Locus 549

Sequence ID X_DroMel_CAF1
Location 1,568,226 – 1,568,324
Length 98
Max. P 0.999731
window862 window863

overview

Window 2

Location 1,568,226 – 1,568,324
Length 98
Sequences 4
Columns 116
Reading direction forward
Mean pairwise identity 77.59
Mean single sequence MFE -36.17
Consensus MFE -14.99
Energy contribution -16.37
Covariance contribution 1.38
Combinations/Pair 1.09
Mean z-score -2.68
Structure conservation index 0.41
SVM decision value 0.02
SVM RNA-class probability 0.541262
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 1568226 98 + 22224390
UGCAGACUCCGGAAUCC-------AAAAUCCGGAAUCCGGAC-------UGAGGACUUUGGCUGUUAGCUGUUAGCUGUCAACUAAAAGCCCUCAGCCAGAG----CGAGCCUUGU
..(((..((((((.(((-------.......))).)))))))-------))(((.(((((((((...(((.((((.......)))).)))...)))))))))----....)))... ( -37.80)
>DroSec_CAF1 29779 98 + 1
UGCAGACUCCGGAAUCC-------AAAAUCCGGAAUCCGGAC-------UGAGGACUUUGGCUGUUAGCUGUUAGCUGUCAACUAAAAGCCCUCAGCCAGAG----CGAGCCUUGC
.((....((((((.(((-------.......))).)))))).-------.((((.(((((((((...(((.((((.......)))).)))...)))))))))----....)))))) ( -37.90)
>DroEre_CAF1 33270 112 + 1
UGCAGAGUCCGGAAUGCAAAAUGCAAAAUCCGGAAUCCGGAAUCCGGACUGCGGACUUUACCAGUUAGCUGUUAGCUGUCAACUAAAAGCCCUCAGCCUGAG----AGAGCCUUGC
.((((((((((((.(((.....)))...(((((...))))).))))))))..((.((((..(((...((((...(((..........)))...)))))))..----)))))))))) ( -40.50)
>DroYak_CAF1 30255 102 + 1
UGCAGACUCCGGAAUCC-------AAAUUCCGAACUGAGGACUGAGGAUUGCGGACUCUCCUAGUUA-------GCUGUCAACUAAAAGCCCUCAGCCCGAAAGAAAGAGCCUUGC
.((((.(((((((((..-------..))))))..((..((.((((((...((((.....))(((((.-------......)))))...)))))))).))...))...)))..)))) ( -28.50)
>consensus
UGCAGACUCCGGAAUCC_______AAAAUCCGGAAUCCGGAC_______UGAGGACUUUGCCAGUUAGCUGUUAGCUGUCAACUAAAAGCCCUCAGCCAGAG____AGAGCCUUGC
.((((..((((((...............))))))..................((.((((........((((...(((..........)))...)))).........)))))))))) (-14.99 = -16.37 +   1.38)

alignment

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secondary structure

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dotplot

Postscript

Window 3

Location 1,568,226 – 1,568,324
Length 98
Sequences 4
Columns 116
Reading direction reverse
Mean pairwise identity 77.59
Mean single sequence MFE -44.00
Consensus MFE -25.09
Energy contribution -27.27
Covariance contribution 2.19
Combinations/Pair 1.09
Mean z-score -4.24
Structure conservation index 0.57
SVM decision value 3.96
SVM RNA-class probability 0.999731
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 1568226 98 - 22224390
ACAAGGCUCG----CUCUGGCUGAGGGCUUUUAGUUGACAGCUAACAGCUAACAGCCAAAGUCCUCA-------GUCCGGAUUCCGGAUUUU-------GGAUUCCGGAGUCUGCA
.........(----(...(((((((((((((..((((..(((.....)))..)))).))))))))))-------))).((((((((((....-------....)))))))))))). ( -44.40)
>DroSec_CAF1 29779 98 - 1
GCAAGGCUCG----CUCUGGCUGAGGGCUUUUAGUUGACAGCUAACAGCUAACAGCCAAAGUCCUCA-------GUCCGGAUUCCGGAUUUU-------GGAUUCCGGAGUCUGCA
(((.(((((.----....(((((((((((((..((((..(((.....)))..)))).))))))))))-------)))((((.((((.....)-------))).)))))))))))). ( -47.20)
>DroEre_CAF1 33270 112 - 1
GCAAGGCUCU----CUCAGGCUGAGGGCUUUUAGUUGACAGCUAACAGCUAACUGGUAAAGUCCGCAGUCCGGAUUCCGGAUUCCGGAUUUUGCAUUUUGCAUUCCGGACUCUGCA
((((((((((----(.......))))))))(((((((........)))))))((((.((((((((.(((((((...))))))).))))))))((.....))...))))....))). ( -42.70)
>DroYak_CAF1 30255 102 - 1
GCAAGGCUCUUUCUUUCGGGCUGAGGGCUUUUAGUUGACAGC-------UAACUAGGAGAGUCCGCAAUCCUCAGUCCUCAGUUCGGAAUUU-------GGAUUCCGGAGUCUGCA
(((.((((((.......((((((((((((..((((((.....-------))))))(((..(....)..)))..))))))))))))(((((..-------..)))))))))))))). ( -41.70)
>consensus
GCAAGGCUCG____CUCUGGCUGAGGGCUUUUAGUUGACAGCUAACAGCUAACAGCCAAAGUCCGCA_______GUCCGGAUUCCGGAUUUU_______GGAUUCCGGAGUCUGCA
....((((..........))))((((((((((((((...(((.....))))))))..)))))))))...........(((((((((((.(((.......))).))))))))))).. (-25.09 = -27.27 +   2.19)

alignment

Postscript

secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:47:28 2006