Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020593.1 Corchorus olitorius cultivar O-4 contig20626, 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: 79551
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31
Found at i:5345 original size:24 final size:24
Alignment explanation
Indices: 5318--5369 Score: 86
Period size: 24 Copynumber: 2.2 Consensus size: 24
5308 AGAATCGATA
* *
5318 GCGTCGTTAATCCGAAGTTTAGCT
1 GCGTCATTAATCCAAAGTTTAGCT
5342 GCGTCATTAATCCAAAGTTTAGCT
1 GCGTCATTAATCCAAAGTTTAGCT
5366 GCGT
1 GCGT
5370 TTCCTAATAG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.23, C:0.21, G:0.23, T:0.33
Consensus pattern (24 bp):
GCGTCATTAATCCAAAGTTTAGCT
Found at i:18458 original size:16 final size:16
Alignment explanation
Indices: 18437--18469 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
18427 AAAGTGAGAG
18437 CATCACAACGGGAGCA
1 CATCACAACGGGAGCA
18453 CATCACAACGGGAGCA
1 CATCACAACGGGAGCA
18469 C
1 C
18470 CGAAGTCTAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.36, C:0.33, G:0.24, T:0.06
Consensus pattern (16 bp):
CATCACAACGGGAGCA
Found at i:27370 original size:19 final size:19
Alignment explanation
Indices: 27346--27383 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
27336 ACTCCATATC
27346 TTATCTAATTTAAGAGGAA
1 TTATCTAATTTAAGAGGAA
27365 TTATCTAATTTAAGAGGAA
1 TTATCTAATTTAAGAGGAA
27384 CAATAAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.42, C:0.05, G:0.16, T:0.37
Consensus pattern (19 bp):
TTATCTAATTTAAGAGGAA
Found at i:27393 original size:19 final size:19
Alignment explanation
Indices: 27352--27394 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 19
27342 TATCTTATCT
** **
27352 AATTTAAGAGGAATTATCT
1 AATTTAAGAGGAACAATAA
27371 AATTTAAGAGGAACAATAA
1 AATTTAAGAGGAACAATAA
27390 AATTT
1 AATTT
27395 CCATTTTTTT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.49, C:0.05, G:0.14, T:0.33
Consensus pattern (19 bp):
AATTTAAGAGGAACAATAA
Found at i:31080 original size:1 final size:1
Alignment explanation
Indices: 31074--31104 Score: 53
Period size: 1 Copynumber: 31.0 Consensus size: 1
31064 ACAGAGCCAC
*
31074 AAAAAAAAAAAAAAAAAAAAAAAAAAGAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
31105 CGAAAGACCG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
1 28 1.00
ACGTcount: A:0.97, C:0.00, G:0.03, T:0.00
Consensus pattern (1 bp):
A
Found at i:31517 original size:1 final size:1
Alignment explanation
Indices: 31511--31552 Score: 84
Period size: 1 Copynumber: 42.0 Consensus size: 1
31501 TGTGTTAGTA
31511 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
31553 CCTTCTTCCT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 41 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:38571 original size:14 final size:15
Alignment explanation
Indices: 38554--38582 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
38544 GATTTTTGCT
38554 AAAT-TTTTTTTAAA
1 AAATATTTTTTTAAA
38568 AAATATTTTTTTAAA
1 AAATATTTTTTTAAA
38583 CAAAAACCTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 4 0.29
15 10 0.71
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
AAATATTTTTTTAAA
Found at i:38688 original size:14 final size:13
Alignment explanation
Indices: 38663--38704 Score: 57
