Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014185.1 Corchorus capsularis cultivar CVL-1 contig14206, 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: 19974
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:911 original size:13 final size:13
Alignment explanation
Indices: 893--923 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
883 TTCATATGCA
893 TTCATATTTAAAT
1 TTCATATTTAAAT
*
906 TTCATATTTATAT
1 TTCATATTTAAAT
919 TTCAT
1 TTCAT
924 TACTATGCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.32, C:0.10, G:0.00, T:0.58
Consensus pattern (13 bp):
TTCATATTTAAAT
Found at i:6932 original size:26 final size:26
Alignment explanation
Indices: 6901--6961 Score: 68
Period size: 28 Copynumber: 2.3 Consensus size: 26
6891 AAAGGAAAAA
6901 CGGAAAAGAAATATTTTTTTTTAAAT
1 CGGAAAAGAAATATTTTTTTTTAAAT
** *
6927 CGGAAACCCTAAATTTTTTTTTTTAAAT
1 CGGAAA--AGAAATATTTTTTTTTAAAT
*
6955 CGCAAAA
1 CGGAAAA
6962 ATTTTTTTTT
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
26 6 0.21
28 22 0.79
ACGTcount: A:0.39, C:0.11, G:0.10, T:0.39
Consensus pattern (26 bp):
CGGAAAAGAAATATTTTTTTTTAAAT
Found at i:7019 original size:32 final size:33
Alignment explanation
Indices: 6966--7031 Score: 98
Period size: 32 Copynumber: 2.0 Consensus size: 33
6956 GCAAAAATTT
*
6966 TTTTTTTTAGAAAAAATCGGAAAAAAGAAAAAC
1 TTTTTTTTAGAAAAAATCGGAAAAAACAAAAAC
* *
6999 TTTTTTTTAGAACAAA-CGGAAAGAACAAAAAC
1 TTTTTTTTAGAAAAAATCGGAAAAAACAAAAAC
7031 T
1 T
7032 AATTCTGGGA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 15 0.50
33 15 0.50
ACGTcount: A:0.52, C:0.09, G:0.12, T:0.27
Consensus pattern (33 bp):
TTTTTTTTAGAAAAAATCGGAAAAAACAAAAAC
Found at i:8983 original size:19 final size:19
Alignment explanation
Indices: 8959--8998 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
8949 TTGAAACAAA
8959 GCACTAAATGGACATAGCC
1 GCACTAAATGGACATAGCC
8978 GCACTAAATGGACATAGCC
1 GCACTAAATGGACATAGCC
8997 GC
1 GC
8999 CCCAAGTGCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.35, C:0.28, G:0.23, T:0.15
Consensus pattern (19 bp):
GCACTAAATGGACATAGCC
Found at i:14157 original size:156 final size:156
Alignment explanation
Indices: 13864--14180 Score: 562
Period size: 156 Copynumber: 2.0 Consensus size: 156
13854 AAAGAATAAA
* *
13864 GATTAGGGGGGTATTGTTTATACCACAATTTACAATTTGGGTAAAATTGTAAATGCACATGGTGG
1 GATTTGGGGGGCATTGTTTATACCACAATTTACAATTTGGGTAAAATTGTAAATGCACATGGTGG
* *
13929 TACACAATGAAGGGTTGAGATTTACTCCCAAAAGTCCTATGGATGGTTAGATTTAATCCACCCTA
66 TACACAATGAAGGGCTGAGATTTACTCCCAAAAGTCCTATGGATGGTTAGATTTAATCCACCATA
