Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008201.1 Corchorus capsularis cultivar CVL-1 contig08222, 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: 22665
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:689 original size:28 final size:28
Alignment explanation
Indices: 620--689 Score: 88
Period size: 28 Copynumber: 2.5 Consensus size: 28
610 TAGTGGACTT
* *
620 AAAATAACCAAAACACCCCTTGAATGCA
1 AAAATGACCAAAATACCCCTTGAATGCA
**
648 AAAATGACCAAAATACACCC-TGAATGTG
1 AAAATGACCAAAATAC-CCCTTGAATGCA
676 AAAATGACCAAAAT
1 AAAATGACCAAAAT
690 GCCCTTATGT
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
28 34 0.92
29 3 0.08
ACGTcount: A:0.51, C:0.23, G:0.10, T:0.16
Consensus pattern (28 bp):
AAAATGACCAAAATACCCCTTGAATGCA
Found at i:3611 original size:18 final size:17
Alignment explanation
Indices: 3588--3625 Score: 58
Period size: 18 Copynumber: 2.2 Consensus size: 17
3578 TTTTCTGACC
*
3588 ATTATTATTGAACTAATT
1 ATTATTATTCAAC-AATT
3606 ATTATTATTCAACAATT
1 ATTATTATTCAACAATT
3623 ATT
1 ATT
3626 CCTAATTTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 7 0.37
18 12 0.63
ACGTcount: A:0.39, C:0.08, G:0.03, T:0.50
Consensus pattern (17 bp):
ATTATTATTCAACAATT
Found at i:5320 original size:31 final size:32
Alignment explanation
Indices: 5285--5348 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 32
5275 TCAATTCTGG
5285 ACAATGAAAG-AAGACTTATCACATCTAACTA
1 ACAATGAAAGAAAGACTTATCACATCTAACTA
**
5316 ACAATGAAAGAAAGACTTATCTGATCTAACTA
1 ACAATGAAAGAAAGACTTATCACATCTAACTA
5348 A
1 A
5349 ACTTCATGGA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
31 10 0.33
32 20 0.67
ACGTcount: A:0.48, C:0.17, G:0.11, T:0.23
Consensus pattern (32 bp):
ACAATGAAAGAAAGACTTATCACATCTAACTA
Found at i:8499 original size:31 final size:31
Alignment explanation
Indices: 8460--8544 Score: 116
Period size: 32 Copynumber: 2.7 Consensus size: 31
8450 GCGTTTACTA
8460 AAGAAAACGCCCTTATTTTGGGCGTCTATAG
1 AAGAAAACGCCCTTATTTTGGGCGTCTATAG
* **
8491 AAGCAAACGCCCTTGCTTTGAGGCGTCTATAG
1 AAGAAAACGCCCTTATTTTG-GGCGTCTATAG
* *
8523 AAGAAAATGCCCCTATTTTGGG
1 AAGAAAACGCCCTTATTTTGGG
8545 GTGTTCAATA
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
31 19 0.42
32 26 0.58
ACGTcount: A:0.28, C:0.21, G:0.24, T:0.27
Consensus pattern (31 bp):
AAGAAAACGCCCTTATTTTGGGCGTCTATAG
Found at i:8591 original size:20 final size:20
Alignment explanation
Indices: 8566--8603 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
8556 AGAAAGGGGA
8566 TTACTAAATACCGCCCCCTT
1 TTACTAAATACCGCCCCCTT
**
8586 TTACTAGGTACCGCCCCC
1 TTACTAAATACCGCCCCC
8604 CCTTTGGACT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.42, G:0.11, T:0.26
Consensus pattern (20 bp):
TTACTAAATACCGCCCCCTT
Found at i:8853 original size:14 final size:14
Alignment explanation
Indices: 8834--8861 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
8824 ATTAAAGTCC
8834 TCTTGCTAATATTA
1 TCTTGCTAATATTA
8848 TCTTGCTAATATTA
1 TCTTGCTAATATTA
8862 ACATATCCAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.14, G:0.07, T:0.50
Consensus pattern (14 bp):
TCTTGCTAATATTA
Found at i:9044 original size:17 final size:18
Alignment explanation
Indices: 9019--9054 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
