Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010915.1 Corchorus capsularis cultivar CVL-1 contig10936, 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: 36873
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:7 original size:2 final size:2
Alignment explanation
Indices: 1--37 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
38 GAAGAAGAAG
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:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:676 original size:16 final size:15
Alignment explanation
Indices: 653--686 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
643 GGTGATTACC
653 AATTCTAATAATTAT
1 AATTCTAATAATTAT
*
668 AATTCCTAATTATTAT
1 AATT-CTAATAATTAT
684 AAT
1 AAT
687 AACATTGCTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 4 0.24
16 13 0.76
ACGTcount: A:0.44, C:0.09, G:0.00, T:0.47
Consensus pattern (15 bp):
AATTCTAATAATTAT
Found at i:3800 original size:20 final size:21
Alignment explanation
Indices: 3764--3805 Score: 52
Period size: 20 Copynumber: 2.0 Consensus size: 21
3754 CAATATTGAA
*
3764 TGCAAGGATCAAGATAT-GAC
1 TGCAAGGATAAAGATATCGAC
3784 TGCAAGGA-AAAGAATATCGAC
1 TGCAAGGATAAAG-ATATCGAC
3805 T
1 T
3806 TCTAGCAACT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
19 3 0.16
20 12 0.63
21 4 0.21
ACGTcount: A:0.43, C:0.14, G:0.24, T:0.19
Consensus pattern (21 bp):
TGCAAGGATAAAGATATCGAC
Found at i:10565 original size:15 final size:16
Alignment explanation
Indices: 10538--10567 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
10528 AAGCAAAACA
10538 TAAGTGAATCTCAAAG
1 TAAGTGAATCTCAAAG
10554 TAAGTG-ATCTCAAA
1 TAAGTGAATCTCAAA
10568 CAAACCAAAC
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:0.43, C:0.13, G:0.17, T:0.27
Consensus pattern (16 bp):
TAAGTGAATCTCAAAG
Found at i:15353 original size:21 final size:21
Alignment explanation
Indices: 15300--15355 Score: 69
Period size: 21 Copynumber: 2.7 Consensus size: 21
15290 TTCTCATTTA
15300 TATAGTATCTAATTTGATATG
1 TATAGTATCTAATTTGATATG
* *
15321 TATAATATCTAATTTGATTTG
1 TATAGTATCTAATTTGATATG
*
15342 T-TCAGTAACTAATT
1 TAT-AGTATCTAATT
15356 ACTAATCGCA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
20 1 0.03
21 29 0.97
ACGTcount: A:0.34, C:0.07, G:0.11, T:0.48
Consensus pattern (21 bp):
TATAGTATCTAATTTGATATG
Found at i:16565 original size:13 final size:13
Alignment explanation
Indices: 16547--16571 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
16537 TGCAATTTAA
16547 AGAAATTAAAGAT
1 AGAAATTAAAGAT
16560 AGAAATTAAAGA
1 AGAAATTAAAGA
16572 AATTGCTATA
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:0.64, C:0.00, G:0.16, T:0.20
Consensus pattern (13 bp):
AGAAATTAAAGAT
Found at i:18247 original size:10 final size:11
Alignment explanation
