Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012948.1 Corchorus capsularis cultivar CVL-1 contig12969, 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: 24313
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:781 original size:41 final size:41
Alignment explanation
Indices: 710--820 Score: 147
Period size: 41 Copynumber: 2.7 Consensus size: 41
700 AATTTCTAAG
*
710 AGTCTTCTCTTGGATTT-TT-AAAAACATTTATTTTCCAAA
1 AGTCTTATCTTGGATTTGTTAAAAAACATTTATTTTCCAAA
*
749 AGTCTTAT-TTCGGATTTGTTAAAAAACATTTATTTTCTAAA
1 AGTCTTATCTT-GGATTTGTTAAAAAACATTTATTTTCCAAA
* *
790 AGTCTTCTCTTGGAATTGCTTAAAAAACATT
1 AGTCTTATCTTGGATTTG-TTAAAAAACATT
821 CTTTTTAAAA
Statistics
Matches: 63, Mismatches: 4, Indels: 7
0.85 0.05 0.09
Matches are distributed among these distances:
38 2 0.03
39 13 0.21
40 2 0.03
41 32 0.51
42 14 0.22
ACGTcount: A:0.32, C:0.14, G:0.10, T:0.44
Consensus pattern (41 bp):
AGTCTTATCTTGGATTTGTTAAAAAACATTTATTTTCCAAA
Found at i:4384 original size:2 final size:2
Alignment explanation
Indices: 4379--4414 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
4369 ACACACACAG
*
4379 AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT -T AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
4415 AATCATGTGC
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:6131 original size:24 final size:24
Alignment explanation
Indices: 6060--6134 Score: 89
Period size: 24 Copynumber: 3.1 Consensus size: 24
6050 ATAAGTCATA
*
6060 GTGGTCGTGAGATTCGATCACATA
1 GTGGTCGTGAGATTCGATCACATG
* * * *
6084 GTGCTGGTGAGA-TCTAACCACATG
1 GTGGTCGTGAGATTC-GATCACATG
6108 GTGGTCGTGAGATTCGATCACATG
1 GTGGTCGTGAGATTCGATCACATG
6132 GTG
1 GTG
6135 ACACACCGGT
Statistics
Matches: 40, Mismatches: 9, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
23 2 0.05
24 36 0.90
25 2 0.05
ACGTcount: A:0.23, C:0.17, G:0.32, T:0.28
Consensus pattern (24 bp):
GTGGTCGTGAGATTCGATCACATG
Found at i:16818 original size:6 final size:6
Alignment explanation
Indices: 16807--16833 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
16797 AAAGCAAAGC
16807 AAATCT AAATCT AAATCT AAATCT AAA
1 AAATCT AAATCT AAATCT AAATCT AAA
16834 GCAGATTATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.56, C:0.15, G:0.00, T:0.30
Consensus pattern (6 bp):
AAATCT
Found at i:19690 original size:15 final size:16
Alignment explanation
Indices: 19666--19697 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
19656 AAAATCCTAA
19666 AAAACAAAAGAAAAAT
1 AAAACAAAAGAAAAAT
19682 AAAAC-AAAGAAAAAT
1 AAAACAAAAGAAAAAT
19697 A
1 A
19698 TTATGGGTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.69
16 5 0.31
ACGTcount: A:0.81, C:0.06, G:0.06, T:0.06
Consensus pattern (16 bp):
AAAACAAAAGAAAAAT
Found at i:22455 original size:21 final size:22
Alignment explanation
Indices: 22429--22472 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
22419 ACTCTTGGAA
*
22429 TTACTGATCAC-CTTTTACTCT
1 TTACTGATCACTATTTTACTCT
*
22450 TTACTGATTACTATTTTACTCT
1 TTACTGATCACTATTTTACTCT
