Locus 4127

Sequence ID X_DroMel_CAF1
Location 10,856,469 – 10,856,588
Length 119
Max. P 0.887899
window6780 window6781

overview

Window 0

Location 10,856,469 – 10,856,588
Length 119
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 87.22
Mean single sequence MFE -27.67
Consensus MFE -19.20
Energy contribution -19.95
Covariance contribution 0.75
Combinations/Pair 1.04
Mean z-score -2.53
Structure conservation index 0.69
SVM decision value 0.95
SVM RNA-class probability 0.887899
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 10856469 119 + 22224390
GCUGACAAGCGAAAUGCGGAUUGAAAUGUCACUGAAGAAAGUCAGUAGUCACAUUUAUCGGUAAGCUGAUUAA-AAUAAACAGAAUGCAUACCAUUAAGUGUAAGAAGUAAUGGUAAACA
(((....)))....((((..(((((((((.((((..(.....)..)))).))))))(((((....)))))...-......)))..))))((((((((..(.....)..)))))))).... ( -26.60)
>DroSec_CAF1 10309 120 + 1
GCUGACAAGCGAAAUGCGGAUUGAAAUGUCACUGAAGAAAGUCAGUAGUCUCAUUUAUCGGUAAGCUGAUUAAAAAUAAGCAAAACGUUUACCAUUAAGUGUACGAAGUAAUGGUAAACA
(((....)))....(((..(((.(((((.((((((......))))).)...)))))(((((....)))))....)))..)))....(((((((((((..(.....)..))))))))))). ( -29.70)
>DroSim_CAF1 12231 120 + 1
GCUGACAAGCAAAAUGCGGAUUGAAAUGUCACUGAAGAAAGUCAGUAGUCACAUUUAUCGGUAAGCUGAUUAAAAAUAAGCAGAACGUUUACCAUUAAGUGUACGAAGUAAUGGUAAACA
(((....)))....(((..(((.((((((.((((..(.....)..)))).))))))(((((....)))))....)))..)))....(((((((((((..(.....)..))))))))))). ( -30.50)
>DroYak_CAF1 10447 110 + 1
GCUGACAAGCGAAAUGCGGAUUGAAAUGUCACUGCAGAAAGUCAGUAGUCACAUUUAUCGAAAAGCUGAUUCAAAAU-AGCAGAACGCUUACAACUAAGUGCUAAAA---------CGCA
(((....)))....(((((((..((((((.(((((.(.....).))))).))))))))).....((((........)-)))....((((((....))))))......---------)))) ( -23.90)
>consensus
GCUGACAAGCGAAAUGCGGAUUGAAAUGUCACUGAAGAAAGUCAGUAGUCACAUUUAUCGGUAAGCUGAUUAAAAAUAAGCAGAACGCUUACCAUUAAGUGUAAGAAGUAAUGGUAAACA
((((((..((.....)).(((......)))..........)))))).....((((((..(((((((....................)))))))..))))))................... (-19.20 = -19.95 +   0.75)

alignment

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secondary structure

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dotplot

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Window 1

Location 10,856,469 – 10,856,588
Length 119
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 87.22
Mean single sequence MFE -23.30
Consensus MFE -15.09
Energy contribution -17.27
Covariance contribution 2.19
Combinations/Pair 1.12
Mean z-score -1.80
Structure conservation index 0.65
SVM decision value 0.04
SVM RNA-class probability 0.551557
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 10856469 119 - 22224390
UGUUUACCAUUACUUCUUACACUUAAUGGUAUGCAUUCUGUUUAUU-UUAAUCAGCUUACCGAUAAAUGUGACUACUGACUUUCUUCAGUGACAUUUCAAUCCGCAUUUCGCUUGUCAGC
(((.((((((((...........)))))))).)))...........-.......(((.((.(((((((((...((((((......))))))))))))..))).((.....))..)).))) ( -20.40)
>DroSec_CAF1 10309 120 - 1
UGUUUACCAUUACUUCGUACACUUAAUGGUAAACGUUUUGCUUAUUUUUAAUCAGCUUACCGAUAAAUGAGACUACUGACUUUCUUCAGUGACAUUUCAAUCCGCAUUUCGCUUGUCAGC
.(((((((((((...........)))))))))))((...(((.((.....)).)))..)).(((((.(((((.((((((......))))))...)))))....((.....)))))))... ( -24.60)
>DroSim_CAF1 12231 120 - 1
UGUUUACCAUUACUUCGUACACUUAAUGGUAAACGUUCUGCUUAUUUUUAAUCAGCUUACCGAUAAAUGUGACUACUGACUUUCUUCAGUGACAUUUCAAUCCGCAUUUUGCUUGUCAGC
.(((((((((((...........)))))))))))....................(((.((.(((((((((...((((((......))))))))))))..))).((.....))..)).))) ( -23.40)
>DroYak_CAF1 10447 110 - 1
UGCG---------UUUUAGCACUUAGUUGUAAGCGUUCUGCU-AUUUUGAAUCAGCUUUUCGAUAAAUGUGACUACUGACUUUCUGCAGUGACAUUUCAAUCCGCAUUUCGCUUGUCAGC
(((.---------.....)))....((((((((((...(((.-...(((((.......))))).((((((.(((.(.(.....).).))).))))))......)))...)))))).)))) ( -24.80)
>consensus
UGUUUACCAUUACUUCGUACACUUAAUGGUAAACGUUCUGCUUAUUUUUAAUCAGCUUACCGAUAAAUGUGACUACUGACUUUCUUCAGUGACAUUUCAAUCCGCAUUUCGCUUGUCAGC
((((((((((((...........))))))))))))...................(((.((.(((((((((...(((((........)))))))))))..))).((.....))..)).))) (-15.09 = -17.27 +   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 11:17:00 2006