Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01009827.1 Corchorus olitorius cultivar O-4 contig09859, 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: 6168
ACGTcount: A:0.34, C:0.16, G:0.19, T:0.31
Found at i:795 original size:321 final size:324
Alignment explanation
Indices: 1--1048 Score: 980
Period size: 333 Copynumber: 3.2 Consensus size: 324
* * **
1 AAAAAGATTGAAAGGCTTTTCACGCTTCTAATATCGGTTATCCATTTTTTTTCCGAATTAATTTC
1 AAAAAGATTGAAA-GC-TTTCACGCTTCTAATATCGTTTTTCC-TAATTTTTCCGAATTAATTTC
* *
66 TAATTAAATCGAAACATGATTCAAATGCTCGTAAAAACAAATCGTTAAATCCAATGTGGTTGAGA
63 TAATTAAATCGAAACATGATTCAAATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGA
* * * * *
131 TTTTGTTAGATGGATATAGATATTTCAATGAGACTTGGCGTCAAAAATCATGCAAAA-TAGAACC
128 TTTCGTTAGATGAATATAGATATTTCAATGAGACTTGACGCCAAAAATCATGCAAAACT-GAGCC
* *
195 GGGACCACAAATCACGCTTTTAGTCAAAACTGTGATGGTTAGTACATGATTTCGGCTAAAATTTT
192 GGGACCACAAAACACGCTTTTAGCCAAAAC-GTGATGG-T-GTA-AT-ATTTCGGCTAAAATTTT
* *
260 GCAAAAATTGACACGAAACATTTCTCCTCAATTTACGGCCACCATATTCATAAAAAATATATAAC
252 GCAAAAATTGACACGAAACATTTCACCTCAATTTACGGCCACCATATTCATAAAAAAAATATAAC
**
325 TCAACGTC
317 TCAACACC
* *
333 AAAAAGATTGAAAGCCTTCTCACGCTTCTAATATTGTTTTTTTTCTAATTTTTCCGAATTAATTT
1 AAAAAGATTGAAAG-CTT-TCACGCTTCTAATATCG--TTTTTCCTAATTTTTCCGAATTAATTT
* * *
398 CTAATTAAATCGAAACCA-GATTGAGATGCTCGTAAAAACAAATCCTTAAATCCTATGTGGCTGA
62 CTAATTAAATCGAAA-CATGATTCAAATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGA
* * * * *
462 GATTTCGTTAGATAAATGTAGATATTTCGATGAGTCTTGACACCAAAAATCATGCAAAACTGAGC
126 GATTTCGTTAGATGAATATAGATATTTCAATGAGACTTGACGCCAAAAATCATGCAAAACTGAGC
* * *
527 CGAGG-CCACAAAACGCGTTTTTAGCCAAAAAC-TG-T-G-GT-AT-TTT-GGCTAAAATTTTGT
191 CG-GGACCACAAAACACGCTTTTAGCC-AAAACGTGATGGTGTAATATTTCGGCTAAAATTTTGC
* *
584 AAAAATTGAGC-CG-AACGAATTT-ACCTCAACTTT-TGGCCACGATATTCATAAAAAAAAATAT
254 AAAAATTGA-CACGAAAC--ATTTCACCTCAA-TTTACGGCCACCATATTCAT-AAAAAAAATAT
*
645 AATTCAACACC
314 AACTCAACACC
* * *
656 AAAAAGATTGAAATGCTATTCACACTCCTAATATCGTTTTTCCTAATTTTTCCGAATTAATTCCT
1 AAAAAGATTGAAA-GCT-TTCACGCTTCTAATATCGTTTTTCCTAATTTTTCCGAATTAATTTCT
* * * * * *
721 AATTGAATCGAGACATGATTCATATGCTCGTAAAAACAAATCCTTAAATTCAATGTGGGTAAGAT
64 AATTAAATCGAAACATGATTCAAATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGAT
* * *
786 TTGGTTAGATGAATATAGATATTTCAATGAGACTTGACGCAAAAAAATCATGCAAAACAGAGCC-
129 TTCGTTAGATGAATATAGATATTTCAATGAGACTTGACGC-CAAAAATCATGCAAAACTGAGCCG
* * * ** * *
850 AGAGCTCCGAA-ACGC-----G-----TCGTGATGGTTAGTACACTATTTCAGCTAAAATTTTGC
193 GGACCACAAAACACGCTTTTAGCCAAAACGTGATGG-T-GTA-A-TATTTCGGCTAAAATTTTGC
* * ** * * * *
904 AAAAATTGACCCGAGAA-ATTTCTCCTCAATTTTGGGCCACAATACTAATAAAAAATATATAACT
254 AAAAATTGACACGA-AACATTTCACCTCAATTTACGGCCACCATATTCATAAAAAAAATATAACT
*
968 CAACGCC
318 CAACACC
* * * * * * **
975 AAAAAGACTGAAGGGTTTCTCACGCTTCTAATATCGCTTATCCTACCTTTTTTTTGAATTAATTT
1 AAAAAGATTGAA-AGCTT-TCACGCTTCTAATATCGTTTTTCCTA--ATTTTTCCGAATTAATTT
*
1040 CTGATTAAA
62 CTAATTAAA
1049 AAAATTATAC
Statistics
Matches: 593, Mismatches: 85, Indels: 87
0.78 0.11 0.11
Matches are distributed among these distances:
309 1 0.00
310 2 0.00
311 1 0.00
312 1 0.00
315 3 0.01
317 1 0.00
318 2 0.00
319 65 0.11
320 46 0.08
321 143 0.24
322 67 0.11
323 58 0.10
324 2 0.00
325 2 0.00
327 2 0.00
330 1 0.00
331 4 0.01
332 32 0.05
333 146 0.25
334 14 0.02
ACGTcount: A:0.36, C:0.18, G:0.15, T:0.32
Consensus pattern (324 bp):
AAAAAGATTGAAAGCTTTCACGCTTCTAATATCGTTTTTCCTAATTTTTCCGAATTAATTTCTAA
TTAAATCGAAACATGATTCAAATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTT
CGTTAGATGAATATAGATATTTCAATGAGACTTGACGCCAAAAATCATGCAAAACTGAGCCGGGA
CCACAAAACACGCTTTTAGCCAAAACGTGATGGTGTAATATTTCGGCTAAAATTTTGCAAAAATT
GACACGAAACATTTCACCTCAATTTACGGCCACCATATTCATAAAAAAAATATAACTCAACACC
Found at i:5450 original size:55 final size:55
Alignment explanation
Indices: 5335--5451 Score: 155
Period size: 55 Copynumber: 2.1 Consensus size: 55
5325 GATTACTCTG
* ** **
5335 TTTGTTTAAAAGTTTATGCTAGGCTCAAATTGAGCAAGTTTGGGAATATGTACCT
1 TTTGTTTAAAAGTTTATGCTAGGCTCAAATTGAGCAAGTTTGAGAATAACTAAAT
* *
5390 CTTGTTTAAAAGTTTATGCTAGGCTCAAATTGAGCAAGTTT-AGATTCAACTAAAT
1 TTTGTTTAAAAGTTTATGCTAGGCTCAAATTGAGCAAGTTTGAGAAT-AACTAAAT
5445 TTTGTTT
1 TTTGTTT
5452 GGACTTCTAT
Statistics
Matches: 53, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
54 3 0.06
55 50 0.94
ACGTcount: A:0.30, C:0.11, G:0.19, T:0.40
Consensus pattern (55 bp):
TTTGTTTAAAAGTTTATGCTAGGCTCAAATTGAGCAAGTTTGAGAATAACTAAAT
Done.