Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01005073.1 Corchorus capsularis cultivar CVL-1 contig05091, 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: 16080
ACGTcount: A:0.36, C:0.13, G:0.15, T:0.36
Found at i:5778 original size:53 final size:53
Alignment explanation
Indices: 5684--5786 Score: 143
Period size: 53 Copynumber: 1.9 Consensus size: 53
5674 GACGTGGCAC
* ** * *
5684 GCCACGTGTACCAAAAAGTGACATGTGACACGCCACTTGTACCAAAAAGTCGT
1 GCCACATGTACCAAAAAGTGACACATGACACACCACGTGTACCAAAAAGTCGT
* *
5737 GCCACATGTATCAAAAAGTGACACATGTCACACCACGTGTACCAAAAAGT
1 GCCACATGTACCAAAAAGTGACACATGACACACCACGTGTACCAAAAAGT
5787 GACACGTGGC
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
53 43 1.00
ACGTcount: A:0.37, C:0.26, G:0.18, T:0.18
Consensus pattern (53 bp):
GCCACATGTACCAAAAAGTGACACATGACACACCACGTGTACCAAAAAGTCGT
Found at i:5814 original size:31 final size:31
Alignment explanation
Indices: 5736--5834 Score: 117
Period size: 31 Copynumber: 3.2 Consensus size: 31
5726 CAAAAAGTCG
* *
5736 TGCCACATGTATCAAAAAGTGACACATGTCA
1 TGCCACATGTATCAAAAAGTGACACGTGGCA
** * *
5767 CACCACGTGTACCAAAAAGTGACACGTGGCA
1 TGCCACATGTATCAAAAAGTGACACGTGGCA
* * *
5798 TGCCACATGTTTCAAAAAATGGCACGTGGCA
1 TGCCACATGTATCAAAAAGTGACACGTGGCA
5829 TGCCAC
1 TGCCAC
5835 GTGCACAAAA
Statistics
Matches: 55, Mismatches: 13, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
31 55 1.00
ACGTcount: A:0.34, C:0.26, G:0.20, T:0.19
Consensus pattern (31 bp):
TGCCACATGTATCAAAAAGTGACACGTGGCA
Found at i:6995 original size:2 final size:2
Alignment explanation
Indices: 6988--7034 Score: 55
Period size: 2 Copynumber: 24.5 Consensus size: 2
6978 ATTGACAACC
*
6988 AT AT AT AT A- ACT A- AT AT AT CT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
7029 -T AT AT A
1 AT AT AT A
7035 AGTCTAAACT
Statistics
Matches: 39, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
1 3 0.08
2 35 0.90
3 1 0.03
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:7334 original size:21 final size:20
Alignment explanation
Indices: 7300--7343 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
7290 ACTAAAAAAT
7300 AACAATTATCTTTTCACGTTA
1 AACAATTATCTTTTCA-GTTA
* * *
7321 AACAATTTTTTTTTGAGTTA
1 AACAATTATCTTTTCAGTTA
7341 AAC
1 AAC
7344 GTTAAACAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 7 0.35
21 13 0.65
ACGTcount: A:0.34, C:0.14, G:0.07, T:0.45
Consensus pattern (20 bp):
AACAATTATCTTTTCAGTTA
Found at i:10397 original size:2 final size:2
Alignment explanation
Indices: 10390--10415 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
10380 TAATAACATC
10390 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
10416 CTTTTTTAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:11566 original size:29 final size:29
Alignment explanation
Indices: 11506--11567 Score: 88
Period size: 29 Copynumber: 2.1 Consensus size: 29
11496 TAAACTAAAT
* **
11506 AATTATGTAACACGTTTATTGGTAGATTG
1 AATTATGTAACACGTATATTGGTAGACGG
*
11535 AATTATGTAGCACGTATATTGGTAGACGG
1 AATTATGTAACACGTATATTGGTAGACGG
11564 AATT
1 AATT
11568 TTAATGATTA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.32, C:0.08, G:0.23, T:0.37
Consensus pattern (29 bp):
AATTATGTAACACGTATATTGGTAGACGG
Found at i:13223 original size:38 final size:38
Alignment explanation
Indices: 13172--13249 Score: 131
Period size: 38 Copynumber: 2.1 Consensus size: 38
13162 TAAAATTACC
*
13172 AAAAATTCAAAGTATTAAGTAAGAATGTAAGATTGTTG
1 AAAAATTCAAAGTATTAAGTAAGAATATAAGATTGTTG
13210 AAAAATGT-AAAGTATTAAGTAAGAATATAAGATTGTTG
1 AAAAAT-TCAAAGTATTAAGTAAGAATATAAGATTGTTG
13248 AA
1 AA
13250 TTTGTTGAAA
Statistics
Matches: 38, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
38 37 0.97
39 1 0.03
ACGTcount: A:0.50, C:0.01, G:0.18, T:0.31
Consensus pattern (38 bp):
AAAAATTCAAAGTATTAAGTAAGAATATAAGATTGTTG
Found at i:14589 original size:26 final size:25
Alignment explanation
Indices: 14532--14589 Score: 64
Period size: 25 Copynumber: 2.3 Consensus size: 25
14522 GACAAAAAGC
14532 TACTAAAATTACAACATATTAAGGT
1 TACTAAAATTACAACATATTAAGGT
* * *
14557 AAATAAAATTACTA-ATGATGTAAGGT
1 TACTAAAATTACAACAT-AT-TAAGGT
14583 TACTAAA
1 TACTAAA
14590 TTTATGGAAA
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
24 2 0.08
25 13 0.50
26 11 0.42
ACGTcount: A:0.50, C:0.09, G:0.10, T:0.31
Consensus pattern (25 bp):
TACTAAAATTACAACATATTAAGGT
Found at i:15721 original size:52 final size:49
Alignment explanation
Indices: 15646--15745 Score: 155
Period size: 52 Copynumber: 2.0 Consensus size: 49
15636 AAGATTATAT
*
15646 TTTTTTATGTTATATTACAAATTATTATGCGATTTATTATATTTATTTA
1 TTTTTTATGTTATATTACAAATTAATATGCGATTTATTATATTTATTTA
*
15695 TTTTTTATGATTTATGATTACGAATTAATATGCGATTTATTATATTTATTT
1 TTTTTTATG--TTAT-ATTACAAATTAATATGCGATTTATTATATTTATTT
15746 GTTTGTTTTT
Statistics
Matches: 46, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
49 9 0.20
51 4 0.09
52 33 0.72
ACGTcount: A:0.30, C:0.04, G:0.08, T:0.58
Consensus pattern (49 bp):
TTTTTTATGTTATATTACAAATTAATATGCGATTTATTATATTTATTTA
Done.