Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01003916.1 Corchorus capsularis cultivar CVL-1 contig03924, 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: 26935
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.34
Found at i:2692 original size:53 final size:53
Alignment explanation
Indices: 2621--2762 Score: 194
Period size: 53 Copynumber: 2.7 Consensus size: 53
2611 GTTTGAATGC
* *
2621 TTTGAAAACCTGATGGGAACTTTCCCACTTTGAAAAAACCTAAATTGAACACT
1 TTTGAAAACTTGATGGGAACTTTCCCACTTTGAAAAAACCAAAATTGAACACT
* * * * * *
2674 TTTGAAAACTTGACGGGAATTTTCCCAGTTTTAAAAGACCAAAATTGAACTCT
1 TTTGAAAACTTGATGGGAACTTTCCCACTTTGAAAAAACCAAAATTGAACACT
* *
2727 TTTAAAAAGTTGATGGGAACTTTCCCACTTTGAAAA
1 TTTGAAAACTTGATGGGAACTTTCCCACTTTGAAAA
2763 CTTTGAAGGA
Statistics
Matches: 75, Mismatches: 14, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
53 75 1.00
ACGTcount: A:0.37, C:0.18, G:0.15, T:0.31
Consensus pattern (53 bp):
TTTGAAAACTTGATGGGAACTTTCCCACTTTGAAAAAACCAAAATTGAACACT
Found at i:4394 original size:22 final size:22
Alignment explanation
Indices: 4368--4431 Score: 76
Period size: 22 Copynumber: 2.9 Consensus size: 22
4358 ATTTGAGACT
* *
4368 GTGGCCGTGAGATTCGGCCTTG
1 GTGGCCGTGAGATTCGGCCATA
4390 GTGGCCGTGAGA-TCTGGCCATA
1 GTGGCCGTGAGATTC-GGCCATA
* *
4412 GTGGTCATGAGATTCGGCCA
1 GTGGCCGTGAGATTCGGCCA
4432 CATGATGGTA
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
21 2 0.06
22 32 0.89
23 2 0.06
ACGTcount: A:0.16, C:0.22, G:0.38, T:0.25
Consensus pattern (22 bp):
GTGGCCGTGAGATTCGGCCATA
Found at i:5088 original size:17 final size:17
Alignment explanation
Indices: 5066--5113 Score: 64
Period size: 15 Copynumber: 2.9 Consensus size: 17
5056 TTTTCTTTTG
*
5066 GACTCTTGTCTACTTGA
1 GACTCTTGTCTACTTAA
*
5083 GACTCTTGTCT-C-CAA
1 GACTCTTGTCTACTTAA
5098 GACTCTTGTCTACTTA
1 GACTCTTGTCTACTTA
5114 CTTGAGACTC
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
15 12 0.46
16 2 0.08
17 12 0.46
ACGTcount: A:0.19, C:0.27, G:0.15, T:0.40
Consensus pattern (17 bp):
GACTCTTGTCTACTTAA
Found at i:6256 original size:17 final size:17
Alignment explanation
Indices: 6234--6281 Score: 64
Period size: 15 Copynumber: 2.9 Consensus size: 17
6224 TTTTCTTTTG
* *
6234 GACTCTTATCTACTTGA
1 GACTCTTGTCTACTTAA
6251 GACTCTTGTCT-C-TAA
1 GACTCTTGTCTACTTAA
6266 GACTCTTGTCTACTTA
1 GACTCTTGTCTACTTA
6282 CTTGAGACTC
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
15 13 0.48
16 2 0.07
17 12 0.44
ACGTcount: A:0.21, C:0.25, G:0.12, T:0.42
Consensus pattern (17 bp):
GACTCTTGTCTACTTAA
Found at i:6289 original size:21 final size:19
Alignment explanation
Indices: 6242--6295 Score: 62
Period size: 15 Copynumber: 2.9 Consensus size: 19
6232 TGGACTCTTA
6242 TCTACTTGAGACTCTTGTC
1 TCTACTTGAGACTCTTGTC
6261 TCTA----AGACTCTTGTC
1 TCTACTTGAGACTCTTGTC
6276 TACTTACTTGAGACTCTTGT
1 T-C-TACTTGAGACTCTTGT
6296 TTCCATCATT
Statistics
Matches: 29, Mismatches: 0, Indels: 10
0.74 0.00 0.26
Matches are distributed among these distances:
15 12 0.41
16 1 0.03
17 2 0.07
19 4 0.14
21 10 0.34
ACGTcount: A:0.19, C:0.24, G:0.15, T:0.43
Consensus pattern (19 bp):
TCTACTTGAGACTCTTGTC
Found at i:7085 original size:29 final size:29
Alignment explanation
Indices: 7030--7104 Score: 69
Period size: 29 Copynumber: 2.6 Consensus size: 29
7020 GGAACCTGGT
***
7030 TTTATTTCAATTAAATTATGTTTTCAAAC
1 TTTATTTCAATTAAATTATGAAATCAAAC
* * *
