Locus 4014

Sequence ID	2L_DroMel_CAF1
Location	11,662,001 – 11,662,126
Length	125
Max. P	0.992623

overview

Window 7

Location	11,662,001 – 11,662,103
Length	102
Sequences	5
Columns	110
Reading direction	reverse
Mean pairwise identity	73.61
Mean single sequence MFE	-35.84
Consensus MFE	-22.13
Energy contribution	-23.54
Covariance contribution	1.41
Combinations/Pair	1.23
Mean z-score	-2.27
Structure conservation index	0.62
SVM decision value	2.34
SVM RNA-class probability	0.992623
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 11662001 102 - 22407834
AA---CUUCA-----GGCUGCGGUGUGUCAUUGCUGGACAAGCAAAGCAGAUUGGCACCCGGACAGCAGGUGGACUGAUGCUGAACUGAAUGCACCGCGGCAUUAGGCAA
..---((...-----.((((((((((((..(((((.....)))))..(((.(..(((.(.(..((.....))..).).)))..).))).))))))))))))...)).... ( -37.60)
>DroSec_CAF1 123308 102 - 1
AA---CUUCA-----GGCUGCGGUGUGUCAUUGCUGGACAAGCAAAGCAGAUUGGCACCCGGACAGCAGGUGGACUGAUGCUGAACUGAAUGCACCGCGGCAUUAGUCAA
.(---((...-----.(((((((.(((((((((((..........)))))..)))))))))..)))).))).(((((((((((...((....))...))))))))))).. ( -38.60)
>DroSim_CAF1 121123 102 - 1
AA---CUUCA-----GGCUGCGGUGUGUCAUUGCUGGACAAGCAAAGCAGAUUGGCACCCGGACAGCAGGUGGACUGAUGCUGAACUGAAUGCACCGCGGCAUUAGGCAA
..---((...-----.((((((((((((..(((((.....)))))..(((.(..(((.(.(..((.....))..).).)))..).))).))))))))))))...)).... ( -37.60)
>DroEre_CAF1 144830 87 - 1
CA---CUUCA-----GGCUGCGGUGUGUCAUUGCUGGACAAGCAAACCAGAUUGCCAGCCGGAU---------------GCUAAACUGAAUGCACCGCGGCAUUAGGCAA
..---((...-----.((((((((((((....(((((.(((.(......).))))))))(((..---------------......))).))))))))))))...)).... ( -31.20)
>DroAna_CAF1 129158 95 - 1
AAUCAUUUUGGAACGGGCC-UUGUCUGUCAUUGUCGCAGUCCCAAACCGAAGUGACAGUUGGCCAACAACUGG-------CUG----GCAUGC---CUGGCAUUAGGCAA
..(((((((((...(((.(-(((.(.......).)).)).)))...)))))))))..((..((((.....)))-------)..----)).(((---(((....)))))). ( -34.20)
>consensus
AA___CUUCA_____GGCUGCGGUGUGUCAUUGCUGGACAAGCAAAGCAGAUUGGCACCCGGACAGCAGGUGGACUGAUGCUGAACUGAAUGCACCGCGGCAUUAGGCAA
................((((((((((((((...(((...........)))..)))).......(((((..........)))))........))))))))))......... (-22.13 = -23.54 +   1.41)

alignment

secondary structure

dotplot

Window 8

Location	11,662,032 – 11,662,126
Length	94
Sequences	5
Columns	95
Reading direction	reverse
Mean pairwise identity	86.12
Mean single sequence MFE	-31.50
Consensus MFE	-23.54
Energy contribution	-24.34
Covariance contribution	0.80
Combinations/Pair	1.00
Mean z-score	-1.63
Structure conservation index	0.75
SVM decision value	0.13
SVM RNA-class probability	0.598116
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 11662032 94 - 22407834
GCAGCAGGAGCGAGGACGAAGGAAACUUCAGGCUGCGGUGUGUCAUUGCUGGACAAGCAAAGCAGAUUGGCACCCGGACAGCAGGUGGACUGAU-
....(((..((......((((....))))..(((((((.(((((((((((..........)))))..)))))))))..))))..))...)))..- ( -32.90)
>DroSec_CAF1 123339 94 - 1
GCAGCAACAGCGAGGACGAAGGAAACUUCAGGCUGCGGUGUGUCAUUGCUGGACAAGCAAAGCAGAUUGGCACCCGGACAGCAGGUGGACUGAU-
.(((...((.(......((((....))))..(((((((.(((((((((((..........)))))..)))))))))..)))).).))..)))..- ( -33.30)
>DroSim_CAF1 121154 94 - 1
GCAGCAGGAGCGAGGACGAAGGAAACUUCAGGCUGCGGUGUGUCAUUGCUGGACAAGCAAAGCAGAUUGGCACCCGGACAGCAGGUGGACUGAU-
....(((..((......((((....))))..(((((((.(((((((((((..........)))))..)))))))))..))))..))...)))..- ( -32.90)
>DroEre_CAF1 144861 79 - 1
GCAGCAGGAGCCAGGACGAAGGACACUUCAGGCUGCGGUGUGUCAUUGCUGGACAAGCAAACCAGAUUGCCAGCCGGAU----------------
..........((.....((((....)))).(((((((((.((...(((((.....)))))..)).)))).)))))))..---------------- ( -25.70)
>DroYak_CAF1 119107 95 - 1
GCAGCAGGAGUAGGGACGAAGGAAACUUCAGGCUGCGGUGCGUCAUCGCUGGACAAGCAAACCAGAUUGGCAGCCGGAAAGCAGGUGGUCCAAUG
(((((....((....))((((....))))..)))))(((..((((...((((.........))))..)))).)))(((..(....)..))).... ( -32.70)
>consensus
GCAGCAGGAGCGAGGACGAAGGAAACUUCAGGCUGCGGUGUGUCAUUGCUGGACAAGCAAAGCAGAUUGGCACCCGGACAGCAGGUGGACUGAU_
(((((....(......)((((....))))..)))))((.((((((...(((...........)))..)))))))).................... (-23.54 = -24.34 +   0.80)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:07:10 2006