Locus 4781

Sequence ID 3L_DroMel_CAF1
Location 13,402,625 – 13,402,759
Length 134
Max. P 0.963296
window7530 window7531

overview

Window 0

Location 13,402,625 – 13,402,725
Length 100
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 75.75
Mean single sequence MFE -16.73
Consensus MFE -11.01
Energy contribution -11.23
Covariance contribution 0.23
Combinations/Pair 1.10
Mean z-score -1.55
Structure conservation index 0.66
SVM decision value 0.48
SVM RNA-class probability 0.751022
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13402625 100 - 23771897
--------------------AAUUUUCUAAACACAAUAUCUCAUAAGUAACCUUGAGAUAAUGUUUAACACCAAUUUCUAAAUUACAUCUGAUGGUCAAAGUCUAUUGGGAAAUUAAGAA
--------------------.......((((((...(((((((..........))))))).))))))........((((.((((...((..((((.......))))..)).)))).)))) ( -16.70)
>DroSec_CAF1 2869 114 - 1
UGACAAGAUAUCUAUCUGAAAGUUUUCUGAACACAAUAUCUCAUAAGUUACCUUGAGAUAAUGUUUAAUACCAACUUCUAAAUUUCAUCUGAAG------GUCUAUUGACAUAUUAGGAA
.....((((....))))..........((((((...(((((((..........))))))).))))))...((..((((............))))------(((....)))......)).. ( -18.20)
>DroSim_CAF1 6179 91 - 1
-----------------------UUUCUGAACACAAUAUCUCAUAAGUUACCUUGAGAUAAUGUUUAAUACCAACUUCUAAAUUACAUCUGAAG------AUCUAUUGACAUAUUAGGAA
-----------------------.((((((......(((((((..........)))))))(((((.((((....((((............))))------...))))))))).)))))). ( -15.30)
>consensus
____________________A_UUUUCUGAACACAAUAUCUCAUAAGUUACCUUGAGAUAAUGUUUAAUACCAACUUCUAAAUUACAUCUGAAG______GUCUAUUGACAUAUUAGGAA
.......................(((((((..(((.(((((((..........))))))).)))..........((((............))))...................))))))) (-11.01 = -11.23 +   0.23)

alignment

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secondary structure

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dotplot

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Window 1

Location 13,402,665 – 13,402,759
Length 94
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 72.07
Mean single sequence MFE -18.00
Consensus MFE -11.73
Energy contribution -11.73
Covariance contribution 0.01
Combinations/Pair 1.15
Mean z-score -1.66
Structure conservation index 0.65
SVM decision value 1.55
SVM RNA-class probability 0.963296
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13402665 94 - 23771897
CAAAAAUUCACGGUAAAUGGGAAUAGAUGUUGUC--------------------------AAUUUUCUAAACACAAUAUCUCAUAAGUAACCUUGAGAUAAUGUUUAACACCAAUUUCUA
...........(((....(..(((.(((...)))--------------------------.)))..)((((((...(((((((..........))))))).))))))..)))........ ( -16.30)
>DroSec_CAF1 2903 119 - 1
-UAUUAUUCACGGUAAAUGGGAAUAAACAUCGGCACGUGAUGACAAGAUAUCUAUCUGAAAGUUUUCUGAACACAAUAUCUCAUAAGUUACCUUGAGAUAAUGUUUAAUACCAACUUCUA
-..........((((...(..(((...(((((.....)))))...((((....))))....)))..)((((((...(((((((..........))))))).)))))).))))........ ( -21.80)
>DroSim_CAF1 6213 85 - 1
-UAUUAUUCACGGUAAAUGGGAAUAAACG----------------------------------UUUCUGAACACAAUAUCUCAUAAGUUACCUUGAGAUAAUGUUUAAUACCAACUUCUA
-..........((((...((((((....)----------------------------------)))))(((((...(((((((..........))))))).)))))..))))........ ( -15.90)
>consensus
_UAUUAUUCACGGUAAAUGGGAAUAAACGU_G_C__________________________A_UUUUCUGAACACAAUAUCUCAUAAGUUACCUUGAGAUAAUGUUUAAUACCAACUUCUA
...........((((.(((........))).....................................((((((...(((((((..........))))))).)))))).))))........ (-11.73 = -11.73 +   0.01)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:33:09 2006