Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013673.1 Corchorus capsularis cultivar CVL-1 contig13694, 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: 21717
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:281 original size:28 final size:28
Alignment explanation
Indices: 218--288 Score: 85
Period size: 28 Copynumber: 2.6 Consensus size: 28
208 CATATCATTG
218 TGCAAAATGATTAA-TTTTTTTGAGAAC
1 TGCAAAATGATTAATTTTTTTTGAGAAC
* *
245 TTG-AGAATGATTAATTTTTTTTGAAGGA-
1 -TGCAAAATGATTAATTTTTTTTG-AGAAC
273 TGCAAAATGATTAATT
1 TGCAAAATGATTAATT
289 AATTGCAATG
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
27 12 0.32
28 22 0.59
29 3 0.08
ACGTcount: A:0.37, C:0.04, G:0.17, T:0.42
Consensus pattern (28 bp):
TGCAAAATGATTAATTTTTTTTGAGAAC
Found at i:4625 original size:167 final size:164
Alignment explanation
Indices: 4252--4700 Score: 526
Period size: 167 Copynumber: 2.7 Consensus size: 164
4242 TGAGTCATTT
* * *
4252 GTCAATTGAGAAATGACCAAAAAGTTTAGTAATTTAATCCCCTCAAGAATAAAAAATTAGGACAT
1 GTCAATTGAGAAATGACCAAAAAG-TTACT-ATTTAATCCCCTCAAGAATCAAAAGTTAGGACAT
* * * * ** * *
4317 TTATGTAATCTGCCAAGTA-GATAAAGAAGAAAAAGATTAGTTCTCTAGCTCATCATCAATCCTT
64 TTAAGTAATCTGCCAAGTAGGA-AAAGACGAAAAAAATAAGTTCTCTAGCTCAAAAGCAAGCCTT
* *
4381 GATGGAGATATTTTAGTAATTCCACTACTGTATTCAA
128 GATGGAGATATTTTAGTAATTCCACTACTCTATTAAA
* * ** *
4418 GTCCATTGAGAAATGACTAAAAAGATTACTTATTTAATCCCCTCAATCATCAAAAGTTAGTACAT
1 GTCAATTGAGAAATGACCAAAAAG-TTAC-TATTTAATCCCCTCAAGAATCAAAAGTTAGGACAT
* *
4483 TTAAGTAATCTGCCAAGTAGGAAAAGTCGAAAAAAATAAGTTCTTTAGCTCCAAAAGCAAGCCTT
64 TTAAGTAATCTGCCAAGTAGGAAAAGACGAAAAAAATAAGTTCTCTAGCT-CAAAAGCAAGCCTT
* * *
4548 GGTAGG-GATCTTTTAGTAATTCCATTACTCTATTAAA
128 GAT-GGAGATATTTTAGTAATTCCACTACTCTATTAAA
*
4585 GTCAATTGAGAAATGACCAAAAAGTCTAACTATTTAATCCCCTCAAGAATCAAAAGTTAGGATAT
1 GTCAATTGAGAAATGACCAAAAAGT-T-ACTATTTAATCCCCTCAAGAATCAAAAGTTAGGACAT
* * * * *
4650 TTAAGTAATATGTCAAGTGGGAAAAAACGAAAAAAATTAA-TTCTCTCGCTC
64 TTAAGTAATCTGCCAAGTAGGAAAAGACGAAAAAAA-TAAGTTCTCTAGCTC
4701 CTCATTATTT
Statistics
Matches: 239, Mismatches: 37, Indels: 14
0.82 0.13 0.05
Matches are distributed among these distances:
166 97 0.41
167 135 0.56
168 7 0.03
ACGTcount: A:0.40, C:0.16, G:0.14, T:0.30
Consensus pattern (164 bp):
GTCAATTGAGAAATGACCAAAAAGTTACTATTTAATCCCCTCAAGAATCAAAAGTTAGGACATTT
AAGTAATCTGCCAAGTAGGAAAAGACGAAAAAAATAAGTTCTCTAGCTCAAAAGCAAGCCTTGAT
GGAGATATTTTAGTAATTCCACTACTCTATTAAA
Found at i:4820 original size:2 final size:2
Alignment explanation
Indices: 4813--4852 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
4803 TAAATAAATC
*
4813 TA TA TA TA TA TA TA TA TA TA TA TA GA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
4853 AACTTTTTGT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
TA
Found at i:5644 original size:22 final size:23