9009 CGCGACCTGC
9019 TGTTCTTCTT-TTTTTTT
1 TGTTCTTCTTCTTTTTTT
*
9036 TGTTTTTCTTCTTTTTTT
1 TGTTCTTCTTCTTTTTTT
9054 T
1 T
9055 TCTTCTTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 9 0.53
18 8 0.47
ACGTcount: A:0.00, C:0.11, G:0.06, T:0.83
Consensus pattern (18 bp):
TGTTCTTCTTCTTTTTTT
Found at i:9052 original size:16 final size:16
Alignment explanation
Indices: 9021--9061 Score: 55
Period size: 17 Copynumber: 2.5 Consensus size: 16
9011 CGACCTGCTG
*
9021 TTCTTCTTTTTTTTTT
1 TTCTTCTTCTTTTTTT
*
9037 GTTTTTCTTCTTTTTTT
1 -TTCTTCTTCTTTTTTT
9054 TTCTTCTT
1 TTCTTCTT
9062 TAAAGGCTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
16 7 0.33
17 14 0.67
ACGTcount: A:0.00, C:0.15, G:0.02, T:0.83
Consensus pattern (16 bp):
TTCTTCTTCTTTTTTT
Found at i:9056 original size:13 final size:14
Alignment explanation
Indices: 9033--9062 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
9023 CTTCTTTTTT
9033 TTTTGTTTTTCTTC
1 TTTTGTTTTTCTTC
9047 TTTT-TTTTTCTTC
1 TTTTGTTTTTCTTC
9060 TTT
1 TTT
9063 AAAGGCTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 12 0.75
14 4 0.25
ACGTcount: A:0.00, C:0.13, G:0.03, T:0.83
Consensus pattern (14 bp):
TTTTGTTTTTCTTC
Found at i:19072 original size:149 final size:149
Alignment explanation
Indices: 18624--19073 Score: 783
Period size: 149 Copynumber: 3.0 Consensus size: 149
18614 GGTTTCTTCA
* * * *
18624 ACAAATCTTGGTCATTGTAAATCTCTCCAAACGTTTGTAGAATTTGAGCCATTGAGATTGGCAGT
1 ACAAATCTTGGTCATTATAAATCTCTCCAAACGTTTGCAGAATTTGAGCCGTTGAGATTGGCAGG
* *
18689 AACAAAGTTCTGTTTGTTAAGGTTGTGTTTAGTAGAGCGGTGCGATTAACTCCATTTGATTGAAA
66 AACAAAGCTCTGTTTGTTAAGGTTGTGTTTAGTAGAGCGGTGCGATTGACTCCATTTGATTGAAA
*
18754 TGGTGAGATTAAACACTAT
131 TGGTGAGATTAAACACTGT
18773 ACAAATCTTGGTCATTATAAATCTCTCCAAACGTTTGCAGAATTTGAGCCGTTGAGATTGGCAGG
1 ACAAATCTTGGTCATTATAAATCTCTCCAAACGTTTGCAGAATTTGAGCCGTTGAGATTGGCAGG
* *
18838 AACAAAGCTCTATTTGTTAAGGTTGTGTTTAGTAGAGCGGTGCGATTGACTTCATTTGATTGAAA
66 AACAAAGCTCTGTTTGTTAAGGTTGTGTTTAGTAGAGCGGTGCGATTGACTCCATTTGATTGAAA
18903 TGGTGAGATTAAACACTGT
131 TGGTGAGATTAAACACTGT
*
18922 ACAAATCTTGGTCATTATAAATCTCTCCAAACGTTTGCAGAATTTGAGCTGTTGAGATTGGCAGG
1 ACAAATCTTGGTCATTATAAATCTCTCCAAACGTTTGCAGAATTTGAGCCGTTGAGATTGGCAGG
* *
18987 AACAAAACTCTGTTTGTTAAGGTTGTGTTTAGTAGAGCGGTGCAATTGACTCCATTTGATTGAAA
66 AACAAAGCTCTGTTTGTTAAGGTTGTGTTTAGTAGAGCGGTGCGATTGACTCCATTTGATTGAAA
*
19052 TGGTGAGATTAAACATTGT
131 TGGTGAGATTAAACACTGT
19071 ACA
1 ACA
19074 GATGAGAATA
Statistics
Matches: 286, Mismatches: 15, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
149 286 1.00
ACGTcount: A:0.30, C:0.14, G:0.23, T:0.34
Consensus pattern (149 bp):
ACAAATCTTGGTCATTATAAATCTCTCCAAACGTTTGCAGAATTTGAGCCGTTGAGATTGGCAGG
AACAAAGCTCTGTTTGTTAAGGTTGTGTTTAGTAGAGCGGTGCGATTGACTCCATTTGATTGAAA
TGGTGAGATTAAACACTGT
Found at i:19758 original size:124 final size:124
Alignment explanation
Indices: 19538--19777 Score: 417
Period size: 124 Copynumber: 1.9 Consensus size: 124
19528 AGGGAAAGAA
19538 TCTATAACTACATATAAAAGCAAAGTACAAGGGCCCTCTCTCACCAAATGTTGACAAGTCGCGCA
1 TCTATAACTACATATAAAAGCAAAGTACAAGGGCCCTCTCTCACCAAATGTTGACAAGTCGCGCA
* *
19603 ATGTGGTGGAGATATTCTATTTGGCCTTATTTAGGCTTATGTGTTGGATATCTATAACT
