Locus 4516

Sequence ID X_DroMel_CAF1
Location 11,914,397 – 11,914,487
Length 90
Max. P 0.876714
window7428 window7429

overview

Window 8

Location 11,914,397 – 11,914,487
Length 90
Sequences 5
Columns 116
Reading direction forward
Mean pairwise identity 84.15
Mean single sequence MFE -25.94
Consensus MFE -19.59
Energy contribution -19.67
Covariance contribution 0.08
Combinations/Pair 1.05
Mean z-score -2.05
Structure conservation index 0.76
SVM decision value 0.90
SVM RNA-class probability 0.876714
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 11914397 90 + 22224390
GGAACUGAAUCGAAAAGGAUUCAGGAUGGGCGUUGG--------------------------CAAUGGCAAUGGUCGCCUAAUAAGCCAACACAGCAGAGCGUGACAAAACAAACA
((..(((((((......)))))))..((((((...(--------------------------(....))......)))))).....))..(((.((...)))))............ ( -22.80)
>DroSec_CAF1 24239 90 + 1
GGAACUGAAUCGAAAAGGAUUCAGGAUGGGCGAUGG--------------------------CAAUGGCAAUGGUCGCCUAAUAAGCCAACACACCAGAGCGUGACAAAACAAACA
((..(((((((......)))))))..((((((((.(--------------------------(....))....)))))))).....))..(((........)))............ ( -25.40)
>DroSim_CAF1 22217 90 + 1
GGAACUGAAUCGAAAAGGAUUCAGGAUGGGCGAUGG--------------------------CAAUGGCAAUGGUCGCCUAAUAAGCCAACACACCAGAGCGUGACAAAACAAACA
((..(((((((......)))))))..((((((((.(--------------------------(....))....)))))))).....))..(((........)))............ ( -25.40)
>DroEre_CAF1 22514 116 + 1
GGUACUGAAUCGAAAGGGAUUCAGGAUGGGCGAUGGGCGAUGGGCGAUGGUGAGGUUGAUGAUGAUGGCAAUGGUCGCCUAAUAAGCCAACACACCAGAGCGUGACAAAACAAACA
(((.(((((((......)))))))....(((..((((((((..((.((.((.(......).)).)).))....))))))))....))).....))).....((......))..... ( -34.90)
>DroYak_CAF1 25492 96 + 1
GGUACUAAAUCGAAAGGGAUUUAGGAUGGGCGAUGGA--------------------GAUGGUGAUGGCAAUGUUCGCCUAAUAAGCCAACACACCAGAGCGUGACAAAACAAACA
....(((((((......))))))).....((..(((.--------------------(.((((...(((.......)))......))))...).)))..))((......))..... ( -21.20)
>consensus
GGAACUGAAUCGAAAAGGAUUCAGGAUGGGCGAUGG__________________________CAAUGGCAAUGGUCGCCUAAUAAGCCAACACACCAGAGCGUGACAAAACAAACA
((..(((((((......)))))))..((((((((.......................................)))))))).....))..(((........)))............ (-19.59 = -19.67 +   0.08)

alignment

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secondary structure

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dotplot

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Window 9

Location 11,914,397 – 11,914,487
Length 90
Sequences 5
Columns 116
Reading direction reverse
Mean pairwise identity 84.15
Mean single sequence MFE -23.27
Consensus MFE -18.56
Energy contribution -18.24
Covariance contribution -0.32
Combinations/Pair 1.05
Mean z-score -1.89
Structure conservation index 0.80
SVM decision value 0.76
SVM RNA-class probability 0.842871
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 11914397 90 - 22224390
UGUUUGUUUUGUCACGCUCUGCUGUGUUGGCUUAUUAGGCGACCAUUGCCAUUG--------------------------CCAACGCCCAUCCUGAAUCCUUUUCGAUUCAGUUCC
.((.((......)).))......((((((((......(((((...)))))...)--------------------------))))))).....(((((((......))))))).... ( -24.20)
>DroSec_CAF1 24239 90 - 1
UGUUUGUUUUGUCACGCUCUGGUGUGUUGGCUUAUUAGGCGACCAUUGCCAUUG--------------------------CCAUCGCCCAUCCUGAAUCCUUUUCGAUUCAGUUCC
.((.((......)).))..(((.(((.((((......(((((...)))))...)--------------------------))).))))))..(((((((......))))))).... ( -24.40)
>DroSim_CAF1 22217 90 - 1
UGUUUGUUUUGUCACGCUCUGGUGUGUUGGCUUAUUAGGCGACCAUUGCCAUUG--------------------------CCAUCGCCCAUCCUGAAUCCUUUUCGAUUCAGUUCC
.((.((......)).))..(((.(((.((((......(((((...)))))...)--------------------------))).))))))..(((((((......))))))).... ( -24.40)
>DroEre_CAF1 22514 116 - 1
UGUUUGUUUUGUCACGCUCUGGUGUGUUGGCUUAUUAGGCGACCAUUGCCAUCAUCAUCAACCUCACCAUCGCCCAUCGCCCAUCGCCCAUCCUGAAUCCCUUUCGAUUCAGUACC
...............((..(((((.(((((.......(((((...))))).......)))))..)))))..))...................(((((((......))))))).... ( -24.94)
>DroYak_CAF1 25492 96 - 1
UGUUUGUUUUGUCACGCUCUGGUGUGUUGGCUUAUUAGGCGAACAUUGCCAUCACCAUC--------------------UCCAUCGCCCAUCCUAAAUCCCUUUCGAUUUAGUACC
(((((((((.(((((((......))).)))).....)))))))))..............--------------------.............(((((((......))))))).... ( -18.40)
>consensus
UGUUUGUUUUGUCACGCUCUGGUGUGUUGGCUUAUUAGGCGACCAUUGCCAUUG__________________________CCAUCGCCCAUCCUGAAUCCUUUUCGAUUCAGUUCC
..........(((((((......))).))))......(((((...)))))..........................................(((((((......))))))).... (-18.56 = -18.24 +  -0.32)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:27:06 2006