Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012505.1 Corchorus capsularis cultivar CVL-1 contig12526, 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: 47822
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31
Found at i:8702 original size:66 final size:66
Alignment explanation
Indices: 8603--8935 Score: 639
Period size: 66 Copynumber: 5.0 Consensus size: 66
8593 CGCTGTCCTT
*
8603 CCAATTGTGAAGGTTCAGAATATTGCTGTCTAGCCATCTGGGGAGAGTTGGACTGCTGGTGTCCG
1 CCAATTGTGAAGGTTCAGAATATTGCTGTCTAGCCATCTGGGGATAGTTGGACTGCTGGTGTCCG
8668 G
66 G
8669 CCAATTGTGAAGGTTCAGAATATTGCTGTCTAGCCATCTGGGGATAGTTGGACTGCTGGTGTCCG
1 CCAATTGTGAAGGTTCAGAATATTGCTGTCTAGCCATCTGGGGATAGTTGGACTGCTGGTGTCCG
8734 G
66 G
8735 CCAATTGTGAAGGTTCAGAATATTGCTGTCTAGCCATCTGGGGATAGTTGGACTGCTGGTGTCCG
1 CCAATTGTGAAGGTTCAGAATATTGCTGTCTAGCCATCTGGGGATAGTTGGACTGCTGGTGTCCG
8800 G
66 G
*
8801 CCAATTGTGAAGGTTCAGAATATTGCTGTCTAGCCATCTGGGGATAGTTGGACTGCTGGTGTCTG
1 CCAATTGTGAAGGTTCAGAATATTGCTGTCTAGCCATCTGGGGATAGTTGGACTGCTGGTGTCCG
8866 G
66 G
*
8867 CCAATTGTGAAGGTTCAGAATATTGCTGTCTAGCCATCTGGGGATAGTTGGACTGCTGGTGTCCT
1 CCAATTGTGAAGGTTCAGAATATTGCTGTCTAGCCATCTGGGGATAGTTGGACTGCTGGTGTCCG
8932 G
66 G
8933 CCA
1 CCA
8936 TCTGAGGAGA
Statistics
Matches: 263, Mismatches: 4, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
66 263 1.00
ACGTcount: A:0.20, C:0.18, G:0.32, T:0.30
Consensus pattern (66 bp):
CCAATTGTGAAGGTTCAGAATATTGCTGTCTAGCCATCTGGGGATAGTTGGACTGCTGGTGTCCG
G
Found at i:10617 original size:15 final size:15
Alignment explanation
Indices: 10597--10627 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
10587 GGGTAGGGTT
10597 GGAGTCTGAATCTGA
1 GGAGTCTGAATCTGA
*
10612 GGAGTCTGAGTCTGA
1 GGAGTCTGAATCTGA
10627 G
1 G
10628 TCTGATTCTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.23, C:0.13, G:0.39, T:0.26
Consensus pattern (15 bp):
GGAGTCTGAATCTGA
Found at i:19380 original size:22 final size:22
Alignment explanation
Indices: 19352--19398 Score: 94
Period size: 22 Copynumber: 2.1 Consensus size: 22
19342 TCGTCGACAC
19352 CATGGGTCCTATTACCATCAAT
1 CATGGGTCCTATTACCATCAAT
19374 CATGGGTCCTATTACCATCAAT
1 CATGGGTCCTATTACCATCAAT
19396 CAT
1 CAT
19399 CTTTAGTTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.28, C:0.28, G:0.13, T:0.32
Consensus pattern (22 bp):
CATGGGTCCTATTACCATCAAT
Found at i:27010 original size:13 final size:13
Alignment explanation
Indices: 26992--27021 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
26982 TAGGCCTGGG
26992 CCTTATTATTTAA
1 CCTTATTATTTAA
27005 CCTTATTATTTAA
1 CCTTATTATTTAA
27018 CCTT
1 CCTT
27022 GTAATAATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.27, C:0.20, G:0.00, T:0.53
Consensus pattern (13 bp):
CCTTATTATTTAA
Found at i:43378 original size:45 final size:45
Alignment explanation
Indices: 43314--43399 Score: 145
Period size: 45 Copynumber: 1.9 Consensus size: 45
43304 TTCTTCAAAT
* * *
43314 AAGAACGTGGGTGGTTACCTCATTCTTGATGAAGTAACTGCTTTG
1 AAGAACGTAGGTGATTACCTCATTCTTGATGAAATAACTGCTTTG
43359 AAGAACGTAGGTGATTACCTCATTCTTGATGAAATAACTGC
1 AAGAACGTAGGTGATTACCTCATTCTTGATGAAATAACTGC
