Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014653.1 Corchorus olitorius cultivar O-4 contig14686, 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: 11167
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32
Found at i:2166 original size:21 final size:21
Alignment explanation
Indices: 2140--2185 Score: 83
Period size: 21 Copynumber: 2.2 Consensus size: 21
2130 CTCTTGTCGA
2140 CTTGCTTTAGTCGACTATCCT
1 CTTGCTTTAGTCGACTATCCT
*
2161 CTTGCTTTAGTCGACTATTCT
1 CTTGCTTTAGTCGACTATCCT
2182 CTTG
1 CTTG
2186 AGCAAGGCCT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.13, C:0.26, G:0.15, T:0.46
Consensus pattern (21 bp):
CTTGCTTTAGTCGACTATCCT
Found at i:10391 original size:332 final size:331
Alignment explanation
Indices: 9713--11167 Score: 2064
Period size: 331 Copynumber: 4.4 Consensus size: 331
9703 GGCTTAATCA
*
9713 GCTTCTAATATCGTTTTTCCTAA-TTTTCCGAATTAATATCTAATTAAATGGAAATCAAATTTTG
1 GCTTCTAATATCGTTTTTCCTAATTTTTCCGAATTAATATCTAATTAAATGGAAATCAGATTTTG
* * *
9777 GTTCTCATAAAAATAAATGCATAAATCCAATGTGGCTGAGATTTGTTTAGAAGAATATAGATATT
66 ATTCTCGTAAAAACAAAT-CATAAATCCAATGTGGCTGAGATTTGTTTAGAAGAATATAGATATT
* * * * * *
9842 GCAATGAGTCTGGGTACCAAAAATCATGCGAAATAGAGCCGGGACCTCGGAATGCGTTTTTAGCC
130 GCAATGAGTCTGGGCACCAAAAATCATGCAAAATAGAGACGGGACCCCAGAACGCGTTTTTAGCC
* * * *
9907 AAAAACCGTGATGGTTAGTACATGATTTCGGCGAAAATTTTGCGAAAACTGGCCCGACAAATTTT
195 AAAAACCGTGATGGTTAGTACATGATTTCGGCTAAAATTTTGCAAAAACTGACCCGACAAACTTT
* * * *
9972 TTCTCAATTTTTGGCCAAAATACTCATGAAAATTATATAATTTAACGCCAAAACGATTGAAGGGA
260 TTCTCAAATTTTGGCCACAATACTCATGAAAATTATATAATTCAACGCCAAAATGATTGAAGGGA
10037 TTTTCAC
325 TTTTCAC
* * * *
10044 TCTTCTAAGATCGTTTTTCCTAATTTTTCCGAATTAATATCTAATTAAATGGATATCAGATTTAG
1 GCTTCTAATATCGTTTTTCCTAATTTTTCCGAATTAATATCTAATTAAATGGAAATCAGATTTTG
* * *
10109 ATTCTCGT-AAAACAAATCTATAAATCCAATGTGGCTAAGATTTGTTTCGAAGATTATAGATATT
66 ATTCTCGTAAAAACAAATC-ATAAATCCAATGTGGCTGAGATTTGTTTAGAAGAATATAGATATT
* * * *
10173 ACAATGAGTCTGGGCACTAAAAATCATGCAAAATAGAGCCGGGGCCCCAGAACGCGTTTTTAGCC
130 GCAATGAGTCTGGGCACCAAAAATCATGCAAAATAGAGACGGGACCCCAGAACGCGTTTTTAGCC
* * * * * **
10238 AAAAAACTGTGGTGGTTAGTACA-GATTTCGGCAAAAAATTTGGCGAAAACTGACCCGACAAGTT
195 -AAAAACCGTGATGGTTAGTACATGATTTCGGC-TAAAATTTTGCAAAAACTGACCCGACAAACT
* * * * *
10302 TTTTCTCAAATTTTGGACACAATACTCTTAGAAAA-TATATAATTCTACGACAAAATAATTGAAG
258 TTTTCTCAAATTTTGGCCACAATACTCAT-GAAAATTATATAATTCAACGCCAAAATGATTGAAG
* *
10366 GGCTTTTCTC
322 GGATTTTCAC
* *
