Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01000234.1 Corchorus capsularis cultivar CVL-1 contig00234, 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, 628
Length: 1048
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34
Found at i:1043 original size:335 final size:336
Alignment explanation
Indices: 438--1048 Score: 767
Period size: 332 Copynumber: 1.8 Consensus size: 336
428 ATTCAAAAAG
* * *
438 AATATGAAAAACGATATGAAAAGCGGGAAAAGTCCTCCAATTTTTTTCGGCAATAAATTATATAT
1 AATATGAAAAACGATATGAAAAGCGCGAAAAGTCCTCCAATCTTTTTCGGCAATAAATTATAAAT
* * *
503 ATATTTCATGACTATTTTATCCAAAAATTATGGAAAATTTTTTGCTAGTCATTTTTTTTAGCAGA
66 ATATTTCATGACTATTTTATCCAAAAATTATGGAAAATATTTTGCGAGTCATTTTTTTTA-CAAA
*
568 ATTTTAACCGAAATTATAGACTAACCACCACAGGTTGTTGCTAAAAACGAGTTTCGGGGCCCTGA
130 ATTTTAACCAAAATTATAGA-TAACCACCACAGGTTGTTGCTAAAAACGAGTTTCGGGGCCCTGA
* * * * * * *
633 CTCAGTTTTGCATGATTTTTGGCGTCGAGACTCCTTGAAATATCTATATTCATTTAATCAAATGT
194 CTCAGATTTGCATGATTATTGGCGCCGACACTCCTTGAAATATCTATATTCATCTAATAAAATCT
*
698 CAATCACATTGCATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAA
259 CAACCACATTGCATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAA
763 ATTAATTAAGAAA
324 ATTAATTAAGAAA
* * **
776 AATATGAAAAACGATATTAAAAGCTCGAAAAGTCC-CCTAATCTTTTT-GGCGTTAAATTATAAA
1 AATATGAAAAACGATATGAAAAGCGCGAAAAGTCCTCC-AATCTTTTTCGGCAATAAATTATAAA
* * *
839 TAT-TTTTATGAGTATTTTATCCAAAAATT-TGAGGAAAA-ATTTT-CGGGTCA-TTTTTTT-CA
65 TATATTTCATGACTATTTTATCCAAAAATTAT--GGAAAATATTTTGCGAGTCATTTTTTTTACA
* * * * *
898 AAATTTTAGCTAAAATCGTGTAG-TAACCATCACA-GTTTTTGGCTAAAAACGCA-TTTCGGGGC
128 AAATTTTAACCAAAAT--TATAGATAACCACCACAGGTTGTT-GCTAAAAACG-AGTTTCGGGGC
*
960 CCTGACTTAGCATTTGCATAGATTATTGGCGCCGACACTTCCTTGAAATATCTATATTCATCTAA
189 CCTGACTCAG-ATTTGCAT-GATTATTGGCGCCGACAC-TCCTTGAAATATCTATATTCATCTAA
* *
1025 TAAAATCTTAGCCACATTGCATTT
251 TAAAATCTCAACCACATTGCATTT
Statistics
Matches: 233, Mismatches: 30, Indels: 23
0.81 0.10 0.08
Matches are distributed among these distances:
331 5 0.02
332 52 0.22
333 8 0.03
334 26 0.11
335 50 0.21
336 28 0.12
337 24 0.10
338 40 0.17
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.36
Consensus pattern (336 bp):
AATATGAAAAACGATATGAAAAGCGCGAAAAGTCCTCCAATCTTTTTCGGCAATAAATTATAAAT
ATATTTCATGACTATTTTATCCAAAAATTATGGAAAATATTTTGCGAGTCATTTTTTTTACAAAA
TTTTAACCAAAATTATAGATAACCACCACAGGTTGTTGCTAAAAACGAGTTTCGGGGCCCTGACT
CAGATTTGCATGATTATTGGCGCCGACACTCCTTGAAATATCTATATTCATCTAATAAAATCTCA
ACCACATTGCATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAAT
TAATTAAGAAA
Done.