22472 T
1 T
22473 ACTAATTACC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 10 0.50
22 10 0.50
ACGTcount: A:0.20, C:0.23, G:0.05, T:0.52
Consensus pattern (22 bp):
TTACTGATCACTATTTTACTCT
Found at i:22474 original size:21 final size:21
Alignment explanation
Indices: 22441--22566 Score: 97
Period size: 21 Copynumber: 6.3 Consensus size: 21
22431 ACTGATCACC
22441 TTTTACTCTTTACTGATTACTA
1 TTTTACTC-TTACTGATTACTA
* *
22463 TTTTACTCTTACTAATTACCA
1 TTTTACTCTTACTGATTACTA
* * ** *
22484 CTTTGCTCCCACTGATTACTG
1 TTTTACTCTTACTGATTACTA
22505 TTTTACTCTTACTGATTAC--
1 TTTTACTCTTACTGATTACTA
* *
22524 -CTTA----TATTGATTACTA
1 TTTTACTCTTACTGATTACTA
*
22540 TTTTACTCTTACTGATTAC-C
1 TTTTACTCTTACTGATTACTA
22560 TTTTACT
1 TTTTACT
22567 GATTACCTTC
Statistics
Matches: 79, Mismatches: 18, Indels: 16
0.70 0.16 0.14
Matches are distributed among these distances:
14 9 0.11
17 3 0.04
18 3 0.04
20 7 0.09
21 49 0.62
22 8 0.10
ACGTcount: A:0.22, C:0.22, G:0.06, T:0.50
Consensus pattern (21 bp):
TTTTACTCTTACTGATTACTA
Found at i:22535 original size:35 final size:34
Alignment explanation
Indices: 22494--22594 Score: 130
Period size: 35 Copynumber: 2.9 Consensus size: 34
22484 CTTTGCTCCC
22494 ACTGATTACTGTTTTACTCTTACTGATTACCTTAT
1 ACTGATTACT-TTTTACTCTTACTGATTACCTTAT
* *
22529 ATTGATTACTATTTTACTCTTACTGATTACCTTTT
1 ACTGATTACT-TTTTACTCTTACTGATTACCTTAT
* * *
22564 ACTGATTACCTTCTTACTCTCATTGATTACC
1 ACTGATTA-CTTTTTACTCTTACTGATTACC
22595 ATTTTGCTCT
Statistics
Matches: 58, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
35 56 0.97
36 2 0.03
ACGTcount: A:0.23, C:0.22, G:0.07, T:0.49
Consensus pattern (34 bp):
ACTGATTACTTTTTACTCTTACTGATTACCTTAT
Found at i:22537 original size:56 final size:55
Alignment explanation
Indices: 22477--22635 Score: 151
Period size: 56 Copynumber: 2.8 Consensus size: 55
22467 ACTCTTACTA
* ** * * *
22477 ATTACCACTTTGCTCCCACTGATTACTGTTTTACTCTTACTGATTAC-CTTATATTG
1 ATTACCATTTTGCTCTTACTGATTACTATTTTACTATTACTGATTACTC-T-CATTG
* * * **
22533 ATTACTATTTTACTCTTACTGATTAC-CTTTTACTGATTACCTTCTTACTCTCATTG
1 ATTACCATTTTGCTCTTACTGATTACTATTTTACT-ATTA-CTGATTACTCTCATTG
*
22589 ATTACCATTTTGCTCTTACTGATTACTATTTTACCTTTTACTGATTA
1 ATTACCATTTTGCTCTTACTGATTACTATTTTA-CTATTACTGATTA
22636 TCATTACTTT
Statistics
Matches: 82, Mismatches: 16, Indels: 10
0.76 0.15 0.09
Matches are distributed among these distances:
55 7 0.09
56 57 0.70
57 15 0.18
58 3 0.04
ACGTcount: A:0.22, C:0.23, G:0.07, T:0.48
Consensus pattern (55 bp):
ATTACCATTTTGCTCTTACTGATTACTATTTTACTATTACTGATTACTCTCATTG
Found at i:22565 original size:14 final size:15
Alignment explanation
Indices: 22546--22581 Score: 65
Period size: 14 Copynumber: 2.5 Consensus size: 15
22536 ACTATTTTAC
22546 TCTTACTGATTACCT
1 TCTTACTGATTACCT
22561 T-TTACTGATTACCT
1 TCTTACTGATTACCT
22575 TCTTACT
1 TCTTACT
22582 CTCATTGATT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 14 0.70
15 6 0.30
ACGTcount: A:0.19, C:0.25, G:0.06, T:0.50
Consensus pattern (15 bp):
TCTTACTGATTACCT
