Locus 5994

Sequence ID X_DroMel_CAF1
Location 15,399,278 – 15,399,436
Length 158
Max. P 0.873365
window9751 window9752 window9753

overview

Window 1

Location 15,399,278 – 15,399,397
Length 119
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 91.44
Mean single sequence MFE -34.40
Consensus MFE -30.23
Energy contribution -30.10
Covariance contribution -0.13
Combinations/Pair 1.06
Mean z-score -1.80
Structure conservation index 0.88
SVM decision value 0.88
SVM RNA-class probability 0.873365
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 15399278 119 + 22224390
AAGGGAGCUGACAAUUUAAUUUGCCAGCCAGGAUGUUCAAAGGACGCAGGACAACGACCUUGCCAAGUGUCCA-AGUGUAACCGAUAGGACAACAUGGAUUACAAUCCAUCCAUCCUGAA
......((((.(((......))).))))(((((((......((((((.((.(((.....)))))..)))))).-.((((..((....))...))))((((....))))...))))))).. ( -35.40)
>DroSec_CAF1 45231 119 + 1
AAGGGAGCUGACAAUUUAAUUUGCCAGCCAGGAUGUUCAAAGGACGCAGGACAACGACCUUGCCAAGUGUCCA-AGUGUAACCGAUACGGCAACGUGGAUUACAAUCCAUUCGUUCUGAA
......((((.(((......))).))))(((((((......((((((.((.(((.....)))))..)))))).-..(((((((...(((....))))).))))).......))))))).. ( -34.90)
>DroEre_CAF1 36595 115 + 1
GAGGGAGCUGACAACUCAAUUUGCCAGCCAGGACGUUCAAAGGACGCAGGACAACGACCUUGCCAAGUGUUCG-AGUGUAACCAAUACGGCAACGUGGAUUACAAUCCAU----CCUGAG
......((((.(((......))).))))(((((........((((((.((.(((.....)))))..))))))(-(.(((((((...(((....))))).))))).))..)----)))).. ( -32.10)
>DroYak_CAF1 39730 116 + 1
AAGGGAGCUGACAAUUUAAUUUGCCAGCCAGGACGUACAAAGGACGCAGGACAACGACCUUGCCAAGUGUCCAAAGUGUAACCGAUACGGCAACGUGGAUUACAAUCCAU----CCUGAA
..((((((((.(((......))).))))..(((........((((((.((.(((.....)))))..))))))....(((((((...(((....))))).))))).))).)----)))... ( -35.20)
>consensus
AAGGGAGCUGACAAUUUAAUUUGCCAGCCAGGACGUUCAAAGGACGCAGGACAACGACCUUGCCAAGUGUCCA_AGUGUAACCGAUACGGCAACGUGGAUUACAAUCCAU____CCUGAA
.((((.((((.(((......))).))))).(((........((((((.((.(((.....)))))..))))))....(((((((...(((....))))).))))).)))......)))... (-30.23 = -30.10 +  -0.13)

