Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012289.1 Corchorus capsularis cultivar CVL-1 contig12310, 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: 20740
ACGTcount: A:0.28, C:0.20, G:0.22, T:0.31
Found at i:1870 original size:27 final size:27
Alignment explanation
Indices: 1840--1925 Score: 93
Period size: 27 Copynumber: 3.1 Consensus size: 27
1830 AGAGAAGAAA
*
1840 AATTGTCTTTGTGTTTAGGGACTTATG
1 AATTGCCTTTGTGTTTAGGGACTTATG
* *
1867 AATTGCCCTTGTGTTT-GAGGACTTTTGAG
1 AATTGCCTTTGTGTTTAG-GGACTTAT--G
* *
1896 AAATGCCTCTGTGTTTAGGGACTTATG
1 AATTGCCTTTGTGTTTAGGGACTTATG
1923 AAT
1 AAT
1926 GCCCAGGTGT
Statistics
Matches: 47, Mismatches: 8, Indels: 8
0.75 0.13 0.13
Matches are distributed among these distances:
26 1 0.02
27 24 0.51
29 21 0.45
30 1 0.02
ACGTcount: A:0.21, C:0.12, G:0.26, T:0.42
Consensus pattern (27 bp):
AATTGCCTTTGTGTTTAGGGACTTATG
Found at i:1935 original size:26 final size:25
Alignment explanation
Indices: 1849--2003 Score: 91
Period size: 26 Copynumber: 5.6 Consensus size: 25
1839 AAATTGTCTT
1849 TGTGTTT-AGGGACTTATGAATTGCCC
1 TGTGTTTGA-GGACTTATGAA-TGCCC
*
1875 TTGTGTTTGAGGACTTTTGAGAAATGCCTC
1 -TGTGTTTGAGGACTTAT--G-AATGCC-C
1905 TGTGTTT-AGGGACTTATGAATGCCC
1 TGTGTTTGA-GGACTTATGAATGCCC
* *
1930 AGGTGTTTGAGGACTTTTTGATAGATATGTCTC
1 -TGTGTTTGAGGAC---TT-AT-GA-ATG-CCC
1963 TGTGTTT-AGGGACTTATGAATGCCC
1 TGTGTTTGA-GGACTTATGAATGCCC
*
1988 AGGTGTTTGAGGACTT
1 -TGTGTTTGAGGACTT
2004 TAATTATTGG
Statistics
Matches: 103, Mismatches: 7, Indels: 37
0.70 0.05 0.25
Matches are distributed among these distances:
25 3 0.03
26 31 0.30
27 19 0.18
28 4 0.04
29 23 0.22
30 5 0.05
31 3 0.03
32 13 0.13
33 2 0.02
ACGTcount: A:0.20, C:0.13, G:0.28, T:0.39
Consensus pattern (25 bp):
TGTGTTTGAGGACTTATGAATGCCC
Found at i:1981 original size:58 final size:56
Alignment explanation
Indices: 1843--2004 Score: 245
Period size: 58 Copynumber: 2.9 Consensus size: 56
1833 GAAGAAAAAT
* **
1843 TGTCTTTGTGTTTAGGGACTTATGAATTGCCCTTGTGTTTGAGGAC-TTTTGAGAAA
1 TGTCTCTGTGTTTAGGGACTTATGAA-TGCCCAGGTGTTTGAGGACTTTTTGAGAAA
* *
1899 TGCCTCTGTGTTTAGGGACTTATGAATGCCCAGGTGTTTGAGGACTTTTTGATAGATA
1 TGTCTCTGTGTTTAGGGACTTATGAATGCCCAGGTGTTTGAGGACTTTTTG--AGAAA
1957 TGTCTCTGTGTTTAGGGACTTATGAATGCCCAGGTGTTTGAGGACTTT
1 TGTCTCTGTGTTTAGGGACTTATGAATGCCCAGGTGTTTGAGGACTTT
2005 AATTATTGGG
Statistics
Matches: 97, Mismatches: 6, Indels: 4
0.91 0.06 0.04
Matches are distributed among these distances:
55 17 0.18
56 29 0.30
58 51 0.53
ACGTcount: A:0.19, C:0.13, G:0.28, T:0.40
Consensus pattern (56 bp):
TGTCTCTGTGTTTAGGGACTTATGAATGCCCAGGTGTTTGAGGACTTTTTGAGAAA
Found at i:6835 original size:8 final size:8
Alignment explanation
Indices: 6824--6853 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
6814 GATATTTCAG
6824 TATTTGGA
1 TATTTGGA
6832 TATTTGG-
1 TATTTGGA
6839 TATTTGGA
1 TATTTGGA
6847 TATTTGG
1 TATTTGG
6854 CATTTGGGTA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
7 7 0.33
8 14 0.67
ACGTcount: A:0.20, C:0.00, G:0.27, T:0.53
