Locus 4281

Sequence ID	3R_DroMel_CAF1
Location	11,406,110 – 11,406,269
Length	159
Max. P	0.996205

overview

Window 9

Location	11,406,110 – 11,406,229
Length	119
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	91.37
Mean single sequence MFE	-31.40
Consensus MFE	-28.66
Energy contribution	-29.46
Covariance contribution	0.80
Combinations/Pair	1.06
Mean z-score	-1.96
Structure conservation index	0.91
SVM decision value	2.67
SVM RNA-class probability	0.996205
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11406110 119 + 27905053
CUCC-GUGUUUCCCACACCAGUUGUGGAAAUCUCUGAGUUGCCUGAUUCGGAAAUUUGCGAAUUUUGAAUUUUGAUUAGAGAUUAAAUUGUCUCUGGCGAUUAGCAUCAAAUCGUUCGCU
....-.......(((((.....)))))((((.((((((((....)))))))).))))(((((((((((........(((((((......)))))))((.....)).)))))..)))))). ( -33.40)
>DroSec_CAF1 153779 119 + 1
CUCC-GUGUUUCCCCCACCACUAGUGGAAAUCUCUGAGUUGCCUGAUUCGGAAAUUUGCGAAUUUUGAAUUUUGAUUAGAGAUUAAAUUGUCUCUGGCGAUUAGCAUCAAAUCGUUCGCU
....-.........((((.....))))((((.((((((((....)))))))).))))(((((((((((........(((((((......)))))))((.....)).)))))..)))))). ( -32.10)
>DroSim_CAF1 145254 119 + 1
CUCC-GUGUUUCCCACACCAGUAGUGGAAAUCUCUGAGUUGCCUGAUUCGGAAAUUUGCGAAUUUUGAAUUUUGAUUAGAGAUUAAAUUGUCUCUGGCGAUUAGCAUCAAAUCGUUCACU
...(-((.....((((.......))))((((.((((((((....)))))))).))))))).....((((((((((((((((((......)))))))((.....))))))))..))))).. ( -30.10)
>DroEre_CAF1 141592 112 + 1
--------CUACCCACUCCAGUAGUGGAAAUCUCCGAGUUGCCCGCUUCGGAAAUUUGCGAAUUUUGAAUUUUGAUUAGAGAUUAAAUUGUCUCUGGCGAUUAGCAUCAACUCGUUCGCU
--------....(((((.....)))))((((.((((((........)))))).))))((((((.((((........(((((((......)))))))((.....)).))))...)))))). ( -31.10)
>DroYak_CAF1 145247 120 + 1
CUCCCACACUUCCCACUCCAGUAGUCGAAAUCUCCGAGUUGCCUGACUCGGAAAUUUGCGAAUUUUGAAUUUUGAUUAGAGAUUAAAUUGUCUCUGGCGAUUAGCAUCCAAUCGUUCGCU
...........................((((.((((((((....)))))))).))))((((((.(((.........(((((((......)))))))((.....))...)))..)))))). ( -30.30)
>consensus
CUCC_GUGUUUCCCACACCAGUAGUGGAAAUCUCUGAGUUGCCUGAUUCGGAAAUUUGCGAAUUUUGAAUUUUGAUUAGAGAUUAAAUUGUCUCUGGCGAUUAGCAUCAAAUCGUUCGCU
............((((.......))))((((.((((((((....)))))))).))))(((((((((((........(((((((......)))))))((.....)).)))))..)))))). (-28.66 = -29.46 +   0.80)

