Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014855.1 Corchorus capsularis cultivar CVL-1 contig14876, 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: 42843
ACGTcount: A:0.31, C:0.20, G:0.17, T:0.32
Found at i:20403 original size:42 final size:44
Alignment explanation
Indices: 20324--20410 Score: 124
Period size: 42 Copynumber: 2.0 Consensus size: 44
20314 CTGTGACCTT
* * *
20324 ATTTAGAAGAGATATAATAAGTCTCGAGTTACTTGAATCAACCAA
1 ATTTAGAAGAGA-ATAACAAGTCTCGAATTACATGAATCAACCAA
20369 ATTTAGAAGAG-AT-ACAAGTCTCGAATTACATGAATCAACCAA
1 ATTTAGAAGAGAATAACAAGTCTCGAATTACATGAATCAACCAA
20411 TTATTGATTG
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
42 26 0.67
43 2 0.05
45 11 0.28
ACGTcount: A:0.44, C:0.15, G:0.15, T:0.26
Consensus pattern (44 bp):
ATTTAGAAGAGAATAACAAGTCTCGAATTACATGAATCAACCAA
Found at i:22415 original size:18 final size:18
Alignment explanation
Indices: 22400--22444 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
22390 GTGGTTCATG
22400 TTCACATGCACATTCACA
1 TTCACATGCACATTCACA
* *
22418 TTCACATGGACATTCTCA
1 TTCACATGCACATTCACA
*
22436 TTCTCATGC
1 TTCACATGC
22445 CCACTCTCAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.27, C:0.31, G:0.09, T:0.33
Consensus pattern (18 bp):
TTCACATGCACATTCACA
Found at i:22746 original size:21 final size:20
Alignment explanation
Indices: 22690--22747 Score: 50
Period size: 21 Copynumber: 3.0 Consensus size: 20
22680 GATCACCATA
22690 ATCATGGACATCAACAT--G
1 ATCATGGACATCAACATGAG
** *
22708 ATCATGCTCAT-AGTCATGAAG
1 ATCATGGACATCA-ACATG-AG
22729 ATCATGGACATCAACATGA
1 ATCATGGACATCAACATGA
22748 TAATGCCCAC
Statistics
Matches: 29, Mismatches: 6, Indels: 8
0.67 0.14 0.19
Matches are distributed among these distances:
17 1 0.03
18 12 0.41
20 1 0.03
21 14 0.48
22 1 0.03
ACGTcount: A:0.38, C:0.21, G:0.17, T:0.24
Consensus pattern (20 bp):
ATCATGGACATCAACATGAG
Found at i:22764 original size:39 final size:39
Alignment explanation
Indices: 22690--22765 Score: 116
Period size: 39 Copynumber: 1.9 Consensus size: 39
22680 GATCACCATA
* * * *
22690 ATCATGGACATCAACATGATCATGCTCATAGTCATGAAG
1 ATCATGGACATCAACATGATAATGCCCACAATCATGAAG
22729 ATCATGGACATCAACATGATAATGCCCACAATCATGA
1 ATCATGGACATCAACATGATAATGCCCACAATCATGA
22766 CCACCATGAT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
39 33 1.00
ACGTcount: A:0.38, C:0.22, G:0.16, T:0.24
Consensus pattern (39 bp):
ATCATGGACATCAACATGATAATGCCCACAATCATGAAG
Found at i:24363 original size:10 final size:10
Alignment explanation
Indices: 24350--24378 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
24340 GGTGAAATGG
24350 GGGAAAGAGA
1 GGGAAAGAGA
24360 GGGAAAGAGA
1 GGGAAAGAGA
24370 GGGAAAGAG
1 GGGAAAGAG
24379 GGAGAGCGGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (10 bp):
GGGAAAGAGA
Found at i:32890 original size:6 final size:6
Alignment explanation
Indices: 32879--32904 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
32869 TATCGGTAAT
32879 TATCTA TATCTA TATCTA TATCTA TA
1 TATCTA TATCTA TATCTA TATCTA TA
32905 CAATATTAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.35, C:0.15, G:0.00, T:0.50
Consensus pattern (6 bp):
TATCTA
Found at i:33080 original size:28 final size:26
Alignment explanation
Indices: 33049--33109 Score: 72
Period size: 24 Copynumber: 2.3 Consensus size: 26
33039 TATTTTTAGA
33049 CAAACTCTTAACCAATTTTAATCTCAAC
1 CAAACTCTT-A-CAATTTTAATCTCAAC
*
33077 CAAACTC--ACAATTTTAATCTCTAC
1 CAAACTCTTACAATTTTAATCTCAAC
*
33101 CAACCTCTT
1 CAAACTCTT
33110 CAAGATTACT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
24 21 0.72
25 1 0.03
28 7 0.24
ACGTcount: A:0.36, C:0.31, G:0.00, T:0.33
Consensus pattern (26 bp):
CAAACTCTTACAATTTTAATCTCAAC
Found at i:34838 original size:18 final size:18
Alignment explanation
Indices: 34815--34852 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
34805 ATGTGGTCTG
34815 TATTTGTGTACTGACTCA
1 TATTTGTGTACTGACTCA
*
34833 TATTTGTGTACTGGCTCA
1 TATTTGTGTACTGACTCA
34851 TA
1 TA
34853 ATTCTTCAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.21, C:0.16, G:0.18, T:0.45
Consensus pattern (18 bp):
TATTTGTGTACTGACTCA
Found at i:35622 original size:85 final size:85
Alignment explanation
Indices: 35476--35651 Score: 307
Period size: 85 Copynumber: 2.1 Consensus size: 85
35466 CAATGATTTG
* *
35476 CAATAACATCAGCTGCCCTAGTAGTTTCCCGGAAGGAGTGCTTCAGTTTGCAATCGGAAATACTT
1 CAATAACATCAACTGCCCTAGTAGTTTCCCGGAAGGAGTGCTTCAGTTTGCAATCGAAAATACTT
35541 TCCTTAAGACCTGCAATCAC
66 TCCTTAAGACCTGCAATCAC
* *
35561 CAATAACATCAATTGCCCTAGTAGTTTCCTGGAAGGAGTGCTTCAGTTTGCAATCGAAAATACTT
1 CAATAACATCAACTGCCCTAGTAGTTTCCCGGAAGGAGTGCTTCAGTTTGCAATCGAAAATACTT
*
35626 TCCTTCAGACCTGCAATCAC
66 TCCTTAAGACCTGCAATCAC
35646 CAATAA
1 CAATAA
35652 GAGTACCTAA
Statistics
Matches: 86, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
85 86 1.00
ACGTcount: A:0.30, C:0.25, G:0.17, T:0.28
Consensus pattern (85 bp):
CAATAACATCAACTGCCCTAGTAGTTTCCCGGAAGGAGTGCTTCAGTTTGCAATCGAAAATACTT
TCCTTAAGACCTGCAATCAC
Found at i:38092 original size:21 final size:21
Alignment explanation
Indices: 38054--38093 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
38044 ATATTTTTCC
*
38054 ACCATTCTCATCTATACAGGA
1 ACCATTCTCACCTATACAGGA
* *
38075 ACCATTCTGACCTGTACAG
1 ACCATTCTCACCTATACAG
38094 TAACTTATCT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.30, C:0.30, G:0.12, T:0.28
Consensus pattern (21 bp):
ACCATTCTCACCTATACAGGA
Done.