Locus 3628

Sequence ID 2R_DroMel_CAF1
Location 12,025,255 – 12,025,347
Length 92
Max. P 0.970503
window5903 window5904

overview

Window 3

Location 12,025,255 – 12,025,347
Length 92
Sequences 6
Columns 101
Reading direction forward
Mean pairwise identity 76.48
Mean single sequence MFE -25.25
Consensus MFE -14.74
Energy contribution -16.30
Covariance contribution 1.56
Combinations/Pair 1.05
Mean z-score -2.29
Structure conservation index 0.58
SVM decision value 1.66
SVM RNA-class probability 0.970503
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 12025255 92 + 20766785
CCAAAUGGCAGAAAUGGCGAGAUGGC------GCA---GCGGCUGCAACUUAGUAAGCCUACUUACUUAAUGGCAACAAAGAAGCAAUCCUUUGUUUGUUC
(((....((((.....(((......)------)).---....)))).....((((((....))))))...))).(((((((........)))))))..... ( -21.30)
>DroSec_CAF1 26570 98 + 1
CCAAAUGGCAGAAAUGGCGAGAUGGCGAGAUGGCA---GCGGCUGCAACUUAGUAAGCCUACUUACUUAAUGGCAACAAAGGAGCAAUCCUUUGUUUGCUC
(((..((.((....)).))...))).(((...(((---(...))))..)))((((((....))))))....((((((((((((....))))))).))))). ( -29.10)
>DroEre_CAF1 26427 83 + 1
CCAAAUGCU---------------GCGAGAUGGCA---GUGGCUGCAACUUAGUAAGCCUACUUACUUAAUGGCAACAAAGGAGCAAUCCUUUGUUUGUUC
......(((---------------((......)))---))....((.....((((((....)))))).....))(((((((((....)))))))))..... ( -26.20)
>DroYak_CAF1 26386 86 + 1
CCAAAUGCU---------------GCGAGAUGGCAGCCGUGGCUGCAACUUAGUAAGCCUACUUACUUAAUGGCAACAAAGGAGCAAGCCUUUGUUUGUUC
(((...(((---------------((......)))))..)))..((.....((((((....)))))).....))((((((((......))))))))..... ( -27.10)
>DroMoj_CAF1 32071 71 + 1
UC----GU-----------------------UGCU---GCAGCUGCAACUUAGUAAGCCUACUUACUUAAUGGCAACAAAGGCACAAUUCAUUGUUUGUGC
..----((-----------------------((((---((....)).....((((((....))))))....))))))....((((((........)))))) ( -19.90)
>DroAna_CAF1 22288 81 + 1
CUAACUGCU---------------UC--GACGGCA---GUUGCUGCAACUUAGUAAGCCUACUUACUUAAUGGCAACAAAGGAGCAAUCCUUUGUUUGUAC
.((((((((---------------..--...))))---))))..((.....((((((....)))))).....))(((((((((....)))))))))..... ( -27.90)
>consensus
CCAAAUGCU_______________GC__GAUGGCA___GCGGCUGCAACUUAGUAAGCCUACUUACUUAAUGGCAACAAAGGAGCAAUCCUUUGUUUGUUC
................................((.......)).((.....((((((....)))))).....))(((((((((....)))))))))..... (-14.74 = -16.30 +   1.56)

alignment

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secondary structure

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dotplot

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Window 4

Location 12,025,255 – 12,025,347
Length 92
Sequences 6
Columns 101
Reading direction reverse
Mean pairwise identity 76.48
Mean single sequence MFE -24.23
Consensus MFE -16.61
Energy contribution -16.83
Covariance contribution 0.22
Combinations/Pair 1.05
Mean z-score -1.98
Structure conservation index 0.69
SVM decision value 1.59
SVM RNA-class probability 0.966127
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 12025255 92 - 20766785
GAACAAACAAAGGAUUGCUUCUUUGUUGCCAUUAAGUAAGUAGGCUUACUAAGUUGCAGCCGC---UGC------GCCAUCUCGCCAUUUCUGCCAUUUGG
.....(((((((((....)))))))))((((((.....))).)))...((((((.((((....---.((------(......))).....)))).)))))) ( -21.60)
>DroSec_CAF1 26570 98 - 1
GAGCAAACAAAGGAUUGCUCCUUUGUUGCCAUUAAGUAAGUAGGCUUACUAAGUUGCAGCCGC---UGCCAUCUCGCCAUCUCGCCAUUUCUGCCAUUUGG
.(((.(((((((((....)))))))))((.(((.((((((....)))))).))).))....))---).........(((....((.......))....))) ( -24.60)
>DroEre_CAF1 26427 83 - 1
GAACAAACAAAGGAUUGCUCCUUUGUUGCCAUUAAGUAAGUAGGCUUACUAAGUUGCAGCCAC---UGCCAUCUCGC---------------AGCAUUUGG
.....(((((((((....)))))))))((.(((.((((((....)))))).))).))..((((---(((......))---------------))....))) ( -24.10)
>DroYak_CAF1 26386 86 - 1
GAACAAACAAAGGCUUGCUCCUUUGUUGCCAUUAAGUAAGUAGGCUUACUAAGUUGCAGCCACGGCUGCCAUCUCGC---------------AGCAUUUGG
.....((((((((......))))))))((.(((.((((((....)))))).))).))..(((..(((((......))---------------)))...))) ( -27.70)
>DroMoj_CAF1 32071 71 - 1
GCACAAACAAUGAAUUGUGCCUUUGUUGCCAUUAAGUAAGUAGGCUUACUAAGUUGCAGCUGC---AGCA-----------------------AC----GA
((((((........))))))..(((((((.....((((((....))))))....(((....))---))))-----------------------))----)) ( -21.50)
>DroAna_CAF1 22288 81 - 1
GUACAAACAAAGGAUUGCUCCUUUGUUGCCAUUAAGUAAGUAGGCUUACUAAGUUGCAGCAAC---UGCCGUC--GA---------------AGCAGUUAG
((...(((((((((....)))))))))((.(((.((((((....)))))).))).)).))(((---(((....--..---------------.)))))).. ( -25.90)
>consensus
GAACAAACAAAGGAUUGCUCCUUUGUUGCCAUUAAGUAAGUAGGCUUACUAAGUUGCAGCCAC___UGCCAUC__GC_______________AGCAUUUGG
.....((((((((......))))))))((.(((.((((((....)))))).))).))............................................ (-16.61 = -16.83 +   0.22)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:00:14 2006