Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01006411.1 Corchorus olitorius cultivar O-4 contig06436, 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, 649
Length: 1083
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.30
Found at i:60 original size:36 final size:35
Alignment explanation
Indices: 2--496 Score: 348
Period size: 35 Copynumber: 13.9 Consensus size: 35
1 C
* * * *
2 GAAGAAAAGATCTCCCTCGATCAAACTAAAATAACTT
1 GAAG-AAAGATCGCCCTGGATC-AACTGAAATAAATT
* * * *
39 GAAGTAAGATCACCCTGGATCAATTGAAATGAATT
1 GAAGAAAGATCGCCCTGGATCAACTGAAATAAATT
* * *
74 GAAGAAAGACCGCCCTGGGTCAACTGAAATAACTT
1 GAAGAAAGATCGCCCTGGATCAACTGAAATAAATT
* * * * *
109 GAAGAATGACCGCCCTGGGTCAGCTAAAATAAATT
1 GAAGAAAGATCGCCCTGGATCAACTGAAATAAATT
* *
144 GAAGGAAAGATCACCCTGGATCGACTGAAATAAATT
1 GAA-GAAAGATCGCCCTGGATCAACTGAAATAAATT
* * *
180 GAATAAAAGATCGCCCTGGATCAACTGGAGTAAATT
1 GAA-GAAAGATCGCCCTGGATCAACTGAAATAAATT
* * * * *
216 GAGGAGAGATCAACCC-GGATCAACTGACATAAACT
1 GAAGAAAGATC-GCCCTGGATCAACTGAAATAAATT
* * * *
251 GAATGAAAAGACCACCCTGGGTCAACTTGAAATAAACT
1 GAA-G-AAAGATCGCCCTGGATCAAC-TGAAATAAATT
* * ** *
289 GAAGAACGGGTCGCCCTGGATCAACTGAGGTAAAAT
1 GAAGAA-AGATCGCCCTGGATCAACTGAAATAAATT
* ** * *
325 GAATAAAAGATCATCCTAGATCAAACTGAAATGAATT
1 GAA-GAAAGATCGCCCTGGATC-AACTGAAATAAATT
* * *
362 GAAGAAAGACCACCCTAGG-TCAATTGAAATAAATT
1 GAAGAAAGATCGCCCT-GGATCAACTGAAATAAATT
* * * * *
397 GAAGAAGGACCGCCCTGGGTCGATTGAAATAAATT
1 GAAGAAAGATCGCCCTGGATCAACTGAAATAAATT
* * * * * *
432 GACGAAGGACCGCCCTGGGTTAACTGAAATAAACT
1 GAAGAAAGATCGCCCTGGATCAACTGAAATAAATT
* *
467 GAATAAAGATCGCCTTGTG-TCAACTGAAAT
1 GAAGAAAGATCGCCCTG-GATCAACTGAAAT
497 GAACTAAAGC
Statistics
Matches: 364, Mismatches: 82, Indels: 26
0.77 0.17 0.06
Matches are distributed among these distances:
34 2 0.01
35 188 0.52
36 115 0.32
37 46 0.13
38 13 0.04
ACGTcount: A:0.40, C:0.19, G:0.21, T:0.20
Consensus pattern (35 bp):
GAAGAAAGATCGCCCTGGATCAACTGAAATAAATT
Found at i:269 original size:72 final size:72
Alignment explanation
Indices: 2--473 Score: 232
Period size: 71 Copynumber: 6.6 Consensus size: 72
1 C
* * * * * *
2 GAAGAAAAGATCTCCCTCGATCAAACTAAAAT-AACTTGAAGT--AAGATCACCCTGGATCAATT
1 GAAGGAAAGATCACCCTGGATC-AACTGAAATAAAC-TGAA-TAAAAGACCACCCTGGATCAACT
* * *
64 GAAATGAATT
63 GGAGTAAATT
* * * * * * * * **
74 GAA-GAAAGACCGCCCTGGGTCAACTGAAAT-AACTTGAA-GAATGACCGCCCTGGGTCAGCTAA
1 GAAGGAAAGATCACCCTGGATCAACTGAAATAAAC-TGAATAAAAGACCACCCTGGATCAACTGG
*
136 AATAAATT
65 AGTAAATT
* * * *
144 GAAGGAAAGATCACCCTGGATCGACTGAAATAAATTGAATAAAAGATCGCCCTGGATCAACTGGA
1 GAAGGAAAGATCACCCTGGATCAACTGAAATAAACTGAATAAAAGACCACCCTGGATCAACTGGA
