Locus 6404

Sequence ID 2L_DroMel_CAF1
Location 17,987,853 – 17,987,944
Length 91
Max. P 0.879757
window10220 window10221

overview

Window 0

Location 17,987,853 – 17,987,944
Length 91
Sequences 6
Columns 101
Reading direction forward
Mean pairwise identity 80.69
Mean single sequence MFE -19.66
Consensus MFE -9.51
Energy contribution -9.84
Covariance contribution 0.33
Combinations/Pair 1.00
Mean z-score -2.47
Structure conservation index 0.48
SVM decision value 0.23
SVM RNA-class probability 0.645467
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 17987853 91 + 22407834
CGGCCAACAGCAGCAAUAAUAAACAAGAAAGUGUGAAAUAAGGCCAAAUGGACAUUC-AAAUUUGUAUGUCCAACACGAG----AAA----CCG-GCAGCA
..(((.......((........(((......)))........))....(((((((.(-(....)).))))))).......----...----..)-)).... ( -17.39)
>DroVir_CAF1 262259 98 + 1
-GGUCGAGCACUGCAAUAAUAAACAAGAAAGUGUGAAAUAAAGCGAAAUGGACAUAACAAAUUUGUAUGUCCAGCGACAGUGGGAAA-GA-GUGAAAAAUA
-.((((.(((((.................)))))..............((((((((.((....)))))))))).)))).........-..-.......... ( -19.43)
>DroPse_CAF1 291674 87 + 1
CGG--AGCCCCAGCAAUAAUAAACAAGAAAGUGUGAAAUAAAGCCAAAUGGACAUAA-AAAUUUGUAUGUCCAACAAGAG----GAG------G-GCGGCA
.(.--.(((((.((........(((......)))........))....((((((((.-.......)))))))).......----).)------)-))..). ( -19.39)
>DroEre_CAF1 194492 91 + 1
CGGCCAACAGCAGCAAUAAUAAACAAGAAAGUGUGAAAUAAGGCCAAAUGGACAUAC-AAAUUUGUAUGUCCAACACGAG----AAA----CUG-GCAGCA
..((((......((........(((......)))........))....(((((((((-(....)))))))))).......----...----.))-)).... ( -22.49)
>DroAna_CAF1 194337 95 + 1
AGGAGCACAACGGCAAUAAUAAACAAGAAAGUGUGAAAUAAAGCCAAAUGGACAUAA-AAAUUUGUAUGUCCUACAAGAG----GAAGUAGUCG-GCUGCG
.(.(((.(.(((((........(((......)))........)))....(((((((.-.......)))))))........----......)).)-))).). ( -19.89)
>DroPer_CAF1 293013 87 + 1
CGG--AGCCCCAGCAAUAAUAAACAAGAAAGUGUGAAAUAAAGCCAAAUGGACAUAA-AAAUUUGUAUGUCCAACAAGAG----GAG------G-GCGGCA
.(.--.(((((.((........(((......)))........))....((((((((.-.......)))))))).......----).)------)-))..). ( -19.39)
>consensus
CGG_CAACAACAGCAAUAAUAAACAAGAAAGUGUGAAAUAAAGCCAAAUGGACAUAA_AAAUUUGUAUGUCCAACAAGAG____AAA______G_GCAGCA
............((........(((......)))........))....((((((((.........))))))))............................ ( -9.51 =  -9.84 +   0.33)

alignment

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secondary structure

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dotplot

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Window 1

Location 17,987,853 – 17,987,944
Length 91
Sequences 6
Columns 101
Reading direction reverse
Mean pairwise identity 80.69
Mean single sequence MFE -20.58
Consensus MFE -10.64
Energy contribution -10.78
Covariance contribution 0.14
Combinations/Pair 1.28
Mean z-score -2.85
Structure conservation index 0.52
SVM decision value 0.91
SVM RNA-class probability 0.879757
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 17987853 91 - 22407834
UGCUGC-CGG----UUU----CUCGUGUUGGACAUACAAAUUU-GAAUGUCCAUUUGGCCUUAUUUCACACUUUCUUGUUUAUUAUUGCUGCUGUUGGCCG
.(((..-(((----(..----.......(((((((.((....)-).)))))))...(((..((....(((......)))....))..)))))))..))).. ( -18.60)
>DroVir_CAF1 262259 98 - 1
UAUUUUUCAC-UC-UUUCCCACUGUCGCUGGACAUACAAAUUUGUUAUGUCCAUUUCGCUUUAUUUCACACUUUCUUGUUUAUUAUUGCAGUGCUCGACC-
..........-..-.....((((((.((((((((((((....)).))))))))....))........(((......)))........)))))).......- ( -16.40)
>DroPse_CAF1 291674 87 - 1
UGCCGC-C------CUC----CUCUUGUUGGACAUACAAAUUU-UUAUGUCCAUUUGGCUUUAUUUCACACUUUCUUGUUUAUUAUUGCUGGGGCU--CCG
....((-(------((.----.......((((((((.......-.))))))))...(((..((....(((......)))....))..)))))))).--... ( -21.40)
>DroEre_CAF1 194492 91 - 1
UGCUGC-CAG----UUU----CUCGUGUUGGACAUACAAAUUU-GUAUGUCCAUUUGGCCUUAUUUCACACUUUCUUGUUUAUUAUUGCUGCUGUUGGCCG
.(((..-(((----(..----.......((((((((((....)-)))))))))...(((..((....(((......)))....))..)))))))..))).. ( -23.90)
>DroAna_CAF1 194337 95 - 1
CGCAGC-CGACUACUUC----CUCUUGUAGGACAUACAAAUUU-UUAUGUCCAUUUGGCUUUAUUUCACACUUUCUUGUUUAUUAUUGCCGUUGUGCUCCU
.(.(((-((((......----........(((((((.......-.)))))))....(((..((....(((......)))....))..))))))).))).). ( -21.80)
>DroPer_CAF1 293013 87 - 1
UGCCGC-C------CUC----CUCUUGUUGGACAUACAAAUUU-UUAUGUCCAUUUGGCUUUAUUUCACACUUUCUUGUUUAUUAUUGCUGGGGCU--CCG
....((-(------((.----.......((((((((.......-.))))))))...(((..((....(((......)))....))..)))))))).--... ( -21.40)
>consensus
UGCUGC_C______UUC____CUCUUGUUGGACAUACAAAUUU_UUAUGUCCAUUUGGCUUUAUUUCACACUUUCUUGUUUAUUAUUGCUGCGGUUG_CCG
.(((.........................(((((((.........)))))))....(((..((....(((......)))....))..)))..)))...... (-10.64 = -10.78 +   0.14)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:10:11 2006