Consensus pattern (8 bp):
TATTTGGA
Found at i:6843 original size:15 final size:15
Alignment explanation
Indices: 6812--6860 Score: 71
Period size: 15 Copynumber: 3.2 Consensus size: 15
6802 TAGAATTTGA
*
6812 TGGATATTTCAGTATT
1 TGGATATTT-GGTATT
6828 TGGATATTTGGTATT
1 TGGATATTTGGTATT
*
6843 TGGATATTTGGCATT
1 TGGATATTTGGTATT
6858 TGG
1 TGG
6861 GTATGTATGA
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
15 22 0.71
16 9 0.29
ACGTcount: A:0.20, C:0.04, G:0.27, T:0.49
Consensus pattern (15 bp):
TGGATATTTGGTATT
Found at i:14551 original size:26 final size:26
Alignment explanation
Indices: 14520--14674 Score: 95
Period size: 32 Copynumber: 5.5 Consensus size: 26
14510 TGAGAAATGC
14520 GTGTTT-AGGGACTTATGAATGCCCAT
1 GTGTTTGA-GGACTTATGAATGCCCAT
14546 GTGTTTGAGGACTTTTTGATAGAAATGCCTC-T
1 GTGTTTGAGGAC---TT-AT-G-AATGCC-CAT
*
14578 GTGTTT-AGGGACTTATGAATGCCCAG
1 GTGTTTGA-GGACTTATGAATGCCCAT
**
14604 GTGTTTGAGGACTTTTTGATAGAGATGCCTTT
1 GTGTTTGAGGAC---TT-AT-GA-ATGCCCAT
*
14636 GTGTTT-AGGGACTTATGAATG-CCAG
1 GTGTTTGA-GGACTTATGAATGCCCAT
14661 GTGTTTGAGGACTT
1 GTGTTTGAGGACTT
14675 TAATTATTGG
Statistics
Matches: 103, Mismatches: 7, Indels: 39
0.69 0.05 0.26
Matches are distributed among these distances:
25 14 0.14
26 30 0.29
27 5 0.05
28 4 0.04
29 8 0.08
30 4 0.04
31 5 0.05
32 32 0.31
33 1 0.01
ACGTcount: A:0.21, C:0.12, G:0.29, T:0.37
Consensus pattern (26 bp):
GTGTTTGAGGACTTATGAATGCCCAT
Found at i:14581 original size:32 final size:32
Alignment explanation
Indices: 14537--14649 Score: 100
Period size: 32 Copynumber: 3.7 Consensus size: 32
14527 GGGACTTATG
14537 AATGCCCATGTGTTT-GAGGACTTTTTGATAGA
1 AATGCCCATGTGTTTAG-GGACTTTTTGATAGA
14569 AATGCCTC-TGTGTTTAGGGAC---TT-AT-G-
1 AATGCC-CATGTGTTTAGGGACTTTTTGATAGA
*
14595 AATGCCCAGGTGTTT-GAGGACTTTTTGATAGA
1 AATGCCCATGTGTTTAG-GGACTTTTTGATAGA
* **
14627 GATGCCTTTGTGTTTAGGGACTT
1 AATGCCCATGTGTTTAGGGACTT
14650 ATGAATGCCA
Statistics
Matches: 65, Mismatches: 5, Indels: 22
0.71 0.05 0.24
Matches are distributed among these distances:
25 2 0.03
26 16 0.25
27 1 0.02
28 2 0.03
29 4 0.06
30 2 0.03
31 1 0.02
32 34 0.52
33 3 0.05
ACGTcount: A:0.21, C:0.13, G:0.27, T:0.38
Consensus pattern (32 bp):
AATGCCCATGTGTTTAGGGACTTTTTGATAGA
Found at i:14592 original size:58 final size:58
Alignment explanation
Indices: 14464--14675 Score: 305
Period size: 58 Copynumber: 3.8 Consensus size: 58
14454 GAAAAATTGT
***
14464 CTCTGTGTTTAGGGACTTATGAATTGCCCTTATGTTTGAGGAC-TTTTG--AGAAATG-
1 CTCTGTGTTTAGGGACTTATGAA-TGCCCAGGTGTTTGAGGACTTTTTGATAGAAATGC
*
14519 --C-GTGTTTAGGGACTTATGAATGCCCATGTGTTTGAGGACTTTTTGATAGAAATGC
1 CTCTGTGTTTAGGGACTTATGAATGCCCAGGTGTTTGAGGACTTTTTGATAGAAATGC
*
14574 CTCTGTGTTTAGGGACTTATGAATGCCCAGGTGTTTGAGGACTTTTTGATAGAGATGC
1 CTCTGTGTTTAGGGACTTATGAATGCCCAGGTGTTTGAGGACTTTTTGATAGAAATGC
*
14632 CTTTGTGTTTAGGGACTTATGAATG-CCAGGTGTTTGAGGACTTT
1 CTCTGTGTTTAGGGACTTATGAATGCCCAGGTGTTTGAGGACTTT
14676 AATTATTGGG
Statistics
Matches: 145, Mismatches: 5, Indels: 12
0.90 0.03 0.07
Matches are distributed among these distances:
