Locus 1640

Sequence ID X_DroMel_CAF1
Location 4,660,072 – 4,660,173
Length 101
Max. P 0.882081
window2691 window2692

overview

Window 1

Location 4,660,072 – 4,660,173
Length 101
Sequences 4
Columns 101
Reading direction forward
Mean pairwise identity 93.22
Mean single sequence MFE -32.12
Consensus MFE -25.20
Energy contribution -25.07
Covariance contribution -0.13
Combinations/Pair 1.08
Mean z-score -3.45
Structure conservation index 0.78
SVM decision value 0.92
SVM RNA-class probability 0.882081
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4660072 101 + 22224390
CGAAGGGGGGGAGCGGAAAAAAAAAAGAAAAUACGGGAAAAGCGUCUACAUGAGACGCAUAUUUAAUUUCCCCCGACCCCUUGGUCCUGUCACGAAAGGAU
....((((((...(((..........(......)((((((.((((((.....))))))........))))))))).)))))).(((((........))))) ( -30.80)
>DroSec_CAF1 21477 94 + 1
CG----GGGGGAGCGAAAA---AAAAGAAAAUACGGGAAAAGCGUCUACAUGAGACGCAUAUUUAAUUCCCCCCGACCCCUUGGUCCUGUCACGAAAGGAU
.(----(((((((..(((.---....(......).......((((((.....))))))...)))..))))))))((((....))))..(((.(....)))) ( -31.60)
>DroSim_CAF1 10425 95 + 1
CG----GGGGGAGCGAAAA--AAAAAGAAAAUACGGGAAAAGCGUCUACAUGAGACGCAUAUUUAAUUCCCCCCGACCCCUUGGUCCUGUCACGAAAGGAU
.(----(((((((..(((.--.....(......).......((((((.....))))))...)))..))))))))((((....))))..(((.(....)))) ( -31.60)
>DroEre_CAF1 22316 95 + 1
CG----GGGGGAGUGAAA--AAAAAGGAAAAUACGGGAAAAGCGUCUACAUGAGACGCAUAUUUAAUUCCCCCCGACCCCUUCGUCCUGUCACGAAAGGAU
((----((((((((.(((--.....(.......).......((((((.....))))))...))).))))))))))..((.(((((......))))).)).. ( -34.50)
>consensus
CG____GGGGGAGCGAAAA__AAAAAGAAAAUACGGGAAAAGCGUCUACAUGAGACGCAUAUUUAAUUCCCCCCGACCCCUUGGUCCUGUCACGAAAGGAU
......(((((((..(((........(......).......((((((.....))))))...)))..))))))).((((....))))..(((.(....)))) (-25.20 = -25.07 +  -0.13)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 2

Location 4,660,072 – 4,660,173
Length 101
Sequences 4
Columns 101
Reading direction reverse
Mean pairwise identity 93.22
Mean single sequence MFE -29.94
Consensus MFE -23.99
Energy contribution -23.80
Covariance contribution -0.19
Combinations/Pair 1.05
Mean z-score -2.46
Structure conservation index 0.80
SVM decision value 0.89
SVM RNA-class probability 0.875576
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4660072 101 - 22224390
AUCCUUUCGUGACAGGACCAAGGGGUCGGGGGAAAUUAAAUAUGCGUCUCAUGUAGACGCUUUUCCCGUAUUUUCUUUUUUUUUUCCGCUCCCCCCCUUCG
.((((........))))..((((((..((((((((..(((...((((((.....)))))).......(......)..)))..))))).)))..)))))).. ( -28.10)
>DroSec_CAF1 21477 94 - 1
AUCCUUUCGUGACAGGACCAAGGGGUCGGGGGGAAUUAAAUAUGCGUCUCAUGUAGACGCUUUUCCCGUAUUUUCUUUU---UUUUCGCUCCCCC----CG
(((((((.((......)).)))))))((((((((.........((((((.....))))))......((...........---....)).))))))----)) ( -28.76)
>DroSim_CAF1 10425 95 - 1
AUCCUUUCGUGACAGGACCAAGGGGUCGGGGGGAAUUAAAUAUGCGUCUCAUGUAGACGCUUUUCCCGUAUUUUCUUUUU--UUUUCGCUCCCCC----CG
(((((((.((......)).)))))))((((((((.........((((((.....)))))).......(......).....--.......))))))----)) ( -28.70)
>DroEre_CAF1 22316 95 - 1
AUCCUUUCGUGACAGGACGAAGGGGUCGGGGGGAAUUAAAUAUGCGUCUCAUGUAGACGCUUUUCCCGUAUUUUCCUUUUU--UUUCACUCCCCC----CG
((((((((((......))))))))))((((((((.........((((((.....)))))).......(......)......--......))))))----)) ( -34.20)
>consensus
AUCCUUUCGUGACAGGACCAAGGGGUCGGGGGGAAUUAAAUAUGCGUCUCAUGUAGACGCUUUUCCCGUAUUUUCUUUUU__UUUUCGCUCCCCC____CG
.((((........))))....((((.((((..((.........((((((.....))))))))..))))......................))))....... (-23.99 = -23.80 +  -0.19)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:15:28 2006