Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008383.1 Corchorus capsularis cultivar CVL-1 contig08404, 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: 35793
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Found at i:6806 original size:114 final size:114
Alignment explanation
Indices: 6604--6831 Score: 384
Period size: 114 Copynumber: 2.0 Consensus size: 114
6594 AGTCATAATG
* * *
6604 GATCTCTGGATACCGGATGAGGTATAAAAAAAATCTCATGTAGTGCACCCTATTAGCGCCATGAG
1 GATCTCTGGATACCGGATGAGGTATAAAAAAAACCCCATGTAATGCACCCTATTAGCGCCATGAG
* *
6669 AAAGAATATGTCCAACAGTTGGGAATGGGATTGACAAAATATGACGCTA
66 AAAGAATATGCCCAACAGCTGGGAATGGGATTGACAAAATATGACGCTA
* *
6718 GATCTTTGGATGCCGGATGAGGTATAAAAAAAACCCCATGTAATGCACCCTATTAGCGCCATGAG
1 GATCTCTGGATACCGGATGAGGTATAAAAAAAACCCCATGTAATGCACCCTATTAGCGCCATGAG
*
6783 AAAGAATATGCCCAATAGCTGGGAATGGGATTGACAAAATATGACGCTA
66 AAAGAATATGCCCAACAGCTGGGAATGGGATTGACAAAATATGACGCTA
6832 TTTCCATCAC
Statistics
Matches: 106, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
114 106 1.00
ACGTcount: A:0.36, C:0.18, G:0.24, T:0.23
Consensus pattern (114 bp):
GATCTCTGGATACCGGATGAGGTATAAAAAAAACCCCATGTAATGCACCCTATTAGCGCCATGAG
AAAGAATATGCCCAACAGCTGGGAATGGGATTGACAAAATATGACGCTA
Found at i:9837 original size:26 final size:27
Alignment explanation
Indices: 9802--9852 Score: 77
Period size: 26 Copynumber: 1.9 Consensus size: 27
9792 ATAATTTTAG
*
9802 TTTTAATTTATAAT-TTATATATAAGT
1 TTTTAATTTATAATAATATATATAAGT
*
9828 TTTTAGTTTATAATAATATATATAA
1 TTTTAATTTATAATAATATATATAA
9853 TTATATTTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 13 0.59
27 9 0.41
ACGTcount: A:0.41, C:0.00, G:0.04, T:0.55
Consensus pattern (27 bp):
TTTTAATTTATAATAATATATATAAGT
Found at i:9961 original size:10 final size:10
Alignment explanation
Indices: 9946--9972 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
9936 ATATAAATCA
9946 AAACCGATCG
1 AAACCGATCG
9956 AAACCGATCG
1 AAACCGATCG
9966 AAACCGA
1 AAACCGA
9973 CCGCCACCAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.44, C:0.30, G:0.19, T:0.07
Consensus pattern (10 bp):
AAACCGATCG
Found at i:11390 original size:32 final size:32
Alignment explanation
Indices: 11316--11391 Score: 120
Period size: 30 Copynumber: 2.4 Consensus size: 32
11306 TTTATACCTT
*
11316 TAATTAATGGAGGGGGAGAGAGAAGATAAATG
1 TAATTAATGGAGAGGGAGAGAGAAGATAAATG
*
11348 T-A-TAAGGGAGAGGGAGAGAGAAGATAAATG
1 TAATTAATGGAGAGGGAGAGAGAAGATAAATG
11378 TAATTAATGGAGAG
1 TAATTAATGGAGAG
11392 TTGGAGTATT
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
30 27 0.69
31 2 0.05
32 10 0.26
ACGTcount: A:0.45, C:0.00, G:0.37, T:0.18
Consensus pattern (32 bp):
TAATTAATGGAGAGGGAGAGAGAAGATAAATG
Found at i:12045 original size:26 final size:27
Alignment explanation
Indices: 11998--12048 Score: 70
Period size: 26 Copynumber: 1.9 Consensus size: 27
11988 TGCAAAGAGT
*