43400 ATATTGGCTT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 38 1.00
ACGTcount: A:0.29, C:0.16, G:0.23, T:0.31
Consensus pattern (45 bp):
AAGAACGTAGGTGATTACCTCATTCTTGATGAAATAACTGCTTTG
Found at i:43466 original size:31 final size:31
Alignment explanation
Indices: 43423--43510 Score: 149
Period size: 31 Copynumber: 2.8 Consensus size: 31
43413 AATACTTGGT
* *
43423 GAGTGTTTACGGTATACCTTTGGTGGGTATG
1 GAGTATTTACGGTATACCTTTGGTGGGTAGG
43454 GAGTATTTACGGTATACCTTTGGTGGGTAGG
1 GAGTATTTACGGTATACCTTTGGTGGGTAGG
43485 GAGTATTTACGGTATACCTTTTGGTG
1 GAGTATTTACGGTATACC-TTTGGTG
43511 AGTAATCATG
Statistics
Matches: 54, Mismatches: 2, Indels: 1
0.95 0.04 0.02
Matches are distributed among these distances:
31 47 0.87
32 7 0.13
ACGTcount: A:0.18, C:0.10, G:0.33, T:0.39
Consensus pattern (31 bp):
GAGTATTTACGGTATACCTTTGGTGGGTAGG
Found at i:43939 original size:10 final size:10
Alignment explanation
Indices: 43924--43956 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
43914 ATTAATTATC
43924 TATATATATT
1 TATATATATT
43934 TATATATATT
1 TATATATATT
*
43944 TTTAT-TATT
1 TATATATATT
43953 TATA
1 TATA
43957 GGATTGACCC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
9 7 0.33
10 14 0.67
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (10 bp):
TATATATATT
Found at i:44123 original size:36 final size:36
Alignment explanation
Indices: 44083--44203 Score: 106
Period size: 35 Copynumber: 3.4 Consensus size: 36
44073 CAGGGTTGGT
44083 GTAATGCCTCCACCCCATT-AGTTTGCTAAGGGG-GGC
1 GTAATGCCTCC-CCCCATTAAG-TTGCTAAGGGGAGGC
** *
44119 GTAATGCCTTCCCCTGATTAAGTTGTTAAGGGGAGGC
1 GTAATGCC-TCCCCCCATTAAGTTGCTAAGGGGAGGC
* * * * *
44156 GTAACGCCT-CCTCAATTAACTT-TTCAAGGGGAGGC
1 GTAATGCCTCCCCCCATTAAGTTGCT-AAGGGGAGGC
44191 GTAATGCCTCCCC
1 GTAATGCCTCCCC
44204 AATTAAATTG
Statistics
Matches: 70, Mismatches: 10, Indels: 10
0.78 0.11 0.11
Matches are distributed among these distances:
34 2 0.03
35 27 0.39
36 26 0.37
37 15 0.21
ACGTcount: A:0.21, C:0.26, G:0.26, T:0.26
Consensus pattern (36 bp):
GTAATGCCTCCCCCCATTAAGTTGCTAAGGGGAGGC
Found at i:44807 original size:28 final size:28
Alignment explanation
Indices: 44775--44870 Score: 78
Period size: 27 Copynumber: 3.5 Consensus size: 28
44765 GGTCGCCCCT
*
44775 CCTTTATGCGCGTAGGGGGGATCGCTCC
1 CCTTTATGCGCATAGGGGGGATCGCTCC
* * *
44803 CC-TT-TGCGCATAGTAAGGGG-TTGCCCC
1 CCTTTATGCGCATAG--GGGGGATCGCTCC
*
44830 CACTTTGTGCGCATA-GGGGGATCGCTCC
1 C-CTTTATGCGCATAGGGGGGATCGCTCC
44858 CCTTTA--CGCATAG
1 CCTTTATGCGCATAG
44871 CAAGGGGGTC
Statistics
Matches: 53, Mismatches: 8, Indels: 16
0.69 0.10 0.21
Matches are distributed among these distances:
25 6 0.11
26 8 0.15
27 16 0.30
28 13 0.25
29 2 0.04
30 8 0.15
ACGTcount: A:0.15, C:0.29, G:0.30, T:0.26
Consensus pattern (28 bp):
CCTTTATGCGCATAGGGGGGATCGCTCC
Found at i:44829 original size:56 final size:55
Alignment explanation
Indices: 44762--44877 Score: 162
Period size: 55 Copynumber: 2.1 Consensus size: 55
44752 CACGCGCACC
* * *
44762 AGGGGTCGCCCCTC-CTTTATGCGCGTAGGGGGGATCGCTCCCCTTTGCGCATAGTA
1 AGGGGTCGCCCC-CACTTTATGCGCATA-GGGGGATCGCTCCCCTTTACGCATAGCA
