Locus 5746

Sequence ID 2R_DroMel_CAF1
Location 18,198,682 – 18,198,816
Length 134
Max. P 0.844998
window9201 window9202

overview

Window 1

Location 18,198,682 – 18,198,780
Length 98
Sequences 6
Columns 107
Reading direction reverse
Mean pairwise identity 81.12
Mean single sequence MFE -28.02
Consensus MFE -19.90
Energy contribution -19.98
Covariance contribution 0.09
Combinations/Pair 1.24
Mean z-score -1.39
Structure conservation index 0.71
SVM decision value 0.17
SVM RNA-class probability 0.617831
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 18198682 98 - 20766785
UAUGCACUUCGAAUUCGCUGGGCUGGCCCAAACAUCAUUAUAUGUGCGUGGGCCAUUUCCCUCAUCCUCAGCUGCCUCA---------UCUGCCCACGGAGAUUGCA
..(((((((((.....((((((.(((((((.((((......))))...)))))))...........)))))).((....---------...))...)))))..)))) ( -29.40)
>DroSec_CAF1 23795 98 - 1
UAUGCACUUCGAAUUCGCUGGGCUGGCUCAUACAUCGGUAUAUCUGCGUGGGCCAUUUCCCUCAUCCUCAGCUGCCUCA---------UCUGCCCACGGAGAUUGCA
..(((((((((.....((((((.((((((((....(((.....))).))))))))...........)))))).((....---------...))...)))))..)))) ( -25.10)
>DroSim_CAF1 25500 98 - 1
UAUGCACUUUGAAUUCGCUGGGCUGGCCCAAACAUCGGUAUAUCUGCGUGGGCCAUUUCCCUCAUCCUCAGCUGCCUCA---------UCUGCCCACGGAGAUUGCA
..((((.......((((.((((((((((((.....(((.....)))..)))))))..............((.((...))---------.)))))))))))...)))) ( -26.60)
>DroEre_CAF1 24439 98 - 1
UAUGCACUUCGAAUUCGCUGGGCUGGCCCAAACAUCGCAAUGGCUGCGUGGGCCAUUUCCCUCAUCCUCAGCUGCCUCA---------UCUGCCCACGAAGAUUGCA
..(((((((((.....((((((.(((((((.....((((.....)))))))))))...........)))))).((....---------...))...)))))..)))) ( -30.10)
>DroYak_CAF1 25262 107 - 1
UAUGCACUUCAAAUUCGCUGGGCUGACCCAAACAUGGUUAUAUCUGCGUGGGCCAUUUCCCUCAUCCUCAGCUGCCUCAUUUGCCUCGUCUGCCCACGGAGAUUGCA
..((((..((...((((.(((((.(((.((((...(((.....(((.(((((........)))))...)))..)))...))))....))).))))))))))).)))) ( -26.90)
>DroPer_CAF1 23306 86 - 1
UAUACAGAUGGAAUCUUCUGGGCUGGCCCAAGCCUCAAGUUUGCUGCGUGGGCCU--CCCCUC---UCUAG-----UCA---------UCUGCCCACAGCCA--GCC
....((((........))))(((((((.(((((.....)))))....((((((..--......---.....-----...---------...)))))).))))--))) ( -30.01)
>consensus
UAUGCACUUCGAAUUCGCUGGGCUGGCCCAAACAUCGGUAUAUCUGCGUGGGCCAUUUCCCUCAUCCUCAGCUGCCUCA_________UCUGCCCACGGAGAUUGCA
...(((..((...((((.((((((((((((..((..........))..))))))).....((.......))....................))))))))))).))). (-19.90 = -19.98 +   0.09)

alignment

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secondary structure

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dotplot

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Window 2

Location 18,198,713 – 18,198,816
Length 103
Sequences 6
Columns 103
Reading direction forward
Mean pairwise identity 81.17
Mean single sequence MFE -34.48
Consensus MFE -24.95
Energy contribution -26.32
Covariance contribution 1.36
Combinations/Pair 1.12
Mean z-score -2.00
Structure conservation index 0.72
SVM decision value 0.77
SVM RNA-class probability 0.844998
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 18198713 103 + 20766785
GGAUGAGGGAAAUGGCCCACGCACAUAUAAUGAUGUUUGGGCCAGCCCAGCGAAUUCGAAGUGCAUAGCUACUUGUCUUAUCUGCGGCCAGCAGAUACAAGAU
......(((...(((((((.((((((...))).))).))))))).)))(((................))).(((((...((((((.....))))))))))).. ( -36.69)
>DroPse_CAF1 23388 98 + 1
A---GAGGGG--AGGCCCACGCAGCAAGCUUGAGGCUUGGGCCAGCCCAGAAGAUUCCAUCUGUAUAGCUACUCGUCUUGCCUACGGAUAUCAGAUUCAAGAU
.---..(((.--.((((((.((..((....))..)).))))))..))).(((......(((((((..((..........)).)))))))......)))..... ( -31.00)
>DroSim_CAF1 25531 103 + 1
GGAUGAGGGAAAUGGCCCACGCAGAUAUACCGAUGUUUGGGCCAGCCCAGCGAAUUCAAAGUGCAUAGCUACUUGUCUUAUCUGCGGCCAGCAGAUACAAGAU
......(((...(((((((.(((..........))).))))))).)))(((................))).(((((...((((((.....))))))))))).. ( -35.89)
>DroEre_CAF1 24470 103 + 1
GGAUGAGGGAAAUGGCCCACGCAGCCAUUGCGAUGUUUGGGCCAGCCCAGCGAAUUCGAAGUGCAUAGCUACUUGUCUUAUCUGCGGCCAGCAGAUACAAGAU
......(((...(((((((.(((((....))..))).))))))).)))(((................))).(((((...((((((.....))))))))))).. ( -36.59)
>DroYak_CAF1 25302 103 + 1
GGAUGAGGGAAAUGGCCCACGCAGAUAUAACCAUGUUUGGGUCAGCCCAGCGAAUUUGAAGUGCAUAGCUACUUGUCUUAUCUGCGGCCAGCAGAUACAAGAU
......(((...(((((((.(((..........))).))))))).)))(((.....((.....))..))).(((((...((((((.....))))))))))).. ( -33.20)
>DroPer_CAF1 23330 98 + 1
A---GAGGGG--AGGCCCACGCAGCAAACUUGAGGCUUGGGCCAGCCCAGAAGAUUCCAUCUGUAUAGCUACUCGUCUUGCCUACGGAUAUCAGAAUCAAGAU
.---..(((.--.((((((.((..((....))..)).))))))..)))....(((((.(((((((..((..........)).)))))))....)))))..... ( -33.50)
>consensus
GGAUGAGGGAAAUGGCCCACGCAGAUAUAACGAUGUUUGGGCCAGCCCAGCGAAUUCGAAGUGCAUAGCUACUUGUCUUAUCUGCGGCCAGCAGAUACAAGAU
......(((...(((((((.(((..........))).))))))).)))..........................(((((((((((.....))))))..))))) (-24.95 = -26.32 +   1.36)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:53:19 2006