Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01009809.1 Corchorus olitorius cultivar O-4 contig09841, 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: 4445
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32
Found at i:4269 original size:327 final size:330
Alignment explanation
Indices: 3513--4444 Score: 1134
Period size: 332 Copynumber: 2.8 Consensus size: 330
3503 TATAATATTG
* * * * * *
3513 TTTTTCCTATTTTTTTCGAATTAATTTATAATTGAATTGAAACAAGATGCAGATGCTCGTAAAAA
1 TTTTTCCTATTTTTTTCAAATTAATTTATAATTAAATCGAAACAAGATTCAAATGTTCGTAAAAA
*
3578 CAAATCCTTAAATCCAATATGGCTAAGATTTGGTTAGATGAATAT--ATATATTTCAAGGAGTCT
66 CAAATCCTTAAATCCAATGTGGCTAAGATTTGGTTAGATGAATATAGATATATTT-AAGGAGTCT
* * ** *
3641 TGTCACCAAAAATCATGCAAAACTGAGCC--GGGCCCCGGAACACGTTTTTAG-CTGAAAACTGT
130 TGCCACCAAAAATCATGCAAAACTGA-CCTGGGGCCCCGGAACGCGTTTTTAGCCAAAAAACCGT
* * * *
3703 GATAGTGTACATGATTTCGGCTAAAATTTTGCAAATATTGACCCGAAAGATTTTTCCTCAGTTTC
194 GAT-G-GTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAATATTTTTCCTCAATTTC
** * * *
3768 TAGTGAAAATACTCATAAAAAATATATAATTCAATGCCAAACAAATTGAAAACCTTTTTCACGCC
257 TAGCCACAATACTCATAAAAAATATATAATTCAACGCC-AACAAATTGAAAACCTTTCTCACGCC
* *
3833 TTTAATATCG
321 TTTAAAATCA
* * * * *
3843 TTTTTCCAATTTTATTTCCAAATTAATTTCTGATTAAATCGAAACAAGATTTAAATACTT-GTAA
1 TTTTTCCTATTTT-TTT-CAAATTAATTTATAATTAAATCGAAACAAGATTCAAAT-GTTCGTAA
* * *
3907 AAACAAATCCTTAAATACAATGTGGCTCAGATTTGGTTAGATTAATATAGATATATTTAAGGAGT
63 AAACAAATCCTTAAATCCAATGTGGCTAAGATTTGGTTAGATGAATATAGATATATTTAAGGAGT
* * * * *
3972 CTTGGCGCTAAAAAT-AGTGCAAAACTGACCTGGGGCCCCGGAATGCATTTTTAGCCAAAAAACC
128 CTTGCCACCAAAAATCA-TGCAAAACTGACCTGGGGCCCCGGAACGCGTTTTTAGCCAAAAAACC
* * *
4036 GCGATGATACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCAAAATATTTTT-CTCAATTTC
192 GTGATGGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAATATTTTTCCTCAATTTC
* ***
4100 TAGCCACAATACTCATAAAAAATATATAATTCAACGCC-AGAAATTGAAGGGC-TTCTCACG-CT
257 TAGCCACAATACTCATAAAAAATATATAATTCAACGCCAACAAATTGAAAACCTTTCTCACGCCT
4162 TCTAAAATCA
322 T-TAAAATCA
*
4172 TTTTTCCTATTTTTTTCAAATTAATTTATAATTAAATCGAAACATGATTCAAATGTTCGTAAAAA
1 TTTTTCCTATTTTTTTCAAATTAATTTATAATTAAATCGAAACAAGATTCAAATGTTCGTAAAAA
* * * *
4237 CAAATCCTTAAATCCAATGTGCCTAAGATTTGGTTCGATGAATATAGATAT-TTCAAGGA-TTTT
66 CAAATCCTTAAATCCAATGTGGCTAAGATTTGGTTAGATGAATATAGATATATTTAAGGAGTCTT
* * * * * *
4300 CGCCACCAAATATCATGCAAAACTGGCATGAGCCCCCGGAACGCGTTTTTAGCCAAAAAATCGTG
131 -GCCACCAAAAATCATGCAAAACTGACCTGGGGCCCCGGAACGCGTTTTTAGCCAAAAAACCGTG
* * * * *
4365 ATGGTAAACGATTTCGGCTAAAATTTTGCAAAAGTTGACCCGAAATATTTTTCCTTAATTTTTTG
195 ATGGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAATATTTTTCCTCAATTTCTAG
*
4430 CCACAATAATCATAA
260 CCACAATACTCATAA
4445 T
Statistics
Matches: 513, Mismatches: 75, Indels: 31
0.83 0.12 0.05
Matches are distributed among these distances:
325 3 0.01
326 107 0.21
327 111 0.22
328 6 0.01
329 25 0.05
330 22 0.04
331 3 0.01
332 123 0.24
333 75 0.15
334 28 0.05
335 10 0.02
ACGTcount: A:0.36, C:0.17, G:0.14, T:0.33
Consensus pattern (330 bp):
TTTTTCCTATTTTTTTCAAATTAATTTATAATTAAATCGAAACAAGATTCAAATGTTCGTAAAAA
CAAATCCTTAAATCCAATGTGGCTAAGATTTGGTTAGATGAATATAGATATATTTAAGGAGTCTT
GCCACCAAAAATCATGCAAAACTGACCTGGGGCCCCGGAACGCGTTTTTAGCCAAAAAACCGTGA
TGGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAATATTTTTCCTCAATTTCTAGC
CACAATACTCATAAAAAATATATAATTCAACGCCAACAAATTGAAAACCTTTCTCACGCCTTTAA
AATCA
Done.