Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015616.1 Corchorus olitorius cultivar O-4 contig15649, 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, 893
Length: 1489
ACGTcount: A:0.31, C:0.19, G:0.21, T:0.29
Found at i:42 original size:32 final size:32
Alignment explanation
Indices: 1--587 Score: 777
Period size: 32 Copynumber: 18.4 Consensus size: 32
* *
1 GTCGGAATAAAACTAAGAAAGACCTGTCTAAG
1 GTCGGAATAAAACTGAGAAAGACCTGTCTGAG
33 GTCGGAATAAAACTGAGAAAGACCTGTCTGAG
1 GTCGGAATAAAACTGAGAAAGACCTGTCTGAG
* *
65 GTCGGAATAAAAAT-ATAAAGACCTGTCTGAG
1 GTCGGAATAAAACTGAGAAAGACCTGTCTGAG
*
96 GTCGAAATAAAACTGAGAAAGACCTGTCTGAG
1 GTCGGAATAAAACTGAGAAAGACCTGTCTGAG
128 GTCGGAATAAAAAGCTGAGAAAGACCTGTCTGAG
1 GTCGGAAT-AAAA-CTGAGAAAGACCTGTCTGAG
**
162 GTCGGAATTGAACTG-GTAAAGACCTGTCTGAG
1 GTCGGAATAAAACTGAG-AAAGACCTGTCTGAG
* *
194 GTCGAAATTAAAAGTTGAGAAAGACCTGTCTGAG
1 GTCGGAA-TAAAA-CTGAGAAAGACCTGTCTGAG
*
228 GTCGG-----AACTGTGAAAGACCTGTCTGAG
1 GTCGGAATAAAACTGAGAAAGACCTGTCTGAG
*
255 GTCGGAATAAAACTGAGAAAGACTTGTCTGAG
1 GTCGGAATAAAACTGAGAAAGACCTGTCTGAG
**
287 GTCGGAATTGAACTG-GTAAAGACCTGTCTGAG
1 GTCGGAATAAAACTGAG-AAAGACCTGTCTGAG
*
319 GTCGAAATTAAAAGCTGAGAAAGACCTGTCTGAG
1 GTCGGAA-TAAAA-CTGAGAAAGACCTGTCTGAG
* * * *
353 GTCGAAATAAAGCTGAAAAAAGACCCGTCTGAG
1 GTCGGAATAAAACTG-AGAAAGACCTGTCTGAG
386 GTC-G----AAACTGAGAAAGACCTGTCTGAG
1 GTCGGAATAAAACTGAGAAAGACCTGTCTGAG
413 GTCGGAATAAAACTGAGAAAGACCTGTCTGAG
1 GTCGGAATAAAACTGAGAAAGACCTGTCTGAG
445 GTCGGAATAAAACTGAGAAAGACCTGTCTGAG
1 GTCGGAATAAAACTGAGAAAGACCTGTCTGAG
477 GTCGGAATAAAACTGAGAAAGACCTGTCTGAG
1 GTCGGAATAAAACTGAGAAAGACCTGTCTGAG
** *
509 GTCGGAATTGAACTGATAAAGACCTGTCTGAG
1 GTCGGAATAAAACTGAGAAAGACCTGTCTGAG
*
541 GTCGAAATTAAAAGCTGAGAAAGACCTGTCTGAG
1 GTCGGAA-TAAAA-CTGAGAAAGACCTGTCTGAG
575 GTCGGAATTAAAA
1 GTCGGAA-TAAAA
588 TCTTCTGCAT
Statistics
Matches: 491, Mismatches: 40, Indels: 46
0.85 0.07 0.08
Matches are distributed among these distances:
27 41 0.08
28 8 0.02
31 30 0.06
32 268 0.55
33 37 0.08
34 105 0.21
35 2 0.00
ACGTcount: A:0.37, C:0.15, G:0.27, T:0.21
