Locus 5433

Sequence ID 2R_DroMel_CAF1
Location 17,487,975 – 17,488,135
Length 160
Max. P 0.998562
window8666 window8667 window8668 window8669

overview

Window 6

Location 17,487,975 – 17,488,095
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 80.97
Mean single sequence MFE -31.05
Consensus MFE -22.45
Energy contribution -23.70
Covariance contribution 1.25
Combinations/Pair 1.00
Mean z-score -1.76
Structure conservation index 0.72
SVM decision value 0.49
SVM RNA-class probability 0.758280
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17487975 120 + 20766785
AUGAUGACGGGAAUAUGUGUGAUCCUAUUAGUUCUCCACUGGCAAAGUGAGAGACUUCAAAUAGCACUCAAGGACUUGUGCUCCUUUCUUAAUCAUGAAGAACGCAACUCCUUGACUUUA
..(((.(((........))).)))((((((((.(((((((.....)))).))))))...)))))...(((((((.(((((.((..(((........))))).))))).)))))))..... ( -30.20)
>DroSec_CAF1 16076 120 + 1
AUGAUGACGGGAAUAUGAGUUAUCCUGUUUGUUCUCCACUGGCAAAGUGAGAGGCUUCAAAUAGCACUCAAGGACUUGUGCUCCUUUCUUAAUUAUGAAGAGCGCAACUCCUUAACUUUG
..((.(((((((.((.....)))))))))...))........((((((..((((((......))).)))(((((.((((((((..(((........))))))))))).))))).)))))) ( -37.50)
>DroSim_CAF1 28393 120 + 1
NNNNNNNNNNNNNNNNNNNAUUCCNUGUUCGUUCUCCACUGGCAAAGUGAGAGGCUUCAAAUAGCGCUCAAGGACUUGUGCUCCUUUCUCAAUUAUGAAGAGCGCAACUCCUUAACUUUG
..........................................((((((..((((((......))).)))(((((.((((((((..(((........))))))))))).))))).)))))) ( -29.80)
>DroYak_CAF1 24288 120 + 1
AUGAUGACUGGAAUAUGUGUGAUCCUGCUAAUUCUCCACUGGCAGAGUGAGAGGCUUCAUAUAGCACUCAAGGAUCUGUGCUCCUUUCUAAAUUAUGAAGAACGCAACGCCUUAGUUUUA
.....((((((.....((((((((((....(((((((...)).)))))..((((((......))).))).))))))((((.((..(((........))))).)))))))).))))))... ( -26.70)
>consensus
AUGAUGACGGGAAUAUGUGUGAUCCUGUUAGUUCUCCACUGGCAAAGUGAGAGGCUUCAAAUAGCACUCAAGGACUUGUGCUCCUUUCUUAAUUAUGAAGAACGCAACUCCUUAACUUUA
.................................(((((((.....)))).)))(((......)))....(((((.((((((((..(((........))))))))))).)))))....... (-22.45 = -23.70 +   1.25)

alignment

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secondary structure

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Window 7

Location 17,487,975 – 17,488,095
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 80.97
Mean single sequence MFE -29.93
Consensus MFE -24.94
Energy contribution -24.62
Covariance contribution -0.31
Combinations/Pair 1.15
Mean z-score -1.57
Structure conservation index 0.83
SVM decision value 0.38
SVM RNA-class probability 0.710991
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17487975 120 - 20766785
UAAAGUCAAGGAGUUGCGUUCUUCAUGAUUAAGAAAGGAGCACAAGUCCUUGAGUGCUAUUUGAAGUCUCUCACUUUGCCAGUGGAGAACUAAUAGGAUCACACAUAUUCCCGUCAUCAU
.....(((((((.(((.(((((((........))..))))).))).)))))))((((((((.....((((.((((.....))))))))...)))))...))).................. ( -32.40)
>DroSec_CAF1 16076 120 - 1
CAAAGUUAAGGAGUUGCGCUCUUCAUAAUUAAGAAAGGAGCACAAGUCCUUGAGUGCUAUUUGAAGCCUCUCACUUUGCCAGUGGAGAACAAACAGGAUAACUCAUAUUCCCGUCAUCAU
...(.(((((((.(((.(((((((........))..))))).))).))))))).)(((......)))(((.((((.....))))))).....((.(((..........))).))...... ( -29.90)
>DroSim_CAF1 28393 120 - 1
CAAAGUUAAGGAGUUGCGCUCUUCAUAAUUGAGAAAGGAGCACAAGUCCUUGAGCGCUAUUUGAAGCCUCUCACUUUGCCAGUGGAGAACGAACANGGAAUNNNNNNNNNNNNNNNNNNN
.....(((((((.(((.((((((((....)))....))))).))).)))))))..(((......)))(((.((((.....)))))))................................. ( -28.70)
>DroYak_CAF1 24288 120 - 1
UAAAACUAAGGCGUUGCGUUCUUCAUAAUUUAGAAAGGAGCACAGAUCCUUGAGUGCUAUAUGAAGCCUCUCACUCUGCCAGUGGAGAAUUAGCAGGAUCACACAUAUUCCAGUCAUCAU
.........(((((((.(((((((((....(((((((((.......)))))(((.(((......))))))....))))...))))))))))))).(((..........))).)))..... ( -28.70)
>consensus
CAAAGUUAAGGAGUUGCGCUCUUCAUAAUUAAGAAAGGAGCACAAGUCCUUGAGUGCUAUUUGAAGCCUCUCACUUUGCCAGUGGAGAACUAACAGGAUAACACAUAUUCCCGUCAUCAU
.....(((((((.(((.(((((((........))..))))).))).)))))))..(((......)))(((.((((.....)))))))................................. (-24.94 = -24.62 +  -0.31)

