Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015253.1 Corchorus capsularis cultivar CVL-1 contig15274, 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: 46389
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.33
Found at i:1546 original size:19 final size:19
Alignment explanation
Indices: 1522--1558 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
1512 CAAGCAACGA
1522 CAATATTATATACCAGCAG
1 CAATATTATATACCAGCAG
1541 CAATATTATATACCAGCA
1 CAATATTATATACCAGCA
1559 ACCATTAGCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.43, C:0.22, G:0.08, T:0.27
Consensus pattern (19 bp):
CAATATTATATACCAGCAG
Found at i:4831 original size:16 final size:16
Alignment explanation
Indices: 4810--4843 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
4800 GAATTGGAAG
*
4810 AAGGAATAAAAGATTA
1 AAGGAATAAAAGAATA
4826 AAGGAATAAAAGAATA
1 AAGGAATAAAAGAATA
4842 AA
1 AA
4844 AAACATCTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.68, C:0.00, G:0.18, T:0.15
Consensus pattern (16 bp):
AAGGAATAAAAGAATA
Found at i:4968 original size:5 final size:6
Alignment explanation
Indices: 4950--4974 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
4940 ACCCATTTAT
4950 AAGAAA AAGAAA AAGAAA AAGAAA A
1 AAGAAA AAGAAA AAGAAA AAGAAA A
4975 TTAGATTTCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (6 bp):
AAGAAA
Found at i:5458 original size:6 final size:6
Alignment explanation
Indices: 5447--5479 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
5437 CATATGTTTT
5447 ATATAA ATATAA ATAT-- ATATAA ATATAA ATATA
1 ATATAA ATATAA ATATAA ATATAA ATATAA ATATA
5480 TATTAAAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
4 4 0.16
6 21 0.84
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (6 bp):
ATATAA
Found at i:5462 original size:21 final size:22
Alignment explanation
Indices: 5420--5462 Score: 52
Period size: 23 Copynumber: 2.0 Consensus size: 22
5410 TATTTTCTGA
* *
5420 TTTTTTATTAATATAATCATATG
1 TTTTATATAAATATAA-CATATG
5443 TTTTATATAAATATAA-ATAT
1 TTTTATATAAATATAACATAT
5463 ATATAAATAT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 4 0.22
23 14 0.78
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.53
Consensus pattern (22 bp):
TTTTATATAAATATAACATATG
Found at i:5467 original size:16 final size:16
Alignment explanation
Indices: 5446--5482 Score: 74
Period size: 16 Copynumber: 2.3 Consensus size: 16
5436 TCATATGTTT
5446 TATATAAATATAAATA
1 TATATAAATATAAATA
5462 TATATAAATATAAATA
1 TATATAAATATAAATA
5478 TATAT
1 TATAT
5483 TAAAAATATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
TATATAAATATAAATA
Found at i:5721 original size:26 final size:26
Alignment explanation
Indices: 5674--5946 Score: 432
Period size: 26 Copynumber: 10.7 Consensus size: 26
5664 GCTCACCTCT
5674 AACCAAGTCC-C-CATGGCTCATGGC
1 AACCAAGTCCTCACATGGCTCATGGC
* *
5698 AACCAAGTCCTTAAATGGCTCATGGC
1 AACCAAGTCCTCACATGGCTCATGGC
*
5724 AACTAAGTCCTCACATGGCTCATGGC
1 AACCAAGTCCTCACATGGCTCATGGC
*
5750 AACCAAGTCCCCACATGGCTCATGGC
1 AACCAAGTCCTCACATGGCTCATGGC
*
5776 AACCAAGTCCCCACATGGCTCATGGC
1 AACCAAGTCCTCACATGGCTCATGGC
5802 AACCAAGTCCTCACATGGCTCATGGC
1 AACCAAGTCCTCACATGGCTCATGGC
5828 AACCAAGTCCTCACATGGCTCATGGC
1 AACCAAGTCCTCACATGGCTCATGGC
*
5854 AACCAAGTCCT--CATGGCTCATGAC
1 AACCAAGTCCTCACATGGCTCATGGC
*
5878 AACCAAGTCCCCACATGGCTCATGGC
1 AACCAAGTCCTCACATGGCTCATGGC
5904 AACCAAGTCC-C-CATGGCTCATGGC
1 AACCAAGTCCTCACATGGCTCATGGC
*
5928 AACCAAGTCCCCACATGGC
1 AACCAAGTCCTCACATGGC
5947 ATATGGAACA
Statistics
Matches: 232, Mismatches: 11, Indels: 10
0.92 0.04 0.04
Matches are distributed among these distances:
24 55 0.24
25 2 0.01
26 175 0.75
ACGTcount: A:0.27, C:0.36, G:0.19, T:0.18
