Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01001940.1 Corchorus capsularis cultivar CVL-1 contig01942, 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: 2873
ACGTcount: A:0.32, C:0.15, G:0.16, T:0.36
Found at i:2310 original size:2 final size:2
Alignment explanation
Indices: 2303--2328 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2293 TTTGACATTG
2303 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
2329 GAGTATTGTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2491 original size:321 final size:314
Alignment explanation
Indices: 1786--2852 Score: 1005
Period size: 323 Copynumber: 3.3 Consensus size: 314
1776 TCATGATTTA
* * * * * * *
1786 AGTTTTGTATGATTTTTGGTGCCAAGAA-TCTTTGAGATATCCATATTCATCTAATCAAATCTCA
1 AGTTTTGCATGATTTTTGGCGCCAA-AACTCCTTAAAATATCTATATTCATCTAACCAAATCTCA
* * * * * *
1850 ACTACATTGGATTTAAGAAATTGTTTTTATGAGCATTTGAATCTTGTTTCGATTTAATTAGAAAT
65 GCCACATTGGATTTAAGGATTTGTTTTTACGAGCATTTGAATTTTGTTTCGATTTAATTAGAAAT
*
1915 TAATTTAGAAAAATATGAAAAATA-ATATTAAAAGCGTGAAAAGTCCTCCAATGTTTTTGGCA-T
130 TAATTTAGAAAAATATGAAAAA-AGATATTAAAAGCGTGAAAAGTCCT-CAATATTTTTGGCATT
* * * *
1978 -TAAATTATATATATTTTACGAGTGTT-TTAGCCAAAAATTGAGGAAAAATTTTTTGAGTCATTT
193 GTAAATTATATATATTTTATGAGTATTGTT-GCTAAAAATTGAGGAAAAATATTTTG-GTC----
* * * * *
2041 TTTGTAAAATTTTAGGCGAAATCGTTTACTAACGGTTTTTTGCT-AAAACGCGTTTCGGGGCCCG
252 ----T--AATTTTAGCCGAAATCGTGTACCATCGGTTTTTGGCTAAAAACGCGTTTCGGGGCCCG
* *
2105 GCTT
311 GGTC
* * * * *
2109 AATTTTGCATGATTTTTGGCGCCGAGACTCCTTGAAATATCTATATTCATCTAATCAAATCTCAG
1 AGTTTTGCATGATTTTTGGCGCCAAAACTCCTTAAAATATCTATATTCATCTAACCAAATCTCAG
* * *
2174 CCACATTGAATTTAAGGATTTGTTTTTACGAACATCTGAATTTTGTTT-GTATTTAATTAGAAAT
66 CCACATTGGATTTAAGGATTTGTTTTTACGAGCATTTGAATTTTGTTTCG-ATTTAATTAGAAAT
* * * *
2238 TAATTTAGAAAAATATGAAAAAAGATCTTAAAAGCTTAAAAAGTCCTCGAATATTTTTGACATTG
130 TAATTTAGAAAAATATGAAAAAAGATATTAAAAGCGTGAAAAGTCCTC-AATATTTTTGGCATTG
2303 ATATATATATATATATATATATATATGAGTATTGTTGCTAAAAATTGAGGAAAAATATTCTTGGT
194 -TA-A-AT-TATATATAT-T-T-TATGAGTATTGTTGCTAAAAATTGAGGAAAAATATT-TTGGT
2368 C-AATTTTAGCCGAAATCGTGTACCATC-GTTTTTGGCTAAAAACGCGTTTCGGGGCCCGGGTC
251 CTAATTTTAGCCGAAATCGTGTACCATCGGTTTTTGGCTAAAAACGCGTTTCGGGGCCCGGGTC
* * *
2430 AGTTTTGCATAATTTTTGGTGTCAAAACTCCTTAAAATATCTATATTCATCTAACCAAATCTCAG
1 AGTTTTGCATGATTTTTGGCGCCAAAACTCCTTAAAATATCTATATTCATCTAACCAAATCTCAG
* * * *
2495 ACACATTGGATATAA-G-TTTTTCTTTTACGAGCATTTGAATTATGTTTCGATTTAATTAGAAAT
66 CCACATTGGATTTAAGGATTTGT-TTTTACGAGCATTTGAATTTTGTTTCGATTTAATTAGAAAT
* * * * * * *
2558 TAATTTGTAAAAAAAAAAGGAAAAATGATATTAGAAGCGTGAGAAG-CCATTCAATCTTTTTGGC
130 TAA-TT-T-AGAAAAATATGAAAAAAGATATTAAAAGCGTGAAAAGTCC--TCAATATTTTTGGC
* * * *
2622 GTTG--AACTATATA-CTTTTATGAGTATTGTTGCTAACAATTGA-GAAAAATATTTTGGGTCAA
190 ATTGTAAATTATATATATTTTATGAGTATTGTTGCTAAAAATTGAGGAAAAATATTTT-GGTC--
* * * *
2683 TTTTTGCAAACTTTTAGCCGAAATCGTGTACCATCACGGTTTTCTGACTAAAAACGTGTTCCGAG
252 ----T---AA-TTTTAGCCGAAATCGTGTACCAT--CGGTTTT-TGGCTAAAAACGCGTTTCGGG
*
2748 ACACCGGGTC
306 GC-CCGGGTC
* * * *
2758 AGTTTTGCATGATTTTTAGCGGCAAGACTCCTTAAAATATATCTATATTTATCTAACCAAATCTC
1 AGTTTTGCATGATTTTTGGCGCCAAAACTCCTT-AAA-ATATCTATATTCATCTAACCAAATCTC
*
2823 AGCCACATTGTATTTAAGGATTTGTTTTTA
64 AGCCACATTGGATTTAAGGATTTGTTTTTA
2853 TGAGTTTCTA
Statistics
Matches: 622, Mismatches: 78, Indels: 80
0.80 0.10 0.10
Matches are distributed among these distances:
311 2 0.00
312 14 0.02
313 24 0.04
314 1 0.00
315 1 0.00
316 1 0.00
317 6 0.01
318 1 0.00
319 5 0.01
320 49 0.08
321 116 0.19
322 9 0.01
323 225 0.36
324 3 0.00
325 1 0.00
326 7 0.01
327 19 0.03
328 37 0.06
329 12 0.02
330 41 0.07
331 7 0.01
332 36 0.06
333 5 0.01
ACGTcount: A:0.33, C:0.13, G:0.16, T:0.38
Consensus pattern (314 bp):
AGTTTTGCATGATTTTTGGCGCCAAAACTCCTTAAAATATCTATATTCATCTAACCAAATCTCAG
CCACATTGGATTTAAGGATTTGTTTTTACGAGCATTTGAATTTTGTTTCGATTTAATTAGAAATT
AATTTAGAAAAATATGAAAAAAGATATTAAAAGCGTGAAAAGTCCTCAATATTTTTGGCATTGTA
AATTATATATATTTTATGAGTATTGTTGCTAAAAATTGAGGAAAAATATTTTGGTCTAATTTTAG
CCGAAATCGTGTACCATCGGTTTTTGGCTAAAAACGCGTTTCGGGGCCCGGGTC
Done.