Locus 1040

Sequence ID	2L_DroMel_CAF1
Location	2,924,105 – 2,924,204
Length	99
Max. P	0.998707

overview

Window 0

Location	2,924,105 – 2,924,204
Length	99
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	76.09
Mean single sequence MFE	-26.79
Consensus MFE	-15.74
Energy contribution	-15.80
Covariance contribution	0.06
Combinations/Pair	1.08
Mean z-score	-2.45
Structure conservation index	0.59
SVM decision value	2.06
SVM RNA-class probability	0.986981
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 2924105 99 + 22407834
GAACUGAAAAUUGUGGGCACGUGUCCUUUGAGUGGACACGCAACAAAAAGCCCAACUGAAUCUAGAAGUGUAUAUAUACA------UGUAGUAUAU---------------GCAUAUAGU
..((((.......(((((.(((((((.......))))))).........))))).............((((((((((...------....))))))---------------)))).)))) ( -27.20)
>DroSec_CAF1 42294 90 + 1
GAACUGAAAAUUGUGGGCACGUGUCCUUUGAGUGGACACGCAACAAAAAGUCCAAGUGGG-CUAGAAAUGUAGAU--ACA------UGCA-UGUAU---------------GUA-----U
...(((....((((..((..((((((.......)))))))).))))..(((((....)))-)).......)))((--(((------((..-..)))---------------)))-----) ( -24.80)
>DroSim_CAF1 43141 90 + 1
GAACUGAAAAUUGUGGGCACGUGUCCUUUGAGUGGACACGCAACAAAAAGCCCAAGUGGA-CUAGAAAUGUAGAU--ACA------UGCA-UGUAU---------------GUA-----U
...(((.......(((((.(((((((.......))))))).........)))))......-.)))........((--(((------((..-..)))---------------)))-----) ( -23.44)
>DroEre_CAF1 43251 116 + 1
GAACUGAAAAUUGUGGGCACGUGUCCUUUGAGGCGACACGCAACAAAAAGCCCAAGUGGG-CUGCCAAUGUAUAU--AUAUGUACAUACA-UACUUAUAUUUUAAAAAGUCGCAUAUAGU
..((((.....(((((((.((((((((....)).))))))........(((((....)))-)))))...(((((.--.(((((....)))-))..)))))..........))))..)))) ( -31.70)
>consensus
GAACUGAAAAUUGUGGGCACGUGUCCUUUGAGUGGACACGCAACAAAAAGCCCAAGUGGA_CUAGAAAUGUAGAU__ACA______UGCA_UAUAU_______________GCA_____U
.............(((((.(((((((.......))))))).........))))).................................................................. (-15.74 = -15.80 +   0.06)

alignment

secondary structure

dotplot

Window 1

Location	2,924,105 – 2,924,204
Length	99
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	76.09
Mean single sequence MFE	-24.27
Consensus MFE	-16.42
Energy contribution	-16.92
Covariance contribution	0.50
Combinations/Pair	1.00
Mean z-score	-2.63
Structure conservation index	0.68
SVM decision value	3.19
SVM RNA-class probability	0.998707
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 2924105 99 - 22407834
ACUAUAUGC---------------AUAUACUACA------UGUAUAUAUACACUUCUAGAUUCAGUUGGGCUUUUUGUUGCGUGUCCACUCAAAGGACACGUGCCCACAAUUUUCAGUUC
..(((((((---------------((.......)------))))))))..........((......(((((........((((((((.......)))))))))))))......))..... ( -26.60)
>DroSec_CAF1 42294 90 - 1
A-----UAC---------------AUACA-UGCA------UGU--AUCUACAUUUCUAG-CCCACUUGGACUUUUUGUUGCGUGUCCACUCAAAGGACACGUGCCCACAAUUUUCAGUUC
(-----(((---------------((...-...)------)))--))............-.......(((((..(((((((((((((.......)))))))))...)))).....))))) ( -18.40)
>DroSim_CAF1 43141 90 - 1
A-----UAC---------------AUACA-UGCA------UGU--AUCUACAUUUCUAG-UCCACUUGGGCUUUUUGUUGCGUGUCCACUCAAAGGACACGUGCCCACAAUUUUCAGUUC
(-----(((---------------((...-...)------)))--))............-......(((((........((((((((.......)))))))))))))............. ( -22.10)
>DroEre_CAF1 43251 116 - 1
ACUAUAUGCGACUUUUUAAAAUAUAAGUA-UGUAUGUACAUAU--AUAUACAUUGGCAG-CCCACUUGGGCUUUUUGUUGCGUGUCGCCUCAAAGGACACGUGCCCACAAUUUUCAGUUC
.........((((.............(((-((((((....)))--))))))...(((((-(((....))))).......(((((((.........))))))))))..........)))). ( -30.00)
>consensus
A_____UAC_______________AUACA_UGCA______UGU__AUAUACAUUUCUAG_CCCACUUGGGCUUUUUGUUGCGUGUCCACUCAAAGGACACGUGCCCACAAUUUUCAGUUC
..................................................................(((((........((((((((.......)))))))))))))............. (-16.42 = -16.92 +   0.50)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:51:46 2006