Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010792.1 Corchorus capsularis cultivar CVL-1 contig10813, 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: 13790
ACGTcount: A:0.26, C:0.24, G:0.19, T:0.30
Found at i:8303 original size:20 final size:20
Alignment explanation
Indices: 8264--8303 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
8254 CATCATTCGA
*
8264 ATTACATCATTCAAATTTTG
1 ATTACATCATCCAAATTTTG
8284 ATTACATCA-CCAAATATTTG
1 ATTACATCATCCAAAT-TTTG
8304 TCTGTTCAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 5 0.28
20 13 0.72
ACGTcount: A:0.38, C:0.17, G:0.05, T:0.40
Consensus pattern (20 bp):
ATTACATCATCCAAATTTTG
Found at i:12089 original size:51 final size:51
Alignment explanation
Indices: 12023--12159 Score: 204
Period size: 51 Copynumber: 2.7 Consensus size: 51
12013 AAAGTGGGTA
*
12023 AAAATAAGCGTCTTCCGTCCGGGAAGGGCAATTTTGAAAAAAAAAGCAAGT
1 AAAATAAGCGCCTTCCGTCCGGGAAGGGCAATTTTGAAAAAAAAAGCAAGT
* * * * *
12074 AAAATAAACGCCTTCCGTCCGGGAAGGGCATTTTTGGAAGAAATAGCAAGT
1 AAAATAAGCGCCTTCCGTCCGGGAAGGGCAATTTTGAAAAAAAAAGCAAGT
*
12125 AAAATAAGTGCCTTCCGTCCGGGAAGGGC-ATTTTG
1 AAAATAAGCGCCTTCCGTCCGGGAAGGGCAATTTTG
12160 GGAAAAACAG
Statistics
Matches: 77, Mismatches: 9, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
50 5 0.06
51 72 0.94
ACGTcount: A:0.35, C:0.18, G:0.26, T:0.22
Consensus pattern (51 bp):
AAAATAAGCGCCTTCCGTCCGGGAAGGGCAATTTTGAAAAAAAAAGCAAGT
Found at i:12147 original size:102 final size:95
Alignment explanation
Indices: 11936--12247 Score: 268
Period size: 99 Copynumber: 3.2 Consensus size: 95
11926 AAATTAACGC
* * * * * ** * *
11936 CTTCTGTCCGGGAAGGGCGTTTTAGGAAAAAGCAAGTAAAAGT-TAGTGCATTCCGTCCGGGAAA
1 CTTCCGTCCGGGAAGGGCATTTT-GAAAAAAACAAGTAAAA-TCAAACGCCTTCCGTCCGGGAAG
* * * *
12000 GGCACTTTGGGAAAAAGTGGGTAAAAATAAGCGT
64 GGCATTTTAGGAAAAA-TAGGT-AAAATAAGTGT
12034 CTTCCGTCCGGGAAGGGCAATTTTGAAAAAAAAAGCAAGTAAAAT-AAACGCCTTCCGTCCGGGA
1 CTTCCGTCCGGGAAGGGC-ATTTTG--AAAAAAA-CAAGTAAAATCAAACGCCTTCCGTCCGGGA
* *
12098 AGGGCATTTTTGGAAGAAATAGCAAGTAAAATAAGTGC
62 AGGGCATTTTAGGAA-AAATAG---GTAAAATAAGTGT
** * * * * *
12136 CTTCCGTCCGGGAAGGGCATTTTGGGAAAAACAGGTAAAATCTAATGTCTTTCGTCCGGGAAGGG
1 CTTCCGTCCGGGAAGGGCATTTTGAAAAAAACAAGTAAAATCAAACGCCTTCCGTCCGGGAAGGG
* *
12201 CGTTTTAGGAAAAATAGGTAAAGATTAGTGT
66 CATTTTAGGAAAAATAGGTAAA-ATAAGTGT
*
12232 ATTCCGTCCGGGAAGG
