Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019332.1 Corchorus olitorius cultivar O-4 contig19365, 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: 18002
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Found at i:9955 original size:436 final size:438
Alignment explanation
Indices: 9098--9957 Score: 1085
Period size: 436 Copynumber: 2.0 Consensus size: 438
9088 TTAAATTGAG
* *
9098 TAAGATAGAATTTGTAAAGGACTAAATAGCATAAAATAAAAAAGTATAAGGGTGATTTAATAACT
1 TAAGATAGAATTTGTAAAGGACTAAATAGCATAAAATAAAAAAGTATAAGGGTCATTTAATAAAT
*
9163 AATTCAAATAAGAAAATATCTGTTAATTAATGGAGATCTTGAAATATAAAAAATTCCCTTTTGAA
66 AATTCAAATAAGAAAATA-CTGTTAATTAATGGAGATCTTGAAACATAAAAAATTCCCTTTTGAA
* * * * * * * *
9228 TACTTTATGAAACTCGTATATTAAATTAATTTCGGGTTCTTCATGAAAGTCGTAGATTATACAAT
130 CACTTAACGAAACTCGTAGATCAAATTAATTTCGGGTCCTTCATGAAAGTCGTAAATCATACAAT
* * * ***
9293 AACCTTTTAACCGACACTTTAATAACTTTAATTGGACATGTGGATCAAAAATTATATGGTATTAA
195 AACCTTTTAACCGACACTTCAATAACTTCAATCGGACATGTGGATCAAAAATTATACAATATTAA
* * * * * **
9358 ATAGACCAACAATCGAAACGACCAAATTTAGGAAGCATTTTTTTGAATTGACATAAAAATTTGCT
260 ATAGACCAACAATCAAAACCACAAAATTTAGGAAGCAATTTTTAGAATAAACATAAAAATTTGCT
** * *
9423 TTTGAGTCCTTCATGAAAGTTGTAGATCATGAAATTACCTTTTAATAGACACATGAATCAACTTC
325 TTTGAGTCCTAAATGAAAATTGTAGATCATGAAATTACCTTTTAATAGACACATGAATCAACTTA
9488 ATTGGACAAATAGAAAAAAGAATAAAAAAATAAAGCTTAAACGTTAGAT
390 ATTGGACAAATAGAAAAAAGAATAAAAAAATAAAGCTTAAACGTTAGAT
* * * * * *
9537 TAAGATAGAATTTGTAAA-GAGCTAAGTAGTATAAAGTAGAAAAGTATGAGGGTCATTTGATAAA
1 TAAGATAGAATTTGTAAAGGA-CTAAATAGCATAAAATAAAAAAGTATAAGGGTCATTTAATAAA
**
9601 TAATTCAAATAAG-AAA-A-TGTTTGTTAATGGAGATCTTGAAACAT-AAAAATTCCCTTTTGAA
65 TAATTCAAATAAGAAAATACTGTTAATTAATGGAGATCTTGAAACATAAAAAATTCCCTTTTGAA
* * * * *
9662 CCCTTAACGAAACTCGTAGGTCAAATTTAGCTTTTGGGTCCTTCATGAAAGTCGTAAATCATGCA
130 CACTTAACGAAACTCGTAGATCAAA-TTA-ATTTCGGGTCCTTCATGAAAGTCGTAAATCATACA
* *
9727 ATAACCTTTTAACTGACACTTCAATAACTTCAATCGGAGATGTGGA-CAAAAAATTATACAATAT
193 ATAACCTTTTAACCGACACTTCAATAACTTCAATCGGACATGTGGATC-AAAAATTATACAATAT
** *
9791 TAAATTA-ACCGGCAATCAAAACCACAAAATTTCA-GAAGCAATTTTTAGAATCAAAACATTAAA
257 TAAA-TAGACCAACAATCAAAACCACAAAATTT-AGGAAGCAATTTTTAGAAT--AAACATAAAA
* * *
9854 A-TTGACTTTTGAGTTCTAAATGAAAATTGTAGATCATGAAATTACCTTTTAATAGACACTTTAA
318 ATTTG-CTTTTGAGTCCTAAATGAAAATTGTAGATCATGAAATTACCTTTTAATAGACACATGAA
* * *
9918 TCATCTTAATTGGATAAATAG-AAAAA-AATACAAAAATAAA
382 TCAACTTAATTGGACAAATAGAAAAAAGAATAAAAAAATAAA
9958 AGCGAACGCG
Statistics
Matches: 360, Mismatches: 52, Indels: 21
0.83 0.12 0.05
Matches are distributed among these distances:
434 35 0.10
435 28 0.08
436 135 0.38
437 12 0.03
438 84 0.23
439 66 0.18
ACGTcount: A:0.43, C:0.12, G:0.14, T:0.31
Consensus pattern (438 bp):
TAAGATAGAATTTGTAAAGGACTAAATAGCATAAAATAAAAAAGTATAAGGGTCATTTAATAAAT
AATTCAAATAAGAAAATACTGTTAATTAATGGAGATCTTGAAACATAAAAAATTCCCTTTTGAAC
ACTTAACGAAACTCGTAGATCAAATTAATTTCGGGTCCTTCATGAAAGTCGTAAATCATACAATA
ACCTTTTAACCGACACTTCAATAACTTCAATCGGACATGTGGATCAAAAATTATACAATATTAAA
TAGACCAACAATCAAAACCACAAAATTTAGGAAGCAATTTTTAGAATAAACATAAAAATTTGCTT
TTGAGTCCTAAATGAAAATTGTAGATCATGAAATTACCTTTTAATAGACACATGAATCAACTTAA
TTGGACAAATAGAAAAAAGAATAAAAAAATAAAGCTTAAACGTTAGAT
Found at i:16899 original size:1 final size:1
Alignment explanation
Indices: 16893--16922 Score: 51
Period size: 1 Copynumber: 30.0 Consensus size: 1
16883 TGCGATCTGG
*
16893 TTTTTTTTTTGTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
16923 CCGGTATTCC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:0.00, C:0.00, G:0.03, T:0.97
Consensus pattern (1 bp):
T
Done.