1 ATGACCCG-AACC-CAA
*
16509 ACGACCC-AACCCAGA
1 ATGACCCGAACCCA-A
16524 ATTGACCCGAACCCAA
1 A-TGACCCGAACCCAA
16540 ATGACCCGA
1 ATGACCCGA
16549 CATTTGATCG
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
14 1 0.03
15 14 0.41
16 7 0.21
17 12 0.35
ACGTcount: A:0.40, C:0.37, G:0.16, T:0.07
Consensus pattern (15 bp):
ATGACCCGAACCCAA
Done.