Locus 5652

Sequence ID	2R_DroMel_CAF1
Location	17,954,719 – 17,954,879
Length	160
Max. P	0.924065

overview

Window 1

Location	17,954,719 – 17,954,839
Length	120
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	97.78
Mean single sequence MFE	-31.05
Consensus MFE	-29.02
Energy contribution	-29.78
Covariance contribution	0.75
Combinations/Pair	1.00
Mean z-score	-2.10
Structure conservation index	0.93
SVM decision value	0.78
SVM RNA-class probability	0.849124
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17954719 120 - 20766785
CGCAGAAAUUGGCUUGCCAAAAUUUAGAAAAUAAACCGAAUUGCUUGCAUCAAUUAGCCGAGCAAUUCGAGGGAGCCCAAACAAACAGGGCAACUUUUUUCGGCUUUUUACAAAGUUUGU
.(((((..(((....(((..................((((((((((((........).)))))))))))(((..((((.........))))..))).....)))......)))..))))) ( -33.20)
>DroSec_CAF1 11984 120 - 1
CGCAGAAAUUGGCUUGCCAAAAUUUAGAAAAUAAACCGAAUUGCUUGCAUUAAUUAGCCGAGCCAUUCGAGGGAGCCCAAACAAACAGGGCAACUUUUUUCGGCUUUUUACAAAGUUUGU
.(((((..(((....(((..................(((((.((((((........).))))).)))))(((..((((.........))))..))).....)))......)))..))))) ( -29.10)
>DroSim_CAF1 7718 120 - 1
CGCAGAAAUUGGCUUGCCAAAAUUUAGAAAAUAAACCGAAUUGCUUGCAUCAAUUAGCCGAGCCAUUCGAGGGAGCCCAAACAAACAGGGCAACUUUUUUCGGCUUUUUACAAAGUUUGU
.(((((..(((....(((..................(((((.((((((........).))))).)))))(((..((((.........))))..))).....)))......)))..))))) ( -29.10)
>DroEre_CAF1 16673 119 - 1
CGCAGAAAUUGGCUUGCCAAAAUUUAGAAAAUAAACCGAAUUGCUUGCAUCAAUUAGCCGAGCAAUUCGAGGGAGCCCAAACAAACAG-GCAACUUUUUUCGGCUUUUCCCAAAGUUUGU
.((.((((..((.(((((..................((((((((((((........).))))))))))).((....)).........)-))))))..)))).))................ ( -32.80)
>consensus
CGCAGAAAUUGGCUUGCCAAAAUUUAGAAAAUAAACCGAAUUGCUUGCAUCAAUUAGCCGAGCAAUUCGAGGGAGCCCAAACAAACAGGGCAACUUUUUUCGGCUUUUUACAAAGUUUGU
.(((((..(((....(((..................((((((((((((........).)))))))))))(((..((((.........))))..))).....)))......)))..))))) (-29.02 = -29.78 +   0.75)

alignment

secondary structure

dotplot

Window 2

Location	17,954,759 – 17,954,879
Length	120
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	98.61
Mean single sequence MFE	-35.08
Consensus MFE	-35.12
Energy contribution	-35.62
Covariance contribution	0.50
Combinations/Pair	1.00
Mean z-score	-2.33
Structure conservation index	1.00
SVM decision value	1.16
SVM RNA-class probability	0.924065
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17954759 120 - 20766785
CUGGCACUCCUGCCAAACGGAGAACUUUAUCCGGGAUUACCGCAGAAAUUGGCUUGCCAAAAUUUAGAAAAUAAACCGAAUUGCUUGCAUCAAUUAGCCGAGCAAUUCGAGGGAGCCCAA
.(((..((((((((((.((((........))))((....)).......))))).......................((((((((((((........).))))))))))).))))).))). ( -37.10)
>DroSec_CAF1 12024 120 - 1
GUGGCACUCCUGCCAAACGGAGAACUUUAUCCGGGAUUACCGCAGAAAUUGGCUUGCCAAAAUUUAGAAAAUAAACCGAAUUGCUUGCAUUAAUUAGCCGAGCCAUUCGAGGGAGCCCAA
.(((..((((((((((.((((........))))((....)).......))))).......................(((((.((((((........).))))).))))).))))).))). ( -33.10)
>DroSim_CAF1 7758 120 - 1
CUGGCACUCCUGCCAAACGGAGAACUUUAUCCGGGAUUACCGCAGAAAUUGGCUUGCCAAAAUUUAGAAAAUAAACCGAAUUGCUUGCAUCAAUUAGCCGAGCCAUUCGAGGGAGCCCAA
.(((..((((((((((.((((........))))((....)).......))))).......................(((((.((((((........).))))).))))).))))).))). ( -33.00)
>DroEre_CAF1 16712 120 - 1
CUGGCACUCCUGCCAAACGGAGAACUUUAUCCGGGAUUACCGCAGAAAUUGGCUUGCCAAAAUUUAGAAAAUAAACCGAAUUGCUUGCAUCAAUUAGCCGAGCAAUUCGAGGGAGCCCAA
.(((..((((((((((.((((........))))((....)).......))))).......................((((((((((((........).))))))))))).))))).))). ( -37.10)
>consensus
CUGGCACUCCUGCCAAACGGAGAACUUUAUCCGGGAUUACCGCAGAAAUUGGCUUGCCAAAAUUUAGAAAAUAAACCGAAUUGCUUGCAUCAAUUAGCCGAGCAAUUCGAGGGAGCCCAA
.(((..((((((((((.((((........))))((....)).......))))).......................((((((((((((........).))))))))))).))))).))). (-35.12 = -35.62 +   0.50)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:51:05 2006