Locus 209

Sequence ID	3L_DroMel_CAF1
Location	575,569 – 575,663
Length	94
Max. P	0.938890

overview

Window 8

Location	575,569 – 575,663
Length	94
Sequences	4
Columns	102
Reading direction	forward
Mean pairwise identity	84.04
Mean single sequence MFE	-32.92
Consensus MFE	-23.15
Energy contribution	-24.02
Covariance contribution	0.88
Combinations/Pair	1.08
Mean z-score	-2.36
Structure conservation index	0.70
SVM decision value	1.27
SVM RNA-class probability	0.938890
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 575569 94 + 23771897
UUCAGGUCCAGCCGCAUCCUGUUUACGGGAACUCCUUGUGAACUCAAGGGUUUUGUCGGAUGGAUGUGGAUAUGGAAAUGGAUCUGGAU-------GC-GGA
((((((((((.((((((((.((((((((.(((.(((((......)))))))))))).)))))))))))).........)))))))))).-------..-... ( -36.60)
>DroSec_CAF1 6996 88 + 1
UUCAGGUCCAGCCGCAUCCUGUUUACGGGAACUCCUGGUAAACUCAAGGGUUUUGUCGGAUGG------AUAUGGAAAUGGAUCUUGAU-------GC-GGA
.(((((((((.(((.((((.((((.((((....))))..(((((....)))))....))))))------)).)))...)))))).))).-------..-... ( -26.20)
>DroSim_CAF1 7593 88 + 1
UUCAGGUCCAGCCGCAUCCUGUUUACGGUAACUCCUGGUGAACUCAAGGGUUUUGUCUGAUGG------AUAUGGAAAUGGAUCUGGAU-------GC-GGA
((((((((((.(((.((((.(((.((((.(((((.(((....).)).)))))))))..)))))------)).)))...)))))))))).-------..-... ( -30.50)
>DroEre_CAF1 6877 96 + 1
UUCAGGUCCAGCCGCAUCCUGUUUACGGGAGUUCCUUGGGAACUCAAGGGUUUCCUCGGGUGG------AUGUGGAUAUGGAUGCGGAUGAAUGAUGCAGGG
.(((..((...((((((((((((((((.....(((..(((((((....)))))))..)))...------.)))))))).))))))))..)).)))....... ( -38.40)
>consensus
UUCAGGUCCAGCCGCAUCCUGUUUACGGGAACUCCUGGUGAACUCAAGGGUUUUGUCGGAUGG______AUAUGGAAAUGGAUCUGGAU_______GC_GGA
((((((((((.((...(((((....)))))..(((....(((((....)))))....))).............))...)))))))))).............. (-23.15 = -24.02 +   0.88)

alignment

secondary structure

dotplot

Window 9

Location	575,569 – 575,663
Length	94
Sequences	4
Columns	102
Reading direction	reverse
Mean pairwise identity	84.04
Mean single sequence MFE	-23.60
Consensus MFE	-13.69
Energy contribution	-14.50
Covariance contribution	0.81
Combinations/Pair	1.06
Mean z-score	-2.19
Structure conservation index	0.58
SVM decision value	0.14
SVM RNA-class probability	0.602469
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 575569 94 - 23771897
UCC-GC-------AUCCAGAUCCAUUUCCAUAUCCACAUCCAUCCGACAAAACCCUUGAGUUCACAAGGAGUUCCCGUAAACAGGAUGCGGCUGGACCUGAA
...-..-------...(((.((((.........((.(((((.....((..((((((((......))))).)))...)).....))))).)).)))).))).. ( -22.50)
>DroSec_CAF1 6996 88 - 1
UCC-GC-------AUCAAGAUCCAUUUCCAUAU------CCAUCCGACAAAACCCUUGAGUUUACCAGGAGUUCCCGUAAACAGGAUGCGGCUGGACCUGAA
...-..-------.(((.(.((((...((.(((------((......(((.....))).((((((..((....)).)))))).))))).)).))))).))). ( -20.60)
>DroSim_CAF1 7593 88 - 1
UCC-GC-------AUCCAGAUCCAUUUCCAUAU------CCAUCAGACAAAACCCUUGAGUUCACCAGGAGUUACCGUAAACAGGAUGCGGCUGGACCUGAA
...-..-------...(((.((((...((.(((------((.....((..(((.((((.(....))))).)))...)).....))))).)).)))).))).. ( -19.40)
>DroEre_CAF1 6877 96 - 1
CCCUGCAUCAUUCAUCCGCAUCCAUAUCCACAU------CCACCCGAGGAAACCCUUGAGUUCCCAAGGAACUCCCGUAAACAGGAUGCGGCUGGACCUGAA
.......(((((((.((((((((..........------......((((....))))(((((((...))))))).........)))))))).))))..))). ( -31.90)
>consensus
UCC_GC_______AUCCAGAUCCAUUUCCAUAU______CCAUCCGACAAAACCCUUGAGUUCACAAGGAGUUCCCGUAAACAGGAUGCGGCUGGACCUGAA
................(((.((((.............................(((((......))))).....(((((.......))))).)))).))).. (-13.69 = -14.50 +   0.81)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:36:13 2006