Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010977.1 Corchorus capsularis cultivar CVL-1 contig10998, 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: 27725
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Found at i:6362 original size:33 final size:33
Alignment explanation
Indices: 6281--6401 Score: 120
Period size: 33 Copynumber: 3.6 Consensus size: 33
6271 CCACGCAACA
* *
6281 CCGGCCACAAGACCAGCCACGCGACATGGACATGT
1 CCGGCCAC-A-ACCGGCCACGCGACATGGACATGC
* *
6316 CCGGCCATC-ACCGGCCACGTGACATGGACATGG
1 CCGGCCA-CAACCGGCCACGCGACATGGACATGC
* ** *
6349 CCGGCTACAACCGGCCAAACGAC-TCGGCCATGC
1 CCGGCCACAACCGGCCACGCGACAT-GGACATGC
6382 CCGGCCACAACCGGCCACGC
1 CCGGCCACAACCGGCCACGC
6402 AACCCTTTGT
Statistics
Matches: 71, Mismatches: 12, Indels: 8
0.78 0.13 0.09
Matches are distributed among these distances:
32 2 0.03
33 61 0.86
35 7 0.10
36 1 0.01
ACGTcount: A:0.24, C:0.41, G:0.26, T:0.08
Consensus pattern (33 bp):
CCGGCCACAACCGGCCACGCGACATGGACATGC
Found at i:6895 original size:18 final size:18
Alignment explanation
Indices: 6874--6911 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
6864 GATAAGCTTA
6874 AGTTAATCAATAAAGTTG
1 AGTTAATCAATAAAGTTG
* *
6892 AGTTGATTAATAAAGTTG
1 AGTTAATCAATAAAGTTG
6910 AG
1 AG
6912 GATTATTTTC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.42, C:0.03, G:0.21, T:0.34
Consensus pattern (18 bp):
AGTTAATCAATAAAGTTG
Found at i:7448 original size:5 final size:5
Alignment explanation
Indices: 7431--7465 Score: 61
Period size: 5 Copynumber: 6.8 Consensus size: 5
7421 GTTATATCGA
7431 AAAAT ATAAAT AAAAT AAAAT AAAAT AAAAT AAAA
1 AAAAT A-AAAT AAAAT AAAAT AAAAT AAAAT AAAA
7466 ATTTCGACCA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
5 24 0.83
6 5 0.17
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
AAAAT
Found at i:13720 original size:17 final size:17
Alignment explanation
Indices: 13698--13731 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
13688 GAATCGGCTA
13698 TGAATTTTTGAAGTTTC
1 TGAATTTTTGAAGTTTC
*
13715 TGAATTTTTGAATTTTC
1 TGAATTTTTGAAGTTTC
13732 AAGAAGGGTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.24, C:0.06, G:0.15, T:0.56
Consensus pattern (17 bp):
TGAATTTTTGAAGTTTC
Found at i:14719 original size:30 final size:33
Alignment explanation
Indices: 14646--14736 Score: 116
Period size: 33 Copynumber: 2.8 Consensus size: 33
14636 TCCGGATGAA
* *
14646 CCAATCGATGTCCGGTTGTGGCCGGTTGGTGCG
1 CCAAGCGATGGCCGGTTGTGGCCGGTTGGTGCG
14679 CCAAGCGATGGCCGGTTGTGGCCGGTT-GT-C-
1 CCAAGCGATGGCCGGTTGTGGCCGGTTGGTGCG
*
14709 CCATGCGATGGCCGGTCATGTGGCCGGT
1 CCAAGCGATGGCCGGT--TGTGGCCGGT
14737 GTTGCGCGGC
Statistics
Matches: 53, Mismatches: 3, Indels: 5
0.87 0.05 0.08
Matches are distributed among these distances:
30 15 0.28
31 1 0.02
32 12 0.23
33 25 0.47
ACGTcount: A:0.10, C:0.26, G:0.40, T:0.24
Consensus pattern (33 bp):
CCAAGCGATGGCCGGTTGTGGCCGGTTGGTGCG
Found at i:14880 original size:23 final size:23
Alignment explanation
Indices: 14854--14899 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
14844 CCTTCTAAGC
14854 CATGATAAGCCCTTGACGCATCA
1 CATGATAAGCCCTTGACGCATCA
*
14877 CATGATAAGCCCTTGGCGCATCA
1 CATGATAAGCCCTTGACGCATCA
14900 AACTTGAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.28, C:0.30, G:0.20, T:0.22
Consensus pattern (23 bp):
CATGATAAGCCCTTGACGCATCA
Found at i:26509 original size:8 final size:8
Alignment explanation
Indices: 26496--26529 Score: 50
Period size: 8 Copynumber: 4.1 Consensus size: 8
26486 CACCTTCTTG
26496 AAAAATTC
1 AAAAATTC
26504 AAAAATTC
1 AAAAATTC
*
26512 AGAAACTTC
1 A-AAAATTC
26521 AAAAATTC
1 AAAAATTC
26529 A
1 A
26530 TAACCGATTC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
8 16 0.70
9 7 0.30
ACGTcount: A:0.59, C:0.15, G:0.03, T:0.24
Consensus pattern (8 bp):
AAAAATTC
Found at i:26618 original size:11 final size:10
Alignment explanation
Indices: 26602--26636 Score: 61
Period size: 10 Copynumber: 3.4 Consensus size: 10
26592 AGTTATATCG
26602 AAAAATATAAA
1 AAAAATA-AAA
26613 AAAAATAAAA
1 AAAAATAAAA
26623 AAAAATAAAA
1 AAAAATAAAA
26633 AAAA
1 AAAA
26637 CTTCGACCAG
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
10 17 0.71
11 7 0.29
ACGTcount: A:0.89, C:0.00, G:0.00, T:0.11
Consensus pattern (10 bp):
AAAAATAAAA
Found at i:26620 original size:9 final size:9
Alignment explanation
Indices: 26602--26636 Score: 52
Period size: 9 Copynumber: 3.8 Consensus size: 9
26592 AGTTATATCG
*
26602 AAAAATATA
1 AAAAAAATA
26611 AAAAAAATAA
1 AAAAAAAT-A
26621 AAAAAAATA
1 AAAAAAATA
26630 AAAAAAA
1 AAAAAAA
26637 CTTCGACCAG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
9 15 0.62
10 9 0.38
ACGTcount: A:0.89, C:0.00, G:0.00, T:0.11
Consensus pattern (9 bp):
AAAAAAATA
Done.