Found at i:22572 original size:21 final size:21
Alignment explanation
Indices: 22531--22572 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
22521 TACCTTATAT
*
22531 TGATTACTATTTTACTCTTAC
1 TGATTACTATTTTACTATTAC
*
22552 TGATTAC-CTTTTACTGATTAC
1 TGATTACTATTTTACT-ATTAC
22573 CTTCTTACTC
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.24, C:0.19, G:0.07, T:0.50
Consensus pattern (21 bp):
TGATTACTATTTTACTATTAC
Found at i:22604 original size:21 final size:21
Alignment explanation
Indices: 22564--22640 Score: 66
Period size: 21 Copynumber: 3.6 Consensus size: 21
22554 ATTACCTTTT
22564 ACTGATTACC-TTCTTACTCTC
1 ACTGATTACCATT-TTACTCTC
* * *
22585 ATTGATTACCATTTTGCTCTT
1 ACTGATTACCATTTTACTCTC
* * *
22606 ACTGATTACTATTTTACCTTTT
1 ACTGATTACCATTTTA-CTCTC
*
22628 ACTGATTATCATT
1 ACTGATTACCATT
22641 ACTTTTTTTA
Statistics
Matches: 45, Mismatches: 9, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
21 28 0.62
22 17 0.38
ACGTcount: A:0.22, C:0.22, G:0.06, T:0.49
Consensus pattern (21 bp):
ACTGATTACCATTTTACTCTC
Found at i:22705 original size:22 final size:22
Alignment explanation
Indices: 22604--22706 Score: 59
Period size: 22 Copynumber: 4.5 Consensus size: 22
22594 CATTTTGCTC
*
22604 TTACTGATTA-CTATTTTACCTT
1 TTACTGATTATCT-TTTTACTTT
*
22626 TTACTGATTATC--ATTACTTTTT
1 TTACTGATTATCTTTTTAC--TTT
* *
22648 TTATTGATTACCTTTTACTACTTCAT
1 TTACTGATTATCTTTT--TACTT--T
**
22674 TCTTTTGATTATCTTTTTACTTT
1 T-TACTGATTATCTTTTTACTTT
22697 TTACTGATTA
1 TTACTGATTA
22707 CCCTTTTATT
Statistics
Matches: 62, Mismatches: 9, Indels: 20
0.68 0.10 0.22
Matches are distributed among these distances:
20 4 0.06
22 29 0.47
23 3 0.05
24 3 0.05
25 5 0.08
26 5 0.08
27 13 0.21
ACGTcount: A:0.21, C:0.16, G:0.05, T:0.58
Consensus pattern (22 bp):
TTACTGATTATCTTTTTACTTT
Found at i:22721 original size:22 final size:21
Alignment explanation
Indices: 22672--22722 Score: 52
Period size: 22 Copynumber: 2.4 Consensus size: 21
22662 TTACTACTTC
* *
22672 ATTCTTT-TGATTATCTTTTT
1 ATTCTTTATGATTACCCTTTT
22692 ACTT-TTTACTGATTACCCTTTT
1 A-TTCTTTA-TGATTACCCTTTT
22714 ATTCTTTAT
1 ATTCTTTAT
22723 CTTCTTCCTT
Statistics
Matches: 25, Mismatches: 2, Indels: 7
0.74 0.06 0.21
Matches are distributed among these distances:
20 4 0.16
21 5 0.20
22 16 0.64
ACGTcount: A:0.18, C:0.16, G:0.04, T:0.63
Consensus pattern (21 bp):
ATTCTTTATGATTACCCTTTT
Found at i:22982 original size:16 final size:16
Alignment explanation
Indices: 22929--22984 Score: 53
Period size: 16 Copynumber: 3.4 Consensus size: 16
22919 CTTAATCTCT
22929 TTTTACTGATTACTATC
1 TTTTACTGATTACTA-C
* *
22946 TTTTACTTAATTGCTGA-
1 TTTTAC-TGATTACT-AC
22963 -TTTACTGATTACTAC
1 TTTTACTGATTACTAC
22978 TTTTACT
1 TTTTACT
22985 CCCTTAATTA
Statistics
Matches: 31, Mismatches: 4, Indels: 9
0.70 0.09 0.20
Matches are distributed among these distances:
14 1 0.03
15 6 0.19
16 11 0.35
17 6 0.19
18 6 0.19
19 1 0.03
ACGTcount: A:0.23, C:0.16, G:0.07, T:0.54
Consensus pattern (16 bp):
TTTTACTGATTACTAC
Done.