209 GTAAATT
66 GTAAATT
* * *
216 G-AGGAGAGATCAACCC-GGATCAACTGACATAAACTGAATGAAAAGACCACCCTGGGTCAACTT
1 GAAGGAAAGATC-ACCCTGGATCAACTGAAATAAACTGAAT-AAAAGACCACCCTGGATCAAC-T
* * *
279 GAAATAAACT
63 GGAGTAAATT
* * * ** * * * *
289 GAA-GAACGGGTCGCCCTGGATCAACTGAGGTAAAATGAATAAAAGATCATCCTAGATCAAACTG
1 GAAGGAA-AGATCACCCTGGATCAACTGAAATAAACTGAATAAAAGACCACCCTGGATC-AACTG
* * *
353 AAATGAATT
64 GAGTAAATT
* * * * * * * * * *
362 GAA-GAAAGACCACCCTAGG-TCAATTGAAATAAATTGAA-GAAGGACCGCCCTGGGTCGATTGA
1 GAAGGAAAGATCACCCT-GGATCAACTGAAATAAACTGAATAAAAGACCACCCTGGATCAACTGG
*
424 AATAAATT
65 AGTAAATT
* * * * * *
432 G-ACGAAGGACCGCCCTGGGTTAACTGAAATAAACTGAATAAA
1 GAAGGAAAGATCACCCTGGATCAACTGAAATAAACTGAATAAA
474 GATCGCCTTG
Statistics
Matches: 310, Mismatches: 74, Indels: 33
0.74 0.18 0.08
Matches are distributed among these distances:
69 3 0.01
70 80 0.26
71 82 0.26
72 73 0.24
73 45 0.15
74 27 0.09
ACGTcount: A:0.40, C:0.19, G:0.21, T:0.20
Consensus pattern (72 bp):
GAAGGAAAGATCACCCTGGATCAACTGAAATAAACTGAATAAAAGACCACCCTGGATCAACTGGA
GTAAATT
Found at i:307 original size:109 final size:109
Alignment explanation
Indices: 2--402 Score: 295
Period size: 109 Copynumber: 3.7 Consensus size: 109
1 C
* * * * * *
2 GAAGAAAAGATC-TCCCTCGATCAAACTAAAAT-AACTTGAAGTAAGATCACCCTGGATCAA-TT
1 GAAGAAAAGATCAACCC-AGATCAAACTGAAATAAAC-TGAAGAAAGACCACCCTGGGTCAACTT
* * * ** **
64 GAAATGAATTGAAG-AAAGACCGCCCTGGGTCAACTGAAATAACTT
64 GAAATAAATTGAAGAAAAGATCGCCCTGGATCAACTGAGGTAAAAT
* ** * * * * * * * *
109 GAAG-AATGA-CCGCCCTGGGTC-AGCTAAAATAAATTGAAGGAAAGATCACCCTGGATCGAC-T
1 GAAGAAAAGATCAACCC-AGATCAAACTGAAATAAACTGAA-GAAAGACCACCCTGGGTCAACTT
* *
170 GAAATAAATTGAATAAAAGATCGCCCTGGATCAACTG-GAGTAAATT
64 GAAATAAATTGAAGAAAAGATCGCCCTGGATCAACTGAG-GTAAAAT
* * * *
216 G-AGGAGAGATCAACCCGGATC-AACTGACATAAACTGAATGAAAAGACCACCCTGGGTCAACTT
1 GAAGAAAAGATCAACCCAGATCAAACTGAAATAAACTGAA-G-AAAGACCACCCTGGGTCAACTT
* ** *
279 GAAATAAACTGAAGAACGGGTCGCCCTGGATCAACTGAGGTAAAAT
64 GAAATAAATTGAAGAAAAGATCGCCCTGGATCAACTGAGGTAAAAT
* * * * * *
325 GAATAAAAGATCATCCTAGATCAAACTGAAATGAATTGAAGAAAGACCACCCTAGGTCAA-TTGA
1 GAAGAAAAGATCAACCCAGATCAAACTGAAATAAACTGAAGAAAGACCACCCTGGGTCAACTTGA
389 AATAAATTGAAGAA
66 AATAAATTGAAGAA
403 GGACCGCCCT
Statistics
Matches: 236, Mismatches: 45, Indels: 25
0.77 0.15 0.08
Matches are distributed among these distances:
105 13 0.06
106 46 0.19
107 51 0.22
108 38 0.16
109 58 0.25
110 16 0.07
111 14 0.06
ACGTcount: A:0.41, C:0.18, G:0.20, T:0.20
Consensus pattern (109 bp):
GAAGAAAAGATCAACCCAGATCAAACTGAAATAAACTGAAGAAAGACCACCCTGGGTCAACTTGA
AATAAATTGAAGAAAAGATCGCCCTGGATCAACTGAGGTAAAAT
Done.