Alignment explanation
Indices: 5605--5647 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
5595 TACAACAACT
5605 TTACAAATTAAATTTGAATGAGG
1 TTACAAATTAAATTTGAATGAGG
*
5628 TTACAAA-TATATTTGAATGA
1 TTACAAATTAAATTTGAATGA
5648 AGATACGTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 12 0.63
23 7 0.37
ACGTcount: A:0.44, C:0.05, G:0.14, T:0.37
Consensus pattern (23 bp):
TTACAAATTAAATTTGAATGAGG
Found at i:6230 original size:11 final size:11
Alignment explanation
Indices: 6214--6240 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
6204 TCAAACAAAT
6214 ACATAGAAAGC
1 ACATAGAAAGC
6225 ACATAGAAAGC
1 ACATAGAAAGC
6236 ACATA
1 ACATA
6241 TGATGTGCAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.56, C:0.19, G:0.15, T:0.11
Consensus pattern (11 bp):
ACATAGAAAGC
Found at i:10298 original size:21 final size:22
Alignment explanation
Indices: 10247--10291 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
10237 TCGAAGGGAG
* *
10247 TTGCTATTTACTGCCTCCTTTT
1 TTGCTACTTACCGCCTCCTTTT
10269 TTGCTACTTACCGCCTCCTTTT
1 TTGCTACTTACCGCCTCCTTTT
10291 T
1 T
10292 GACACTTTTG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.09, C:0.31, G:0.09, T:0.51
Consensus pattern (22 bp):
TTGCTACTTACCGCCTCCTTTT
Found at i:11151 original size:13 final size:13
Alignment explanation
Indices: 11133--11157 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
11123 TTCAATGTTC
11133 TAAATATTATTTA
1 TAAATATTATTTA
11146 TAAATATTATTT
1 TAAATATTATTT
11158 GGAATTCTAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
TAAATATTATTTA
Found at i:11291 original size:3 final size:3
Alignment explanation
Indices: 11283--11328 Score: 83
Period size: 3 Copynumber: 15.3 Consensus size: 3
11273 TAAGGTATAG
*
11283 ATA ATA ATA ATA ATA ATA ATA ATA GTA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
11329 AGACTGAGTC
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:12738 original size:3 final size:3
Alignment explanation
Indices: 12723--12766 Score: 54
Period size: 3 Copynumber: 14.7 Consensus size: 3
12713 AAAGAGATAT
* *
12723 ATA ATA TTA ATA ATA ATA ATA ATA ATA ATG A-A ATA ATA GATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA -ATA AT
12767 CATTTCTAGA
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
2 1 0.03
3 31 0.89
4 3 0.09
ACGTcount: A:0.61, C:0.00, G:0.05, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:14077 original size:22 final size:22
Alignment explanation
Indices: 14050--14093 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
14040 TTTTTTAAGT
*
14050 AAAAAT-TATATTAATTATAATA
1 AAAAATGTATA-TAATCATAATA
14072 AAAAATGTATATAATCATAATA
1 AAAAATGTATATAATCATAATA
14094 TATTGAAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 16 0.80
23 4 0.20
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.36