7059 TTTATTTCAATTAAGTTTTGAAATCAATC
1 TTTATTTCAATTAAATTATGAAATCAAAC
* *
7088 TATATTTCCAATAAAAT
1 TTTATTT-CAATTAAAT
7105 CTCATATAAC
Statistics
Matches: 36, Mismatches: 9, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
29 29 0.81
30 7 0.19
ACGTcount: A:0.37, C:0.11, G:0.04, T:0.48
Consensus pattern (29 bp):
TTTATTTCAATTAAATTATGAAATCAAAC
Found at i:8367 original size:17 final size:18
Alignment explanation
Indices: 8345--8378 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
8335 ATCAAGGGGC
8345 CAAATT-AAAAAAAAGGA
1 CAAATTCAAAAAAAAGGA
8362 CAAATTCAAAAAAAAGG
1 CAAATTCAAAAAAAAGG
8379 GGGGGGGGGG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.68, C:0.09, G:0.12, T:0.12
Consensus pattern (18 bp):
CAAATTCAAAAAAAAGGA
Found at i:12241 original size:16 final size:16
Alignment explanation
Indices: 12222--12267 Score: 65
Period size: 16 Copynumber: 2.9 Consensus size: 16
12212 CGTGACCCAA
*
12222 ATAATCCGAGACCCGT
1 ATAATCCGAAACCCGT
*
12238 ATAACCCGAAACCCGT
1 ATAATCCGAAACCCGT
*
12254 ATGATCCGAAACCC
1 ATAATCCGAAACCC
12268 CAAACCCGTG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.35, C:0.35, G:0.15, T:0.15
Consensus pattern (16 bp):
ATAATCCGAAACCCGT
Found at i:12892 original size:16 final size:16
Alignment explanation
Indices: 12864--12996 Score: 126
Period size: 16 Copynumber: 8.4 Consensus size: 16
12854 CCGAAGTTTA
12864 AACCCGA-ACCCGAAT
1 AACCCGAGACCCGAAT
* *
12879 AATCCGAGACCCGATT
1 AACCCGAGACCCGAAT
* *
12895 AACCCAAGAACCGAAT
1 AACCCGAGACCCGAAT
* *
12911 GACCCGAAACCCGAAT
1 AACCCGAGACCCGAAT
*
12927 AATCCGAGACCCGAAT
1 AACCCGAGACCCGAAT
* *
12943 AACCTGAGACCCGATT
1 AACCCGAGACCCGAAT
* * *
12959 GACCCGAAACCCGATT
1 AACCCGAGACCCGAAT
*
12975 AACCCGA-ACCCAAAT
1 AACCCGAGACCCGAAT
*
12990 GACCCGA
1 AACCCGA
12997 AATCCGAATG
Statistics
Matches: 94, Mismatches: 23, Indels: 2
0.79 0.19 0.02
Matches are distributed among these distances:
15 18 0.19
16 76 0.81
ACGTcount: A:0.38, C:0.35, G:0.17, T:0.11
Consensus pattern (16 bp):
AACCCGAGACCCGAAT
Found at i:12927 original size:48 final size:48
Alignment explanation
Indices: 12865--13007 Score: 166
Period size: 48 Copynumber: 3.0 Consensus size: 48
12855 CGAAGTTTAA
*
12865 ACCCG-AACCCGAATAATCCGAGACCCGATTAACCCAAGAACCGAATG
1 ACCCGAAACCCGAATAATCCGAGACCCGAATAACCCAAGAACCGAATG
** * *
12912 ACCCGAAACCCGAATAATCCGAGACCCGAATAACCTGAGACCCGATTG
1 ACCCGAAACCCGAATAATCCGAGACCCGAATAACCCAAGAACCGAATG
* * * * *
12960 ACCCGAAACCCGATTAACCCGA-ACCCAAATGACCCGAA-ATCCGAATG
1 ACCCGAAACCCGAATAATCCGAGACCCGAATAACCC-AAGAACCGAATG
13007 A
1 A
13008 TTCGAAAAAA
Statistics
Matches: 81, Mismatches: 13, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
47 23 0.28
48 58 0.72
ACGTcount: A:0.38, C:0.34, G:0.17, T:0.11
Consensus pattern (48 bp):
ACCCGAAACCCGAATAATCCGAGACCCGAATAACCCAAGAACCGAATG
Found at i:17341 original size:23 final size:24
Alignment explanation
Indices: 17283--17346 Score: 66
Period size: 23 Copynumber: 2.8 Consensus size: 24
17273 AGGGATCCAG
17283 TAAAGAATGTGATATAT--ATAGAA
1 TAAAGAATGTGATAT-TGGATAGAA
* *
17306 TATAG-ATAT-ATATTGGATA-AA
1 TAAAGAATGTGATATTGGATAGAA
17327 TAAAGAATGTGATATTGGAT
1 TAAAGAATGTGATATTGGAT
17347 GTTTATAAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
20 1 0.03
21 10 0.30
22 9 0.27
23 13 0.39
ACGTcount: A:0.47, C:0.00, G:0.19, T:0.34
Consensus pattern (24 bp):
TAAAGAATGTGATATTGGATAGAA
Done.