Consensus pattern (26 bp):
AACCAAGTCCTCACATGGCTCATGGC
Found at i:8918 original size:12 final size:11
Alignment explanation
Indices: 8903--8950 Score: 51
Period size: 12 Copynumber: 4.1 Consensus size: 11
8893 ATTACTCGTA
8903 TTATTATTTAAT
1 TTATT-TTTAAT
*
8915 TTATTCTTATAT
1 TTATTTTTA-AT
*
8927 TTATATTTAAT
1 TTATTTTTAAT
8938 TTAATTTTTAAT
1 TT-ATTTTTAAT
8950 T
1 T
8951 ACTAAGAAGA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
11 7 0.23
12 23 0.77
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (11 bp):
TTATTTTTAAT
Found at i:12300 original size:14 final size:14
Alignment explanation
Indices: 12281--12311 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
12271 TTTTACTTCC
12281 TAGCTTGCTGAATT
1 TAGCTTGCTGAATT
12295 TAGCTTGCTGAATT
1 TAGCTTGCTGAATT
12309 TAG
1 TAG
12312 AGCAGAATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.23, C:0.13, G:0.23, T:0.42
Consensus pattern (14 bp):
TAGCTTGCTGAATT
Found at i:17888 original size:2 final size:2
Alignment explanation
Indices: 17876--17910 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
17866 TTGAAATAAA
*
17876 AT AT GT AT AT AT AT AT AT AT A- 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 AT
17911 TACTTTCTTC
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Found at i:17902 original size:13 final size:13
Alignment explanation
Indices: 17884--17909 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
17874 AAATATGTAT
17884 ATATATATATATA
1 ATATATATATATA
17897 ATATATATATATA
1 ATATATATATATA
17910 TTACTTTCTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (13 bp):
ATATATATATATA
Found at i:17902 original size:15 final size:15
Alignment explanation
Indices: 17882--17910 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
17872 TAAAATATGT
17882 ATATATATATATATA
1 ATATATATATATATA
17897 ATATATATATATAT
1 ATATATATATATAT
17911 TACTTTCTTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATATATATATATATA
Found at i:20084 original size:5 final size:5
Alignment explanation
Indices: 20071--20102 Score: 55
Period size: 5 Copynumber: 6.4 Consensus size: 5
20061 CAAAATTTCA
*
20071 AAAAA AAAAC AAAAC AAAAC AAAAC AAAAC AA
1 AAAAC AAAAC AAAAC AAAAC AAAAC AAAAC AA
20103 GAATATAATT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.84, C:0.16, G:0.00, T:0.00
Consensus pattern (5 bp):
AAAAC
Found at i:33200 original size:24 final size:22
Alignment explanation
Indices: 33159--33205 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 22
33149 ATTTTTAAAT
33159 AAAATAAAAATTAAAATATTTA
1 AAAATAAAAATTAAAATATTTA
33181 AAAATAAAATTATTAAAATATTTA
1 AAAATAAAA--ATTAAAATATTTA
33205 A
1 A
33206 TAACAAGTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
22 9 0.39
24 14 0.61
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (22 bp):
AAAATAAAAATTAAAATATTTA
Found at i:38518 original size:93 final size:93
Alignment explanation
Indices: 38354--38535 Score: 328
Period size: 93 Copynumber: 2.0 Consensus size: 93
38344 AAAGGGGGAG
38354 AAGAAATATGAATTGAGCTTATTGAATATATGTTATATATGTTGTGGAATTTAATGTTCTTATCT
1 AAGAAATATGAATTGAGCTTATTGAATATATGTTATATATGTTGTGGAATTTAATGTTCTTATCT
*
38419 ACTGTGTTCAGCATTTGAAAACCAACAA
66 ACTGTGTTCAACATTTGAAAACCAACAA
* *
38447 AAGAAATATGAATTGAGCTTATTTAATATCTGTTATATATGTTGTGGAATTTAATGTTCTTATCT
1 AAGAAATATGAATTGAGCTTATTGAATATATGTTATATATGTTGTGGAATTTAATGTTCTTATCT
*
38512 AGTGTGTTCAACATTTGAAAACCA
66 ACTGTGTTCAACATTTGAAAACCA
38536 GCATGCTTGA
Statistics
Matches: 85, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 85 1.00
ACGTcount: A:0.35, C:0.09, G:0.16, T:0.40
Consensus pattern (93 bp):
AAGAAATATGAATTGAGCTTATTGAATATATGTTATATATGTTGTGGAATTTAATGTTCTTATCT
ACTGTGTTCAACATTTGAAAACCAACAA
Done.