Locus 4029

Sequence ID 2R_DroMel_CAF1
Location 13,304,640 – 13,304,744
Length 104
Max. P 0.610733
window6495 window6496

overview

Window 5

Location 13,304,640 – 13,304,744
Length 104
Sequences 6
Columns 112
Reading direction forward
Mean pairwise identity 81.62
Mean single sequence MFE -26.80
Consensus MFE -19.55
Energy contribution -19.67
Covariance contribution 0.11
Combinations/Pair 1.17
Mean z-score -1.36
Structure conservation index 0.73
SVM decision value 0.11
SVM RNA-class probability 0.588066
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 13304640 104 + 20766785
GAAAGGAUUCGGAACCCACAAAUGAAGUGGUGGCCAGUUCCGAGGCUUCCGAAAACGAGGAGGAGGAGGAGGUAAGACCCAUUGACAG---UGAUAUAAA---AAGUCAU--
....((.((((((((((((..........))))...))))))))((((((.....(.....).....)))))).....))..((((..---.........---..)))).-- ( -25.62)
>DroSec_CAF1 4940 102 + 1
GAAAGGAUUCGGAACCCACAAAUGAAGUGGUGGCCAGUUCCGAGGCUUCCGAAAACGAGGAGGAGGAGGAGGUAAGACCCGUUAACAG---UGAUAUA-----AAGUCAU--
....((.((((((((((((..........))))...))))))))((((((.....(.....).....)))))).....)).......(---((((...-----..)))))-- ( -25.90)
>DroSim_CAF1 4066 102 + 1
GAAAGGAUUCGGAACCCACAAAUGAAGUGGUGGCCAGUUCCGAGGCUUCCGAAAACGAGGAGGAGGAGGAGGUAAGACCCAUUAACAG---UGAUAUA-----AAGUCAU--
....((.((((((((((((..........))))...))))))))((((((.....(.....).....)))))).....)).......(---((((...-----..)))))-- ( -25.90)
>DroEre_CAF1 4973 104 + 1
GAAAGGAGUCGGAGCCCAUAAAUAAAGUGGUGGCCAGUUCUGAGGCGUCCGAAAAUGAGGAGGAAGAGGAGGUAAGUACCAUUGACGA---GGAAAUAAU---AAGUUGU--
.......(((((...))........((((((((((..((((....(.(((........))).).))))..)))...))))))))))..---.........---.......-- ( -21.20)
>DroYak_CAF1 4943 109 + 1
GAAAGGAUGCGGAGCCCACAAAUGAAGUGGUGGCCAGUUCCGAGGCUUCCGAAAAUGAGGAGGAGGAGGAGGUAAGACCCAUUGACGA---GGAAAUACUCAGAAAUUGUAC
.....((((.((..(((((.......)))).)(((..((((....(((((........))))).))))..)))....))))))...((---(......)))........... ( -27.90)
>DroAna_CAF1 3138 98 + 1
GGAAAGAGCCGGAGCCCACAAAUGAAGUGGCCGCCAGUUCCGAGGCCUCCGACAACGAGGAGG---AGGAGGUAAGC----UUGGCACUUUUCAUUUU-----AAAUCAC--
((((((.((((.(((((((.......))))..(((...(((....(((((........)))))---.))))))..))----))))).)))))).....-----.......-- ( -34.30)
>consensus
GAAAGGAUUCGGAACCCACAAAUGAAGUGGUGGCCAGUUCCGAGGCUUCCGAAAACGAGGAGGAGGAGGAGGUAAGACCCAUUGACAG___UGAUAUA_____AAGUCAU__
....((....((...((((.......))))...))(.((((....(((((........)))))....)))).).....))................................ (-19.55 = -19.67 +   0.11)

alignment

Postscript

secondary structure

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dotplot

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Window 6

Location 13,304,640 – 13,304,744
Length 104
Sequences 6
Columns 112
Reading direction reverse
Mean pairwise identity 81.62
Mean single sequence MFE -21.91
Consensus MFE -16.32
Energy contribution -16.65
Covariance contribution 0.33
Combinations/Pair 1.21
Mean z-score -1.38
Structure conservation index 0.74
SVM decision value 0.16
SVM RNA-class probability 0.610733
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 13304640 104 - 20766785
--AUGACUU---UUUAUAUCA---CUGUCAAUGGGUCUUACCUCCUCCUCCUCCUCGUUUUCGGAAGCCUCGGAACUGGCCACCACUUCAUUUGUGGGUUCCGAAUCCUUUC
--.((((..---.........---..))))..((......))..............(..((((((((((........)))..((((.......)))).)))))))..).... ( -23.52)
>DroSec_CAF1 4940 102 - 1
--AUGACUU-----UAUAUCA---CUGUUAACGGGUCUUACCUCCUCCUCCUCCUCGUUUUCGGAAGCCUCGGAACUGGCCACCACUUCAUUUGUGGGUUCCGAAUCCUUUC
--.((((..-----.......---..))))..((......))..............(..((((((((((........)))..((((.......)))).)))))))..).... ( -21.80)
>DroSim_CAF1 4066 102 - 1
--AUGACUU-----UAUAUCA---CUGUUAAUGGGUCUUACCUCCUCCUCCUCCUCGUUUUCGGAAGCCUCGGAACUGGCCACCACUUCAUUUGUGGGUUCCGAAUCCUUUC
--..(((((-----.......---........)))))...................(..((((((((((........)))..((((.......)))).)))))))..).... ( -21.76)
>DroEre_CAF1 4973 104 - 1
--ACAACUU---AUUAUUUCC---UCGUCAAUGGUACUUACCUCCUCUUCCUCCUCAUUUUCGGACGCCUCAGAACUGGCCACCACUUUAUUUAUGGGCUCCGACUCCUUUC
--.......---.........---..(((...(((....)))....................(((.(((.(((((.(((...))).))).....)))))))))))....... ( -14.60)
>DroYak_CAF1 4943 109 - 1
GUACAAUUUCUGAGUAUUUCC---UCGUCAAUGGGUCUUACCUCCUCCUCCUCCUCAUUUUCGGAAGCCUCGGAACUGGCCACCACUUCAUUUGUGGGCUCCGCAUCCUUUC
((.....(((((((..(((((---..(..((((((..................))))))..)))))).)))))))..((...((((.......))))...))))........ ( -20.97)
>DroAna_CAF1 3138 98 - 1
--GUGAUUU-----AAAAUGAAAAGUGCCAA----GCUUACCUCCU---CCUCCUCGUUGUCGGAGGCCUCGGAACUGGCGGCCACUUCAUUUGUGGGCUCCGGCUCUUUCC
--.......-----.......((((.(((..----(((....(((.---(((((........)))))....)))...)))(.((((.......)))).)...))).)))).. ( -28.80)
>consensus
__AUGACUU_____UAUAUCA___CUGUCAAUGGGUCUUACCUCCUCCUCCUCCUCGUUUUCGGAAGCCUCGGAACUGGCCACCACUUCAUUUGUGGGCUCCGAAUCCUUUC
...........................................................((((((((((........)))..((((.......)))).)))))))....... (-16.32 = -16.65 +   0.33)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:10:00 2006