66 ATGCGGTGGAGATATTCTATTTGGCCTTATTTAGGCTTATGTGGTGGATATCTATAACT
* * *
19662 TCTATAACTACATATAAAAGCAAGGTACAAGGGCTCTCTCTCACCAAATGTTGACAAGTGGCGCA
1 TCTATAACTACATATAAAAGCAAAGTACAAGGGCCCTCTCTCACCAAATGTTGACAAGTCGCGCA
**
19727 ATGCGGTGGAGATATTCTATTTGGGTTTATTTAGGCTTATGTGGTGGATAT
66 ATGCGGTGGAGATATTCTATTTGGCCTTATTTAGGCTTATGTGGTGGATAT
19778 ATTCTATTTG
Statistics
Matches: 109, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
124 109 1.00
ACGTcount: A:0.29, C:0.17, G:0.22, T:0.32
Consensus pattern (124 bp):
TCTATAACTACATATAAAAGCAAAGTACAAGGGCCCTCTCTCACCAAATGTTGACAAGTCGCGCA
ATGCGGTGGAGATATTCTATTTGGCCTTATTTAGGCTTATGTGGTGGATATCTATAACT
Found at i:19991 original size:48 final size:48
Alignment explanation
Indices: 19936--20054 Score: 150
Period size: 48 Copynumber: 2.5 Consensus size: 48
19926 ATTTATGTTG
* * * *
19936 GGTTATCTATTACCTAATTAGTC-AAATGTTATTTTTTTGTTAACATTA
1 GGTTATCTAATACCTAATT-CTCTAAAGGTAATTTTTTTGTTAACATTA
* ** *
19984 TGTTATCTAATACCTAATTCTCTCTAGGTAATTTTTTTGTTAGCATTA
1 GGTTATCTAATACCTAATTCTCTAAAGGTAATTTTTTTGTTAACATTA
20032 GGTTATCTAATACCTAATTCTCT
1 GGTTATCTAATACCTAATTCTCT
20055 TTAGGTCATT
Statistics
Matches: 61, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
47 2 0.03
48 59 0.97
ACGTcount: A:0.27, C:0.14, G:0.10, T:0.49
Consensus pattern (48 bp):
GGTTATCTAATACCTAATTCTCTAAAGGTAATTTTTTTGTTAACATTA
Found at i:20060 original size:48 final size:48
Alignment explanation
Indices: 19966--20060 Score: 163
Period size: 48 Copynumber: 2.0 Consensus size: 48
19956 GTCAAATGTT
*
19966 ATTTTTTTGTTAACATTATGTTATCTAATACCTAATTCTCTCTAGGTA
1 ATTTTTTTGTTAACATTAGGTTATCTAATACCTAATTCTCTCTAGGTA
* *
20014 ATTTTTTTGTTAGCATTAGGTTATCTAATACCTAATTCTCTTTAGGT
1 ATTTTTTTGTTAACATTAGGTTATCTAATACCTAATTCTCTCTAGGT
20061 CATTGAACAA
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
48 44 1.00
ACGTcount: A:0.25, C:0.14, G:0.11, T:0.51
Consensus pattern (48 bp):
ATTTTTTTGTTAACATTAGGTTATCTAATACCTAATTCTCTCTAGGTA
Found at i:20261 original size:167 final size:167
Alignment explanation
Indices: 20070--20378 Score: 555
Period size: 167 Copynumber: 1.9 Consensus size: 167
20060 TCATTGAACA
* *
20070 AACTACTCTTTGTGCTAATTGTGTTTTGGCTAAAAATTTATTGTACTTTAATTCCCAAGTGTTAT
1 AACTACTATTTGTGCTAATTGTGTTTTGGCTAAAAATTAATTGTACTTTAATTCCCAAGTGTTAT
* ** *
20135 TTTTGGGTCTGCATTATATTTCCTTTCCTTTAACCTATTACTAATTGTGTTTTGGCTAAAAAATT
66 TTTTGGGTCTGCATCATATTTCCTTTCCTTTAACCTACCACTAATTGTGTTTTGGCAAAAAAATT
20200 ATTTTACTCTAACTACTATTTTTTTTATCAATACTCT
131 ATTTTACTCTAACTACTATTTTTTTTATCAATACTCT
*
20237 AACTACTATTTGTGCTAATTGTGTTTTGGCTTAAAATTAATTGTACTTTAATTCCCAAGTGTTAT
1 AACTACTATTTGTGCTAATTGTGTTTTGGCTAAAAATTAATTGTACTTTAATTCCCAAGTGTTAT
20302 TTTTGGGTCTGCATCATATTTCCTTTCCTTTAACCTACCACTAATTGTGTTTTGGCAAAAAAATT
66 TTTTGGGTCTGCATCATATTTCCTTTCCTTTAACCTACCACTAATTGTGTTTTGGCAAAAAAATT
20367 ATTTTACTCTAA
131 ATTTTACTCTAA
20379 TGCCCAATTC
Statistics
Matches: 135, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
167 135 1.00
ACGTcount: A:0.26, C:0.16, G:0.11, T:0.47
Consensus pattern (167 bp):
AACTACTATTTGTGCTAATTGTGTTTTGGCTAAAAATTAATTGTACTTTAATTCCCAAGTGTTAT
TTTTGGGTCTGCATCATATTTCCTTTCCTTTAACCTACCACTAATTGTGTTTTGGCAAAAAAATT
ATTTTACTCTAACTACTATTTTTTTTATCAATACTCT
Done.