Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015701.1 Corchorus capsularis cultivar CVL-1 contig15722, 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: 44138
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.35
Found at i:48 original size:2 final size:2
Alignment explanation
Indices: 41--77 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
31 AAAATAATTC
41 AT AT AT AT AT 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 AT AT AT AT AT A
78 CTTTTTTTCC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:6085 original size:2 final size:2
Alignment explanation
Indices: 6078--6107 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
6068 CAATTTGAGG
6078 TA TA 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
6108 GAGAGAGAGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:6112 original size:2 final size:2
Alignment explanation
Indices: 6107--6135 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
6097 ATATATATAT
6107 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
6136 TTTATGTTTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:7017 original size:315 final size:315
Alignment explanation
Indices: 6445--7069 Score: 1043
Period size: 315 Copynumber: 2.0 Consensus size: 315
6435 ACGAATATTG
*
6445 TTTTAATCCTGAAAGTGAAGAAGCCAGTGACCCCTGCTGAATTTAGACCAATTAGTTTGTGCAAT
1 TTTTAATCCTCAAAGTGAAGAAGCCAGTGACCCCTGCTGAATTTAGACCAATTAGTTTGTGCAAT
6510 GTGTTGTACAAAATTGTGTCTAAGGTTTAAGCGAACCGTTTAAAGCAAATTTTGCCTAAGAACAA
66 GTGTTGTACAAAATTGTGTCTAAGGTTTAAGCGAACCGTTTAAAGCAAATTTTGCCTAAGAACAA
* *
6575 TAGTGAGAACCATAGTGCATCTGTTATGGGGAGATTGATTTTTGACAATACTCTGGTTGCATATG
131 TAGTGAGAACCATAGTGCATCTGTCACGGGGAGATTGATTTTTGACAATACTCTGGTTGCATATG
*
6640 AAACAGTTCATAAATTAAAAAACAAGAAGTGTGGCAAAGATGGTTTTATGGCCTTGAAACTTGAC
196 AAACAGTTCATAAATTAAAAAACAAGAAGTGTGGCAAAGATGGTTTTATAGCCTTGAAACTTGAC
* * * *
6705 ATGAGTAATGCCTATGACAAAGTAGAGTGGGTCTATTTGGAGAATGTAATATTTT
261 ATGAGTAAGGCCTATGACAAAGTAGAGTAGGACTATTTAGAGAATGTAATATTTT
*
6760 TTTTAATCCTCAAAGTGTAGAAGCCAGTGACCCCTGCTGAATTTAGACCAATTAGTTTGTGCAAT
1 TTTTAATCCTCAAAGTGAAGAAGCCAGTGACCCCTGCTGAATTTAGACCAATTAGTTTGTGCAAT
* * * * * *
6825 GTGTTGTGCAAAATTGTGTCTAAGGTTTTAGCGAACCGTTTGAAGCAAATTTTGCCTGAGATCAT
66 GTGTTGTACAAAATTGTGTCTAAGGTTTAAGCGAACCGTTTAAAGCAAATTTTGCCTAAGAACAA
* * * *
6890 TAGTGAGAACCATAGTGCATTTGTCCCGGGGAGATTTATTTTTGACAATGCTCTGGTTGCATATG
131 TAGTGAGAACCATAGTGCATCTGTCACGGGGAGATTGATTTTTGACAATACTCTGGTTGCATATG
** *
6955 AAATGGTTCATAAATTGAAAAACAAGAAGTGTGGCAAAGATGGTTTTATAGCCTTGAAACTTGAC
196 AAACAGTTCATAAATTAAAAAACAAGAAGTGTGGCAAAGATGGTTTTATAGCCTTGAAACTTGAC
*
7020 ATGAGTAAGGCCTATGACAGAGTAGAGTAGGACTATTTAGAGAATGTAAT
261 ATGAGTAAGGCCTATGACAAAGTAGAGTAGGACTATTTAGAGAATGTAAT
7070 GCGGATTATG
Statistics
Matches: 287, Mismatches: 23, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
