Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020744.1 Corchorus olitorius cultivar O-4 contig20777, 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: 39831
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.33
Found at i:8799 original size:35 final size:35
Alignment explanation
Indices: 8753--8843 Score: 146
Period size: 35 Copynumber: 2.6 Consensus size: 35
8743 GGCTTTAGAT
8753 GGGTGATCGGATCACCCCTCTGAGGGATGATCTGG
1 GGGTGATCGGATCACCCCTCTGAGGGATGATCTGG
* *
8788 GGGTGATCGGATCACCCCTCTGAGGGGTGATTTGG
1 GGGTGATCGGATCACCCCTCTGAGGGATGATCTGG
* *
8823 GGGTAATCGGATCACCACTCT
1 GGGTGATCGGATCACCCCTCT
8844 TTAAAAAAAG
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
35 52 1.00
ACGTcount: A:0.18, C:0.23, G:0.35, T:0.24
Consensus pattern (35 bp):
GGGTGATCGGATCACCCCTCTGAGGGATGATCTGG
Found at i:9058 original size:33 final size:33
Alignment explanation
Indices: 9021--9087 Score: 125
Period size: 33 Copynumber: 2.0 Consensus size: 33
9011 ATCTATAGTC
9021 TATACATATAACAATTGATTTGGATATAGGGTT
1 TATACATATAACAATTGATTTGGATATAGGGTT
*
9054 TATACATATAACAATTGATTTGGATGTAGGGTT
1 TATACATATAACAATTGATTTGGATATAGGGTT
9087 T
1 T
9088 CATGAGATTA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.34, C:0.06, G:0.19, T:0.40
Consensus pattern (33 bp):
TATACATATAACAATTGATTTGGATATAGGGTT
Found at i:15021 original size:31 final size:29
Alignment explanation
Indices: 14985--15056 Score: 92
Period size: 29 Copynumber: 2.4 Consensus size: 29
14975 GGAAGTTTTG
14985 GGGCAAAATGTCCTAAATTTAGAAATTC-AA
1 GGGCAAAATGTCCT-AATTTA-AAATTCAAA
* *
15015 GAGGCAAAACGTCCTAATTTAAAGTTCAAA
1 G-GGCAAAATGTCCTAATTTAAAATTCAAA
15045 GGGCAAAATGTC
1 GGGCAAAATGTC
15057 GTTGACGCAA
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
29 15 0.41
30 10 0.27
31 12 0.32
ACGTcount: A:0.42, C:0.15, G:0.19, T:0.24
Consensus pattern (29 bp):
GGGCAAAATGTCCTAATTTAAAATTCAAA
Found at i:17500 original size:28 final size:31
Alignment explanation
Indices: 17438--17505 Score: 115
Period size: 28 Copynumber: 2.3 Consensus size: 31
17428 AAAGGAATGT
17438 ATCAATATTTTTTGAGTAGTATATTGCATGC
1 ATCAATATTTTTTGAGTAGTATATTGCATGC
17469 ATCAATATTTTTTGAGT-G-A-ATTGCATGC
1 ATCAATATTTTTTGAGTAGTATATTGCATGC
17497 ATCAATATT
1 ATCAATATT
17506 GAGCTTTAAG
Statistics
Matches: 37, Mismatches: 0, Indels: 3
0.93 0.00 0.08
Matches are distributed among these distances:
28 18 0.49
29 1 0.03
30 1 0.03
31 17 0.46
ACGTcount: A:0.31, C:0.10, G:0.15, T:0.44
Consensus pattern (31 bp):
ATCAATATTTTTTGAGTAGTATATTGCATGC
Found at i:21349 original size:21 final size:19
Alignment explanation
Indices: 21324--21381 Score: 71
Period size: 19 Copynumber: 2.9 Consensus size: 19
21314 GTTGTTCTAA
*
21324 TAATCTCATCTGTATAGTACC
1 TAATCTCATCTGTACAGT--C
* *
21345 TAATCTAATCTGTACAGTG
1 TAATCTCATCTGTACAGTC
21364 TAATCTCATCTGTACAGT
1 TAATCTCATCTGTACAGT
21382 TGTTAAAACA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
19 17 0.52
21 16 0.48
ACGTcount: A:0.29, C:0.21, G:0.12, T:0.38
Consensus pattern (19 bp):
TAATCTCATCTGTACAGTC
Found at i:23547 original size:19 final size:19
Alignment explanation
Indices: 23521--23579 Score: 73
Period size: 19 Copynumber: 3.0 Consensus size: 19