Period size: 14 Copynumber: 3.0 Consensus size: 13
38653 GAAAATTTCG
38663 TTTTTTACTTTTTT
1 TTTTTTA-TTTTTT
38677 TGTTTTTATTTTTT
1 T-TTTTTATTTTTT
38691 TTGTTTTATTTTTT
1 TT-TTTTATTTTTT
38705 AATTCAAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
13 1 0.04
14 19 0.73
15 6 0.23
ACGTcount: A:0.07, C:0.02, G:0.05, T:0.86
Consensus pattern (13 bp):
TTTTTTATTTTTT
Found at i:38703 original size:15 final size:15
Alignment explanation
Indices: 38664--38704 Score: 66
Period size: 15 Copynumber: 2.8 Consensus size: 15
38654 AAAATTTCGT
*
38664 TTTTTACTTTTTTTG
1 TTTTTATTTTTTTTG
38679 TTTTTATTTTTTTTG
1 TTTTTATTTTTTTTG
38694 -TTTTATTTTTT
1 TTTTTATTTTTT
38705 AATTCAAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
14 11 0.44
15 14 0.56
ACGTcount: A:0.07, C:0.02, G:0.05, T:0.85
Consensus pattern (15 bp):
TTTTTATTTTTTTTG
Found at i:48226 original size:14 final size:16
Alignment explanation
Indices: 48199--48231 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
48189 ATTCCTGTTT
48199 TTGTTGCTTTCCTC-C
1 TTGTTGCTTTCCTCTC
48214 TTGTTGC-TTCCTCTC
1 TTGTTGCTTTCCTCTC
48229 TTG
1 TTG
48232 GCCCTGTTCT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 6 0.35
15 11 0.65
ACGTcount: A:0.00, C:0.30, G:0.15, T:0.55
Consensus pattern (16 bp):
TTGTTGCTTTCCTCTC
Found at i:63254 original size:18 final size:18
Alignment explanation
Indices: 63231--63266 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
63221 AAAAAAGCGA
63231 AGAGCACACGATGCCACG
1 AGAGCACACGATGCCACG
63249 AGAGCACACGATGCCACG
1 AGAGCACACGATGCCACG
63267 CTTTGGGCCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.33, C:0.33, G:0.28, T:0.06
Consensus pattern (18 bp):
AGAGCACACGATGCCACG
Found at i:65991 original size:31 final size:31
Alignment explanation
Indices: 65956--66017 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 31
65946 GGATAACAGG
* * *
65956 GCAAAAGTATAAAATTGGTCGCTGAAGTGAA
1 GCAAAAGTAGAAAATTGGTCCCTCAAGTGAA
*
65987 GCAAAAGTAGCAAATTGGTCCCTCAAGTGAA
1 GCAAAAGTAGAAAATTGGTCCCTCAAGTGAA
66018 AAATATGTAA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.40, C:0.15, G:0.24, T:0.21
Consensus pattern (31 bp):
GCAAAAGTAGAAAATTGGTCCCTCAAGTGAA
Found at i:66185 original size:17 final size:17
Alignment explanation
Indices: 66158--66207 Score: 57
Period size: 16 Copynumber: 2.9 Consensus size: 17
66148 CCACGTCCTT
66158 TTTTTTATTAAAAAAATA
1 TTTTTT-TTAAAAAAATA
*
66176 TTTTTTTTAAAAAACTA
1 TTTTTTTTAAAAAAATA
* *
66193 -ATTTCTTAAAAAAAT
1 TTTTTTTTAAAAAAAT
66208 TGGGTCAGGG
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
16 12 0.43
17 10 0.36
18 6 0.21
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (17 bp):
TTTTTTTTAAAAAAATA
Found at i:78910 original size:15 final size:15
Alignment explanation
Indices: 78852--78911 Score: 57
Period size: 15 Copynumber: 4.0 Consensus size: 15
78842 GGGTTGGTAT
*
78852 GGCATAGGTGGCAAC
1 GGCATAGGTGGAAAC
* * *
78867 GGCATACGCGGATAC
1 GGCATAGGTGGAAAC
* *
78882 GGCAAAGGTTGAAAC
1 GGCATAGGTGGAAAC
*
78897 GCCATAGGTGGAAAC
1 GGCATAGGTGGAAAC
78912 ATCATTGGCG
Statistics
Matches: 33, Mismatches: 12, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
15 33 1.00
ACGTcount: A:0.32, C:0.20, G:0.35, T:0.13
Consensus pattern (15 bp):
GGCATAGGTGGAAAC
Done.