Indices: 18224--18261 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
18214 AGTTATATCG
*
18224 AAAAATATCAA
1 AAAAATATAAA
18235 AAAAATA-AAA
1 AAAAATATAAA
*
18245 AAAAATATATA
1 AAAAATATAAA
18256 AAAAAT
1 AAAAAT
18262 TTTTTGACCA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
10 9 0.38
11 15 0.62
ACGTcount: A:0.79, C:0.03, G:0.00, T:0.18
Consensus pattern (11 bp):
AAAAATATAAA
Found at i:22604 original size:176 final size:176
Alignment explanation
Indices: 22310--22660 Score: 684
Period size: 176 Copynumber: 2.0 Consensus size: 176
22300 CATTGGAGAC
22310 CATGTCTTGGATAAACATGGAGATGTCTTGGAGATTCAAGAAGATGCCACGGATGATCCCGGATT
1 CATGTCTTGGATAAACATGGAGATGTCTTGGAGATTCAAGAAGATGCCACGGATGATCCCGGATT
22375 GAACACAAGCTTGGCGGAGCAAGGAGTTGAGGACCGGCCACCATCGCATGGAGCAACCGGCCAAC
66 GAACACAAGCTTGGCGGAGCAAGGAGTTGAGGACCGGCCACCATCGCATGGAGCAACCGGCCAAC
* *
22440 GCATGGGACATCGCACGGGCCATCTGGCCACAACCGGCCACTTGAT
131 GCATGGGACATCGCACGGGCCATCCGGCCACAACCGACCACTTGAT
22486 CATGTCTTGGATAAACATGGAGATGTCTTGGAGATTCAAGAAGATGCCACGGATGATCCCGGATT
1 CATGTCTTGGATAAACATGGAGATGTCTTGGAGATTCAAGAAGATGCCACGGATGATCCCGGATT
22551 GAACACAAGCTTGGCGGAGCAAGGAGTTGAGGACCGGCCACCATCGCATGGAGCAACCGGCCAAC
66 GAACACAAGCTTGGCGGAGCAAGGAGTTGAGGACCGGCCACCATCGCATGGAGCAACCGGCCAAC
22616 GCATGGGACATCGCACGGGCCATCCGGCCACAACCGACCACTTGA
131 GCATGGGACATCGCACGGGCCATCCGGCCACAACCGACCACTTGA
22661 CCCTTTAGCC
Statistics
Matches: 173, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
176 173 1.00
ACGTcount: A:0.28, C:0.26, G:0.29, T:0.17
Consensus pattern (176 bp):
CATGTCTTGGATAAACATGGAGATGTCTTGGAGATTCAAGAAGATGCCACGGATGATCCCGGATT
GAACACAAGCTTGGCGGAGCAAGGAGTTGAGGACCGGCCACCATCGCATGGAGCAACCGGCCAAC
GCATGGGACATCGCACGGGCCATCCGGCCACAACCGACCACTTGAT
Found at i:30341 original size:49 final size:48
Alignment explanation
Indices: 30311--30537 Score: 285
Period size: 48 Copynumber: 4.7 Consensus size: 48
30301 ATTAACGCCC
* * *
30311 TCCGTCCGGGAAGGGCATTTTA-GGAAAAAGCAAATAAAAGAAGTGCCT
1 TCCGTCCGGGAAGGGC-GTTTAGGGAAAAAGCAAGTAAAATAAGTGCCT
* *
30359 TCCGTCCAGGAAGGGCGTTTAGGGAAAAAGCAAGTAAAAATTGAGTGCCT
1 TCCGTCCGGGAAGGGCGTTTAGGGAAAAAGCAAGT-AAAA-TAAGTGCCT
* *
30409 TACGTCCGGGAAAGGCGTTTAGGGAAAAAGCAAGTAAAAATAAGTGCCT
1 TCCGTCCGGGAAGGGCGTTTAGGGAAAAAGCAAGT-AAAATAAGTGCCT
** *
30458 TCCGTCTAGGAAGGGCGTTTTGGGAAAAAGCAAGTAAAATAAGTGCCT
1 TCCGTCCGGGAAGGGCGTTTAGGGAAAAAGCAAGTAAAATAAGTGCCT
* * * *
30506 TCCGTCCGAGAAGGGTGTTTTGGGAAATAGCA
1 TCCGTCCGGGAAGGGCGTTTAGGGAAAAAGCA
30538 TATAAAAACT
Statistics
Matches: 157, Mismatches: 19, Indels: 6
0.86 0.10 0.03
Matches are distributed among these distances:
47 4 0.03
48 67 0.43
49 42 0.27
50 44 0.28
ACGTcount: A:0.34, C:0.15, G:0.30, T:0.21
Consensus pattern (48 bp):
TCCGTCCGGGAAGGGCGTTTAGGGAAAAAGCAAGTAAAATAAGTGCCT
Done.