1 CTTCCGTCCGGGAAGG
12248 ACGTTTTAGG
Statistics
Matches: 178, Mismatches: 26, Indels: 22
0.79 0.12 0.10
Matches are distributed among these distances:
95 5 0.03
96 21 0.12
98 33 0.19
99 37 0.21
100 35 0.20
101 18 0.10
102 27 0.15
103 2 0.01
ACGTcount: A:0.33, C:0.15, G:0.29, T:0.23
Consensus pattern (95 bp):
CTTCCGTCCGGGAAGGGCATTTTGAAAAAAACAAGTAAAATCAAACGCCTTCCGTCCGGGAAGGG
CATTTTAGGAAAAATAGGTAAAATAAGTGT
Found at i:12212 original size:48 final size:48
Alignment explanation
Indices: 11900--12449 Score: 367
Period size: 48 Copynumber: 11.4 Consensus size: 48
11890 TTCGTCTGGA
* * * * * *
11900 AAGGGTATTTTAAGAAAAAGC-GAGCAAAATTAACGCCTTCTGTCCGGG
1 AAGGGCATTTTAGGAAAAAGCAG-GTAAAATTAATGTCTTCCGTCCGGG
* * *
11948 AAGGGCGTTTTAGGAAAAAGCAAGTAAAAGTTAGTG-CATTCCGTCCGGG
1 AAGGGCATTTTAGGAAAAAGCAGGTAAAA-TTAATGTC-TTCCGTCCGGG
* * * ** * *
11997 AAAGGCACTTTGGGAAAAAGTGGGTAAAAATAAGCGTCTTCCGTCCGGG
1 AAGGGCATTTTAGGAAAAAGCAGGTAAAATTAA-TGTCTTCCGTCCGGG
** * * * *
12046 AAGGGCAATTTTGAAAAAAAAAGCAAGTAAAATAAACGCCTTCCGTCCGGG
1 AAGGGC-ATTTT--AGGAAAAAGCAGGTAAAATTAATGTCTTCCGTCCGGG
* * *
12097 AAGGGCATTTTTGGAAGAAATAGCAAGTAAAA-TAAGTGCCTTCCGTCCGGG
1 AAGGGCATTTTAGG-A-AAA-AGCAGGTAAAATTAA-TGTCTTCCGTCCGGG
* *
12148 AAGGGCATTTTGGGAAAAA-CAGGTAAAATCTAATGTCTTTCGTCCGGG
1 AAGGGCATTTTAGGAAAAAGCAGGTAAAAT-TAATGTCTTCCGTCCGGG
* * * *
12196 AAGGGCGTTTTAGGAAAAA-TAGGTAAAGATTAGTGTATTCCGTCCGGG
1 AAGGGCATTTTAGGAAAAAGCAGGTAAA-ATTAATGTCTTCCGTCCGGG
* * *
12244 AAGGACGTTTTAGGAAAAA-CAGGTAAAGATTAGTGTCTTCCGTCCGGG
1 AAGGGCATTTTAGGAAAAAGCAGGTAAA-ATTAATGTCTTCCGTCCGGG
* ** * * * * *
12292 AAGGGCGTTTCGGGAAAAA-CGGGTAAAACTAAATGCCTTCCATCCGAG
1 AAGGGCATTTTAGGAAAAAGCAGGTAAAA-TTAATGTCTTCCGTCCGGG
* * * *
12340 AA-GG-----T-GGAAATTAGCAGGTAAAAGTAAATATCTTCCATCCGGG
1 AAGGGCATTTTAGGAAA-AAGCAGGTAAAA-TTAATGTCTTCCGTCCGGG
* * *
12383 AAGGGCCTTTTAGGAAATAGC-GG-ATAAATCAAATGTCTTCCGTCCGGG
1 AAGGGCATTTTAGGAAAAAGCAGGTA-AAAT-TAATGTCTTCCGTCCGGG
*
12431 AAGGGCATTTTGGGAAAAA
1 AAGGGCATTTTAGGAAAAA
12450 ATAAAATTTG
Statistics
Matches: 407, Mismatches: 68, Indels: 54
0.77 0.13 0.10
Matches are distributed among these distances:
41 5 0.01
42 1 0.00
43 26 0.06
44 2 0.00
47 13 0.03
48 200 0.49
49 67 0.16
50 21 0.05
51 58 0.14
52 14 0.03
ACGTcount: A:0.34, C:0.15, G:0.28, T:0.23
Consensus pattern (48 bp):
AAGGGCATTTTAGGAAAAAGCAGGTAAAATTAATGTCTTCCGTCCGGG
Done.