10376 GCTTCTAATATCGTTTTTCCTATTTTTTCCGAATTAATATCTAATTAAATGGAAATCGGATTTTG
1 GCTTCTAATATCGTTTTTCCTAATTTTTCCGAATTAATATCTAATTAAATGGAAATCAGATTTTG
*
10441 ATTCTCGTTAAAACAAATCCATAAATCCAATGTGGCTGAGATTTGTTTAGAAGAATATAGATATT
66 ATTCTCGTAAAAACAAAT-CATAAATCCAATGTGGCTGAGATTTGTTTAGAAGAATATAGATATT
* * *
10506 GCAATTAGTTTGGGCACCAAAAATCATGCAAAATAGAGACGGGACCCCGGAACGCGTTTTTAGCC
130 GCAATGAGTCTGGGCACCAAAAATCATGCAAAATAGAGACGGGACCCCAGAACGCGTTTTTAGCC
* *
10571 AAAAACCGTGATGGTTAGTACATGAATTCGGCTAAAATTCTGCAAAAACTGACCCGACAAACTTT
195 AAAAACCGTGATGGTTAGTACATGATTTCGGCTAAAATTTTGCAAAAACTGACCCGACAAACTTT
*
10636 TTCTCAATTTTTGGCCACAATACTCATAGAAAA-TATATAATTCAACGCCAAAATGATTGAAGGG
260 TTCTCAAATTTTGGCCACAATACTCAT-GAAAATTATATAATTCAACGCCAAAATGATTGAAGGG
* **
10700 CTTTTGTC
324 ATTTTCAC
* * *
10708 GCTTCTAATATCGTTTTTAC-AATCTTTTCCAAATTAATATCTAATTAAATAGAAATC-GAATTT
1 GCTTCTAATATCGTTTTTCCTAAT-TTTTCCGAATTAATATCTAATTAAATGGAAATCAG-ATTT
* * * * *
10771 AGATTCTCGTAAAAAAAAATCATAAATCCAATTTGGCTGAAATTTGTTTAGAAGTATATAGATAT
64 TGATTCTCGTAAAAACAAATCATAAATCCAATGTGGCTGAGATTTGTTTAGAAGAATATAGATAT
* *
10836 TGCAATGAGTTTGGGCACCAAAAATCATGCAAAATAGAGACGGGACCCCAGAATGCGTTTTTAGC
129 TGCAATGAGTCTGGGCACCAAAAATCATGCAAAATAGAGACGGGACCCCAGAACGCGTTTTTAGC
* * *
10901 CTAAAACCGTGATGGTTAGTACATAATTTCGGCTAAAATTTTGCAAAAACTGGCCCGACAAACTT
194 CAAAAACCGTGATGGTTAGTACATGATTTCGGCTAAAATTTTGCAAAAACTGACCCGACAAACTT
* * *
10966 TTTCTC-AATTTTCTGCCACAATACTCATGAAAATTATATAATTCAACGCCAAAATGATGGAAAG
259 TTTCTCAAATTTT-GGCCACAATACTCATGAAAATTATATAATTCAACGCCAAAATGATTGAAGG
11030 GATTTTCAC
323 GATTTTCAC
** * *
11039 GCTTCTAATATCGTTTTTCCTTTTTTTTCCGAATTAATATCTAATTAAATGGATATCGGATTTTG
1 GCTTCTAATATCGTTTTTCCTAATTTTTCCGAATTAATATCTAATTAAATGGAAATCAGATTTTG
*
11104 ATTCTCGTAAAAACAAATCTATAAATCCAATGTGGCTGAGATTT-TTTAGATGAATATAGATATT
66 ATTCTCGTAAAAACAAATC-ATAAATCCAATGTGGCTGAGATTTGTTTAGAAGAATATAGATATT
Statistics
Matches: 1004, Mismatches: 105, Indels: 30
0.88 0.09 0.03
Matches are distributed among these distances:
330 11 0.01
331 448 0.45
332 422 0.42
333 122 0.12
334 1 0.00
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Consensus pattern (331 bp):
GCTTCTAATATCGTTTTTCCTAATTTTTCCGAATTAATATCTAATTAAATGGAAATCAGATTTTG
ATTCTCGTAAAAACAAATCATAAATCCAATGTGGCTGAGATTTGTTTAGAAGAATATAGATATTG
CAATGAGTCTGGGCACCAAAAATCATGCAAAATAGAGACGGGACCCCAGAACGCGTTTTTAGCCA
AAAACCGTGATGGTTAGTACATGATTTCGGCTAAAATTTTGCAAAAACTGACCCGACAAACTTTT
TCTCAAATTTTGGCCACAATACTCATGAAAATTATATAATTCAACGCCAAAATGATTGAAGGGAT
TTTCAC
Done.