315 287 1.00
ACGTcount: A:0.32, C:0.13, G:0.23, T:0.32
Consensus pattern (315 bp):
TTTTAATCCTCAAAGTGAAGAAGCCAGTGACCCCTGCTGAATTTAGACCAATTAGTTTGTGCAAT
GTGTTGTACAAAATTGTGTCTAAGGTTTAAGCGAACCGTTTAAAGCAAATTTTGCCTAAGAACAA
TAGTGAGAACCATAGTGCATCTGTCACGGGGAGATTGATTTTTGACAATACTCTGGTTGCATATG
AAACAGTTCATAAATTAAAAAACAAGAAGTGTGGCAAAGATGGTTTTATAGCCTTGAAACTTGAC
ATGAGTAAGGCCTATGACAAAGTAGAGTAGGACTATTTAGAGAATGTAATATTTT
Found at i:12782 original size:15 final size:16
Alignment explanation
Indices: 12762--12794 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
12752 TGGCTCCGAA
12762 AATCAAAC-AATACCC
1 AATCAAACGAATACCC
*
12777 AATCAAACGAGTACCC
1 AATCAAACGAATACCC
12793 AA
1 AA
12795 AGTTGCGTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.52, C:0.30, G:0.06, T:0.12
Consensus pattern (16 bp):
AATCAAACGAATACCC
Found at i:15678 original size:6 final size:6
Alignment explanation
Indices: 15667--15691 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
15657 ATATATATTA
15667 ACTTTG ACTTTG ACTTTG ACTTTG A
1 ACTTTG ACTTTG ACTTTG ACTTTG A
15692 AGAGAGTGAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.20, C:0.16, G:0.16, T:0.48
Consensus pattern (6 bp):
ACTTTG
Found at i:16755 original size:32 final size:30
Alignment explanation
Indices: 16710--16770 Score: 88
Period size: 32 Copynumber: 2.0 Consensus size: 30
16700 CATAGGAGAA
16710 TAAATTTTCCTAAATTTAAAAAGTTCAAAGGG
1 TAAATTTTCCTAAATTTAAAAA-TT-AAAGGG
16742 TAAATTGTT-CTAAATTTAAAAATTAAAGG
1 TAAATT-TTCCTAAATTTAAAAATTAAAGG
16771 ACAAGTTATT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
30 5 0.18
31 2 0.07
32 19 0.68
33 2 0.07
ACGTcount: A:0.46, C:0.07, G:0.11, T:0.36
Consensus pattern (30 bp):
TAAATTTTCCTAAATTTAAAAATTAAAGGG
Found at i:17475 original size:11 final size:11
Alignment explanation
Indices: 17461--17486 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
17451 ACTAAGATTA
17461 TATATATATAT
1 TATATATATAT
17472 TATATATATAT
1 TATATATATAT
17483 TATA
1 TATA
17487 AAATAATAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (11 bp):
TATATATATAT
Found at i:17482 original size:13 final size:13
Alignment explanation
Indices: 17457--17482 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
17447 ATATACTAAG
17457 ATTATATATATAT
1 ATTATATATATAT
17470 ATTATATATATAT
1 ATTATATATATAT
17483 TATAAAATAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (13 bp):
ATTATATATATAT
Found at i:19188 original size:10 final size:10
Alignment explanation
Indices: 19173--19202 Score: 60
Period size: 10 Copynumber: 3.0 Consensus size: 10
19163 AAGTGGCTCG
19173 AACCCGAATT
1 AACCCGAATT
19183 AACCCGAATT
1 AACCCGAATT
19193 AACCCGAATT
1 AACCCGAATT
19203 GAATTAACTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.40, C:0.30, G:0.10, T:0.20
