Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018161.1 Corchorus olitorius cultivar O-4 contig18194, 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, 778
Length: 1297
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.34
Found at i:796 original size:333 final size:331
Alignment explanation
Indices: 4--935 Score: 1439
Period size: 333 Copynumber: 2.8 Consensus size: 331
1 TGG
* * *
4 ATTTA-TTTTAATT-AATCG-AAC-AGATTCAGATGTTCGT-AAATCAAATTCTTGAATCGAATA
1 ATTTATTTTTAATTGAATCGAAACAAGATTCAGATGTTCGTAAAAACAAATCCTTAAATCGAAT-
* * * *
64 GTGGTTAGGGATATTGGTCTTGATGAATATAGATATTTTAGTGAGTTTTTACGCC-AAAATCATA
65 GTGGCT-GCGATA-T-GACTCGATGAATATAGATA-TTTAGTGAGTTTTTACGCCAAAAATCATA
128 CAAAACTGAGCCGGGGACCCGGAACGCGTTTTTAGCCAAAAACCGTGATAGTTAATATACGATTT
126 CAAAACTGAGCCGGGGACCCGGAACGCGTTTTTAGCCAAAAACCGTGATAGTTAATATACGATTT
* ** * *
193 CGGCTAAAATTTTGCAAAAACTCACCCGGAAAATTTTTCCGCAAATTTTTTGTCACAATACTC-A
191 CGGCTAAAATTTTGCAAAAACTAACCCAAAAAATTTTTCCTCAATTTTTTTGTCACAATACTCAA
257 AAAAATGTATAATTCAATGCCGAAAAATTGAAGGATTTTTCACGCTTCTAATATCATTTTTGTAT
256 AAAAATGTATAATTCAATGCCGAAAAATTGAAGGATTTTTCACGCTTCTAATATCATTTTTGTAT
322 TTTTTTCCTGA
321 TTTTTTCCTGA
* * *
333 ATTTATTTTTAAATGAATCGAAACAAGATTCAGATATTCATAAAAACAAATCCTTAAATCGAATG
1 ATTTATTTTTAATTGAATCGAAACAAGATTCAGATGTTCGTAAAAACAAATCCTTAAATCGAATG
*
398 TGGCTGCGATATGGCTCGATGAATATAGATAATTTAGTGAGTTTTTACGCCAAAAATCATACAAA
66 TGGCTGCGATATGACTCGATGAATATAGAT-ATTTAGTGAGTTTTTACGCCAAAAATCATACAAA
* * *
463 ACTAAGCCGGGGACCCGGAACGCGATTTTAGCCAAAAACAGTGATAGTTAATATACGATTTCGGC
130 ACTGAGCCGGGGACCCGGAACGCGTTTTTAGCCAAAAACCGTGATAGTTAATATACGATTTCGGC
*
528 TAAAATTTTACAAAAACTAACCCAAAAAATTTTTCCTCAATTTTTTTGTCACAATACTCAAAAAA
195 TAAAATTTTGCAAAAACTAACCCAAAAAATTTTTCCTCAATTTTTTTGTCACAATACTCAAAAAA
*
593 ATGTATAATTCAATGCCGAAAAATTGAAGGATTTTTCACGCTTCTAATATCGTTTTTGTATGTTT
260 ATGTATAATTCAATGCCGAAAAATTGAAGGATTTTTCACGCTTCTAATATCATTTTTGTAT-TTT
658 TTTCCTGA
324 TTTCCTGA
666 ATTTATTTTTAATTGAATCGAAACAAGATTCAGATGTTCGTAAAAACAAATCCTTAAATCGAATG
1 ATTTATTTTTAATTGAATCGAAACAAGATTCAGATGTTCGTAAAAACAAATCCTTAAATCGAATG
*
731 TGGCTGTGATATGACTCGATGAATATAGATATTTCAGTGAGTTTTTACGCCAAAAATCATACAAA
66 TGGCTGCGATATGACTCGATGAATATAGATATTT-AGTGAGTTTTTACGCCAAAAATCATACAAA
* * * *
796 ACTGAGCCGGGGACCCGGAACGCGTTTTTAGCCAAAAACCGTGATAGATAACACACGATTTCGTC
130 ACTGAGCCGGGGACCCGGAACGCGTTTTTAGCCAAAAACCGTGATAGTTAATATACGATTTCGGC
* *
861 TAAAATTTTGCAAAAAACTGACCCGAAAAATTTTTTCCTCAATTTTTTTG-CACAATACTCATAA
195 TAAAATTTTGC-AAAAACTAACCC-AAAAAATTTTTCCTCAATTTTTTTGTCACAATACTCA-AA
* *
925 AACATATATAA
257 AAAATGTATAA
936 ACCCTCTGTC
Statistics
Matches: 553, Mismatches: 37, Indels: 20
0.91 0.06 0.03
Matches are distributed among these distances:
329 5 0.01
330 42 0.08
331 135 0.24
332 77 0.14
333 218 0.39
334 41 0.07
335 35 0.06
ACGTcount: A:0.36, C:0.16, G:0.15, T:0.33
Consensus pattern (331 bp):
ATTTATTTTTAATTGAATCGAAACAAGATTCAGATGTTCGTAAAAACAAATCCTTAAATCGAATG
TGGCTGCGATATGACTCGATGAATATAGATATTTAGTGAGTTTTTACGCCAAAAATCATACAAAA
CTGAGCCGGGGACCCGGAACGCGTTTTTAGCCAAAAACCGTGATAGTTAATATACGATTTCGGCT
AAAATTTTGCAAAAACTAACCCAAAAAATTTTTCCTCAATTTTTTTGTCACAATACTCAAAAAAA
TGTATAATTCAATGCCGAAAAATTGAAGGATTTTTCACGCTTCTAATATCATTTTTGTATTTTTT
TCCTGA
Done.