Locus 4877

Sequence ID	3L_DroMel_CAF1
Location	13,614,526 – 13,614,619
Length	93
Max. P	0.747326

overview

Window 8

Location	13,614,526 – 13,614,619
Length	93
Sequences	5
Columns	102
Reading direction	forward
Mean pairwise identity	84.25
Mean single sequence MFE	-25.22
Consensus MFE	-16.01
Energy contribution	-15.61
Covariance contribution	-0.40
Combinations/Pair	1.09
Mean z-score	-2.19
Structure conservation index	0.63
SVM decision value	0.47
SVM RNA-class probability	0.747326
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13614526 93 + 23771897
UGCAAAAAUCAGUGCAGUCUGCACAUAUACGU------AUACGUAUACGUUAUACGUACGUAUUGAUCAGGCCAGU---CAAUGCCGUGUUGAUGAAGCCUG
.......((((((((.....))))..((((((------..(((((((...)))))))))))))))))(((((..((---((((.....))))))...))))) ( -29.10)
>DroSec_CAF1 21547 78 + 1
UGCAGAAAUCAGUGCAGUCUGCACACAUACGA------ACAC---------------ACGUAUUGAUCAGGCCAGU---CAAUGCCGUGUUGAUGAAGCCUG
.......((((((((.....))))..(((((.------....---------------.)))))))))(((((..((---((((.....))))))...))))) ( -22.20)
>DroSim_CAF1 30630 78 + 1
UGCAGAAAUCAGUGCAGUCUGCACAUAUACGU------ACAC---------------ACGUAUUGAUCAGGCCAGU---CAAUGCCGUGUUGAUGGAGCCUG
.......((((((((.....))))..((((((------....---------------))))))))))((((((.((---((((.....)))))).).))))) ( -23.60)
>DroEre_CAF1 24303 81 + 1
UGCAAAAAUCAGUGCAGCCUGCACAUAUACGU------AUAC---------------ACGUAUUGAUCAGGCCAGUCGUCAAUGGCGUGUUGAUGAAGCCUG
.......((((((((.....))))..((((((------....---------------))))))))))(((((...((((((((.....)))))))).))))) ( -26.70)
>DroYak_CAF1 28623 84 + 1
UGCAAAAAUCAGUGCAGCUUGCACAUAUACGUAUACGUAUAC---------------UCGUAUUGAUCAGGCCAGU---CAAUGCCGUGUUGAUGAAGCCUG
.......((((((((.....)))).((((((....)))))).---------------......))))(((((..((---((((.....))))))...))))) ( -24.50)
>consensus
UGCAAAAAUCAGUGCAGUCUGCACAUAUACGU______AUAC_______________ACGUAUUGAUCAGGCCAGU___CAAUGCCGUGUUGAUGAAGCCUG
.((....(((((..(.(((((..((.(((((...........................)))))))..)))))((........))..)..)))))...))... (-16.01 = -15.61 +  -0.40)

alignment

secondary structure

dotplot

Window 9

Location	13,614,526 – 13,614,619
Length	93
Sequences	5
Columns	102
Reading direction	reverse
Mean pairwise identity	84.25
Mean single sequence MFE	-23.06
Consensus MFE	-15.75
Energy contribution	-15.75
Covariance contribution	0.00
Combinations/Pair	1.00
Mean z-score	-1.71
Structure conservation index	0.68
SVM decision value	0.07
SVM RNA-class probability	0.570506
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13614526 93 - 23771897
CAGGCUUCAUCAACACGGCAUUG---ACUGGCCUGAUCAAUACGUACGUAUAACGUAUACGUAU------ACGUAUAUGUGCAGACUGCACUGAUUUUUGCA
((((((...((((.......)))---)..))))))((((....(((((((((.((....)))))------))))))..((((.....))))))))....... ( -28.00)
>DroSec_CAF1 21547 78 - 1
CAGGCUUCAUCAACACGGCAUUG---ACUGGCCUGAUCAAUACGU---------------GUGU------UCGUAUGUGUGCAGACUGCACUGAUUUCUGCA
((((((...((((.......)))---)..))))))(((((((((.---------------....------.)))))..((((.....))))))))....... ( -20.80)
>DroSim_CAF1 30630 78 - 1
CAGGCUCCAUCAACACGGCAUUG---ACUGGCCUGAUCAAUACGU---------------GUGU------ACGUAUAUGUGCAGACUGCACUGAUUUCUGCA
((((((...((((.......)))---)..))))))((((((((((---------------....------))))))..((((.....))))))))....... ( -20.80)
>DroEre_CAF1 24303 81 - 1
CAGGCUUCAUCAACACGCCAUUGACGACUGGCCUGAUCAAUACGU---------------GUAU------ACGUAUAUGUGCAGGCUGCACUGAUUUUUGCA
((((((((.((((.......)))).))..))))))((((((((((---------------....------))))))..((((.....))))))))....... ( -22.00)
>DroYak_CAF1 28623 84 - 1
CAGGCUUCAUCAACACGGCAUUG---ACUGGCCUGAUCAAUACGA---------------GUAUACGUAUACGUAUAUGUGCAAGCUGCACUGAUUUUUGCA
((((((...((((.......)))---)..))))))((((......---------------(((((((....)))))))((((.....))))))))....... ( -23.70)
>consensus
CAGGCUUCAUCAACACGGCAUUG___ACUGGCCUGAUCAAUACGU_______________GUAU______ACGUAUAUGUGCAGACUGCACUGAUUUUUGCA
((((((....(((.......)))......))))))(((((((((...........................)))))..((((.....))))))))....... (-15.75 = -15.75 +   0.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:35:54 2006