Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007900.1 Corchorus capsularis cultivar CVL-1 contig07921, 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: 18818
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Found at i:810 original size:21 final size:22
Alignment explanation
Indices: 779--834 Score: 62
Period size: 21 Copynumber: 2.6 Consensus size: 22
769 CAAAAGCTTT
* * *
779 GGATTGCGCGGCATGGGCTCGT
1 GGATGGCGCGGCATGGGCGCGC
*
801 GG-TGGCGCGG-TTGGGCGCGC
1 GGATGGCGCGGCATGGGCGCGC
821 GGATGGCGCGGCAT
1 GGATGGCGCGGCAT
835 AGTCATATTC
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
20 9 0.33
21 15 0.56
22 3 0.11
ACGTcount: A:0.07, C:0.23, G:0.52, T:0.18
Consensus pattern (22 bp):
GGATGGCGCGGCATGGGCGCGC
Found at i:4120 original size:24 final size:24
Alignment explanation
Indices: 4065--4120 Score: 71
Period size: 24 Copynumber: 2.4 Consensus size: 24
4055 AAAAGAAAAA
*
4065 CTTTTTTTTTTTAAATCGGAAACC
1 CTTTTTTTTTTTAAATCGCAAACC
**
4089 CTAATTTTTTTTAAATCGCAAA--
1 CTTTTTTTTTTTAAATCGCAAACC
4111 CTTTTTTTTT
1 CTTTTTTTTT
4121 AAAAGTAAAA
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
22 8 0.30
24 19 0.70
ACGTcount: A:0.25, C:0.14, G:0.05, T:0.55
Consensus pattern (24 bp):
CTTTTTTTTTTTAAATCGCAAACC
Found at i:5777 original size:11 final size:10
Alignment explanation
Indices: 5759--5792 Score: 50
Period size: 11 Copynumber: 3.2 Consensus size: 10
5749 AATTGTCTTC
5759 AAATCTTCAA
1 AAATCTTCAA
5769 AATATCTTCAA
1 AA-ATCTTCAA
5780 GAAATCTTCAA
1 -AAATCTTCAA
5791 AA
1 AA
5793 CACGAACTTC
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
10 4 0.18
11 16 0.73
12 2 0.09
ACGTcount: A:0.50, C:0.18, G:0.03, T:0.29
Consensus pattern (10 bp):
AAATCTTCAA
Found at i:6751 original size:12 final size:13
Alignment explanation
Indices: 6722--6764 Score: 61
Period size: 13 Copynumber: 3.4 Consensus size: 13
6712 CCCTTAATTT
*
6722 GAAAACCTAAAAA
1 GAAAAACTAAAAA
6735 GAAAAAC-AAAAA
1 GAAAAACTAAAAA
*
6747 CAAAAACTAAAAA
1 GAAAAACTAAAAA
6760 GAAAA
1 GAAAA
6765 TTAAAATGTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
12 11 0.42
13 15 0.58
ACGTcount: A:0.77, C:0.12, G:0.07, T:0.05
Consensus pattern (13 bp):
GAAAAACTAAAAA
Found at i:8369 original size:108 final size:108
Alignment explanation
Indices: 8180--8396 Score: 416
Period size: 108 Copynumber: 2.0 Consensus size: 108
8170 TAAATTGCTA
8180 TATGTTTTCCGTCATGGTGTTGAGCAGCTTCCTTGCTTCATCAGGGGTTTTGAGTGTAAAACTCC
1 TATGTTTTCCGTCATGGTGTTGAGCAGCTTCCTTGCTTCATCAGGGGTTTTGAGTGTAAAACTCC
8245 CTCCACTTGCAGAATCAATATATGTTCGATCTTTATAGAGGAG
66 CTCCACTTGCAGAATCAATATATGTTCGATCTTTATAGAGGAG
**
8288 TATGTTTTCTTTCATGGTGTTGAGCAGCTTCCTTGCTTCATCAGGGGTTTTGAGTGTAAAACTCC
1 TATGTTTTCCGTCATGGTGTTGAGCAGCTTCCTTGCTTCATCAGGGGTTTTGAGTGTAAAACTCC
8353 CTCCACTTGCAGAATCAATATATGTTCGATCTTTATAGAGGAG
66 CTCCACTTGCAGAATCAATATATGTTCGATCTTTATAGAGGAG
8396 T
1 T
8397 CCATCATAAA
Statistics
Matches: 107, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
108 107 1.00
ACGTcount: A:0.22, C:0.19, G:0.22, T:0.37
Consensus pattern (108 bp):
TATGTTTTCCGTCATGGTGTTGAGCAGCTTCCTTGCTTCATCAGGGGTTTTGAGTGTAAAACTCC
CTCCACTTGCAGAATCAATATATGTTCGATCTTTATAGAGGAG
Found at i:10602 original size:19 final size:18
Alignment explanation
Indices: 10569--10604 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
10559 TTAAAATAAT
10569 TCTTCAATGATCTTCAAA
1 TCTTCAATGATCTTCAAA
*
10587 TCTTCAAATTATCTTCAA
1 TCTTC-AATGATCTTCAA
10605 GAAATCTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.33, C:0.22, G:0.03, T:0.42
Consensus pattern (18 bp):
TCTTCAATGATCTTCAAA
Found at i:10867 original size:2 final size:2
Alignment explanation
Indices: 10854--10884 Score: 53
Period size: 2 Copynumber: 15.0 Consensus size: 2
10844 GACAAAAATA
10854 AT AT AT AGT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT
10885 TAGTTTATCG
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 26 0.93
3 2 0.07
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:18470 original size:6 final size:6
Alignment explanation
Indices: 18459--18491 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
18449 AAAGCAAAGC
18459 AAATCT AAATCT AAATCT AAATCT AAATCT AAA
1 AAATCT AAATCT AAATCT AAATCT AAATCT AAA
18492 GCAGAATTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.55, C:0.15, G:0.00, T:0.30
Consensus pattern (6 bp):
AAATCT
Done.