*
13994 GGTCAAAGTCAATTAAGAAAAAGATT
131 GGCCAAAGTCAATTAAGAAAAAGATT
14020 GATTTGGGGGGCATTGTTTATACCACAATTTACAATTTGGGTAAAATTGTAAATGCACATGGTGG
1 GATTTGGGGGGCATTGTTTATACCACAATTTACAATTTGGGTAAAATTGTAAATGCACATGGTGG
* * *
14085 TACATAATGAAGGGCTGAGATTTACTCCCAAAAGTCCTATGGATGGTTGGTTTTAATCCACCATA
66 TACACAATGAAGGGCTGAGATTTACTCCCAAAAGTCCTATGGATGGTTAGATTTAATCCACCATA
14150 GGCCAAAGTCAATTAAGAAAAAGATT
131 GGCCAAAGTCAATTAAGAAAAAGATT
14176 GATTT
1 GATTT
14181 TTGATTTAAA
Statistics
Matches: 153, Mismatches: 8, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
156 153 1.00
ACGTcount: A:0.34, C:0.14, G:0.22, T:0.31
Consensus pattern (156 bp):
GATTTGGGGGGCATTGTTTATACCACAATTTACAATTTGGGTAAAATTGTAAATGCACATGGTGG
TACACAATGAAGGGCTGAGATTTACTCCCAAAAGTCCTATGGATGGTTAGATTTAATCCACCATA
GGCCAAAGTCAATTAAGAAAAAGATT
Found at i:15567 original size:22 final size:22
Alignment explanation
Indices: 15532--15586 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 22
15522 TATCCTCTTC
* **
15532 TTACTGATTGCCATCTTACTTT
1 TTACTGATTACCATCTTACCCT
* *
15554 TTACTAATTACCATTTTACCCT
1 TTACTGATTACCATCTTACCCT
15576 TTACTGATTAC
1 TTACTGATTAC
15587 GTTTTACTTT
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.24, C:0.24, G:0.05, T:0.47
Consensus pattern (22 bp):
TTACTGATTACCATCTTACCCT
Found at i:15637 original size:44 final size:44
Alignment explanation
Indices: 15609--15708 Score: 105
Period size: 44 Copynumber: 2.3 Consensus size: 44
15599 ACCATTTTAC
*
15609 CTTTTTACT-CTTAATATTTCACTCTTTACTTATTGCCTTCTTA
1 CTTTTTACTGATTAATATTTCACTCTTTACTTATTGCCTTCTTA
* * * * * * *
15652 CTTTTTGCTGATTACTATTTTACTCTTTACTGATTACCATCTTG
1 CTTTTTACTGATTAATATTTCACTCTTTACTTATTGCCTTCTTA
*
15696 C-TCTTACTGATTA
1 CTTTTTACTGATTA
15709 CCCTTTACTC
Statistics
Matches: 46, Mismatches: 10, Indels: 2
0.79 0.17 0.03
Matches are distributed among these distances:
43 18 0.39
44 28 0.61
ACGTcount: A:0.19, C:0.22, G:0.06, T:0.53
Consensus pattern (44 bp):
CTTTTTACTGATTAATATTTCACTCTTTACTTATTGCCTTCTTA
Found at i:15704 original size:21 final size:22
Alignment explanation
Indices: 15629--15722 Score: 93
Period size: 22 Copynumber: 4.4 Consensus size: 22
15619 TTAATATTTC
* * *
15629 ACTCTTTACTTATTGCCTTCTT
1 ACTCTTTACTGATTACCATCTT
* * * *
15651 ACTTTTTGCTGATTACTATTTT
1 ACTCTTTACTGATTACCATCTT
15673 ACTCTTTACTGATTACCATCTT
1 ACTCTTTACTGATTACCATCTT
* *
15695 GCTC-TTACTGATTACCCT-TT
1 ACTCTTTACTGATTACCATCTT
15715 ACTCTTTA
1 ACTCTTTA
15723 TCATTCTTCC
Statistics
Matches: 57, Mismatches: 14, Indels: 3