* *
44818 AGGGGTTGCCCCCACTTTGTGCGCATAGGGGGATCGCTCCCCTTTACGCATAGCA
1 AGGGGTCGCCCCCACTTTATGCGCATAGGGGGATCGCTCCCCTTTACGCATAGCA
44873 AGGGG
1 AGGGG
44878 GTCACCCCTT
Statistics
Matches: 54, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
55 32 0.59
56 22 0.41
ACGTcount: A:0.15, C:0.29, G:0.33, T:0.23
Consensus pattern (55 bp):
AGGGGTCGCCCCCACTTTATGCGCATAGGGGGATCGCTCCCCTTTACGCATAGCA
Found at i:44830 original size:26 final size:26
Alignment explanation
Indices: 44801--44896 Score: 72
Period size: 26 Copynumber: 3.6 Consensus size: 26
44791 GGGGATCGCT
*
44801 CCCCTTTGCGCATAGTAAGGGGTTGCC
1 CCCCTTTGCGCATAG-AAGGGGTTGCA
* *
44828 CCCACTTTGTGCGCATAG--GGGGATCGCT
1 CCC-C-TT-TGCGCATAGAAGGGG-TTGCA
* *
44856 CCCCTTTACGCATAGCAAGGGGGT-CA
1 CCCCTTTGCGCATAG-AAGGGGTTGCA
44882 CCCCTTTGCGCATAG
1 CCCCTTTGCGCATAG
44897 CAAAGCTCAA
Statistics
Matches: 55, Mismatches: 7, Indels: 15
0.71 0.09 0.19
Matches are distributed among these distances:
25 8 0.15
26 17 0.31
27 8 0.15
28 11 0.20
29 2 0.04
30 9 0.16
ACGTcount: A:0.17, C:0.31, G:0.28, T:0.24
Consensus pattern (26 bp):
CCCCTTTGCGCATAGAAGGGGTTGCA
Found at i:44879 original size:56 final size:56
Alignment explanation
Indices: 44762--44886 Score: 164
Period size: 56 Copynumber: 2.2 Consensus size: 56
44752 CACGCGCACC
* * *
44762 AGGGGTCGCCCCTCCTTTATGCGCGTAGGGGGGATCGCTCCCCTTTGCGCATAGTA
1 AGGGGTCGCCCCTCCTTTATGCGCATAGGGGGGATCGCTCCCCTTTACGCATAGCA
* *
44818 AGGGGTTGCCCC-CACTTTGTGCGCATA-GGGGGATCGCTCCCCTTTACGCATAGCA
1 AGGGGTCGCCCCTC-CTTTATGCGCATAGGGGGGATCGCTCCCCTTTACGCATAGCA
*
44873 AGGGGGTCACCCCT
1 A-GGGGTCGCCCCT
44887 TTGCGCATAG
Statistics
Matches: 59, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
55 28 0.47
56 31 0.53
ACGTcount: A:0.14, C:0.31, G:0.31, T:0.23
Consensus pattern (56 bp):
AGGGGTCGCCCCTCCTTTATGCGCATAGGGGGGATCGCTCCCCTTTACGCATAGCA
Found at i:46198 original size:24 final size:23
Alignment explanation
Indices: 46168--46238 Score: 124
Period size: 24 Copynumber: 3.0 Consensus size: 23
46158 CAACGGGGTT
46168 GCGCCATACCCACTCTTAGAGGGC
1 GCGCCATACCCACTCTTAG-GGGC
46192 GCGCCATACCCACTCTTAGGGGGC
1 GCGCCATACCCACTCTTA-GGGGC
46216 GCGCCATACCCACTCTTAGGGGC
1 GCGCCATACCCACTCTTAGGGGC
46239 CCTTTCTTGA
Statistics
Matches: 46, Mismatches: 0, Indels: 3
0.94 0.00 0.06
Matches are distributed among these distances:
23 5 0.11
24 40 0.87
25 1 0.02
ACGTcount: A:0.18, C:0.38, G:0.27, T:0.17
Consensus pattern (23 bp):
GCGCCATACCCACTCTTAGGGGC
Found at i:46550 original size:36 final size:36
Alignment explanation
Indices: 46456--46552 Score: 149
Period size: 36 Copynumber: 2.7 Consensus size: 36
46446 AGCCAATTAT
* * *
46456 GTATTAGGCGACTTAGGCCAGCAGCGTTATAGCCAA
1 GTATTGGGCGACTAAGGCCAGCGGCGTTATAGCCAA
* *
46492 GCATTGGGCGACTAAGGCCAGCGGTGTTATAGCCAA
1 GTATTGGGCGACTAAGGCCAGCGGCGTTATAGCCAA
46528 GTATTGGGCGACTAAGGCCAGCGGC
1 GTATTGGGCGACTAAGGCCAGCGGC
46553 ACTACAACCA
Statistics
Matches: 54, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
36 54 1.00
ACGTcount: A:0.25, C:0.23, G:0.33, T:0.20
Consensus pattern (36 bp):
GTATTGGGCGACTAAGGCCAGCGGCGTTATAGCCAA
Done.