Consensus pattern (22 bp):
AAAAATGTATATAATCATAATA
Found at i:16096 original size:146 final size:146
Alignment explanation
Indices: 15832--16119 Score: 490
Period size: 146 Copynumber: 2.0 Consensus size: 146
15822 ACCCAAAGTA
*
15832 AGGTTTGAGATTCAAATACCCCACCCTGATAAGAGCAACAACAAAGCCACGAAATTTAACCAAAT
1 AGGTTTGAGATTCAAATACCCCACCCTGATAAGAGCAACAACAAAGCCACGAAATTAAACCAAAT
* *
15897 CAAATTTGAGAAAATTAGAGCTATCTAAAATTTTTAAAAGATCATATGAAACCATGAGGCTAGCT
66 CAAATTTGAGAAAATTAGACCTATCTAAAATTTTTAAAAGATCATATGAAACCATGAGGCTACCT
15962 ATTATGATAAAAAAAT
131 ATTATGATAAAAAAAT
*
15978 AGGTTTGAGATTCAAATACCCCA-CCTCGATAAGAGCAACAACAAAGCCATGAAATTAAACCAAA
1 AGGTTTGAGATTCAAATACCCCACCCT-GATAAGAGCAACAACAAAGCCACGAAATTAAACCAAA
* *
16042 TCAAATTTGA-AGACATTAGACCTATCTAAAGTTTTTAAAAGATCATATGAAACCATGAGGCTAC
65 TCAAATTTGAGA-AAATTAGACCTATCTAAAATTTTTAAAAGATCATATGAAACCATGAGGCTAC
16106 CTATTATGATAAAA
129 CTATTATGATAAAA
16120 TAATTCCAAC
Statistics
Matches: 134, Mismatches: 6, Indels: 4
0.93 0.04 0.03
Matches are distributed among these distances:
145 4 0.03
146 130 0.97
ACGTcount: A:0.44, C:0.17, G:0.14, T:0.25
Consensus pattern (146 bp):
AGGTTTGAGATTCAAATACCCCACCCTGATAAGAGCAACAACAAAGCCACGAAATTAAACCAAAT
CAAATTTGAGAAAATTAGACCTATCTAAAATTTTTAAAAGATCATATGAAACCATGAGGCTACCT
ATTATGATAAAAAAAT
Found at i:17543 original size:21 final size:21
Alignment explanation
Indices: 17505--17545 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
17495 CCCATTTTTA
*
17505 CTTTCATTCTCTTCCTCTCTG
1 CTTTCATTCTCTCCCTCTCTG
17526 CTTTC-TTCTCTCCTCTCTCT
1 CTTTCATTCTCTCC-CTCTCT
17546 CCCGTTCTCT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.02, C:0.41, G:0.02, T:0.54
Consensus pattern (21 bp):
CTTTCATTCTCTCCCTCTCTG
Found at i:18631 original size:2 final size:2
Alignment explanation
Indices: 18624--18660 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
18614 TTTAGTAAAG
18624 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
18661 AATTATGATT
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:19874 original size:54 final size:54
Alignment explanation
Indices: 19811--19975 Score: 330
Period size: 54 Copynumber: 3.1 Consensus size: 54
19801 ATGGTATACT
19811 CAAATCAAACCAAACCAAAGAACAACCCCTTATGCTTTAATAAATTATGGGCTG
1 CAAATCAAACCAAACCAAAGAACAACCCCTTATGCTTTAATAAATTATGGGCTG
19865 CAAATCAAACCAAACCAAAGAACAACCCCTTATGCTTTAATAAATTATGGGCTG
1 CAAATCAAACCAAACCAAAGAACAACCCCTTATGCTTTAATAAATTATGGGCTG
19919 CAAATCAAACCAAACCAAAGAACAACCCCTTATGCTTTAATAAATTATGGGCTG
1 CAAATCAAACCAAACCAAAGAACAACCCCTTATGCTTTAATAAATTATGGGCTG
19973 CAA
1 CAA
19976 CTTCTTTCCG
Statistics
Matches: 111, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 111 1.00
ACGTcount: A:0.43, C:0.24, G:0.11, T:0.22
Consensus pattern (54 bp):
CAAATCAAACCAAACCAAAGAACAACCCCTTATGCTTTAATAAATTATGGGCTG
Done.