0.77 0.19 0.04
Matches are distributed among these distances:
20 5 0.09
21 16 0.28
22 36 0.63
ACGTcount: A:0.18, C:0.24, G:0.06, T:0.51
Consensus pattern (22 bp):
ACTCTTTACTGATTACCATCTT
Found at i:15715 original size:35 final size:35
Alignment explanation
Indices: 15671--15758 Score: 115
Period size: 35 Copynumber: 2.5 Consensus size: 35
15661 GATTACTATT
*
15671 TTACTCTTTACTGATTACCA-TCTTGCTCTTACTGA
1 TTACTCTTTACTGATTACCATTCTTCCT-TTACTGA
* ** *
15706 TTACCCTTTACTCTTTATCATTCTTCCTTTACTGA
1 TTACTCTTTACTGATTACCATTCTTCCTTTACTGA
15741 TTACTCTTTACTGATTAC
1 TTACTCTTTACTGATTAC
15759 TTTTGCCTGA
Statistics
Matches: 43, Mismatches: 9, Indels: 2
0.80 0.17 0.04
Matches are distributed among these distances:
35 37 0.86
36 6 0.14
ACGTcount: A:0.19, C:0.26, G:0.06, T:0.49
Consensus pattern (35 bp):
TTACTCTTTACTGATTACCATTCTTCCTTTACTGA
Found at i:15749 original size:14 final size:14
Alignment explanation
Indices: 15732--15883 Score: 77
Period size: 14 Copynumber: 11.0 Consensus size: 14
15722 ATCATTCTTC
15732 CTTTACTGATTACT
1 CTTTACTGATTACT
15746 CTTTACTGATTACT
1 CTTTACTGATTACT
* *
15760 -TTTGCCTGAATAC-
1 CTTT-ACTGATTACT
*
15773 CTTT--T-ACTACT
1 CTTTACTGATTACT
* **
15784 CTTTGCCATTTTTACT
1 CTTT-AC-TGATTACT
*
15800 -TTTCGCTGATTACT
1 CTTT-ACTGATTACT
15814 CTTTACTGATTACT
1 CTTTACTGATTACT
**
15828 -TTTACCATTTTTACT
1 CTTTA-C-TGATTACT
15843 -TTTACTGATTACT
1 CTTTACTGATTACT
** *
15856 CTTTACTTTTTCCT
1 CTTTACTGATTACT
*
15870 CTTTAATGATTACT
1 CTTTACTGATTACT
15884 ATTTTACTCT
Statistics
Matches: 105, Mismatches: 21, Indels: 24
0.70 0.14 0.16
Matches are distributed among these distances:
10 4 0.04
11 5 0.05
13 13 0.12
14 61 0.58
15 18 0.17
16 4 0.04
ACGTcount: A:0.19, C:0.22, G:0.07, T:0.53
Consensus pattern (14 bp):
CTTTACTGATTACT
Found at i:15860 original size:42 final size:44
Alignment explanation
Indices: 15732--15862 Score: 136
Period size: 43 Copynumber: 3.2 Consensus size: 44
15722 ATCATTCTTC
** *
15732 CTTTACTGATTACTCTTTA-C-TGATTACTTTTGC-CTGAATAC-
1 CTTTACTGATTACTCTTTACCATTTTTACTTTT-CACTGATTACT
* * *
15773 CTTT--T-ACTACTCTTTGCCATTTTTACTTTTCGCTGATTACT
1 CTTTACTGATTACTCTTTACCATTTTTACTTTTCACTGATTACT
15814 CTTTACTGATTACT-TTTACCATTTTTACTTTT-ACTGATTACT
1 CTTTACTGATTACTCTTTACCATTTTTACTTTTCACTGATTACT
15856 CTTTACT
1 CTTTACT
15863 TTTTCCTCTT
Statistics
Matches: 75, Mismatches: 8, Indels: 13
0.78 0.08 0.14
Matches are distributed among these distances:
38 9 0.12
39 3 0.04
40 16 0.21
41 8 0.11
42 16 0.21
43 18 0.24
44 5 0.07
