Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014143.1 Corchorus capsularis cultivar CVL-1 contig14164, 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: 4635
ACGTcount: A:0.29, C:0.21, G:0.15, T:0.35
Found at i:587 original size:17 final size:19
Alignment explanation
Indices: 555--592 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
545 TGCAAAATGC
*
555 AAAGCGAAAGAAC-AAAGA
1 AAAGCGAAACAACAAAAGA
573 AAAGC-AAACAACAAAAGA
1 AAAGCGAAACAACAAAAGA
591 AA
1 AA
593 TTAGTTAGTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 6 0.33
18 12 0.67
ACGTcount: A:0.71, C:0.13, G:0.16, T:0.00
Consensus pattern (19 bp):
AAAGCGAAACAACAAAAGA
Found at i:1694 original size:28 final size:26
Alignment explanation
Indices: 1645--1713 Score: 70
Period size: 28 Copynumber: 2.6 Consensus size: 26
1635 TTTTTACTCT
1645 TTTCTTACTCT-TTTACTAATTACCC
1 TTTCTTACTCTCTTTACTAATTACCC
* *
1670 TTTCCTTACTCTCTTTCATTGATTACCAC
1 TTT-CTTACTCTCTTT-ACTAATTACC-C
1699 TTT-TTACTCTTCTTT
1 TTTCTTACTC-TCTTT
1714 TTTTCTTATA
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
25 3 0.08
26 8 0.22
27 9 0.24
28 13 0.35
29 4 0.11
ACGTcount: A:0.16, C:0.28, G:0.01, T:0.55
Consensus pattern (26 bp):
TTTCTTACTCTCTTTACTAATTACCC
Found at i:1813 original size:35 final size:35
Alignment explanation
Indices: 1774--1863 Score: 94
Period size: 35 Copynumber: 2.6 Consensus size: 35
1764 AGTCTTTATT
*
1774 GATTACTCCTTACTAATTACCATT-TTGCTCTTACA
1 GATTACTCCTTACTAATTACCATTCTTCCT-TTACA
** * *
1809 GATTAC-CCTTTACTCTTTATCATTCTTCCTTTACT
1 GATTACTCC-TTACTAATTACCATTCTTCCTTTACA
*
1844 GATTACTCCTTACTGATTAC
1 GATTACTCCTTACTAATTAC
1864 TTTTGCCTGA
Statistics
Matches: 44, Mismatches: 8, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
34 2 0.05
35 36 0.82
36 6 0.14
ACGTcount: A:0.22, C:0.27, G:0.06, T:0.46
Consensus pattern (35 bp):
GATTACTCCTTACTAATTACCATTCTTCCTTTACA
Found at i:1927 original size:14 final size:14
Alignment explanation
Indices: 1910--1988 Score: 81
Period size: 14 Copynumber: 5.6 Consensus size: 14
1900 TTACTTTTCG
1910 CTGATTACTCTTTA
1 CTGATTACTCTTTA
1924 CTGATTACT-TTTA
1 CTGATTACTCTTTA
**
1937 CCATTTTTACT-TTTA
1 -C-TGATTACTCTTTA
1952 CTGATTACTCTTTA
1 CTGATTACTCTTTA
** *
1966 CTTTTTCCTCTTTA
1 CTGATTACTCTTTA
1980 CTGATTACT
1 CTGATTACT
1989 ATTTTACTCT
Statistics
Matches: 52, Mismatches: 10, Indels: 6
0.76 0.15 0.09
Matches are distributed among these distances:
13 10 0.19
14 32 0.62
15 10 0.19
ACGTcount: A:0.19, C:0.22, G:0.05, T:0.54
Consensus pattern (14 bp):
CTGATTACTCTTTA
Found at i:1933 original size:28 final size:27
Alignment explanation
Indices: 1900--1988 Score: 99
Period size: 28 Copynumber: 3.2 Consensus size: 27
1890 CCTGCCATTT
**
1900 TTACTTTTCGCTGATTACTCTTTACTGA
1 TTACTTTTC-CTTTTTACTCTTTACTGA
1928 TTACTTTTACCATTTTTACT-TTTACTGA
1 TTACTTTT-CC-TTTTTACTCTTTACTGA
* *
1956 TTACTCTTTACTTTTTCCTCTTTACTGA
1 TTACT-TTTCCTTTTTACTCTTTACTGA
1984 TTACT
1 TTACT
1989 ATTTTACTCT
Statistics
Matches: 53, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
27 7 0.13
28 36 0.68
29 10 0.19
ACGTcount: A:0.18, C:0.21, G:0.06, T:0.55
Consensus pattern (27 bp):
TTACTTTTCCTTTTTACTCTTTACTGA
Found at i:2018 original size:26 final size:25
Alignment explanation
Indices: 1983--2080 Score: 97
Period size: 26 Copynumber: 3.6 Consensus size: 25
1973 CTCTTTACTG
1983 ATTACTATTTTACTCTCTTGAATTTA
1 ATTACTATTTTACTCT-TTGAATTTA
2009 ATTACTATTTTCACTCTTTGAATTTA
