Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011976.1 Corchorus olitorius cultivar O-4 contig12009, 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: 11042
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31
Found at i:4457 original size:438 final size:435
Alignment explanation
Indices: 3623--4630 Score: 1211
Period size: 438 Copynumber: 2.3 Consensus size: 435
3613 AAAATTTCAA
* *
3623 AAGCATTTTTTAGAATTGAAACATAAAAATTAGCTTTTGAGTCTTTCATGAAAGTTGCAGATCAT
1 AAGCATTTTTTAGAATTGAAACATAAAAATTAGCTTTTGAGTCCTTCATGAAAGTTGTAGATCAT
* * * * *
3688 AAAATTACCTTTTAATAGACACCTGAATTACCTTAATTGGACACATAGAACAAAGAAAATAAAAA
66 GAAATTACCTTTTAATAGACACATGAATCACTTTAATTGGACAAATAGAACAAAG--AAT---AA
* * * *
3753 AAAAATGAAGTGTTAAATCGAGTAAGATATAATTTGTAAAGGACTAAGTAGCATAAAATGAAAAA
126 AAAAATAAAGTCTTAAATCGAGTAAGATAGAATTTGTAAAGAACTAAGTAGCATAAAATGAAAAA
* * * *
3818 GTATGAGGGTGATTTGATAACTAATTAAAATCAGAAAATATTTGTTAATGGAGATCTTAAAACAT
191 GTATGAGGGTCATTTGATAAATAATCAAAATAAGAAAATATTTGTTAATGGAGATCTTAAAACAT
* * * * * *
3883 AAAAATTCCCTTTTGAACTCTTCATGAAATTTATAGATCAAATTAACTTTCGGGTTATTCATGAA
256 AAAAATTCCCTTTTGAACCCTTCACGAAACTCATAGATCAAATTAACTTTCGGATCATTCATGAA
* * * * * * * * *
3948 AGTCGTAGATCATACAGTAACCTTTTAACCGACAGTTGAATAACTTTAATTGGACATGTGGATCG
321 AGTCGTAAATCACACAATAACCATTTAACCGACACTTCAATAACTTCAATCGGACATGTGGATCA
* * *
4013 AAAATTATATGGTATTAAA-TAGACCAACAATCAAAACGACCAAA-TTTAGG
386 AAAATTATACGATATTAAATTA-ACCAACAATCAAAACCA-CAAACTTTAGG
* * * *
4063 AAGCATTTTTTTTGAATTGAAACATAAAAATTTGCTTTTGAGTCCATCATGAAAGTTATAGATCA
1 AAGCA-TTTTTTAGAATTGAAACATAAAAATTAGCTTTTGAGTCCTTCATGAAAGTTGTAGATCA
* *
4128 TGAAATTACCTTTTGATAGACACATGAATCAATTTAATTGGACAAATAGAACAAAGAATAAAAAA
65 TGAAATTACCTTTTAATAGACACATGAATCACTTTAATTGGACAAATAGAACAAAGAATAAAAAA
* *
4193 ATAAAG-CTTAAA-CGTTAGATTAAGATAGAATTTGTAAAGAACTAAGTAGTATAAAGT-AGAAA
130 ATAAAGTCTTAAATCG--AG--TAAGATAGAATTTGTAAAGAACTAAGTAGCATAAAATGA-AAA
* * *
4255 AGTATGAGGGTCATTTGATAAATAATCCAAATAAGAAAATGTTTGTTAATGGAGATCTTGAAACA
190 AGTATGAGGGTCATTTGATAAATAATCAAAATAAGAAAATATTTGTTAATGGAGATCTTAAAACA
* * *
4320 TAAAAATTCCCTTTTGAACCCTTCACGAAACTCGTAGATCAAATTTAGCTTTCGGATCCTT-ATG
255 TAAAAATTCCCTTTTGAACCCTTCACGAAACTCATAGATCAAA-TTAACTTTCGGATCATTCATG
*
4384 AAAGTCGTAAATCACGCAATAACCATTTAACCGACACTTCAATAACTTCAATCGGACATGTGGA-
319 AAAGTCGTAAATCACACAATAACCATTTAACCGACACTTCAATAACTTCAATCGGACATGTGGAT
** *
4448 CAAAAAATTATACGATATTAAATTAACCGGCAATCAAAACCACAAACTTTCGG
384 C-AAAAATTATACGATATTAAATTAACCAACAATCAAAACCACAAACTTTAGG
** * * * ** * * *
4501 AAGCATTTTTTAGAATCAAAACATTATAATTGGCTTTCAAGTTCTTAATGAAAATTGTAGATCAT
1 AAGCATTTTTTAGAATTGAAACATAAAAATTAGCTTTTGAGTCCTTCATGAAAGTTGTAGATCAT
* * * * * *
4566 GAAATAACCTTTTAATAGACACTTGAATCACCTTATAATCGGATAAATAGAAAAAAAAATAAAAA
66 GAAATTACCTTTTAATAGACACATGAATCA-CTT-TAATTGGACAAATAGAACAAAGAATAAAAA
4631 TAAAAGCCAA
Statistics
Matches: 484, Mismatches: 72, Indels: 25
0.83 0.12 0.04
Matches are distributed among these distances:
434 2 0.00
435 5 0.01
436 13 0.03
437 80 0.17
438 233 0.48
439 44 0.09
440 5 0.01
441 102 0.21
ACGTcount: A:0.43, C:0.13, G:0.14, T:0.30
Consensus pattern (435 bp):
AAGCATTTTTTAGAATTGAAACATAAAAATTAGCTTTTGAGTCCTTCATGAAAGTTGTAGATCAT
GAAATTACCTTTTAATAGACACATGAATCACTTTAATTGGACAAATAGAACAAAGAATAAAAAAA
TAAAGTCTTAAATCGAGTAAGATAGAATTTGTAAAGAACTAAGTAGCATAAAATGAAAAAGTATG
AGGGTCATTTGATAAATAATCAAAATAAGAAAATATTTGTTAATGGAGATCTTAAAACATAAAAA
TTCCCTTTTGAACCCTTCACGAAACTCATAGATCAAATTAACTTTCGGATCATTCATGAAAGTCG
TAAATCACACAATAACCATTTAACCGACACTTCAATAACTTCAATCGGACATGTGGATCAAAAAT
TATACGATATTAAATTAACCAACAATCAAAACCACAAACTTTAGG
Done.