Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01005430.1 Corchorus capsularis cultivar CVL-1 contig05448, 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: 20439
ACGTcount: A:0.36, C:0.14, G:0.15, T:0.34
Found at i:646 original size:36 final size:36
Alignment explanation
Indices: 592--687 Score: 131
Period size: 36 Copynumber: 2.6 Consensus size: 36
582 AAAAAACACA
592 TGGAGTCAACATAAAGAACTTAATTAAGGG-TAATTAAG
1 TGGAGTC-A-ATAAAGAACTTAATT-AGGGATAATTAAG
*
630 TGGAGTCAATAAAGAACTTAATTTGGGATAATTAAG
1 TGGAGTCAATAAAGAACTTAATTAGGGATAATTAAG
* *
666 TCGAGCCAATAAAGAACTTAAT
1 TGGAGTCAATAAAGAACTTAAT
688 CAAAAAAGAG
Statistics
Matches: 54, Mismatches: 3, Indels: 4
0.89 0.05 0.07
Matches are distributed among these distances:
35 3 0.06
36 43 0.80
37 1 0.02
38 7 0.13
ACGTcount: A:0.44, C:0.09, G:0.20, T:0.27
Consensus pattern (36 bp):
TGGAGTCAATAAAGAACTTAATTAGGGATAATTAAG
Found at i:5926 original size:30 final size:27
Alignment explanation
Indices: 5887--5957 Score: 81
Period size: 29 Copynumber: 2.4 Consensus size: 27
5877 AGTCTTTTAT
5887 CAAACTATAACATTTTGAAAATTTATTTCC
1 CAAACTATAACA-TTT--AAATTTATTTCC
5917 CAATA-TATAATACATTTAAATTTATTTCC
1 CAA-ACTAT-A-ACATTTAAATTTATTTCC
5946 CAAACTATAACA
1 CAAACTATAACA
5958 ATTCTTGCCA
Statistics
Matches: 37, Mismatches: 0, Indels: 11
0.77 0.00 0.23
Matches are distributed among these distances:
27 3 0.08
28 2 0.05
29 18 0.49
30 6 0.16
31 5 0.14
32 3 0.08
ACGTcount: A:0.44, C:0.17, G:0.01, T:0.38
Consensus pattern (27 bp):
CAAACTATAACATTTAAATTTATTTCC
Found at i:6661 original size:17 final size:17
Alignment explanation
Indices: 6632--6672 Score: 57
Period size: 17 Copynumber: 2.4 Consensus size: 17
6622 ATTTATTTTG
6632 AGAAGAAAAAAAAG-AAA
1 AGAA-AAAAAAAAGAAAA
6649 AGAAAAAAGAAAAGAAAA
1 AGAAAAAA-AAAAGAAAA
6667 AGAAAA
1 AGAAAA
6673 TATGACATGT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.18
17 9 0.41
18 9 0.41
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (17 bp):
AGAAAAAAAAAAGAAAA
Found at i:6666 original size:11 final size:12
Alignment explanation
Indices: 6639--6672 Score: 61
Period size: 12 Copynumber: 2.9 Consensus size: 12
6629 TTGAGAAGAA
6639 AAAAAAGAAAAG
1 AAAAAAGAAAAG
6651 AAAAAAGAAAAG
1 AAAAAAGAAAAG
6663 -AAAAAGAAAA
1 AAAAAAGAAAA
6673 TATGACATGT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
11 10 0.45
12 12 0.55
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (12 bp):
AAAAAAGAAAAG
Found at i:6902 original size:27 final size:26
Alignment explanation
Indices: 6864--6918 Score: 83
Period size: 27 Copynumber: 2.1 Consensus size: 26
6854 GAAGGTAGTC
*
6864 AATTTTCTTATTTAAAATTGATTTAAA
1 AATTTTCTTATTTAAAATT-ACTTAAA
*
6891 AATTTTTTTATTTAAAATTACTTAAA
1 AATTTTCTTATTTAAAATTACTTAAA
6917 AA
1 AA
6919 GCTATATAGT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
26 8 0.31
27 18 0.69