Consensus pattern (32 bp):
GTCGGAATAAAACTGAGAAAGACCTGTCTGAG
Found at i:454 original size:190 final size:190
Alignment explanation
Indices: 9--578 Score: 784
Period size: 190 Copynumber: 3.0 Consensus size: 190
1 GTCGGAAT
* *
9 AAAACTAAGAAAGACCTGTCTAAGGTCGGAATAAAACTGAGAAAGACCTGTCTGAGGTCGGAATA
1 AAAACTGAGAAAGACCTGTCTGAGGTCGGAATAAAACTGAGAAAGACCTGTCTGAGGTCGGAATA
* * * *
74 AAAAT-ATAAAGACCTGTCTGAGGTCGAAATAAAACTGAGAAAGACCTGTCTGAGGTCGGAATAA
66 AAACTGAGAAAGACCTGTCTGAGGTCGGAATAAAACTGAGAAAGACCTGTCTGAGGTCGGAATTA
* * **
138 AAAGCTGAGAAAGACCTGTCTGAGGTCGGAATTGAA-CTGGTAAAGACCTGTCTGAGGTCG
131 AAAGCTGAGAAAGACCTGTCTGAGGTC-GAAATAAAGCTGAAAAAGACCTGTCTGAGGTCG
* *
198 AAATTAAAAGTTGAGAAAGACCTGTCTGAGGTCGG-----AACTGTGAAAGACCTGTCTGAGGTC
1 -----AAAA-CTGAGAAAGACCTGTCTGAGGTCGGAATAAAACTGAGAAAGACCTGTCTGAGGTC
* **
258 GGAATAAAACTGAGAAAGACTTGTCTGAGGTCGGAATTGAACTG-GTAAAGACCTGTCTGAGGTC
60 GGAATAAAACTGAGAAAGACCTGTCTGAGGTCGGAATAAAACTGAG-AAAGACCTGTCTGAGGTC
* *
322 GAAATTAAAAGCTGAGAAAGACCTGTCTGAGGTCGAAATAAAGCTGAAAAAAGACCCGTCTGAGG
124 GGAATTAAAAGCTGAGAAAGACCTGTCTGAGGTCGAAATAAAGCTG-AAAAAGACCTGTCTGAGG
387 TCG
188 TCG
390 -AAACTGAGAAAGACCTGTCTGAGGTCGGAATAAAACTGAGAAAGACCTGTCTGAGGTCGGAATA
1 AAAACTGAGAAAGACCTGTCTGAGGTCGGAATAAAACTGAGAAAGACCTGTCTGAGGTCGGAATA
454 AAACTGAGAAAGACCTGTCTGAGGTCGGAATAAAACTGAGAAAGACCTGTCTGAGGTCGGAATT-
66 AAACTGAGAAAGACCTGTCTGAGGTCGGAATAAAACTGAGAAAGACCTGTCTGAGGTCGGAATTA
* * *
518 GAA-CTGATAAAGACCTGTCTGAGGTCGAAATTAAAAGCTGAGAAAGACCTGTCTGAGGTCG
131 AAAGCTGAGAAAGACCTGTCTGAGGTCGAAA-T-AAAGCTGAAAAAGACCTGTCTGAGGTCG
579 GAATTAAAAT
Statistics
Matches: 336, Mismatches: 27, Indels: 31
0.85 0.07 0.08
Matches are distributed among these distances:
185 24 0.07
186 3 0.01
188 26 0.08
189 22 0.07
190 136 0.40
191 81 0.24
192 18 0.05
194 4 0.01
195 22 0.07
ACGTcount: A:0.36, C:0.15, G:0.28, T:0.21
Consensus pattern (190 bp):
AAAACTGAGAAAGACCTGTCTGAGGTCGGAATAAAACTGAGAAAGACCTGTCTGAGGTCGGAATA
AAACTGAGAAAGACCTGTCTGAGGTCGGAATAAAACTGAGAAAGACCTGTCTGAGGTCGGAATTA
AAAGCTGAGAAAGACCTGTCTGAGGTCGAAATAAAGCTGAAAAAGACCTGTCTGAGGTCG
