Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01010575.1 Corchorus olitorius cultivar O-4 contig10607, 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, 1000
Length: 1857
ACGTcount: A:0.35, C:0.18, G:0.15, T:0.32
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:880 original size:324 final size:321
Alignment explanation
Indices: 4--937 Score: 1032
Period size: 326 Copynumber: 2.9 Consensus size: 321
1 CCT
* * * *
4 AAAAACCGTGACGGTTAGTACATGA-TTTCGGCAAAAACT-AACC-CGAATTTTTTTCTGAATTT
1 AAAAACCGTGATGGTTAGTACA-AATTTTCGGCAAAAACTGACCCACAAATTTTTTTCTGAATTT
* * * *
66 TCTGCTA-AGATACTCAG-AAAAATAAATAATTCAACACC-AAAAAATTGACGGGCTTCTCACGC
65 TCTGCCACA-ATACTCAGAAAAAATATATAATTCAACACCGAAAAAATTGACAGGCTTTTCACGC
*
128 TTCTAATATCG-TTTTGCATTTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGAT
129 TTCTAATATCGTTTTTCCATTTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGAT
* * * * * * *
192 GCTCGTAAAAACAAATCGC-TACATCGAATTTGGCTGGGAATTGGTTCGATGAATATAGGTGTTT
194 GCTCGTAAAAACAAATC-CTTAAATCCAATGTGGCTGAGATTTGGTTCGATGAATATAGATATTT
* * * * * * *
256 CAAGGAGTCTTTACGCCAAAAATCATGCAAAACTGAGCCGGGACCCCGGAATGTGTTTTTAGCA
258 AAAGGAGTCTTTACGCCAAAAACCATCCAAAACTGAGCAGGGACACCGAAACGTGTTTTTAGCA
* * * * *
320 AGAAAACCGTGATACGGTTTCAACTA-AAATTTT--GAAAAAATTGACCCGA-AAAGTTTTTCCT
1 A-AAAACCGTGAT--GG-TT--AGTACAAATTTTCGGCAAAAACTGACCC-ACAAATTTTTTTCT
* * * ** * * * *
381 CAATTATTTTGCGACAATTGTCAGAAAAAATATATAATTCAA-TCGGAAAAAAATTGAAAGGTTT
59 GAATT-TTCTGCCACAATACTCAGAAAAAATATATAATTCAACACCG-AAAAAATTGACAGGCTT
* * * * * *
445 TTCTCGCTTCTAATATCATTTTTCCATTTTTTTTCCAAATTTATTTCAAATTAAATAGAAACAAG
122 TTCACGCTTCTAATATCGTTTTTCCA-TTTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAG
* * * *
510 ATACATATGCTCGTAAAAATAAATCCTTAAATCCAATGTGGCTGAGATTTGGTTAGATGAATATA
186 ATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGGTTCGATGAATATA
* * *
575 GATATTTAAAGGAGTCTTTATGCCAAAACCCATCCAAAACTGAGCAGGGGCACCGAAACGTGTTT
251 GATATTTAAAGGAGTCTTTACGCCAAAAACCATCCAAAACTGAGCAGGGACACCGAAACGTGTTT
*
640 TTAGCCC
316 TTAG-CA
* *
647 AAAAACTGTGATGGTTAGTACACATTTTCGGCTAAAAACTGACCCACAAATTTTTTTCTTGAATT
1 AAAAACCGTGATGGTTAGTACAAATTTTCGGC-AAAAACTGACCCACAAATTTTTTTC-TGAATT
* * **
712 TTCCGCCACAATACTCAGAAAAAATATATAATTCAACACCGAAAATATTGACAGGCTTTTCACTA
64 TTCTGCCACAATACTCAGAAAAAATATATAATTCAACACCGAAAAAATTGACAGGCTTTTCACGC
* *
777 TTGTAATATCGTTTTTCCATTTTTTTCCGAATTAATTTCTAATTAAATCGAAAGAAGATTCAGAT
129 TTCTAATATCGTTTTTCCATTTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGAT
* *
842 GCTCGTAAAAACAAATCCTTATATCCAATGTCGCTGAGATTTGGTTCGATGAATATAGATATTTC
194 GCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGGTTCGATGAATATAGATATTT-
* * *
907 AAA-GAGGTCTTTGCCCCAAAAACCATGCAAA
258 AAAGGA-GTCTTTACGCCAAAAACCATCCAAA
938 TCATAGTCGG
Statistics
Matches: 501, Mismatches: 89, Indels: 47
0.79 0.14 0.07
Matches are distributed among these distances:
316 1 0.00
317 10 0.02
319 9 0.02
320 6 0.01
321 20 0.04
322 22 0.04
323 19 0.04
324 134 0.27
325 116 0.23
326 162 0.32
327 2 0.00
ACGTcount: A:0.36, C:0.17, G:0.15, T:0.32
Consensus pattern (321 bp):
AAAAACCGTGATGGTTAGTACAAATTTTCGGCAAAAACTGACCCACAAATTTTTTTCTGAATTTT
CTGCCACAATACTCAGAAAAAATATATAATTCAACACCGAAAAAATTGACAGGCTTTTCACGCTT
CTAATATCGTTTTTCCATTTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGC
TCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGGTTCGATGAATATAGATATTTAAA
GGAGTCTTTACGCCAAAAACCATCCAAAACTGAGCAGGGACACCGAAACGTGTTTTTAGCA
Done.