ACGTcount: A:0.19, C:0.22, G:0.07, T:0.52
Consensus pattern (44 bp):
CTTTACTGATTACTCTTTACCATTTTTACTTTTCACTGATTACT
Found at i:15866 original size:28 final size:28
Alignment explanation
Indices: 15809--15883 Score: 100
Period size: 28 Copynumber: 2.7 Consensus size: 28
15799 TTTTCGCTGA
15809 TTACTCTTTACTGATTACTTTTACCATTT
1 TTACTCTTTACTGATTACTTTTACC-TTT
15838 TTACT-TTTACTGATTACTCTTTA-CTTT
1 TTACTCTTTACTGATTACT-TTTACCTTT
* *
15865 TTCCTCTTTAATGATTACT
1 TTACTCTTTACTGATTACT
15884 ATTTTACTCT
Statistics
Matches: 42, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
27 7 0.17
28 26 0.62
29 9 0.21
ACGTcount: A:0.20, C:0.20, G:0.04, T:0.56
Consensus pattern (28 bp):
TTACTCTTTACTGATTACTTTTACCTTT
Found at i:15914 original size:26 final size:26
Alignment explanation
Indices: 15878--15931 Score: 92
Period size: 26 Copynumber: 2.1 Consensus size: 26
15868 CTCTTTAATG
15878 ATTACTATTTT-ACTCTCTTGAATTTA
1 ATTACTATTTTCACTCT-TTGAATTTA
15904 ATTACTATTTTCACTCTTTGAATTTA
1 ATTACTATTTTCACTCTTTGAATTTA
15930 AT
1 AT
15932 CACCATTTGT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
26 22 0.81
27 5 0.19
ACGTcount: A:0.28, C:0.15, G:0.04, T:0.54
Consensus pattern (26 bp):
ATTACTATTTTCACTCTTTGAATTTA
Found at i:15939 original size:26 final size:26
Alignment explanation
Indices: 15884--15939 Score: 78
Period size: 26 Copynumber: 2.2 Consensus size: 26
15874 AATGATTACT
* *
15884 ATTTTACTCTCTTGAATTTAATTACT
1 ATTTTACTCTCTTGAATTTAATCACC
15910 ATTTTCACTCT-TTGAATTTAATCACC
1 ATTTT-ACTCTCTTGAATTTAATCACC
15936 ATTT
1 ATTT
15940 GTCATTTTAC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
26 22 0.81
27 5 0.19
ACGTcount: A:0.27, C:0.18, G:0.04, T:0.52
Consensus pattern (26 bp):
ATTTTACTCTCTTGAATTTAATCACC
Found at i:15985 original size:33 final size:33
Alignment explanation
Indices: 15905--15987 Score: 116
Period size: 32 Copynumber: 2.5 Consensus size: 33
15895 TTGAATTTAA
*
15905 TTACTATTTTCACTCTTTGAATTTAATCACCATT
1 TTACTATTTT-ACGCTTTGAATTTAATCACCATT
*
15939 TGT-C-ATTTTACGCTTTGAATTTAATTACCATT
1 T-TACTATTTTACGCTTTGAATTTAATCACCATT
15971 TTACTATTTTACGCTTT
1 TTACTATTTTACGCTTT
15988 ACCGATTACT
Statistics
Matches: 44, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
31 1 0.02
32 23 0.52
33 17 0.39
34 2 0.05
35 1 0.02
ACGTcount: A:0.24, C:0.18, G:0.06, T:0.52
Consensus pattern (33 bp):
TTACTATTTTACGCTTTGAATTTAATCACCATT
Found at i:16032 original size:45 final size:46
Alignment explanation
Indices: 15978--16094 Score: 191
Period size: 45 Copynumber: 2.5 Consensus size: 46