11998 TTGAGAGAAAAGCGCGGAGCTTGAAAA
1 TTGAGAGAAAAGCACGGAGCTTGAAAA
12025 TTGAGAG-AAAGCACAGG-GCTTGAA
1 TTGAGAGAAAAGCAC-GGAGCTTGAA
12049 GTTTTGCACG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
26 13 0.59
27 9 0.41
ACGTcount: A:0.39, C:0.12, G:0.33, T:0.16
Consensus pattern (27 bp):
TTGAGAGAAAAGCACGGAGCTTGAAAA
Found at i:18424 original size:39 final size:39
Alignment explanation
Indices: 18370--18447 Score: 156
Period size: 39 Copynumber: 2.0 Consensus size: 39
18360 AATCTTCTTA
18370 AGCTTTGGTGAATATCAGAATAAGAACATCTGAAATATT
1 AGCTTTGGTGAATATCAGAATAAGAACATCTGAAATATT
18409 AGCTTTGGTGAATATCAGAATAAGAACATCTGAAATATT
1 AGCTTTGGTGAATATCAGAATAAGAACATCTGAAATATT
18448 TCAGAGCTTT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.41, C:0.10, G:0.18, T:0.31
Consensus pattern (39 bp):
AGCTTTGGTGAATATCAGAATAAGAACATCTGAAATATT
Found at i:30027 original size:30 final size:31
Alignment explanation
Indices: 29978--30042 Score: 114
Period size: 30 Copynumber: 2.1 Consensus size: 31
29968 AATTTTATGT
*
29978 TTTCCGATTATACCCCTTTTTTAAAAATATA
1 TTTCCGATTATACCCCTTTTTAAAAAATATA
30009 TTTCCGATTATA-CCCTTTTTAAAAAATATA
1 TTTCCGATTATACCCCTTTTTAAAAAATATA
30039 TTTC
1 TTTC
30043 TAAATTGCCA
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
30 21 0.64
31 12 0.36
ACGTcount: A:0.32, C:0.18, G:0.03, T:0.46
Consensus pattern (31 bp):
TTTCCGATTATACCCCTTTTTAAAAAATATA
Found at i:33120 original size:16 final size:16
Alignment explanation
Indices: 33099--33129 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
33089 TTCTTCTCCA
33099 TATTCTATTGTCTTTC
1 TATTCTATTGTCTTTC
*
33115 TATTCTCTTGTCTTT
1 TATTCTATTGTCTTT
33130 TACATACTTC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.10, C:0.19, G:0.06, T:0.65
Consensus pattern (16 bp):
TATTCTATTGTCTTTC
Found at i:33252 original size:53 final size:53
Alignment explanation
Indices: 33172--33278 Score: 205
Period size: 53 Copynumber: 2.0 Consensus size: 53
33162 TTGTTATCAT
*
33172 TTCACAACAAAATTTGATTTCTTAACTGAATTTTCTTAAGAGAATTTATAAAA
1 TTCACAACAAAATTTGATTTCTTAACTGAATTTTCTTAAAAGAATTTATAAAA
33225 TTCACAACAAAATTTGATTTCTTAACTGAATTTTCTTAAAAGAATTTATAAAA
1 TTCACAACAAAATTTGATTTCTTAACTGAATTTTCTTAAAAGAATTTATAAAA
33278 T
1 T
33279 AAAATAGCTG
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
53 53 1.00
ACGTcount: A:0.42, C:0.11, G:0.07, T:0.40
Consensus pattern (53 bp):
TTCACAACAAAATTTGATTTCTTAACTGAATTTTCTTAAAAGAATTTATAAAA
Found at i:34033 original size:15 final size:15
Alignment explanation
Indices: 34013--34048 Score: 65
Period size: 14 Copynumber: 2.5 Consensus size: 15
34003 ATGGCCAAAA
34013 ATTCTTTACTGCCTT
1 ATTCTTTACTGCCTT
34028 ATTC-TTACTGCCTT
1 ATTCTTTACTGCCTT
34042 ATTCTTT
1 ATTCTTT
34049 TTGTCCATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 14 0.70
15 6 0.30
ACGTcount: A:0.14, C:0.25, G:0.06, T:0.56
Consensus pattern (15 bp):
ATTCTTTACTGCCTT
Done.