Consensus pattern (10 bp):
AACCCGAATT
Found at i:19782 original size:21 final size:21
Alignment explanation
Indices: 19756--19797 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
19746 CTTTTTTTTA
*
19756 GACCCGAATCCGA-TTACACTC
1 GACCCGAAACCGACTTA-ACTC
19777 GACCCGAAACCGACTTAACTC
1 GACCCGAAACCGACTTAACTC
19798 TTAAAATTGC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 16 0.84
22 3 0.16
ACGTcount: A:0.31, C:0.38, G:0.14, T:0.17
Consensus pattern (21 bp):
GACCCGAAACCGACTTAACTC
Found at i:32829 original size:92 final size:92
Alignment explanation
Indices: 32723--32921 Score: 389
Period size: 92 Copynumber: 2.2 Consensus size: 92
32713 TTATGGAAAA
32723 CTGAGGCGTGATAGTTTGGTTTGAAATAGGTTTGATTTTAATTTATTAAGCATGTAAGATCTATA
1 CTGAGGCGTGATAGTTTGGTTTGAAATAGGTTTGATTTTAATTTATTAAGCATGTAAGATCTATA
32788 ATTGAACTTAATGCTTTATTCTTGTTT
66 ATTGAACTTAATGCTTTATTCTTGTTT
*
32815 CTGAGGCGTGATAGTTTGGTTTGAAATAGGTTTGATTTTAATTTATTAAGCATGTGAGATCTATA
1 CTGAGGCGTGATAGTTTGGTTTGAAATAGGTTTGATTTTAATTTATTAAGCATGTAAGATCTATA
32880 ATTGAACTTAATGCTTTATTCTTGTTT
66 ATTGAACTTAATGCTTTATTCTTGTTT
32907 CTGAGGCGTGATAGT
1 CTGAGGCGTGATAGT
32922 ACGGAACCTT
Statistics
Matches: 106, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
92 106 1.00
ACGTcount: A:0.26, C:0.08, G:0.22, T:0.44
Consensus pattern (92 bp):
CTGAGGCGTGATAGTTTGGTTTGAAATAGGTTTGATTTTAATTTATTAAGCATGTAAGATCTATA
ATTGAACTTAATGCTTTATTCTTGTTT
Found at i:39348 original size:2 final size:2
Alignment explanation
Indices: 39343--39390 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
39333 CTCACACAAT
39343 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
39385 CA CA CA
1 CA CA CA
39391 AAAGTCTAAA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:41788 original size:22 final size:22
Alignment explanation
Indices: 41755--41832 Score: 54
Period size: 21 Copynumber: 3.6 Consensus size: 22
41745 GTTTGTTCTC
41755 TCTTCTTC-TTTCAATTCCAGTT
1 TCTT-TTCTTTTCAATTCCAGTT
* * *
41777 TCTTTTCTTTTC-TTTTCATTT
1 TCTTTTCTTTTCAATTCCAGTT
* *
41798 TCCTTT-TTTACAATTCCAGATT
1 TCTTTTCTTTTCAATTCCAG-TT
* *
41820 TCGTTTCTGTTCA
1 TCTTTTCTTTTCA
41833 TCTTTTTTGT
Statistics
Matches: 41, Mismatches: 11, Indels: 7
0.69 0.19 0.12
Matches are distributed among these distances:
20 4 0.10
21 18 0.44
22 15 0.37
23 4 0.10
ACGTcount: A:0.13, C:0.23, G:0.05, T:0.59
Consensus pattern (22 bp):
TCTTTTCTTTTCAATTCCAGTT
Found at i:42794 original size:15 final size:16
Alignment explanation
Indices: 42767--42796 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
42757 TTTCTTTCTT
42767 TTTTGTAATAATTTCC
1 TTTTGTAATAATTTCC
42783 TTTTGT-ATAATTTC
1 TTTTGTAATAATTTC
42797 TCTGTTTATG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.23, C:0.10, G:0.07, T:0.60
Consensus pattern (16 bp):
TTTTGTAATAATTTCC
Done.