Locus 2896

Sequence ID	2R_DroMel_CAF1
Location	10,002,528 – 10,002,629
Length	101
Max. P	0.999307

overview

Window 9

Location	10,002,528 – 10,002,629
Length	101
Sequences	5
Columns	101
Reading direction	forward
Mean pairwise identity	79.91
Mean single sequence MFE	-19.86
Consensus MFE	-13.08
Energy contribution	-13.48
Covariance contribution	0.40
Combinations/Pair	1.12
Mean z-score	-3.69
Structure conservation index	0.66
SVM decision value	3.50
SVM RNA-class probability	0.999307
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 10002528 101 + 20766785
GCUGGUCAAUCACAGUUAACCACCCCUUUGACCCCACAUAAAUACAUAUGGAAAAAUAAAUACAUUUAUGUACAUACAUAUACAUAUGACCAGCUGCUUGC
((((((((.((...(((((........)))))....((((......))))))..............((((((........))))))))))))))....... ( -19.90)
>DroSec_CAF1 5682 89 + 1
GCUGGUCAAUCAGAGUUAACCACCCCUUUGACCCCACAUAAAUACAUAUGGAAAAAUAAAUACAUAUAUGU------------AUAUGACCAGCUGCUUGU
((((((((.((((((..........))))))..........(((((((((..............)))))))------------)).))))))))....... ( -23.84)
>DroSim_CAF1 6059 89 + 1
GCUGGUCAAUCAGAGUUAACCACCCCUUUAACCCCACAUAAAUACAUAUGGAAAAAUAAAUACAUAUAUGU------------AUAUGACCAGCUGCUUGC
((((((((......(((((........))))).........(((((((((..............)))))))------------)).))))))))....... ( -21.44)
>DroEre_CAF1 5943 77 + 1
ACUGGUCAAUCAGAGUUAGCCACCCCUUUAACCCUGCAUAAAUA--UAUGAAAAAAUACAU----------------------AUAUGACCAGCUGCUCGC
.((((((...(((.(((((........))))).))).....(((--((((........)))----------------------))))))))))........ ( -18.10)
>DroYak_CAF1 5968 77 + 1
ACUGGUCAAUCAGAGUUAACCACCCCUUAACCCCCUCAUAAAUA--UAUGGAAAAAUACAU----------------------AUAUGACCAGCUGGUGGC
.((((((.......(((((.......)))))..........(((--((((........)))----------------------))))))))))........ ( -16.00)
>consensus
GCUGGUCAAUCAGAGUUAACCACCCCUUUAACCCCACAUAAAUACAUAUGGAAAAAUAAAUACAU_UAUGU____________AUAUGACCAGCUGCUUGC
((((((((......(((((........)))))....((((......))))....................................))))))))....... (-13.08 = -13.48 +   0.40)

alignment

secondary structure

dotplot

Window 0

Location	10,002,528 – 10,002,629
Length	101
Sequences	5
Columns	101
Reading direction	reverse
Mean pairwise identity	79.91
Mean single sequence MFE	-25.04
Consensus MFE	-19.46
Energy contribution	-20.66
Covariance contribution	1.20
Combinations/Pair	1.09
Mean z-score	-2.63
Structure conservation index	0.78
SVM decision value	2.39
SVM RNA-class probability	0.993378
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 10002528 101 - 20766785
GCAAGCAGCUGGUCAUAUGUAUAUGUAUGUACAUAAAUGUAUUUAUUUUUCCAUAUGUAUUUAUGUGGGGUCAAAGGGGUGGUUAACUGUGAUUGACCAGC
.......((((((((((((((((....))))))))..............((((((((....))))))))((((.((..(....)..)).)))))))))))) ( -28.90)
>DroSec_CAF1 5682 89 - 1
ACAAGCAGCUGGUCAUAU------------ACAUAUAUGUAUUUAUUUUUCCAUAUGUAUUUAUGUGGGGUCAAAGGGGUGGUUAACUCUGAUUGACCAGC
.......((((((((.((------------(((....)))))......(((((((((....))))))))).....(((((.....)))))...)))))))) ( -26.20)
>DroSim_CAF1 6059 89 - 1
GCAAGCAGCUGGUCAUAU------------ACAUAUAUGUAUUUAUUUUUCCAUAUGUAUUUAUGUGGGGUUAAAGGGGUGGUUAACUCUGAUUGACCAGC
.......((((((((..(------------(((....))))((((...(((((((((....))))))))).))))(((((.....)))))...)))))))) ( -26.40)
>DroEre_CAF1 5943 77 - 1
GCGAGCAGCUGGUCAUAU----------------------AUGUAUUUUUUCAUA--UAUUUAUGCAGGGUUAAAGGGGUGGCUAACUCUGAUUGACCAGU
.......(((((((((((----------------------(((........))))--))......((((((((..........))))))))..)))))))) ( -22.90)
>DroYak_CAF1 5968 77 - 1
GCCACCAGCUGGUCAUAU----------------------AUGUAUUUUUCCAUA--UAUUUAUGAGGGGGUUAAGGGGUGGUUAACUCUGAUUGACCAGU
.......(((((((((((----------------------(((........))))--))........((((((((.......))))))))...)))))))) ( -20.80)
>consensus
GCAAGCAGCUGGUCAUAU____________ACAUA_AUGUAUUUAUUUUUCCAUAUGUAUUUAUGUGGGGUUAAAGGGGUGGUUAACUCUGAUUGACCAGC
.......((((((((.................................(((((((((....))))))))).....(((((.....)))))...)))))))) (-19.46 = -20.66 +   1.20)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:42:10 2006