alignment

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secondary structure

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dotplot

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Window 8

Location 17,488,015 – 17,488,135
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 81.94
Mean single sequence MFE -35.68
Consensus MFE -25.96
Energy contribution -29.65
Covariance contribution 3.69
Combinations/Pair 1.13
Mean z-score -3.38
Structure conservation index 0.73
SVM decision value 3.14
SVM RNA-class probability 0.998562
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17488015 120 + 20766785
GGCAAAGUGAGAGACUUCAAAUAGCACUCAAGGACUUGUGCUCCUUUCUUAAUCAUGAAGAACGCAACUCCUUGACUUUAUCAGAAAACAAGGCCAAUAGAUCCCUCGGAAAAUUGGCUA
.((....((((....))))....))..(((((((.(((((.((..(((........))))).))))).)))))))................(((((((...(((...)))..))))))). ( -29.10)
>DroSec_CAF1 16116 103 + 1
GGCAAAGUGAGAGGCUUCAAAUAGCACUCAAGGACUUGUGCUCCUUUCUUAAUUAUGAAGAGCGCAACUCCUUAACUUUGUCAGAAAACAAGGACGAUAGAUC-----------------
((((((((..((((((......))).)))(((((.((((((((..(((........))))))))))).))))).)))))))).....................----------------- ( -35.30)
>DroSim_CAF1 28433 120 + 1
GGCAAAGUGAGAGGCUUCAAAUAGCGCUCAAGGACUUGUGCUCCUUUCUCAAUUAUGAAGAGCGCAACUCCUUAACUUUGUCAGAAAACAAGGCCGAUAGAUCCCUAGGAAAAUUGGCUA
((((((((..((((((......))).)))(((((.((((((((..(((........))))))))))).))))).)))))))).........(((((((...(((...)))..))))))). ( -44.70)
>DroYak_CAF1 24328 120 + 1
GGCAGAGUGAGAGGCUUCAUAUAGCACUCAAGGAUCUGUGCUCCUUUCUAAAUUAUGAAGAACGCAACGCCUUAGUUUUAUCAACAGAUAAGGCUAAUAGAUCCCUUAGAAUCCUGGCUA
(.(((..((((..(((......))).)))).((((((((((...((((........))))...)).......((((((((((....)))))))))))))))))).........))).).. ( -33.60)
>consensus
GGCAAAGUGAGAGGCUUCAAAUAGCACUCAAGGACUUGUGCUCCUUUCUUAAUUAUGAAGAACGCAACUCCUUAACUUUAUCAGAAAACAAGGCCAAUAGAUCCCU_GGAAAAUUGGCUA
((((((((..((((((......))).)))(((((.((((((((..(((........))))))))))).))))).)))))))).........(((((((...((.....))..))))))). (-25.96 = -29.65 +   3.69)

alignment

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secondary structure

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dotplot

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Window 9

Location 17,488,015 – 17,488,135
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 81.94
Mean single sequence MFE -31.62
Consensus MFE -24.27
Energy contribution -23.28
Covariance contribution -1.00
Combinations/Pair 1.31
Mean z-score -1.69
Structure conservation index 0.77
SVM decision value 0.41
SVM RNA-class probability 0.726197
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17488015 120 - 20766785
UAGCCAAUUUUCCGAGGGAUCUAUUGGCCUUGUUUUCUGAUAAAGUCAAGGAGUUGCGUUCUUCAUGAUUAAGAAAGGAGCACAAGUCCUUGAGUGCUAUUUGAAGUCUCUCACUUUGCC
..((((((..(((...)))...)))))).....((((.((((.(.(((((((.(((.(((((((........))..))))).))).))))))).)..)))).)))).............. ( -33.70)
>DroSec_CAF1 16116 103 - 1
-----------------GAUCUAUCGUCCUUGUUUUCUGACAAAGUUAAGGAGUUGCGCUCUUCAUAAUUAAGAAAGGAGCACAAGUCCUUGAGUGCUAUUUGAAGCCUCUCACUUUGCC
-----------------.......................((((((.(((((.(((.(((((((........))..))))).))).)))))(((.(((......))))))..)))))).. ( -27.60)
>DroSim_CAF1 28433 120 - 1
UAGCCAAUUUUCCUAGGGAUCUAUCGGCCUUGUUUUCUGACAAAGUUAAGGAGUUGCGCUCUUCAUAAUUGAGAAAGGAGCACAAGUCCUUGAGCGCUAUUUGAAGCCUCUCACUUUGCC
..(((.((..(((...)))...)).)))............((((((.(((((.(((.((((((((....)))....))))).))).)))))(((.(((......))))))..)))))).. ( -33.90)
>DroYak_CAF1 24328 120 - 1
UAGCCAGGAUUCUAAGGGAUCUAUUAGCCUUAUCUGUUGAUAAAACUAAGGCGUUGCGUUCUUCAUAAUUUAGAAAGGAGCACAGAUCCUUGAGUGCUAUAUGAAGCCUCUCACUCUGCC
....((((......((((((((....((((((...(((.....)))))))))(((.(.((((.........)))).).)))..))))))))(((.(((......))))))....)))).. ( -31.30)
>consensus
UAGCCAAUUUUCC_AGGGAUCUAUCGGCCUUGUUUUCUGACAAAGUUAAGGAGUUGCGCUCUUCAUAAUUAAGAAAGGAGCACAAGUCCUUGAGUGCUAUUUGAAGCCUCUCACUUUGCC
.........................(((.(((((....))))).)))(((((.(((.(((((((........))..))))).))).)))))(((.(((......)))))).......... (-24.27 = -23.28 +  -1.00)

alignment

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secondary structure

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dotplot

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Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:44:44 2006