Locus 1650

Sequence ID X_DroMel_CAF1
Location 4,666,070 – 4,666,197
Length 127
Max. P 0.876934
window2712 window2713

overview

Window 2

Location 4,666,070 – 4,666,166
Length 96
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 76.69
Mean single sequence MFE -23.87
Consensus MFE -14.23
Energy contribution -14.98
Covariance contribution 0.75
Combinations/Pair 1.05
Mean z-score -2.04
Structure conservation index 0.60
SVM decision value 0.90
SVM RNA-class probability 0.876934
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4666070 96 + 22224390
GCUAAUCGAUGAGC---------------------AAAUAGUGCACUCGUCUAAUCGAUGACUUUCUGAUAGCCUCGAUUGCACUUC---CUUCACUUAUUUCCCAGCCCAAUCGCUGCU
.......((((((.---------------------....((((((.(((.(((.((((......)).)))))...))).))))))..---.....))))))...((((......)))).. ( -19.60)
>DroSec_CAF1 27398 90 + 1
GCUAAUCGAUUGGC---------------------AAAUAGUGCACUCGUCUAAUCGAUGACUUUCUGAUAGUCUCGAUUCCCCCUC---C------UAUUUCCCAGUCCAAUCGCUGCU
((.....((((((.---------------------((((((.(.........((((((.((((.......))))))))))......)---)------))))).)))))).....)).... ( -20.56)
>DroEre_CAF1 28135 99 + 1
GCUAAUCGAUUGGC---------------------AAAUAGUGCACUCGUCUAAUCGAUGACUUUCUGAUAGUCUCGAUUGCACUUCUACUCCUACUUAGUGCCCACCCCAAUUGCUGCU
((....(((((((.---------------------.................((((((.((((.......))))))))))(((((.............))))).....)))))))..)). ( -22.62)
>DroYak_CAF1 24605 118 + 1
GCUAAUCGAUUGGUAAAUGGCAAAUGGUAAAUGGUAAAUAGUGCACUAUUCUAAUCGAUGACUUUCUGAUAGUCUCGAUUGCACUU--GCCUCUACUUAUUUCCCGCCCCAAUUGCUGCU
((....(((((((....(((.((((((((...((((...((((((........(((((.((((.......))))))))))))))))--)))..))).))))).)))..)))))))..)). ( -32.70)
>consensus
GCUAAUCGAUUGGC_____________________AAAUAGUGCACUCGUCUAAUCGAUGACUUUCUGAUAGUCUCGAUUGCACUUC___CUCUACUUAUUUCCCACCCCAAUCGCUGCU
((....(((((((..........................((....))....(((((((.((((.......)))))))))))...........................)))))))..)). (-14.23 = -14.98 +   0.75)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 3

Location 4,666,089 – 4,666,197
Length 108
Sequences 4
Columns 111
Reading direction forward
Mean pairwise identity 87.44
Mean single sequence MFE -26.70
Consensus MFE -19.15
Energy contribution -19.65
Covariance contribution 0.50
Combinations/Pair 1.04
Mean z-score -1.90
Structure conservation index 0.72
SVM decision value 0.48
SVM RNA-class probability 0.753638
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4666089 108 + 22224390
GUGCACUCGUCUAAUCGAUGACUUUCUGAUAGCCUCGAUUGCACUUC---CUUCACUUAUUUCCCAGCCCAAUCGCUGCUCGAUUCACGCCUCAUUUGAGUGGGGCCAAAA
(((((.(((.(((.((((......)).)))))...))).)))))...---..............((((......))))..........(((((((....)))))))..... ( -25.60)
>DroSec_CAF1 27417 102 + 1
GUGCACUCGUCUAAUCGAUGACUUUCUGAUAGUCUCGAUUCCCCCUC---C------UAUUUCCCAGUCCAAUCGCUGCUCGAUUCACGCCUCAUUUGAGUGGGGCCAAAA
(((...(((...((((((.((((.......)))))))))).......---.------.......((((......))))..)))..)))(((((((....)))))))..... ( -24.80)
>DroEre_CAF1 28154 110 + 1
GUGCACUCGUCUAAUCGAUGACUUUCUGAUAGUCUCGAUUGCACUUCUACUCCUACUUAGUGCCCACCCCAAUUGCUGCUCGAUUCACGCCUCAUUUGAGUGG-GCCAAAA
(((((........(((((.((((.......))))))))))))))...............(.((((((..(((.((..((.........))..)).))).))))-))).... ( -28.60)
>DroYak_CAF1 24645 109 + 1
GUGCACUAUUCUAAUCGAUGACUUUCUGAUAGUCUCGAUUGCACUU--GCCUCUACUUAUUUCCCGCCCCAAUUGCUGCUCGAUUCACGCCUCAUUUGAGUGGGGCCAAAA
(((((........(((((.((((.......))))))))))))))..--(((.(((((((......((...(((((.....)))))...))......))))))))))..... ( -27.80)
>consensus
GUGCACUCGUCUAAUCGAUGACUUUCUGAUAGUCUCGAUUGCACUUC___CUCUACUUAUUUCCCACCCCAAUCGCUGCUCGAUUCACGCCUCAUUUGAGUGGGGCCAAAA
(((........(((((((.((((.......))))))))))).............................(((((.....))))))))(((((((....)))))))..... (-19.15 = -19.65 +   0.50)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:15:47 2006