Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013893.1 Corchorus capsularis cultivar CVL-1 contig13914, 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: 52965
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.31
Found at i:3509 original size:13 final size:13
Alignment explanation
Indices: 3487--3524 Score: 58
Period size: 13 Copynumber: 2.9 Consensus size: 13
3477 GGATAATTGT
*
3487 ATTTGACCCTCCA
1 ATTTGTCCCTCCA
*
3500 ATTTGTCCCTGCA
1 ATTTGTCCCTCCA
3513 ATTTGTCCCTCC
1 ATTTGTCCCTCC
3525 TAATAATCAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.16, C:0.37, G:0.11, T:0.37
Consensus pattern (13 bp):
ATTTGTCCCTCCA
Found at i:3582 original size:40 final size:40
Alignment explanation
Indices: 3527--3602 Score: 125
Period size: 40 Copynumber: 1.9 Consensus size: 40
3517 GTCCCTCCTA
*
3527 ATAATCAAGGAAACAAATTAAATTCAGGTTTAGCCCCCTG
1 ATAATCAAGGAAACAAATTAAATCCAGGTTTAGCCCCCTG
* *
3567 ATAATTAAGGTAACAAATTAAATCCAGGTTTAGCCC
1 ATAATCAAGGAAACAAATTAAATCCAGGTTTAGCCC
3603 ATAGTTATAA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 33 1.00
ACGTcount: A:0.41, C:0.18, G:0.14, T:0.26
Consensus pattern (40 bp):
ATAATCAAGGAAACAAATTAAATCCAGGTTTAGCCCCCTG
Found at i:20867 original size:12 final size:13
Alignment explanation
Indices: 20847--20878 Score: 57
Period size: 12 Copynumber: 2.5 Consensus size: 13
20837 AACTCTTCCT
20847 TAAACTTCAAATG
1 TAAACTTCAAATG
20860 TAAA-TTCAAATG
1 TAAACTTCAAATG
20872 TAAACTT
1 TAAACTT
20879 GCTGCTGATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 12 0.67
13 6 0.33
ACGTcount: A:0.47, C:0.12, G:0.06, T:0.34
Consensus pattern (13 bp):
TAAACTTCAAATG
Found at i:29437 original size:16 final size:16
Alignment explanation
Indices: 29416--29464 Score: 80
Period size: 16 Copynumber: 3.1 Consensus size: 16
29406 TGAACCAAAA
29416 AAAAAAAGAAAGAAAG
1 AAAAAAAGAAAGAAAG
29432 AAAAAAAGAAAGAAAG
1 AAAAAAAGAAAGAAAG
* *
29448 AAAGAAAGAAGGAAAG
1 AAAAAAAGAAAGAAAG
29464 A
1 A
29465 TCTGAGCAAC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 31 1.00
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (16 bp):
AAAAAAAGAAAGAAAG
Found at i:29443 original size:4 final size:4
Alignment explanation
Indices: 29420--29464 Score: 72
Period size: 4 Copynumber: 11.2 Consensus size: 4
29410 CCAAAAAAAA
* *
29420 AAAG AAAG AAAG AAAA AAAG AAAG AAAG AAAG AAAG AAGG AAAG A
1 AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG A
29465 TCTGAGCAAC
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
4 37 1.00
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (4 bp):
AAAG
Found at i:30888 original size:14 final size:14
Alignment explanation
Indices: 30847--30892 Score: 65
Period size: 14 Copynumber: 3.2 Consensus size: 14
30837 TTTCTTTCCT
30847 TATTATAGGTACCG
1 TATTATAGGTACCG
*
30861 TATAATACGGTACCG
1 TATTATA-GGTACCG
*
30876 TATTGTAGGTACCG
1 TATTATAGGTACCG
30890 TAT
1 TAT
30893 CAATCTAGTT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
14 16 0.57
15 12 0.43
ACGTcount: A:0.28, C:0.15, G:0.22, T:0.35
Consensus pattern (14 bp):
TATTATAGGTACCG
Found at i:39478 original size:2 final size:2
Alignment explanation
Indices: 39471--39496 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
39461 ATAGTTTTAA
39471 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
39497 TTATCTAAAA
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:40257 original size:17 final size:18
Alignment explanation
Indices: 40235--40272 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
40225 GAGACAATTG
*
40235 AATATGGAGAAGAAGA-A
1 AATATGAAGAAGAAGAGA
*
40252 AATATGAAGAATAAGAGA
1 AATATGAAGAAGAAGAGA
40270 AAT
1 AAT
40273 TGTTCTCATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 14 0.78
18 4 0.22
ACGTcount: A:0.61, C:0.00, G:0.24, T:0.16
Consensus pattern (18 bp):
AATATGAAGAAGAAGAGA
Found at i:41205 original size:165 final size:169
Alignment explanation
Indices: 40903--41253 Score: 430
Period size: 169 Copynumber: 2.1 Consensus size: 169
40893 CAATGCTTGC
* * * * * *
40903 TTGGTTATTTCTCAATTGACTTTAATAGAGTAGTGGAATTACTAAAAGATCTCTACCTAGACTTG
1 TTGGTCATTTCTCAATGGACTTGAATAGAGTAGTGGAATTAATAAAAGATCTCCACCAAGACTTG
* ** * * * *
40968 CTTTTGGAGTTAGAGAACTTATTTTTTTTTTCGTATTTTCCTACTTGGCAGATTACTTAAATGTC
66 ATGATGGAGCTAGAGAACTTA-TATTTTTTTCGTATTTACCTACTTGGCAGATTACTTAAATGTA
*
41033 CTAACTTTTAACTCTTGA-GGGATTAAATAAGT-AATCTTT
130 CTAACTTTTAACTCTTGAGGGGATTAAATAACTAAAT-TTT
*
41072 TTGGTCATTTCTCAATGGACTTGAATAGAGTAGTGGAATTAATAAAAGAT-TCCCATCAAGGA-T
1 TTGGTCATTTCTCAATGGACTTGAATAGAGTAGTGGAATTAATAAAAGATCT-CCACCAA-GACT
*
41135 TGATGAT-GAGCTAGAGAAC-TA-ATTTTTTTCGTCTTTACCTA-TTGGGCAGATTACTTAAATG
64 TGATGATGGAGCTAGAGAACTTATATTTTTTTCGTATTTACCTACTT-GGCAGATTACTTAAATG
* * *
41196 TACTAACTTTTGATTCTTGAGGGGATTAAATATCTAAATTTT
128 TACTAACTTTTAACTCTTGAGGGGATTAAATAACTAAATTTT
41238 TTGGTCATTTCTCAAT
1 TTGGTCATTTCTCAAT
41254 TGACAAATGA
Statistics
Matches: 158, Mismatches: 19, Indels: 13
0.83 0.10 0.07
Matches are distributed among these distances:
164 2 0.01
165 51 0.32
166 31 0.20
167 5 0.03
168 12 0.08
169 55 0.35
170 2 0.01
ACGTcount: A:0.29, C:0.13, G:0.17, T:0.41
Consensus pattern (169 bp):
TTGGTCATTTCTCAATGGACTTGAATAGAGTAGTGGAATTAATAAAAGATCTCCACCAAGACTTG
ATGATGGAGCTAGAGAACTTATATTTTTTTCGTATTTACCTACTTGGCAGATTACTTAAATGTAC
TAACTTTTAACTCTTGAGGGGATTAAATAACTAAATTTT
Done.