Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006578.1 Corchorus capsularis cultivar CVL-1 contig06599, 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, 606
Length: 1010
ACGTcount: A:0.27, C:0.19, G:0.23, T:0.32
Found at i:850 original size:454 final size:454
Alignment explanation
Indices: 1--1010 Score: 1694
Period size: 454 Copynumber: 2.2 Consensus size: 454
* *
1 TAGATTTATCATGCAAAGACCAATGGGTGCGATCATACCAACACTAATGCACCGGATCCCATTAG
1 TAGATTTATCATGCAAAGACCAATGGGTGCGATCATACCAGCACTAATGCACCGGATCCCATCAG
*
66 AACTCCGCAGTTAAGCGTGCTTGGTCGAGAGTAGTACTAGGAAGGGTGACCTCCTGGAAGTCCTC
66 AACTCCGCAGTTAAGCGTGCTTGGGCGAGAGTAGTACTAGGAAGGGTGACCTCCTGGAAGTCCTC
* *
131 GATTTGCACCCCTTTTTCATTTTTTTTTTCTTTAGTTTTCTTCTACTTTTGGAATTTCTTATGGG
131 GATTTGCACCCCTTTTTCA-TTTTTTTTTCTTTAGATTTCTTCTACTTTCGGAATTTCTTATGGG
*
196 AAGCAATCGGTTCATGTAAGCATTAAGTCTTAGTATGGCTGCGAATGAACAACATGTTCGATGAA
195 AAGCAATCGGTTAATGTAAGCATTAAGTCTTAGTATGGCTGCGAATGAACAACATGTTCGATGAA
261 CGGCACGTGAACAAGCTGGATCAAAGGCCGTTTATGTTCGCTCGGTAAGGTTTCCAAAGAGAAAT
260 CGGCACGTGAACAAGCTGGATCAAAGGCCGTTTATGTTCGCTCGGTAAGGTTTCCAAAGAGAAAT
326 AAATTTTTCTTCTTCTTTCGAAAAATTTTTTGGGATCATCGGTTGAAGTAAGTATTAAGTCTTAG
325 AAATTTTTCTTCTTCTTTCGAAAAATTTTTTGGGATCATCGGTTGAAGTAAGTATTAAGTCTTAG
391 TACGTATGACGTATACGATCATTATGTTGGCAACAATGCACCGGATCCAATGAGATGTGGCTTGT
390 TACGTATGACGTATACGATCA-TATGTTGGCAACAATGCACCGGATCCAATGAGATGTGGCTTGT
456 A
454 A
* * *
457 TAGATTTATCATGCAAAAACC-ATAGGGTGCGGTCATACCGGCACTAATGCACCGGAT-CCATCA
1 TAGATTTATCATGCAAAGACCAAT-GGGTGCGATCATACCAGCACTAATGCACCGGATCCCATCA
* * * *
520 GAACTTCGCAGTTAAGTGTGCTTGGGCTAGAGTAGTACTAGGATGGGTGACCTCCTGGGAAGTCC
65 GAACTCCGCAGTTAAGCGTGCTTGGGCGAGAGTAGTACTAGGAAGGGTGACCTCCT-GGAAGTCC
*
585 TC-TTGTTGCACCCCTTTTTACA-TTTTTTTTCTTTA-ATTTCTTCTACTTTCGGAATTTCTTAT
129 TCGAT-TTGCACCCCTTTTT-CATTTTTTTTTCTTTAGATTTCTTCTACTTTCGGAATTTCTTAT
*
647 GGGAAGCAATCGGTTAATGTAAGCATTACGTCTTAGTATGGCTGCGAATGAACAACATGTTCGAT
192 GGGAAGCAATCGGTTAATGTAAGCATTAAGTCTTAGTATGGCTGCGAATGAACAACATGTTCGAT
*
712 GAACGGCACGTGAACAAGCTGGATCAAAGGTCGTTTATGTTCGCTCGGTAAGGTTTCCAAAGAGA
257 GAACGGCACGTGAACAAGCTGGATCAAAGGCCGTTTATGTTCGCTCGGTAAGGTTTCCAAAGAGA
*
777 AATAATTTTTTCTT-TTCTCTT-G-AAAATTTTTTGGGTAGTCATCGGTTGAAGTAAGTATTAAG
322 AATAAATTTTTCTTCTTCT-TTCGAAAAATTTTTTGGG-A-TCATCGGTTGAAGTAAGTATTAAG
*
839 TCTTAGTACGTATGGCGTATACGATCATATGTTGGCAACAATGCACCGGATCCAATGAGATGTGG
384 TCTTAGTACGTATGACGTATACGATCATATGTTGGCAACAATGCACCGGATCCAATGAGATGTGG
904 CTTGTA
449 CTTGTA
* *
910 TAGATTCATCATGCAAAGACCAATGGGTGTGATCATACCAGCACTAATGCACCGGATCCCATCAG
1 TAGATTTATCATGCAAAGACCAATGGGTGCGATCATACCAGCACTAATGCACCGGATCCCATCAG
*
975 AACTCCGCAGTAAAGCGTGCTTGGGCGAGAGTAGTA
66 AACTCCGCAGTTAAGCGTGCTTGGGCGAGAGTAGTA
Statistics
Matches: 518, Mismatches: 27, Indels: 20
0.92 0.05 0.04
Matches are distributed among these distances:
452 13 0.03
453 99 0.19
454 258 0.50
455 72 0.14
456 74 0.14
457 2 0.00
ACGTcount: A:0.27, C:0.19, G:0.23, T:0.32
Consensus pattern (454 bp):
TAGATTTATCATGCAAAGACCAATGGGTGCGATCATACCAGCACTAATGCACCGGATCCCATCAG
AACTCCGCAGTTAAGCGTGCTTGGGCGAGAGTAGTACTAGGAAGGGTGACCTCCTGGAAGTCCTC
GATTTGCACCCCTTTTTCATTTTTTTTTCTTTAGATTTCTTCTACTTTCGGAATTTCTTATGGGA
AGCAATCGGTTAATGTAAGCATTAAGTCTTAGTATGGCTGCGAATGAACAACATGTTCGATGAAC
GGCACGTGAACAAGCTGGATCAAAGGCCGTTTATGTTCGCTCGGTAAGGTTTCCAAAGAGAAATA
AATTTTTCTTCTTCTTTCGAAAAATTTTTTGGGATCATCGGTTGAAGTAAGTATTAAGTCTTAGT
ACGTATGACGTATACGATCATATGTTGGCAACAATGCACCGGATCCAATGAGATGTGGCTTGTA
Done.