51 17 0.12
52 24 0.17
53 1 0.01
54 7 0.05
57 20 0.14
58 76 0.52
ACGTcount: A:0.21, C:0.13, G:0.28, T:0.38
Consensus pattern (58 bp):
CTCTGTGTTTAGGGACTTATGAATGCCCAGGTGTTTGAGGACTTTTTGATAGAAATGC
Found at i:15079 original size:6 final size:6
Alignment explanation
Indices: 15068--15097 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
15058 AAAGCAAAGC
15068 AAATCT AAATCT AAATCT AAATCT AAATCT
1 AAATCT AAATCT AAATCT AAATCT AAATCT
15098 GAAGCAGAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.50, C:0.17, G:0.00, T:0.33
Consensus pattern (6 bp):
AAATCT
Found at i:16045 original size:10 final size:10
Alignment explanation
Indices: 16026--16055 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
16016 AGATAAGGAC
16026 TCTAGAATTT
1 TCTAGAATTT
*
16036 TCTGGAATTT
1 TCTAGAATTT
16046 TCTAGAATTT
1 TCTAGAATTT
16056 AGCAGCAACT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.27, C:0.10, G:0.13, T:0.50
Consensus pattern (10 bp):
TCTAGAATTT
Found at i:17041 original size:9 final size:9
Alignment explanation
Indices: 17027--17059 Score: 57
Period size: 9 Copynumber: 3.7 Consensus size: 9
17017 GAATGTCAAA
17027 CAACCACCT
1 CAACCACCT
17036 CAACCACCT
1 CAACCACCT
*
17045 CAACAACCT
1 CAACCACCT
17054 CAACCA
1 CAACCA
17060 GAGACAAAAG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.39, C:0.52, G:0.00, T:0.09
Consensus pattern (9 bp):
CAACCACCT
Found at i:18297 original size:45 final size:45
Alignment explanation
Indices: 18192--18341 Score: 192
Period size: 45 Copynumber: 3.3 Consensus size: 45
18182 AGGCTGTTTG
* * * *
18192 GTTTATTTTGAACAAGGTAACAAATAGTCTTTAATGGCTATTTTTA
1 GTTTAGTTTGAACATGGTTACAAATAGTCTTTCATGGCTA-TTTTA
* * * *
18238 GTTTAGTTTGAACATGGTTAGAAATGGTCTTTCATGGATATTTGA
1 GTTTAGTTTGAACATGGTTACAAATAGTCTTTCATGGCTATTTTA
* * *
18283 TTTTAGTTTGAACATGGTTTCAAATAGTCTTTCATGGCTGTTTTA
1 GTTTAGTTTGAACATGGTTACAAATAGTCTTTCATGGCTATTTTA
18328 GTTTAGTTTGAACA
1 GTTTAGTTTGAACA
18342 AACAATGGTT
Statistics
Matches: 88, Mismatches: 16, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
45 55 0.62
46 33 0.38
ACGTcount: A:0.27, C:0.09, G:0.19, T:0.45
Consensus pattern (45 bp):
GTTTAGTTTGAACATGGTTACAAATAGTCTTTCATGGCTATTTTA
Found at i:18587 original size:2 final size:2
Alignment explanation
Indices: 18580--18613 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
18570 CTGATACTGG
18580 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
18614 TGAACAACGA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:18850 original size:19 final size:18
Alignment explanation
Indices: 18799--18852 Score: 63
Period size: 19 Copynumber: 2.8 Consensus size: 18
18789 TTAGTTTCCC
18799 TTCATTATTTAGCAAAAATT
1 TTCATTA-TTAGC-AAAATT
*
18819 TTCAATACTTAGCAAAATT
1 TTCATTA-TTAGCAAAATT
18838 TTCATTATATAGCAA
1 TTCATTAT-TAGCAA
18853 GGGTAAAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
18 1 0.03
19 18 0.60
20 11 0.37
ACGTcount: A:0.41, C:0.13, G:0.06, T:0.41
Consensus pattern (18 bp):
TTCATTATTAGCAAAATT
Done.