Locus 5025

Sequence ID	3L_DroMel_CAF1
Location	13,777,747 – 13,777,855
Length	108
Max. P	0.999956

overview

Window 4

Location	13,777,747 – 13,777,855
Length	108
Sequences	5
Columns	108
Reading direction	forward
Mean pairwise identity	97.04
Mean single sequence MFE	-41.24
Consensus MFE	-39.30
Energy contribution	-39.58
Covariance contribution	0.28
Combinations/Pair	1.06
Mean z-score	-3.52
Structure conservation index	0.95
SVM decision value	4.86
SVM RNA-class probability	0.999956
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13777747 108 + 23771897
GCUGGCGCCUGCGCUAGGACCUCACACAUGUAGUGGUCCUAGGACGACGAGGCCUAGACUAGAAAAUAGGCCUAAGCGAAUCAACAUUAAGCAGGAGUGCAGCCCACA
((((((.(((((.((((((((.(((....)).).))))))))..((...(((((((..........)))))))...))............))))).)).))))..... ( -45.70)
>DroSec_CAF1 24310 108 + 1
GCUGGCGCCUGCGCCAGGACCUCACACAUGUAGUGGUCCUAGGACGACAAGGCCUAGACUAGAAAAUAGGCCUAAGCGAAUCAACAUUAAGCAGGAGUGCAGCCCGCA
((.(((.(((((.((((((((.(((....)).).)))))).)).((...(((((((..........)))))))...))............)))))......))).)). ( -42.80)
>DroSim_CAF1 20464 108 + 1
GCUGGCGCCUGCGCCAGGACCUCACACAUGUAGUGGUCCUAGGACGACAAGGCCUAGACUAGAAAAUAGGCCUAAGCGAAUCAACAUUAAGCAGGAGUGCAGCCCACA
((((((.(((((.((((((((.(((....)).).)))))).)).((...(((((((..........)))))))...))............))))).)).))))..... ( -42.60)
>DroEre_CAF1 23827 108 + 1
GCUGGCGCCUGCGCCAGGAUCUCACACAUGUAGUGGUCCUAGGACGAAACGGCCUAGACUAGAAAAUAGGCCUAAGCGAAUCAACAUUAAGCAGAAGUGCAGCCCACA
((((.(((((((.((((((((.(((....)).).)))))).)).((....((((((..........))))))....))............))))..)))))))..... ( -35.40)
>DroYak_CAF1 22610 108 + 1
GCUGGCGCCUGCGCCAGGACCUCACACAUGUAGUGGUCCUAGGACGAAAAGGCCUAGACUAGAAAAUAGGCCUAAGCGAAUCAACAUUAAGCAGAAGUGCAGCCCACA
((((.(((((((.((((((((.(((....)).).)))))).)).((...(((((((..........)))))))...))............))))..)))))))..... ( -39.70)
>consensus
GCUGGCGCCUGCGCCAGGACCUCACACAUGUAGUGGUCCUAGGACGACAAGGCCUAGACUAGAAAAUAGGCCUAAGCGAAUCAACAUUAAGCAGGAGUGCAGCCCACA
((((((.(((((.((((((((.(((....)).).)))))).)).((...(((((((..........)))))))...))............))))).)).))))..... (-39.30 = -39.58 +   0.28)

alignment

secondary structure

dotplot

Window 5

Location	13,777,747 – 13,777,855
Length	108
Sequences	5
Columns	108
Reading direction	reverse
Mean pairwise identity	97.04
Mean single sequence MFE	-36.36
Consensus MFE	-34.72
Energy contribution	-34.92
Covariance contribution	0.20
Combinations/Pair	1.06
Mean z-score	-1.14
Structure conservation index	0.95
SVM decision value	0.19
SVM RNA-class probability	0.627045
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13777747 108 - 23771897
UGUGGGCUGCACUCCUGCUUAAUGUUGAUUCGCUUAGGCCUAUUUUCUAGUCUAGGCCUCGUCGUCCUAGGACCACUACAUGUGUGAGGUCCUAGCGCAGGCGCCAGC
.....((((..(.(((((........(((..((((((((..........))))))))...)))...((((((((..(((....))).)))))))).))))).).)))) ( -37.50)
>DroSec_CAF1 24310 108 - 1
UGCGGGCUGCACUCCUGCUUAAUGUUGAUUCGCUUAGGCCUAUUUUCUAGUCUAGGCCUUGUCGUCCUAGGACCACUACAUGUGUGAGGUCCUGGCGCAGGCGCCAGC
.(((((.......))))).....((((...((((((((((((..........)))))))....((.((((((((..(((....))).)))))))).))))))).)))) ( -38.20)
>DroSim_CAF1 20464 108 - 1
UGUGGGCUGCACUCCUGCUUAAUGUUGAUUCGCUUAGGCCUAUUUUCUAGUCUAGGCCUUGUCGUCCUAGGACCACUACAUGUGUGAGGUCCUGGCGCAGGCGCCAGC
.....((((..(.(((((........(((..((((((((..........))))))))...)))...((((((((..(((....))).)))))))).))))).).)))) ( -37.90)
>DroEre_CAF1 23827 108 - 1
UGUGGGCUGCACUUCUGCUUAAUGUUGAUUCGCUUAGGCCUAUUUUCUAGUCUAGGCCGUUUCGUCCUAGGACCACUACAUGUGUGAGAUCCUGGCGCAGGCGCCAGC
....(((.(((....))).............((((.((((((..........)))))).....((.((((((((((.......))).).)))))).)))))))))... ( -32.30)
>DroYak_CAF1 22610 108 - 1
UGUGGGCUGCACUUCUGCUUAAUGUUGAUUCGCUUAGGCCUAUUUUCUAGUCUAGGCCUUUUCGUCCUAGGACCACUACAUGUGUGAGGUCCUGGCGCAGGCGCCAGC
....(((.(((....))).............(((((((((((..........)))))))....((.((((((((..(((....))).)))))))).)))))))))... ( -35.90)
>consensus
UGUGGGCUGCACUCCUGCUUAAUGUUGAUUCGCUUAGGCCUAUUUUCUAGUCUAGGCCUUGUCGUCCUAGGACCACUACAUGUGUGAGGUCCUGGCGCAGGCGCCAGC
.....((((..(.(((((........(((..((((((((..........))))))))...)))...((((((((..(((....))).)))))))).))))).).)))) (-34.72 = -34.92 +   0.20)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:39:58 2006