Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007030.1 Corchorus capsularis cultivar CVL-1 contig07051, 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: 44817
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.29
Found at i:6227 original size:15 final size:15
Alignment explanation
Indices: 6203--6246 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
6193 TGCTAGGGTG
*
6203 AATGGCGCAAACAAC
1 AATGGTGCAAACAAC
* *
6218 AATGGTGCAAACCAT
1 AATGGTGCAAACAAC
*
6233 AATGGTGCGAACAA
1 AATGGTGCAAACAA
6247 TCATGTTGTG
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.43, C:0.20, G:0.23, T:0.14
Consensus pattern (15 bp):
AATGGTGCAAACAAC
Found at i:26881 original size:2 final size:2
Alignment explanation
Indices: 26874--26902 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
26864 AAAATGACAA
26874 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
26903 GTAACAAGGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:33663 original size:18 final size:19
Alignment explanation
Indices: 33637--33672 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
33627 AGAACTTTAT
*
33637 TCTATTTTCTCTC-CTCTA
1 TCTAATTTCTCTCTCTCTA
33655 TCTAATTTCTCTCTCTCT
1 TCTAATTTCTCTCTCTCT
33673 GGTTTACGAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.11, C:0.33, G:0.00, T:0.56
Consensus pattern (19 bp):
TCTAATTTCTCTCTCTCTA
Found at i:39440 original size:46 final size:46
Alignment explanation
Indices: 39371--39459 Score: 151
Period size: 46 Copynumber: 1.9 Consensus size: 46
39361 GTGTCACTGT
*
39371 TTTAAGGCGTCAATCATGAGATTTATGGTAAGAAAGAAATATCTGA
1 TTTAAAGCGTCAATCATGAGATTTATGGTAAGAAAGAAATATCTGA
* *
39417 TTTAAAGCGTCAATCATGGGATTTATGGTAAGAAGGAAATATC
1 TTTAAAGCGTCAATCATGAGATTTATGGTAAGAAAGAAATATC
39460 GAGGAAGATG
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
46 40 1.00
ACGTcount: A:0.38, C:0.09, G:0.22, T:0.30
Consensus pattern (46 bp):
TTTAAAGCGTCAATCATGAGATTTATGGTAAGAAAGAAATATCTGA
Found at i:40532 original size:24 final size:25
Alignment explanation
Indices: 40474--40534 Score: 79
Period size: 25 Copynumber: 2.5 Consensus size: 25
40464 CGTTATGGCA
* *
40474 AAATACCTTTTGATAATACTCATGG
1 AAATACCTTATGACAATACTCATGG
* *
40499 TAATACCTTATGACAATACT-GTGG
1 AAATACCTTATGACAATACTCATGG
40523 AAATACCTTATG
1 AAATACCTTATG
40535 TTAATACCTT
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
24 14 0.45
25 17 0.55
ACGTcount: A:0.36, C:0.16, G:0.13, T:0.34
Consensus pattern (25 bp):
AAATACCTTATGACAATACTCATGG
Found at i:40540 original size:24 final size:25
Alignment explanation
Indices: 40474--40541 Score: 84
Period size: 24 Copynumber: 2.8 Consensus size: 25
40464 CGTTATGGCA
*
40474 AAATACCTTTTGATAATACTCATGG
1 AAATACCTTATGATAATACTCATGG
* * *
40499 TAATACCTTATGACAATACT-GTGG
1 AAATACCTTATGATAATACTCATGG
*
40523 AAATACCTTATGTTAATAC
1 AAATACCTTATGATAATAC
40542 CTTGTGACAA
Statistics
Matches: 36, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
24 19 0.53
25 17 0.47
ACGTcount: A:0.37, C:0.16, G:0.12, T:0.35
Consensus pattern (25 bp):
AAATACCTTATGATAATACTCATGG
Found at i:43438 original size:46 final size:46
Alignment explanation
Indices: 43367--43505 Score: 188
Period size: 46 Copynumber: 3.0 Consensus size: 46
43357 CTTTGCAAGA
* * * * * *
43367 AGCTACCGTATAAAGAATTCCTTCTGAAGATGGGTGCTCACATAAG
1 AGCTACTGTATAGAGTATTCTTTCTGAAGAAGTGTGCTCACATAAG
*
43413 AGCTACTGTATAGAGTATTCTTTCTGAAGAAGTGTGCTCACATAAA
1 AGCTACTGTATAGAGTATTCTTTCTGAAGAAGTGTGCTCACATAAG
* * *
43459 AGCTATTGTATAGAGTATTTTTTCTGCAGAAGTGTGCTCACATAAG
1 AGCTACTGTATAGAGTATTCTTTCTGAAGAAGTGTGCTCACATAAG
43505 A
1 A
43506 TGCATCTCCT
Statistics
Matches: 82, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
46 82 1.00
ACGTcount: A:0.32, C:0.16, G:0.21, T:0.32
Consensus pattern (46 bp):
AGCTACTGTATAGAGTATTCTTTCTGAAGAAGTGTGCTCACATAAG
Found at i:44100 original size:45 final size:45
Alignment explanation
Indices: 44045--44146 Score: 152
Period size: 45 Copynumber: 2.3 Consensus size: 45
44035 CACCATGTGT
44045 AAGAGAGTATAATGCTTGTCATTGGAAGCACCACCACT-ATGTTGG
1 AAGAGAGTATAATGCTTGTCATTGGAAGCACCACC-CTCATGTTGG
* * *
44090 AAGAGGGTATAATTCTTGTCATTGGAAGCGCCACCCTCATGTTGG
1 AAGAGAGTATAATGCTTGTCATTGGAAGCACCACCCTCATGTTGG
*
44135 AGGAGAGTATAA
1 AAGAGAGTATAA
44147 ATAATGTCGT
Statistics
Matches: 51, Mismatches: 5, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
44 2 0.04
45 49 0.96
ACGTcount: A:0.30, C:0.17, G:0.26, T:0.26
Consensus pattern (45 bp):
AAGAGAGTATAATGCTTGTCATTGGAAGCACCACCCTCATGTTGG
Found at i:44160 original size:45 final size:45
Alignment explanation
Indices: 44061--44167 Score: 126
Period size: 45 Copynumber: 2.4 Consensus size: 45
44051 GTATAATGCT
* * * **
44061 TGTCATTGGAAGCACCACCACTATGTTGGAAGAGGGTATAATTCT
1 TGTCATTGGAAGCGCCACCACTATGTTGGAAGAGAGTATAAATAA
*
44106 TGTCATTGGAAGCGCCACC-CTCATGTTGGAGGAGAGTATAAATAA
1 TGTCATTGGAAGCGCCACCACT-ATGTTGGAAGAGAGTATAAATAA
* *
44151 TGTCGTTGGAAGTGCCA
1 TGTCATTGGAAGCGCCA
44168 TCACCCTGGA
Statistics
Matches: 53, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
44 2 0.04
45 51 0.96
ACGTcount: A:0.28, C:0.18, G:0.27, T:0.27
Consensus pattern (45 bp):
TGTCATTGGAAGCGCCACCACTATGTTGGAAGAGAGTATAAATAA
Done.