1 ATTACTATTTT-ACTCTTTGAATTTA
*
2035 ATCACCATTTGTCATTTTACTCTTTGAATTTA
1 ATTA-C-----T-ATTTTACTCTTTGAATTTA
*
2067 ATTACCATTTTACT
1 ATTACTATTTTACT
2081 ATTTTACTCT
Statistics
Matches: 61, Mismatches: 3, Indels: 17
0.75 0.04 0.21
Matches are distributed among these distances:
25 8 0.13
26 23 0.38
27 6 0.10
31 1 0.02
32 18 0.30
33 5 0.08
ACGTcount: A:0.27, C:0.17, G:0.04, T:0.52
Consensus pattern (25 bp):
ATTACTATTTTACTCTTTGAATTTA
Found at i:2090 original size:33 final size:33
Alignment explanation
Indices: 2010--2090 Score: 121
Period size: 32 Copynumber: 2.5 Consensus size: 33
2000 TTGAATTTAA
2010 TTACTATTTTCACTCTTTGAATTTAATCACCATT
1 TTACTATTTT-ACTCTTTGAATTTAATCACCATT
*
2044 TGT-C-ATTTTACTCTTTGAATTTAATTACCATT
1 T-TACTATTTTACTCTTTGAATTTAATCACCATT
2076 TTACTATTTTACTCT
1 TTACTATTTTACTCT
2091 CAACCGATTA
Statistics
Matches: 43, Mismatches: 1, Indels: 7
0.84 0.02 0.14
Matches are distributed among these distances:
31 1 0.02
32 24 0.56
33 15 0.35
34 2 0.05
35 1 0.02
ACGTcount: A:0.25, C:0.19, G:0.04, T:0.53
Consensus pattern (33 bp):
TTACTATTTTACTCTTTGAATTTAATCACCATT
Found at i:2180 original size:40 final size:39
Alignment explanation
Indices: 2128--2206 Score: 108
Period size: 40 Copynumber: 2.0 Consensus size: 39
2118 TTTTTTATTC
2128 TTTACCGATTTACCGATTAC-CTCTTTTACTTTTACTCTTA
1 TTTACCGATTTACCGATTACTC-CTTTTAC-TTTACTCTTA
*
2168 TTTACC-ATTTTACTGATTACTCCTTTTACTTTACTCTTA
1 TTTACCGA-TTTACCGATTACTCCTTTTACTTTACTCTTA
2207 ATTCTACTGA
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
39 11 0.31
40 24 0.67
41 1 0.03
ACGTcount: A:0.20, C:0.24, G:0.04, T:0.52
Consensus pattern (39 bp):
TTTACCGATTTACCGATTACTCCTTTTACTTTACTCTTA
Found at i:2195 original size:24 final size:24
Alignment explanation
Indices: 2151--2196 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
2141 CGATTACCTC
* *
2151 TTTTACTTTTACTCTTATTTACCA
1 TTTTACTATTACTCCTATTTACCA
2175 TTTTACTGATTACTCCT-TTTAC
1 TTTTACT-ATTACTCCTATTTAC
2197 TTTACTCTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
24 12 0.63
25 7 0.37
ACGTcount: A:0.20, C:0.22, G:0.02, T:0.57
Consensus pattern (24 bp):
TTTTACTATTACTCCTATTTACCA
Found at i:2469 original size:38 final size:40
Alignment explanation
Indices: 2404--2478 Score: 100
Period size: 38 Copynumber: 1.9 Consensus size: 40
2394 CTGATTGCTA
* * *
2404 CTTTTACTTCCTCTCTTAGTTATCAATTTACTAATTAATC
1 CTTTTACTTCCTCTCTTAGTCACCAATTGACTAATTAATC
*
2444 CTTTTACTTCCTCT-TTA-TCACCAATTGACTGATTA
1 CTTTTACTTCCTCTCTTAGTCACCAATTGACTAATTA
2479 CTACTTTTTA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
38 14 0.45
39 3 0.10
40 14 0.45
ACGTcount: A:0.24, C:0.24, G:0.04, T:0.48
Consensus pattern (40 bp):
CTTTTACTTCCTCTCTTAGTCACCAATTGACTAATTAATC
Found at i:2486 original size:38 final size:39
Alignment explanation
Indices: 2389--2486 Score: 110
Period size: 40 Copynumber: 2.5 Consensus size: 39
2379 TTTGACCCTT
* * *
2389 AATTACTGATTGCTACTTTTACTTCCTCTCTTAGTTATC
1 AATTACTGATTACTACTTTTACTTCCTCTCTTAGTCACC
* * *
2428 AATTTACTAATTAATCCTTTTACTTCCTCT-TTA-TCACC
1 AA-TTACTGATTACTACTTTTACTTCCTCTCTTAGTCACC
2466 AATTGACTGATTACTACTTTT
1 AATT-ACTGATTACTACTTTT
2487 TATCTTTTCA
Statistics
Matches: 48, Mismatches: 9, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
37 2 0.04
38 18 0.38
39 5 0.10
40 23 0.48
ACGTcount: A:0.24, C:0.22, G:0.05, T:0.48
Consensus pattern (39 bp):
AATTACTGATTACTACTTTTACTTCCTCTCTTAGTCACC
Done.