23511 CTGTTTAACA
23521 ACTGTACAGATGAGATTAT
1 ACTGTACAGATGAGATTAT
* *
23540 ATTGTACAGATTAGATTAGGT
1 ACTGTACAGATGAGATTA--T
*
23561 ACTGTACAAATGAGATTAT
1 ACTGTACAGATGAGATTAT
23580 TAGAGCAGCG
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
19 17 0.52
21 16 0.48
ACGTcount: A:0.37, C:0.08, G:0.20, T:0.34
Consensus pattern (19 bp):
ACTGTACAGATGAGATTAT
Found at i:24022 original size:15 final size:17
Alignment explanation
Indices: 23997--24029 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 17
23987 CCCAACAAAT
23997 TCAACTTAATTAA-ACA
1 TCAACTTAATTAATACA
24013 TCAA-TTAATTAATACA
1 TCAACTTAATTAATACA
24029 T
1 T
24030 GGGTATTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.48, C:0.15, G:0.00, T:0.36
Consensus pattern (17 bp):
TCAACTTAATTAATACA
Found at i:31913 original size:14 final size:14
Alignment explanation
Indices: 31875--31913 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
31865 ATATCAAAGT
**
31875 GAAAAAAAAAGCTA
1 GAAAAAAAAATATA
31889 GAAAAAAAAATATA
1 GAAAAAAAAATATA
*
31903 TAAAAAAAAAT
1 GAAAAAAAAAT
31914 CAAAACCCAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.77, C:0.03, G:0.08, T:0.13
Consensus pattern (14 bp):
GAAAAAAAAATATA
Found at i:37613 original size:29 final size:29
Alignment explanation
Indices: 37563--37622 Score: 86
Period size: 29 Copynumber: 2.1 Consensus size: 29
37553 TTTTAAGAAG
*
37563 TATTCTTTTTAATCATTTAACTTTTTTAT
1 TATTCTTTTTAATCATTCAACTTTTTTAT
*
37592 TATT-TTTTTAGATGATTCAACTTTTTTAT
1 TATTCTTTTTA-ATCATTCAACTTTTTTAT
37621 TA
1 TA
37623 ATATTATTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
28 6 0.21
29 22 0.79
ACGTcount: A:0.25, C:0.08, G:0.03, T:0.63
Consensus pattern (29 bp):
TATTCTTTTTAATCATTCAACTTTTTTAT
Found at i:37701 original size:18 final size:18
Alignment explanation
Indices: 37660--37711 Score: 63
Period size: 18 Copynumber: 3.0 Consensus size: 18
37650 AATAACTTAC
*
37660 TATAATAATA-ATTTT-T
1 TATAATATTATATTTTAT
*
37676 TATTATATTATATTTTAT
1 TATAATATTATATTTTAT
*
37694 TATAATATTATAATTTAT
1 TATAATATTATATTTTAT
37712 AATCATGAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
16 8 0.27
17 5 0.17
18 17 0.57
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (18 bp):
TATAATATTATATTTTAT
Found at i:39113 original size:330 final size:320
Alignment explanation
Indices: 38031--39286 Score: 1078
Period size: 330 Copynumber: 3.9 Consensus size: 320
38021 TTAGCAATGA
** * * * *
38031 CTCAGTTTTGCATGATTTTTTACGTAAATACTCCTTGAAATATCTATATTCATCGAACAAAATCC
1 CTCAGTTTTGCATGATTTTTGGCG-AAAGACTCCTTGAAATATATATATTCATCGAACCAAATCT
** * * * * * * *
38096 CAGCCACGGTCGATTTAAGTATTTGTTTTTACGAGGCATCCGAATCTTGTTTCAATTTAATTAAA
65 CAGCCACATTAGATTTAAGGATTTATTTTTACGA-GCATCTGAATATTGTTTCGATTTAATTAGA
* * *** **
38161 AATTAATTCAG-AAAAAATGGAAAAACGATA-TTAGAAGCGTGAAAAGCCCGTCAATATTTTTGG
129 AATTAATTCGGAAAAAAATGGAAAAATGATATTTA-AAGCGTGAAAA--ATTTCAAT-TTTTTTT
* * * * *
38224 CGTTGAATTATATATTTTTT-TGAGTATTATGGCAAAAAAA-TGAGAAAAAACTTTTCCG-ATAA
190 CGTTGAATTATATATTTTTTCTGACTATTGTGGCAAAAAAATTGAGAAAAAAATTTT-CGTGTCA
* * * * *
38286 GTTTATAGCCG-AAAT-C-GT-GT-A-CATCACGGTTTTTCGCTAAAAACGCGTTCC-TGAGCCC
254 GTTTTTAACCGAAAATCCTGTACTAACCATCACGGTTTTTGGCTAAAAACGCGTTCCGGGA-CCC
