Locus 4654

Sequence ID X_DroMel_CAF1
Location 12,169,713 – 12,169,865
Length 152
Max. P 0.922744
window7640 window7641

overview

Window 0

Location 12,169,713 – 12,169,833
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 72.32
Mean single sequence MFE -16.79
Consensus MFE -12.50
Energy contribution -13.17
Covariance contribution 0.67
Combinations/Pair 1.00
Mean z-score -1.16
Structure conservation index 0.74
SVM decision value 0.60
SVM RNA-class probability 0.794722
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 12169713 120 + 22224390
CAAAGCCAGUGCAUCACCACAUACCCCAUCAUCCCCGCCGUUACCAUCCCAUCCUCUAUCUCCAUCUGCAACUGCAGCUGCAGUUAAAUAUUCAAAUUUAUACAAAGCAUCUUCAGGUGC
....(((.(((......)))..............................................(((((((((....))))))((((......)))).......)))......))).. ( -13.90)
>DroEre_CAF1 22052 94 + 1
--------------------CUCAACCAGCAGCUCCUCCAUU------CCAAUCUGCAUCUGCAACUACAGCUACAGCUGCAGUUAAAUAUUCAAAUUUAUACAAAGCAUCUUCAGGUGC
--------------------....(((.((((..........------.....))))...(((((((.((((....)))).))))((((......)))).......)))......))).. ( -16.06)
>DroYak_CAF1 22707 114 + 1
CAAAGCAAGUGCAUCGCCACCUUCGCCACCAUCACCGCCGUC------GCAAUCUCCAUCUCCAUCUGCAGCUGCAGCUGCAGUUAAAUAUUCAAAUUUAUACAAAGCAUCUUCAGGUGC
....((....)).....(((((..((..........))....------((...............(((((((....))))))).(((((......)))))......))......))))). ( -20.40)
>consensus
CAAAGC_AGUGCAUC_CCACCUACACCACCAUCACCGCCGUU______CCAAUCUCCAUCUCCAUCUGCAGCUGCAGCUGCAGUUAAAUAUUCAAAUUUAUACAAAGCAUCUUCAGGUGC
.................................................................(((((((....))))))).......................(((((....))))) (-12.50 = -13.17 +   0.67)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 1

Location 12,169,753 – 12,169,865
Length 112
Sequences 3
Columns 112
Reading direction forward
Mean pairwise identity 89.09
Mean single sequence MFE -25.53
Consensus MFE -24.01
Energy contribution -24.23
Covariance contribution 0.23
Combinations/Pair 1.07
Mean z-score -1.98
Structure conservation index 0.94
SVM decision value 1.15
SVM RNA-class probability 0.922744
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 12169753 112 + 22224390
UUACCAUCCCAUCCUCUAUCUCCAUCUGCAACUGCAGCUGCAGUUAAAUAUUCAAAUUUAUACAAAGCAUCUUCAGGUGCUCGUUGAGCAGUUUUGUGUUGCCUGUUUACCA
...........................(((((.((((((((...(((((......)))))..(((((((((....))))))..))).)))))..)))))))).......... ( -22.20)
>DroEre_CAF1 22072 106 + 1
UU------CCAAUCUGCAUCUGCAACUACAGCUACAGCUGCAGUUAAAUAUUCAAAUUUAUACAAAGCAUCUUCAGGUGCUCGUUGAGCAGUUGUGUGUUGCCUGUUUACCA
..------.((((..(((.((((((((.((((....)))).)))).................(((((((((....))))))..))).)))).)))..))))........... ( -27.40)
>DroYak_CAF1 22747 106 + 1
UC------GCAAUCUCCAUCUCCAUCUGCAGCUGCAGCUGCAGUUAAAUAUUCAAAUUUAUACAAAGCAUCUUCAGGUGCUCGUUGAGCAGUUGUGUGUUGCCUGUUUACCA
..------...................((((((((((((((...(((((......)))))..(((((((((....))))))..))).))))))))).))))).......... ( -27.00)
>consensus
UU______CCAAUCUCCAUCUCCAUCUGCAGCUGCAGCUGCAGUUAAAUAUUCAAAUUUAUACAAAGCAUCUUCAGGUGCUCGUUGAGCAGUUGUGUGUUGCCUGUUUACCA
...........................((((((((((((((...(((((......)))))..(((((((((....))))))..))).))))))))).))))).......... (-24.01 = -24.23 +   0.23)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:30:14 2006