Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021169.1 Corchorus olitorius cultivar O-4 contig21202, 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: 35640
ACGTcount: A:0.29, C:0.20, G:0.19, T:0.31
Found at i:1117 original size:25 final size:25
Alignment explanation
Indices: 1088--1136 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
1078 AATCTTGAAA
1088 TGAGTCGGCACTAAACGGCGCCGTC
1 TGAGTCGGCACTAAACGGCGCCGTC
* *
1113 TGAGTCTGTACTAAACGGCGCCGT
1 TGAGTCGGCACTAAACGGCGCCGT
1137 TTTGGTTAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.20, C:0.29, G:0.31, T:0.20
Consensus pattern (25 bp):
TGAGTCGGCACTAAACGGCGCCGTC
Found at i:11941 original size:21 final size:21
Alignment explanation
Indices: 11917--11961 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
11907 GGCGCCCACA
* *
11917 TGGTTTCCTTGAGCACCCATG
1 TGGTTTCCTTGAGAACCCAGG
*
11938 TGGTTTGCTTGAGAACCCAGG
1 TGGTTTCCTTGAGAACCCAGG
11959 TGG
1 TGG
11962 GCAATGTCAC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.22, G:0.31, T:0.31
Consensus pattern (21 bp):
TGGTTTCCTTGAGAACCCAGG
Found at i:12046 original size:76 final size:76
Alignment explanation
Indices: 11896--12039 Score: 177
Period size: 76 Copynumber: 1.9 Consensus size: 76
11886 CAAGGACCCT
* *
11896 GACTCCACCTGGGCGCCCACATGGTTTCCTTGAGCACCCATGTGGTTTGCTTGAGAACCCAGGTG
1 GACTCCACCTGGGCGCCCACATGGTTTCCTTGAGCACCCATGTGGTTTGCCTGAGAACCCAGATG
11961 GGCAATGTCAC
66 GGCAATGTCAC
* * * **
11972 GACTCCAGCTGGGTGCCCACATGGTTTAGC-TGAAG-ACCCATGT-GTTTCGCCTGATCACCCAG
1 GACTCCACCTGGGCGCCCACATGGTTT-CCTTG-AGCACCCATGTGGTTT-GCCTGAGAACCCAG
12034 ATGGGC
63 ATGGGC
12040 TGTGTCATAG
Statistics
Matches: 58, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
75 4 0.07
76 51 0.88
77 3 0.05
ACGTcount: A:0.19, C:0.30, G:0.28, T:0.24
Consensus pattern (76 bp):
GACTCCACCTGGGCGCCCACATGGTTTCCTTGAGCACCCATGTGGTTTGCCTGAGAACCCAGATG
GGCAATGTCAC
Found at i:13467 original size:39 final size:39
Alignment explanation
Indices: 13254--13467 Score: 338
Period size: 39 Copynumber: 5.5 Consensus size: 39
13244 ACGGAACAGA
* * *
13254 GACCTAAGCAGGTTTGCATAACCGGAAATTCTAAACAAG
1 GACCTAAGCAGGTTTGCTTAAACGAAAATTCTAAACAAG
*
13293 GACCTAAGCAGGTTTGCTGAAACGAAAATTCTAAACAAG
1 GACCTAAGCAGGTTTGCTTAAACGAAAATTCTAAACAAG
*
13332 GACCTAAGCAGGTTTGCTTAAACGGAAATTCTAAACAAG
1 GACCTAAGCAGGTTTGCTTAAACGAAAATTCTAAACAAG
* * *
13371 GACCTAAGCAGGTATGCTGAAACAAAAATTCTAAACAAG
1 GACCTAAGCAGGTTTGCTTAAACGAAAATTCTAAACAAG
*
13410 AACCTAAGCAGGTTTGCTTAAACGAAAATTCTAAACAAG
1 GACCTAAGCAGGTTTGCTTAAACGAAAATTCTAAACAAG
*
13449 GAGCTAAGCAGGTTTGCTT
1 GACCTAAGCAGGTTTGCTT
13468 CGAAATGGGG
Statistics
Matches: 159, Mismatches: 16, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
39 159 1.00
ACGTcount: A:0.40, C:0.18, G:0.20, T:0.22
Consensus pattern (39 bp):
GACCTAAGCAGGTTTGCTTAAACGAAAATTCTAAACAAG
Found at i:27282 original size:11 final size:11
Alignment explanation
Indices: 27266--27291 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
27256 GTTTTAGATC
27266 TTTTCTTCTAG
1 TTTTCTTCTAG
27277 TTTTCTTCTAG
1 TTTTCTTCTAG
27288 TTTT
1 TTTT
27292 TTAGGCAAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.08, C:0.15, G:0.08, T:0.69
Consensus pattern (11 bp):
TTTTCTTCTAG
Found at i:32713 original size:17 final size:18
Alignment explanation
Indices: 32691--32725 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
32681 AAAGGGTAGT
*
32691 TAAAAA-AATTGTTTTCA
1 TAAAAACAAGTGTTTTCA
32708 TAAAAACAAGTGTTTTCA
1 TAAAAACAAGTGTTTTCA
32726 AGCGAGAGGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.46, C:0.09, G:0.09, T:0.37
Consensus pattern (18 bp):
TAAAAACAAGTGTTTTCA
Found at i:34286 original size:11 final size:11
Alignment explanation
Indices: 34270--34295 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
34260 GTTTTAGATC
34270 TTTTCTTCTAG
1 TTTTCTTCTAG
34281 TTTTCTTCTAG
1 TTTTCTTCTAG
34292 TTTT
1 TTTT
34296 TTAGGCAAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.08, C:0.15, G:0.08, T:0.69
Consensus pattern (11 bp):
TTTTCTTCTAG
Done.