alignment

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secondary structure

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dotplot

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Window 2

Location 15,399,278 – 15,399,397
Length 119
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 91.44
Mean single sequence MFE -37.55
Consensus MFE -30.95
Energy contribution -31.33
Covariance contribution 0.37
Combinations/Pair 1.09
Mean z-score -2.00
Structure conservation index 0.82
SVM decision value 0.86
SVM RNA-class probability 0.868329
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 15399278 119 - 22224390
UUCAGGAUGGAUGGAUUGUAAUCCAUGUUGUCCUAUCGGUUACACU-UGGACACUUGGCAAGGUCGUUGUCCUGCGUCCUUUGAACAUCCUGGCUGGCAAAUUAAAUUGUCAGCUCCCUU
..(((((((.((((((....))))))..(((((....(....)...-.)))))......((((.(((......))).))))....)))))))((((((((......))))))))...... ( -39.90)
>DroSec_CAF1 45231 119 - 1
UUCAGAACGAAUGGAUUGUAAUCCACGUUGCCGUAUCGGUUACACU-UGGACACUUGGCAAGGUCGUUGUCCUGCGUCCUUUGAACAUCCUGGCUGGCAAAUUAAAUUGUCAGCUCCCUU
((((((.....(((((....))))).((.((((...)))).))...-.((((.(..(((((.....)))))..).))))))))))......(((((((((......)))))))))..... ( -33.60)
>DroEre_CAF1 36595 115 - 1
CUCAGG----AUGGAUUGUAAUCCACGUUGCCGUAUUGGUUACACU-CGAACACUUGGCAAGGUCGUUGUCCUGCGUCCUUUGAACGUCCUGGCUGGCAAAUUGAGUUGUCAGCUCCCUC
..((((----(((((.(((((((.(((....)))...))))))).)-)...........((((.(((......))).))))....)))))))((((((((......))))))))...... ( -37.60)
>DroYak_CAF1 39730 116 - 1
UUCAGG----AUGGAUUGUAAUCCACGUUGCCGUAUCGGUUACACUUUGGACACUUGGCAAGGUCGUUGUCCUGCGUCCUUUGUACGUCCUGGCUGGCAAAUUAAAUUGUCAGCUCCCUU
..((((----(((....((((((.(((....)))...))))))((...((((.(..(((((.....)))))..).))))...)).)))))))((((((((......))))))))...... ( -39.10)
>consensus
UUCAGG____AUGGAUUGUAAUCCACGUUGCCGUAUCGGUUACACU_UGGACACUUGGCAAGGUCGUUGUCCUGCGUCCUUUGAACAUCCUGGCUGGCAAAUUAAAUUGUCAGCUCCCUU
..((((......((((....))))(((((((((.....(((........)))...))))((((.(((......))).))))..)))))))))((((((((......))))))))...... (-30.95 = -31.33 +   0.37)

alignment

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secondary structure

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dotplot

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Window 3

Location 15,399,318 – 15,399,436
Length 118
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 89.86
Mean single sequence MFE -30.10
Consensus MFE -23.15
Energy contribution -23.15
Covariance contribution 0.00
Combinations/Pair 1.14
Mean z-score -2.07
Structure conservation index 0.77
SVM decision value 0.73
SVM RNA-class probability 0.833924
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 15399318 118 + 22224390
AGGACGCAGGACAACGACCUUGCCAAGUGUCCA-AGUGUAACCGAUAGGACAACAUGGAUUACAAUCCAUCCAUCCUGAAUCCAUUAGGAAUCAAAACCGAGCGAAAU-UUGCCGCACAA
.((((((.((.(((.....)))))..)))))).-.((((....(((.(((.....(((((....)))))))).((((((.....)))))))))......(.((((...-))))))))).. ( -30.80)
>DroSec_CAF1 45271 119 + 1
AGGACGCAGGACAACGACCUUGCCAAGUGUCCA-AGUGUAACCGAUACGGCAACGUGGAUUACAAUCCAUUCGUUCUGAAUCCAUUAGGAAUCAAGACCGAGCGAAAUUUUGCCACACAA
.((((((.((.(((.....)))))..)))))).-.((((.....))))(((((..(((((....)))))((((((((((.(((....))).))).....)))))))...)))))...... ( -36.20)
>DroEre_CAF1 36635 114 + 1
AGGACGCAGGACAACGACCUUGCCAAGUGUUCG-AGUGUAACCAAUACGGCAACGUGGAUUACAAUCCAU----CCUGAGUCCAUUAGAAAUCAAAACCAACCGAAAU-UUGCCGCACAA
.((((.(((((.....((.(((((..(((((.(-........))))))))))).))((((....)))).)----)))).)))).........................-........... ( -27.00)
>DroYak_CAF1 39770 115 + 1
AGGACGCAGGACAACGACCUUGCCAAGUGUCCAAAGUGUAACCGAUACGGCAACGUGGAUUACAAUCCAU----CCUGAAUCCAUUAGGAAUCAAAACCAACCGAAAU-UUACCAGACAA
.(((..(((((.....((.(((((..(((((............)))))))))).))((((....)))).)----))))..)))....((........)).........-........... ( -26.40)
>consensus
AGGACGCAGGACAACGACCUUGCCAAGUGUCCA_AGUGUAACCGAUACGGCAACGUGGAUUACAAUCCAU____CCUGAAUCCAUUAGGAAUCAAAACCAACCGAAAU_UUGCCACACAA
.((((((.((.(((.....)))))..))))))...((((.........((....((((((....))))))....))(((.(((....))).)))....................)))).. (-23.15 = -23.15 +   0.00)

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 12:01:44 2006