Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01008039.1 Corchorus olitorius cultivar O-4 contig08066, 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, 938
Length: 1564
ACGTcount: A:0.33, C:0.14, G:0.15, T:0.38
Found at i:774 original size:319 final size:320
Alignment explanation
Indices: 7--825 Score: 889
Period size: 329 Copynumber: 2.5 Consensus size: 320
1 GAACCT
* * * * * * ** * *
7 GGGTCATTTTTGCATGATCTTTGCCGCC-AAGACTCTTTGAGATATCCATATTCACCTAATCAAA
1 GGGTCAATTTTGCATGATTTTTGGCGCCGAA-ACTCCTTAAAATATATATATTCATCTAACCAAA
* * * *
71 TCTCAGCTACATTGGATTTAAGAATTTGTTTTTACGAGCATCTGATTCTTGTTTCGTTTTAATTA
65 TCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTA
* * * * * * *
136 GAAATTAATTCAGAAAAATATAAAAAATGATATTAAAAGCGTGAAAAGTCCTCCAATCTTTTTGG
130 GAAATTAATT-TGAAAAAAATGAAAAACGATATTAGAAGCGCGAAAAGCCCTCCAATCTTTTTGG
*
201 CTTTAAATTATATATACTTTATGAGTATTTAGACAAAAATTGAGAAAAAAATTTCAAGTCATTTT
194 CGTTAAATTATATATACTTTATGAGTA-TT-----AAAATTGAGAAAAAAATTTCAAGTCATTTT
*
266 TTGCAAAATTATAGCCGAAATCGTGTACAACCATCACGGTTTTTTGGCTAAAAACGCGTTCCGGG
253 TTGCAAAATTATAGCCGAAATCGTGT--AACCATCACGGTTTTTTAGCTAAAAACGCGTTCCGGG
331 GCCCC
316 GCCCC
* * * * *
336 GGGTCAATTTTGCATGATTTTTGGTGGCGAAATTCCTTGAAATATCTATATTCATCTAACCAAAT
1 GGGTCAATTTTGCATGATTTTTGGCGCCGAAACTCCTTAAAATATATATATTCATCTAACCAAAT
* * * * *
401 CTTAGCCACATTGGATTTAGGGATTTGTTTTTACAAGCATTTGAATCATGTTTCGATTTAATTAG
66 CTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAG
* **
466 AAATTAATTTGAAAAAAATGATAAAACGATATTAGAAGCGCGAGAAGCCCTTTAATCTTTTTGGC
131 AAATTAATTTGAAAAAAATGA-AAAACGATATTAGAAGCGCGAAAAGCCCTCCAATCTTTTTGGC
* * * * *
531 GTTGAATTATATATTC-TTATGAGTA-T-AAATTGAG-AAAATATTTC-GGATCATTTTTTGTAA
195 GTTAAATTATATATACTTTATGAGTATTAAAATTGAGAAAAAAATTTCAAG-TCATTTTTTGCAA
* * * * *
591 AATTTTAGTCGAAATCGTGT-ACCATCACGGTTTTTTAGCTAGAAACGCGTTTCGTGG-CCC
259 AATTATAGCCGAAATCGTGTAACCATCACGGTTTTTTAGCTAAAAACGCGTTCCGGGGCCCC
* * * * *
651 GTGTCAGTTTTGCATGATTTTTTGCGCCTAGACTCCTTAAAAAATATATATATATTCATCTAACC
1 GGGTCAATTTTGCATGATTTTTGGCGCCGAAACTCCTT---AAA-ATATATATATTCATCTAACC
* * * * *
716 AAATCTCAACCATATTGTATTTAAGGATTTGTTTTTACGAGTATCTAAATCTTGTTTCGATTTAA
62 AAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAA
*
781 TCAGAAATTAATTTGGAAATAAAATAGGAAAAACGATATTAGAAG
127 TTAGAAATTAATTT-GAAA-AAAAT--GAAAAACGATATTAGAAG
826 TGTGAAAAAG
Statistics
Matches: 416, Mismatches: 63, Indels: 29
0.82 0.12 0.06
Matches are distributed among these distances:
315 33 0.08
316 33 0.08
318 3 0.01
319 126 0.30
320 12 0.03
321 5 0.01
322 16 0.04
323 2 0.00
326 1 0.00
328 18 0.04
329 165 0.40
330 2 0.00
ACGTcount: A:0.33, C:0.14, G:0.16, T:0.37
Consensus pattern (320 bp):
GGGTCAATTTTGCATGATTTTTGGCGCCGAAACTCCTTAAAATATATATATTCATCTAACCAAAT
CTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAG
AAATTAATTTGAAAAAAATGAAAAACGATATTAGAAGCGCGAAAAGCCCTCCAATCTTTTTGGCG
TTAAATTATATATACTTTATGAGTATTAAAATTGAGAAAAAAATTTCAAGTCATTTTTTGCAAAA
TTATAGCCGAAATCGTGTAACCATCACGGTTTTTTAGCTAAAAACGCGTTCCGGGGCCCC
Done.