alignment

secondary structure

dotplot

Window 0

Location	11,406,149 – 11,406,269
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	98.00
Mean single sequence MFE	-33.66
Consensus MFE	-31.26
Energy contribution	-31.86
Covariance contribution	0.60
Combinations/Pair	1.00
Mean z-score	-1.75
Structure conservation index	0.93
SVM decision value	1.75
SVM RNA-class probability	0.975290
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11406149 120 + 27905053
GCCUGAUUCGGAAAUUUGCGAAUUUUGAAUUUUGAUUAGAGAUUAAAUUGUCUCUGGCGAUUAGCAUCAAAUCGUUCGCUCUGCUCGCUGAGCACUGUGCAAACAAGCGUAUGUUUGCAU
....((((((........))))))..(((((((((((((((((......)))))))((.....))))))))..))))((((........))))...(((((((((......))))))))) ( -34.00)
>DroSec_CAF1 153818 120 + 1
GCCUGAUUCGGAAAUUUGCGAAUUUUGAAUUUUGAUUAGAGAUUAAAUUGUCUCUGGCGAUUAGCAUCAAAUCGUUCGCUCUGCUCGCUGAGCACUGUGCAAACAAGCGUAUGUUUGCAU
....((((((........))))))..(((((((((((((((((......)))))))((.....))))))))..))))((((........))))...(((((((((......))))))))) ( -34.00)
>DroSim_CAF1 145293 120 + 1
GCCUGAUUCGGAAAUUUGCGAAUUUUGAAUUUUGAUUAGAGAUUAAAUUGUCUCUGGCGAUUAGCAUCAAAUCGUUCACUCUGCUCGCUGAGCACUGUGCAAACAAGCGUAUGUUUGCAU
....((((((........)))))).((((((((((((((((((......)))))))((.....))))))))..)))))...(((((...)))))..(((((((((......))))))))) ( -32.70)
>DroEre_CAF1 141624 120 + 1
GCCCGCUUCGGAAAUUUGCGAAUUUUGAAUUUUGAUUAGAGAUUAAAUUGUCUCUGGCGAUUAGCAUCAACUCGUUCGCUCUGCUCGCUGAGCACUGUGCAAACAAGCGUAUGUUUGCAU
....(((.(((......((((((.((((........(((((((......)))))))((.....)).))))...))))))........))))))...(((((((((......))))))))) ( -34.04)
>DroYak_CAF1 145287 120 + 1
GCCUGACUCGGAAAUUUGCGAAUUUUGAAUUUUGAUUAGAGAUUAAAUUGUCUCUGGCGAUUAGCAUCCAAUCGUUCGCUCUGCUCGCUGAGCACUGUGCAAACAAGCGUAUGUUUGCAU
...((.(((((......((((((.(((.........(((((((......)))))))((.....))...)))..))))))........)))))))..(((((((((......))))))))) ( -33.54)
>consensus
GCCUGAUUCGGAAAUUUGCGAAUUUUGAAUUUUGAUUAGAGAUUAAAUUGUCUCUGGCGAUUAGCAUCAAAUCGUUCGCUCUGCUCGCUGAGCACUGUGCAAACAAGCGUAUGUUUGCAU
.((......))......(((((((((((........(((((((......)))))))((.....)).)))))..))))))..(((((...)))))..(((((((((......))))))))) (-31.26 = -31.86 +   0.60)

alignment

secondary structure

dotplot

Window 1

Location	11,406,149 – 11,406,269
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	98.00
Mean single sequence MFE	-28.72
Consensus MFE	-27.34
Energy contribution	-27.38
Covariance contribution	0.04
Combinations/Pair	1.03
Mean z-score	-1.66
Structure conservation index	0.95
SVM decision value	1.72
SVM RNA-class probability	0.973828
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11406149 120 - 27905053
AUGCAAACAUACGCUUGUUUGCACAGUGCUCAGCGAGCAGAGCGAACGAUUUGAUGCUAAUCGCCAGAGACAAUUUAAUCUCUAAUCAAAAUUCAAAAUUCGCAAAUUUCCGAAUCAGGC
.((((((((......))))))))...(((((...)))))..((((((((((.......)))))..(((((........)))))...............)))))......((......)). ( -28.40)
>DroSec_CAF1 153818 120 - 1
AUGCAAACAUACGCUUGUUUGCACAGUGCUCAGCGAGCAGAGCGAACGAUUUGAUGCUAAUCGCCAGAGACAAUUUAAUCUCUAAUCAAAAUUCAAAAUUCGCAAAUUUCCGAAUCAGGC
.((((((((......))))))))...(((((...)))))..((((((((((.......)))))..(((((........)))))...............)))))......((......)). ( -28.40)
>DroSim_CAF1 145293 120 - 1
AUGCAAACAUACGCUUGUUUGCACAGUGCUCAGCGAGCAGAGUGAACGAUUUGAUGCUAAUCGCCAGAGACAAUUUAAUCUCUAAUCAAAAUUCAAAAUUCGCAAAUUUCCGAAUCAGGC
.((((((((......))))))))...(((((...)))))..((((((((((.......)))))..(((((........)))))...............)))))......((......)). ( -26.50)
>DroEre_CAF1 141624 120 - 1
AUGCAAACAUACGCUUGUUUGCACAGUGCUCAGCGAGCAGAGCGAACGAGUUGAUGCUAAUCGCCAGAGACAAUUUAAUCUCUAAUCAAAAUUCAAAAUUCGCAAAUUUCCGAAGCGGGC
.((((((((......))))))))...(((((...)))))..(((((.((((((((....)))...(((((........)))))......)))))....))))).....((((...)))). ( -29.40)
>DroYak_CAF1 145287 120 - 1
AUGCAAACAUACGCUUGUUUGCACAGUGCUCAGCGAGCAGAGCGAACGAUUGGAUGCUAAUCGCCAGAGACAAUUUAAUCUCUAAUCAAAAUUCAAAAUUCGCAAAUUUCCGAGUCAGGC
.((((((((......))))))))...(((((...)))))..((((((((((((...)))))))..(((((........)))))...............)))))......((......)). ( -30.90)
>consensus
AUGCAAACAUACGCUUGUUUGCACAGUGCUCAGCGAGCAGAGCGAACGAUUUGAUGCUAAUCGCCAGAGACAAUUUAAUCUCUAAUCAAAAUUCAAAAUUCGCAAAUUUCCGAAUCAGGC
.((((((((......))))))))...(((((...)))))..((((((((((.......)))))..(((((........)))))...............)))))......((......)). (-27.34 = -27.38 +   0.04)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:24:32 2006