ACGTcount: A:0.44, C:0.04, G:0.02, T:0.51
Consensus pattern (26 bp):
AATTTTCTTATTTAAAATTACTTAAA
Found at i:9653 original size:19 final size:19
Alignment explanation
Indices: 9629--9667 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
9619 AATAATACAT
9629 TCTGAATATTACTACACAA
1 TCTGAATATTACTACACAA
9648 TCTGAATATTACTACACAA
1 TCTGAATATTACTACACAA
9667 T
1 T
9668 GTTAAGACTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.41, C:0.21, G:0.05, T:0.33
Consensus pattern (19 bp):
TCTGAATATTACTACACAA
Found at i:10971 original size:2 final size:2
Alignment explanation
Indices: 10942--11053 Score: 55
Period size: 2 Copynumber: 60.5 Consensus size: 2
10932 ATTTTATAAT
* * *
10942 TA TA TT TA TGA TA TA T- TA TA -A TA T- TA TA TA TA TA TA AA CA
1 TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * * *
10982 AA T- TA AA TA TA -A TA TA -A AA CA TA AA TA TA TA -A TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
11020 TA -A CA TA TA -A TA TA TA TA TA T- TA TA TA TA AA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
11054 CTTTAGTCGG
Statistics
Matches: 84, Mismatches: 15, Indels: 22
0.69 0.12 0.18
Matches are distributed among these distances:
1 10 0.12
2 72 0.86
3 2 0.02
ACGTcount: A:0.54, C:0.03, G:0.01, T:0.42
Consensus pattern (2 bp):
TA
Found at i:10998 original size:20 final size:20
Alignment explanation
Indices: 10966--11039 Score: 62
Period size: 20 Copynumber: 3.5 Consensus size: 20
10956 ATTATAATAT
*
10966 TATATATATATAAACAAATTAA
1 TATATA-ATATAAA-AAATAAA
*
10988 -ATATAATATAAAACATAAA
1 TATATAATATAAAAAATAAA
*
11007 TATATAATATATATAACATATAA
1 TATATAATATA-A-AAAATA-AA
11030 TATAT-ATATA
1 TATATAATATA
11040 TTATATATAA
Statistics
Matches: 46, Mismatches: 2, Indels: 8
0.82 0.04 0.14
Matches are distributed among these distances:
19 5 0.11
20 17 0.37
21 6 0.13
22 11 0.24
23 7 0.15
ACGTcount: A:0.59, C:0.04, G:0.00, T:0.36
Consensus pattern (20 bp):
TATATAATATAAAAAATAAA
Found at i:11008 original size:18 final size:20
Alignment explanation
Indices: 10985--11040 Score: 64
Period size: 20 Copynumber: 2.8 Consensus size: 20
10975 ATAAACAAAT
10985 TAAATATAATATA-A-AACA
1 TAAATATAATATATATAACA
11003 TAAATATATAATATATATAACA
1 T-AA-ATATAATATATATAACA
11025 TATAATAT-ATATATAT
1 TA-AATATAATATATAT
11041 TATATATAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
18 1 0.03
19 2 0.06
20 18 0.55
21 6 0.18
22 6 0.18
ACGTcount: A:0.59, C:0.04, G:0.00, T:0.38
Consensus pattern (20 bp):
TAAATATAATATATATAACA
Found at i:11015 original size:7 final size:7
Alignment explanation
Indices: 10988--11053 Score: 57
Period size: 7 Copynumber: 9.6 Consensus size: 7
10978 AACAAATTAA
10988 ATATAAT
1 ATATAAT
* *
10995 ATAAAAC
1 ATATAAT
11002 ATA-AAT
1 ATATAAT
11008 ATATAATAT
1 ATAT-A-AT
*
11017 ATATAAC
1 ATATAAT
11024 ATATAAT
1 ATATAAT
11031 ATAT-AT
1 ATATAAT
*
11037 ATATTAT
1 ATATAAT