*
38344 CGA
318 CGG
* * * * * *
38347 CTCAATTTTACATGATTTTTGGCGCAAAGACTCCTTGCAATATCTATATTCATCAAACCAAATGT
1 CTCAGTTTTGCATGATTTTTGGCG-AAAGACTCCTTGAAATATATATATTCATCGAACCAAATCT
* ** * * *
38412 CAGCCACATTGGACATAAGGATTTGTTTTTACGAGCATCTGAATGTTGCTTCGATTTAATTAGAA
65 CAGCCACATTAGATTTAAGGATTTATTTTTACGAGCATCTGAATATTGTTTCGATTTAATTAGAA
* * * **
38477 ATTAATTCGGAAAAAAAATGGAAAATTAATATTAAAAGCGTGAAAAGACCATCAATTTTTTTGGT
130 ATTAATTCGG-AAAAAAATGGAAAAATGATATTTAAAGCGTGAAAA-A-TTTCAATTTTTTT--T
* * * * * * * * *
38542 -GTTGGATAATATAATTTTTCTGAGTATTGTGGCAAAAAAA-TCAGAAAAAAAATTCCGGGTTAG
190 CGTTGAATTATATATTTTTTCTGACTATTGTGGCAAAAAAATTGAGAAAAAAATTTTCGTGTCAG
* * * * *
38605 TTTTTAGCCGAAAATCGTGTACTAACCATCATGGTTTTTGGGCTAAAAACGCGTTTCGGGGGCCC
255 TTTTTAACCGAAAATCCTGTACTAACCATCACGGTTTTT-GGCTAAAAACGCG-TTCCGGGACCC
38670 CGG
318 CGG
* *
38673 CTCAGTTTTGCATGATTTTTGCCAGAAAGACTCTTTGAAATATATATATTCATCTAGCCAATCTC
1 CTCAGTTTTGCATGATTTTTGGC-GAAAGACTCCTTGAAATATATATATTCATC--G--AA-C-C
* *
38738 AGGATCTCAGCCACATTAGATTTAAGGATTTGA-TTTTACGAGCATCTAAATATTGTTTCGATTT
59 A-AATCTCAGCCACATTAGATTTAAGGATTT-ATTTTTACGAGCATCTGAATATTGTTTCGATTT
* * * **
38802 AATTTGAAA-TAGATTCGGAAACAAATAGAAAAATGATATTTAAAGCAAGAAAATATTTCAATTT
122 AATTAGAAATTA-ATTCGGAAAAAAATGGAAAAATGATATTTAAAGCGTGAAAA-ATTTCAATTT
* * * *
38866 TTTTTCGTTGAATTGTGTATTTTTTCTGACTATTGTGGCAAAAAAATTGAGGAAAAATTTTTCGT
185 TTTTTCGTTGAATTATATATTTTTTCTGACTATTGTGGCAAAAAAATTGAGAAAAAAATTTTCGT
* * *
38931 GTCAGTTTTTGCAAAACTTTCGCTGAAATCCTGTACTAACCATCACGGTGTTTT-GCTAAAACCA
250 GTCAGTTTTT----AAC---CG--AAAATCCTGTACTAACCATCACGGT-TTTTGGCTAAAAACG
38995 CGTTCCGGGACCCCGG
305 CGTTCCGGGACCCCGG
* * *
39011 CTCAGTTTTGCATGA-TTTTGGCGTAAAAACTCCTTGAAATATTTATATTCATCGAACCAAATCC
1 CTCAGTTTTGCATGATTTTTGGCG-AAAGACTCCTTGAAATATATATATTCATCGAACCAAATCT
* * * * * * *
39075 CAGCCAAATTCGATTTAACGATTTATTTTTATGAGCATCTGAATCTTGTTTCGTTTTGATTAGAA
65 CAGCCACATTAGATTTAAGGATTTATTTTTACGAGCATCTGAATATTGTTTCGATTTAATTAGAA
* * **
39140 ATTAATTCGAAAAAAAATGGAAAAATGATA-TTAGAAGTGTGAAAAATCATTCAATTTTTTGGCG
130 ATTAATTCGGAAAAAAATGGAAAAATGATATTTA-AAGCGTGAAAAAT--TTCAATTTTTTTTCG
** * * * *
39204 TAAAATTATATATTTTTTATGACTATTGTCGC-AAAAAATTGAGAAAAAAATTTTCGTCTCAATT
192 TTGAATTATATATTTTTTCTGACTATTGTGGCAAAAAAATTGAGAAAAAAATTTTCGTGTCAGTT
* *
39268 TTTAGCCG-AAATCGTGTAC
257 TTTAACCGAAAATCCTGTAC
39287 ATTTGGCTAA
Statistics
Matches: 761, Mismatches: 134, Indels: 86
0.78 0.14 0.09
Matches are distributed among these distances:
315 35 0.05
316 87 0.11
317 51 0.07
318 44 0.06
319 4 0.01
320 10 0.01
321 2 0.00
322 1 0.00
323 3 0.00
324 12 0.02
325 12 0.02
326 56 0.07
327 2 0.00
329 7 0.01
330 156 0.20
331 76 0.10
332 34 0.04
333 68 0.09
335 3 0.00
336 1 0.00
337 32 0.04
338 29 0.04
339 10 0.01
340 22 0.03
341 4 0.01
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.35
Consensus pattern (320 bp):
CTCAGTTTTGCATGATTTTTGGCGAAAGACTCCTTGAAATATATATATTCATCGAACCAAATCTC
AGCCACATTAGATTTAAGGATTTATTTTTACGAGCATCTGAATATTGTTTCGATTTAATTAGAAA
TTAATTCGGAAAAAAATGGAAAAATGATATTTAAAGCGTGAAAAATTTCAATTTTTTTTCGTTGA
ATTATATATTTTTTCTGACTATTGTGGCAAAAAAATTGAGAAAAAAATTTTCGTGTCAGTTTTTA
ACCGAAAATCCTGTACTAACCATCACGGTTTTTGGCTAAAAACGCGTTCCGGGACCCCGG
Done.