Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01008821.1 Corchorus olitorius cultivar O-4 contig08848, 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: 1011
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.35
Found at i:854 original size:338 final size:317
Alignment explanation
Indices: 36--1011 Score: 933
Period size: 324 Copynumber: 3.0 Consensus size: 317
26 TTTTTGCCAA
* * * *
36 CGAAATCGTGTACTAACTATCACAGTTTTTGGC-AAAAACGCGTTCCGGATTCCCGGCTCAATTT
1 CGAAATCGTGTACTAACCATCACGGTTTTTGGCTAAAAACGCGTTCTGGA-TACCGGCTCAATTT
** * *
100 TGCATGATTTTTGGCGTAAAGACTCCTTGAAATATCTATATTCATCGAACCAAATCTC-TGTCAC
65 TGCATGATTTTTGGCACAAAGACTCCTTGAAATATCTTTATTCATCGAACCAAATCTCAT-CCAC
* * *
164 ATTGTATATAAGGATTTGTTTTTACGAGCATC-CGAACCTTGTTTCGATTTAATTAGAATTTAAT
129 ATTGGATATAAGGATTTGTTTTTACGAGCATCTC-AATCTTGTTTCGATTTAATTAGAA-ATAAT
* * * * *
228 TC-AGAAAAAATGGAAAAACGATATTAGAATTTAGAAGCGTGAAAAGCCCGTCAATATTTTTGGT
192 TCGAAAAAAAATGGAAAAATG--A-T---A-TTAGAAGCGTGAAAAACACGTCAATATTTTTGGC
* * * *
292 GTTGAATTATATATTTTTCTAAATATTTTGCAAAAAATTGAGAAAAACTGTTCGGGTTAGTTTTT
250 GTTAAATTATATATTCTTCTAAATATTTTGAAAAAAATTGAGAAAAACTGTTCGGGTCAGTTTTT
357 AGC
315 AGC
* * * * *
360 CGAAATCATGTACTAACCATCACGATTTTTGGCTAAAAACGCGTT-TCGGATAACGACTCAGTTT
1 CGAAATCGTGTACTAACCATCACGGTTTTTGGCTAAAAACGCGTTCT-GGATACCGGCTCAATTT
** * * * *
424 TAAATGATTTTTGGCAGAAAGACTCCTTGAAATAT-TTATATTCATCTAACAAAATCTCAGCCAC
65 TGCATGATTTTTGGCACAAAGACTCCTTGAAATATCTT-TATTCATCGAACCAAATCTCATCCAC
* * * * *
488 AATGGATTTAAGAATTTGTTTTTACGAGCATCTCAATCTTTGTATCGATTTAATTAGAAACAGAT
129 ATTGGATATAAGGATTTGTTTTTACGAGCATCTCAATC-TTGTTTCGATTTAATTAGAAATA-AT
* * * *
553 TCGGAAAAAAAATTGAAAAATGATATTAGAAGCGTGAAAAACAC-TATAATTTTTTTTTGCGTTA
192 TC-GAAAAAAAATGGAAAAATGATATTAGAAGCGTGAAAAACACGT-CAA-TATTTTTGGCGTTA
* * * *
617 AATTATATATTACTTCTGAGTATTTTGGAAAAAAAAATTGAGGAAAAACTTTTTGGGTCAGTTTT
254 AATTATATATT-CTTCTAAATATTTT-G--AAAAAAATTGA-GAAAAACTGTTCGGGTCAG----
682 TGCAAAATTTTAGC
310 T------TTTTAGC
* *
696 CGAAATCGGTGTACTAACCATCACGGTTTTTGGCTAAAAACGCGTTCTGGAGTGCCGGTTCAATT
1 CGAAATC-GTGTACTAACCATCACGGTTTTTGGCTAAAAACGCGTTCTGGA-TACCGGCTCAATT
* * * *
761 TTGCAGGATTTTTTGCACAAAGACTCCTTGAAATATCTTTGTTCATCGAACCAAATGTCATCCAC
64 TTGCATGATTTTTGGCACAAAGACTCCTTGAAATATCTTTATTCATCGAACCAAATCTCATCCAC
* * *
826 ATTGGATATAAGGATTTCTTTTTACGAGCATGTCAATCTTGTTTTGATTTAATTAGAAATTAATT
129 ATTGGATATAAGGATTTGTTTTTACGAGCATCTCAATCTTGTTTCGATTTAATTAGAAA-TAATT
* * * * * * * * *
891 C-AGAAACAAATGGAAAAATGATATTAAAAGCGTGAAAAGCCCGTCACTCTTTTTGACATTGAAT
193 CGA-AAAAAAATGGAAAAATGATATTAGAAGCGTGAAAAACACGTCAATATTTTTGGCGTTAAAT
* ** * *
955 TATATATTTTTTCTAAATATTACGCAAAAAATTGAGAAAAAAACTTTTCGGGTCAGT
257 TATATA-TTCTTCTAAATATTTTGAAAAAAATTGAG--AAAAACTGTTCGGGTCAGT
Statistics
Matches: 529, Mismatches: 87, Indels: 67
0.77 0.13 0.10
Matches are distributed among these distances:
319 1 0.00
320 19 0.04
321 22 0.04
322 11 0.02
323 2 0.00
324 124 0.23
325 49 0.09
326 16 0.03
327 15 0.03
329 1 0.00
330 1 0.00
331 1 0.00
332 10 0.02
333 17 0.03
334 1 0.00
335 28 0.05
336 51 0.10
337 63 0.12
338 95 0.18
339 2 0.00
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.35
Consensus pattern (317 bp):
CGAAATCGTGTACTAACCATCACGGTTTTTGGCTAAAAACGCGTTCTGGATACCGGCTCAATTTT
GCATGATTTTTGGCACAAAGACTCCTTGAAATATCTTTATTCATCGAACCAAATCTCATCCACAT
TGGATATAAGGATTTGTTTTTACGAGCATCTCAATCTTGTTTCGATTTAATTAGAAATAATTCGA
AAAAAAATGGAAAAATGATATTAGAAGCGTGAAAAACACGTCAATATTTTTGGCGTTAAATTATA
TATTCTTCTAAATATTTTGAAAAAAATTGAGAAAAACTGTTCGGGTCAGTTTTTAGC
Done.