Found at i:467 original size:222 final size:227
Alignment explanation
Indices: 1--587 Score: 889
Period size: 222 Copynumber: 2.6 Consensus size: 227
* *
1 GTCGGAATAAAACTAAGAAAGACCTGTCTAAGGTCGGAATAAAACTGAGAAAGACCTGTCTGAGG
1 GTCGGAATAAAACTGAGAAAGACCTGTCTGAGGTCGGAATAAAACTGAGAAAGACCTGTCTGAGG
** *
66 TCGGAATAAAAAT-ATAAAGACCTGTCTGAGGTCGAAA-TAAAA-CTGAGAAAGACCTGTCTGAG
66 TCGGAATTGAACTGATAAAGACCTGTCTGAGGTCGAAATTAAAAGCTGAGAAAGACCTGTCTGAG
* *
128 GTCGGAATAAAAAGCTGAGAAAGACCTGTCTGAGGTCGGAATTGAACTGGTAAAGACCTGTCTGA
131 GTC-GAATAAAAAGCTGAAAAAGACCCGTCTGAGGTCGGAA-T-AACTGGTAAAGACCTGTCTGA
*
193 GGTCGAAATTAAAAGTTGAGAAAGACCTGTCTGAG
193 GGTCGAAATTAAAAGCTGAGAAAGACCTGTCTGAG
* *
228 GTCGG-----AACTGTGAAAGACCTGTCTGAGGTCGGAATAAAACTGAGAAAGACTTGTCTGAGG
1 GTCGGAATAAAACTGAGAAAGACCTGTCTGAGGTCGGAATAAAACTGAGAAAGACCTGTCTGAGG
*
288 TCGGAATTGAACTGGTAAAGACCTGTCTGAGGTCGAAATTAAAAGCTGAGAAAGACCTGTCTGAG
66 TCGGAATTGAACTGATAAAGACCTGTCTGAGGTCGAAATTAAAAGCTGAGAAAGACCTGTCTGAG
*
353 GTCGAA-ATAAAGCTGAAAAAAGACCCGTCTGAGGTC-G-A-AACTGAG-AAAGACCTGTCTGAG
131 GTCGAATAAAAAGCTG-AAAAAGACCCGTCTGAGGTCGGAATAACTG-GTAAAGACCTGTCTGAG
*
413 GTCGGAA-TAAAA-CTGAGAAAGACCTGTCTGAG
194 GTCGAAATTAAAAGCTGAGAAAGACCTGTCTGAG
445 GTCGGAATAAAACTGAGAAAGACCTGTCTGAGGTCGGAATAAAACTGAGAAAGACCTGTCTGAGG
1 GTCGGAATAAAACTGAGAAAGACCTGTCTGAGGTCGGAATAAAACTGAGAAAGACCTGTCTGAGG
510 TCGGAATTGAACTGATAAAGACCTGTCTGAGGTCGAAATTAAAAGCTGAGAAAGACCTGTCTGAG
66 TCGGAATTGAACTGATAAAGACCTGTCTGAGGTCGAAATTAAAAGCTGAGAAAGACCTGTCTGAG
*
575 GTCGGAATTAAAA
131 GTC-GAATAAAAA
588 TCTTCTGCAT
Statistics
Matches: 330, Mismatches: 18, Indels: 27
0.88 0.05 0.07
Matches are distributed among these distances:
217 24 0.07
218 5 0.02
219 26 0.08
220 1 0.00
222 182 0.55
223 35 0.11
224 29 0.09
225 23 0.07
227 5 0.02
ACGTcount: A:0.37, C:0.15, G:0.27, T:0.21
Consensus pattern (227 bp):
GTCGGAATAAAACTGAGAAAGACCTGTCTGAGGTCGGAATAAAACTGAGAAAGACCTGTCTGAGG
TCGGAATTGAACTGATAAAGACCTGTCTGAGGTCGAAATTAAAAGCTGAGAAAGACCTGTCTGAG
GTCGAATAAAAAGCTGAAAAAGACCCGTCTGAGGTCGGAATAACTGGTAAAGACCTGTCTGAGGT
CGAAATTAAAAGCTGAGAAAGACCTGTCTGAG
Done.