11044 ATATAA-
1 ATATAAT
11050 ATAT
1 ATAT
11054 CTTTAGTCGG
Statistics
Matches: 49, Mismatches: 6, Indels: 9
0.77 0.09 0.14
Matches are distributed among these distances:
6 15 0.31
7 26 0.53
8 2 0.04
9 6 0.12
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (7 bp):
ATATAAT
Found at i:11018 original size:22 final size:22
Alignment explanation
Indices: 10958--11040 Score: 91
Period size: 22 Copynumber: 3.7 Consensus size: 22
10948 TATGATATAT
10958 TATAATATTATATATATATAAACA
1 TATAATA-TATATATATA-AAACA
*
10982 AATTAA-ATATA-ATATAAAACA
1 TA-TAATATATATATATAAAACA
*
11003 TA-AATATATAATATATATAACA
1 TATAATATAT-ATATATAAAACA
11025 TATAATATATATATAT
1 TATAATATATATATAT
11041 TATATATAAA
Statistics
Matches: 51, Mismatches: 3, Indels: 12
0.77 0.05 0.18
Matches are distributed among these distances:
19 2 0.04
20 4 0.08
21 7 0.14
22 22 0.43
23 11 0.22
24 2 0.04
25 3 0.06
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.39
Consensus pattern (22 bp):
TATAATATATATATATAAAACA
Found at i:11038 original size:11 final size:11
Alignment explanation
Indices: 10936--11053 Score: 59
Period size: 11 Copynumber: 10.7 Consensus size: 11
10926 TTTATCATTT
*
10936 TATAATTATATT
1 TATAA-TATATA
*
10948 TATGATATAT-
1 TATAATATATA
10958 TATAATAT-TA
1 TATAATATATA
10968 TAT-ATATATA
1 TATAATATATA
* * *
10978 AACAA-ATTAAA
1 TATAATA-TATA
*
10989 TATAATATAAAA
1 TATAATAT-ATA
*
11001 CATAA-ATATA
1 TATAATATATA
*
11011 TAATATATATAACA
1 T-ATA-ATAT-ATA
11025 TATAATATATA
1 TATAATATATA
*
11036 TATATTATATA
1 TATAATATATA
11047 TA-AATAT
1 TATAATAT
11054 CTTTAGTCGG
Statistics
Matches: 82, Mismatches: 14, Indels: 22
0.69 0.12 0.19
Matches are distributed among these distances:
9 5 0.06
10 20 0.24
11 32 0.39
12 17 0.21
13 5 0.06
14 3 0.04
ACGTcount: A:0.54, C:0.03, G:0.01, T:0.42
Consensus pattern (11 bp):
TATAATATATA
Found at i:16494 original size:32 final size:31
Alignment explanation
Indices: 16458--16527 Score: 104
Period size: 31 Copynumber: 2.2 Consensus size: 31
16448 AAGATATTGA
*
16458 AATTTTTAGAAAGGTACACATAAACGTATCTT
1 AATTTTT-GAAAGGTACACATAAACGTATCCT
* *
16490 AATTTATGGAAGGTACACATAAACGTATCCT
1 AATTTTTGAAAGGTACACATAAACGTATCCT
16521 AATTTTT
1 AATTTTT
16528 TTCATGTTAA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
31 28 0.82
32 6 0.18
ACGTcount: A:0.39, C:0.13, G:0.13, T:0.36
Consensus pattern (31 bp):
AATTTTTGAAAGGTACACATAAACGTATCCT
Found at i:16989 original size:25 final size:26
Alignment explanation
Indices: 16935--16987 Score: 88
Period size: 26 Copynumber: 2.0 Consensus size: 26
16925 AGAATATCAG
*
16935 AATTTGTTTTGTTTTTAAAATTCAAA
1 AATTTGTTTTGCTTTTAAAATTCAAA
*
16961 AATTTTTTTTGCTTTTAAAATTCAAA
1 AATTTGTTTTGCTTTTAAAATTCAAA
16987 A
1 A
16988 TTATTTCCTA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.36, C:0.06, G:0.06, T:0.53
Consensus pattern (26 bp):
AATTTGTTTTGCTTTTAAAATTCAAA
Done.