Locus 1684

Sequence ID 2R_DroMel_CAF1
Location 6,377,944 – 6,378,062
Length 118
Max. P 0.783484
window2807 window2808

overview

Window 7

Location 6,377,944 – 6,378,062
Length 118
Sequences 5
Columns 119
Reading direction forward
Mean pairwise identity 77.90
Mean single sequence MFE -32.14
Consensus MFE -17.55
Energy contribution -17.71
Covariance contribution 0.16
Combinations/Pair 1.14
Mean z-score -1.74
Structure conservation index 0.55
SVM decision value -0.03
SVM RNA-class probability 0.518803
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 6377944 118 + 20766785
CAGAAUCCCUGCGCUCUUGGAUACCAAGUGCUUUUGGAGAGCAGCCAAGUUGGUGGAAAUUCAUCAGCAAUGUUCAGGCUU-UCCACCUCCUUGAAAUUAGUCAAGGAAAUCCGAGAAG
(((.....)))...((((((((............((((((((.((...((((((((....))))))))...))....))))-))))..(((((((......))))))).)))))))).. ( -38.70)
>DroSec_CAF1 18679 101 + 1
CAGAAUCCCUGCGCUCUU-----------------GGAGAGUGGCCAAGUUGGUGGAAAUUCAUCAGCACUGCUCAGGCUU-UCCACCUCCUUGAAAUUAGUCAAGGAAAUCCGAGGAG
.......(((.((....(-----------------((((((((((...((((((((....))))))))...)))...))))-))))..(((((((......)))))))....))))).. ( -32.60)
>DroSim_CAF1 19951 101 + 1
CAGAAUCCCUGCGCUCUU-----------------GGAGAGUGGCCAAGUUGGUGGAAAUUCAUAAGCACUGUUCAGGCUU-UCCACCUCCUUGAAAUUAGUCAAGGAAAUCCGAGGAG
(((.....)))...((((-----------------(((.............(((((((.......(((.((....))))))-))))))(((((((......)))))))..))))))).. ( -29.91)
>DroEre_CAF1 19849 97 + 1
CAGAAUCCUUGUACUCUGGGAUCCC-U--------GGAGA------------GUGGAAAUUU-UCAGCAAUGUUCAGGCUUUUCCACCUCCUUGAAAUUAGUCGAGGAAAUCCAAGGAG
.....((((((..(((..((...))-.--------.))).------------(((((((...-..(((.........)))))))))).(((((((......)))))))....)))))). ( -31.70)
>DroYak_CAF1 19896 105 + 1
CAGAAUCCCUGUACUCUUGCAUCCC-UGUGCUCGUGGAGA------------GUGGAAAUUU-UCAGCAAUGUUCAGGCUUUUCCACCUCCUUGAAAUUAGUCCAGGAAAUCCGAGGAG
.......((((.(((...((((...-.))))(((.((((.------------(((((((...-..(((.........)))))))))))))).)))....))).))))...((....)). ( -27.80)
>consensus
CAGAAUCCCUGCGCUCUUG_AU_CC__________GGAGAG__GCCAAGUUGGUGGAAAUUCAUCAGCAAUGUUCAGGCUU_UCCACCUCCUUGAAAUUAGUCAAGGAAAUCCGAGGAG
(((.....)))........................(((.............((((((........(((...)))........))))))(((((((......)))))))..)))...... (-17.55 = -17.71 +   0.16)

alignment

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secondary structure

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dotplot

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Window 8

Location 6,377,944 – 6,378,062
Length 118
Sequences 5
Columns 119
Reading direction reverse
Mean pairwise identity 77.90
Mean single sequence MFE -32.27
Consensus MFE -17.38
Energy contribution -17.86
Covariance contribution 0.48
Combinations/Pair 1.10
Mean z-score -1.97
Structure conservation index 0.54
SVM decision value 0.56
SVM RNA-class probability 0.783484
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 6377944 118 - 20766785
CUUCUCGGAUUUCCUUGACUAAUUUCAAGGAGGUGGA-AAGCCUGAACAUUGCUGAUGAAUUUCCACCAACUUGGCUGCUCUCCAAAAGCACUUGGUAUCCAAGAGCGCAGGGAUUCUG
.....((((..((((((........((((..((((((-((..(..............)..))))))))..))))((((((.......))).(((((...)))))))).)))))).)))) ( -35.94)
>DroSec_CAF1 18679 101 - 1
CUCCUCGGAUUUCCUUGACUAAUUUCAAGGAGGUGGA-AAGCCUGAGCAGUGCUGAUGAAUUUCCACCAACUUGGCCACUCUCC-----------------AAGAGCGCAGGGAUUCUG
.((((((....(((((((......)))))))((((((-((..((.(((...))).).)..))))))))..(((((.......))-----------------)))..)).))))...... ( -32.80)
>DroSim_CAF1 19951 101 - 1
CUCCUCGGAUUUCCUUGACUAAUUUCAAGGAGGUGGA-AAGCCUGAACAGUGCUUAUGAAUUUCCACCAACUUGGCCACUCUCC-----------------AAGAGCGCAGGGAUUCUG
.((((((....(((((((......)))))))((((((-((((((....)).))).......)))))))..(((((.......))-----------------)))..)).))))...... ( -31.11)
>DroEre_CAF1 19849 97 - 1
CUCCUUGGAUUUCCUCGACUAAUUUCAAGGAGGUGGAAAAGCCUGAACAUUGCUGA-AAAUUUCCAC------------UCUCC--------A-GGGAUCCCAGAGUACAAGGAUUCUG
.((((((((..((((.((......)).))))(((((((((((.........)))..-...)))))))------------).)))--------)-))))...((((((......)))))) ( -29.20)
>DroYak_CAF1 19896 105 - 1
CUCCUCGGAUUUCCUGGACUAAUUUCAAGGAGGUGGAAAAGCCUGAACAUUGCUGA-AAAUUUCCAC------------UCUCCACGAGCACA-GGGAUGCAAGAGUACAGGGAUUCUG
.....((((.((((((.(((........((((((((((((((.........)))..-...)))))))------------.))))....(((..-....)))...))).)))))).)))) ( -32.30)
>consensus
CUCCUCGGAUUUCCUUGACUAAUUUCAAGGAGGUGGA_AAGCCUGAACAUUGCUGAUGAAUUUCCACCAACUUGGC__CUCUCC__________GG_AU_CAAGAGCGCAGGGAUUCUG
.((((.(....(((((((......)))))))((((((..(((.........)))........))))))........................................).))))..... (-17.38 = -17.86 +   0.48)

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 10:10:34 2006