15968 ATTTTACTAT
15978 TTTACGCTTTACCGATTACTCTTTGCTTTTTACCATTTTTT-ATTC
1 TTTACGCTTTACCGATTACTCTTTGCTTTTTACCATTTTTTCATTC
16023 TTTACGCTTTACCGATTACTCTTTGCTTTTTACCATTTTTTCATTC
1 TTTACGCTTTACCGATTACTCTTTGCTTTTTACCATTTTTTCATTC
* *
16069 TTTACCGATTTACTGATTACCTCTTT
1 TTTA-CGCTTTACCGATTA-CTCTTT
16095 TACTTTTACT
Statistics
Matches: 67, Mismatches: 2, Indels: 3
0.93 0.03 0.04
Matches are distributed among these distances:
45 41 0.61
46 8 0.12
47 12 0.18
48 6 0.09
ACGTcount: A:0.16, C:0.23, G:0.07, T:0.54
Consensus pattern (46 bp):
TTTACGCTTTACCGATTACTCTTTGCTTTTTACCATTTTTTCATTC
Found at i:16157 original size:34 final size:36
Alignment explanation
Indices: 16078--16159 Score: 98
Period size: 40 Copynumber: 2.2 Consensus size: 36
16068 CTTTACCGAT
16078 TTACTGATTACCTCTTTTACTTTTACTCTTAATTACC
1 TTACTGATTACCTCTTTTACTTTTACTCTTAATTA-C
16115 ATTTTACTGATTA-CTCCTTTTACTTTTACTCTTAATT-C
1 ---TTACTGATTACCT-CTTTTACTTTTACTCTTAATTAC
16153 -TACTGAT
1 TTACTGAT
16160 CACTTCCTCT
Statistics
Matches: 41, Mismatches: 0, Indels: 8
0.84 0.00 0.16
Matches are distributed among these distances:
34 7 0.17
38 1 0.02
39 2 0.05
40 31 0.76
ACGTcount: A:0.22, C:0.22, G:0.04, T:0.52
Consensus pattern (36 bp):
TTACTGATTACCTCTTTTACTTTTACTCTTAATTAC
Found at i:16349 original size:32 final size:32
Alignment explanation
Indices: 16281--16353 Score: 85
Period size: 32 Copynumber: 2.3 Consensus size: 32
16271 CTAATTAATC
* * * *
16281 CTTTTACCTTGACTCTTAATTATTGACTTACC
1 CTTTTACTTTGACCCTTAATTACTGACTTACA
*
16313 CTTTTACTTTGACCCTTAATTACTGA-TTGCTA
1 CTTTTACTTTGACCCTTAATTACTGACTTAC-A
16345 CTTTTACTT
1 CTTTTACTT
16354 CCTCTCTTAG
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
31 3 0.09
32 32 0.91
ACGTcount: A:0.21, C:0.23, G:0.07, T:0.49
Consensus pattern (32 bp):
CTTTTACTTTGACCCTTAATTACTGACTTACA
Found at i:16427 original size:38 final size:39
Alignment explanation
Indices: 16330--16427 Score: 101
Period size: 38 Copynumber: 2.5 Consensus size: 39
16320 TTTGACCCTT
* * * *
16330 AATTACTGATTGCTACTTTTACTTCCTCTCTTAGTTATC
1 AATTACTGATTACTACTTTTACTTCCTCTCTTAATCAAC
* * *
16369 AATTTACTAATTAATCCTTTTACTT-C-CTCTTAATCAAC
1 AA-TTACTGATTACTACTTTTACTTCCTCTCTTAATCAAC
16407 AATTGACTGATTACTACTTTT
1 AATT-ACTGATTACTACTTTT
16428 TTATTATTTC
Statistics
Matches: 47, Mismatches: 10, Indels: 5
0.76 0.16 0.08
Matches are distributed among these distances:
37 2 0.04
38 24 0.51
39 3 0.06
40 18 0.38
ACGTcount: A:0.27, C:0.21, G:0.05, T:0.47
Consensus pattern (39 bp):
AATTACTGATTACTACTTTTACTTCCTCTCTTAATCAAC
Done.