Locus 8410

Sequence ID	X_DroMel_CAF1
Location	20,882,783 – 20,882,893
Length	110
Max. P	0.575353

overview

Window 2

Location	20,882,783 – 20,882,893
Length	110
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	91.12
Mean single sequence MFE	-29.80
Consensus MFE	-20.05
Energy contribution	-22.54
Covariance contribution	2.50
Combinations/Pair	1.00
Mean z-score	-3.25
Structure conservation index	0.67
SVM decision value	0.08
SVM RNA-class probability	0.575353
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 20882783 110 + 22224390
----AGACAUAAAACAGAGCCAUAAAACCAACGAUCGAUCGAGUGGGG-AAAUAAUUAAACCCGAUCAGCGAUAAUUAAACCGCAUAAGUGUCC-CCAUAAUGGAUCGA----UCGAUCG
----...........................(((((((((((((((((-(..((((((....((.....)).))))))...(((....))))))-))))......))))----))))))) ( -29.10)
>DroSec_CAF1 2644 114 + 1
----AGAUAUAAAACAGAGCCAUAAAACCGACGAUCGAUCGAUUGGGG-AAAUAAUUAAACCCGAUCAGCGAUAAUUAAACCGCAUAAGUGUCC-CCAUAAUGGAUCGAUCGAUCGAUCG
----........................(((((((((((((((((((.-...........))))))).(((..........)))......((((-.......)))).))))))))).))) ( -32.10)
>DroSim_CAF1 3445 114 + 1
----AGACAUAAAACAGAGCCAUAAAACCGACGAUCGAUCGAGUGGGG-AAAUAAUUAAACCCGAUCAGCGAUAAUUAAACCGCAUAAGUGUCC-CCAUAAUGGAUCGAUCGAUCGAUCG
----........................((((((((((((((((((((-(..((((((....((.....)).))))))...(((....))))))-))))......))))))))))).))) ( -32.10)
>DroYak_CAF1 3580 112 + 1
AAUAAGACAUAAAACAGAGCCAUAAAAUCAACGAUCGAUCGAGUGGGGCAACUAAUUAAACCCGAUCAGCGAUAAUUAAACCGCAUAAGUGUCCCCCAUAAUGGAUC--------GAUCG
...............................(((((((((.(((((((..(((.(((......)))..(((..........)))...)))...))))))..).))))--------))))) ( -25.90)
>consensus
____AGACAUAAAACAGAGCCAUAAAACCAACGAUCGAUCGAGUGGGG_AAAUAAUUAAACCCGAUCAGCGAUAAUUAAACCGCAUAAGUGUCC_CCAUAAUGGAUCGA____UCGAUCG
...............................(((((((((((..(((.............)))((((.(((..........)))....(((.....)))....))))..))))))))))) (-20.05 = -22.54 +   2.50)

alignment

secondary structure

dotplot

Window 3

Location	20,882,783 – 20,882,893
Length	110
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	91.12
Mean single sequence MFE	-31.88
Consensus MFE	-21.57
Energy contribution	-22.14
Covariance contribution	0.56
Combinations/Pair	1.03
Mean z-score	-2.43
Structure conservation index	0.68
SVM decision value	-0.03
SVM RNA-class probability	0.517193
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 20882783 110 - 22224390
CGAUCGA----UCGAUCCAUUAUGG-GGACACUUAUGCGGUUUAAUUAUCGCUGAUCGGGUUUAAUUAUUU-CCCCACUCGAUCGAUCGUUGGUUUUAUGGCUCUGUUUUAUGUCU----
(((((((----((((((.....((.-...)).....(((((......))))).))))(((...........-.)))....)))))))))..........(((..........))).---- ( -29.80)
>DroSec_CAF1 2644 114 - 1
CGAUCGAUCGAUCGAUCCAUUAUGG-GGACACUUAUGCGGUUUAAUUAUCGCUGAUCGGGUUUAAUUAUUU-CCCCAAUCGAUCGAUCGUCGGUUUUAUGGCUCUGUUUUAUAUCU----
(((.((((((((((((......(((-(((.......(((((......)))))(((......)))......)-))))))))))))))))))))........................---- ( -35.30)
>DroSim_CAF1 3445 114 - 1
CGAUCGAUCGAUCGAUCCAUUAUGG-GGACACUUAUGCGGUUUAAUUAUCGCUGAUCGGGUUUAAUUAUUU-CCCCACUCGAUCGAUCGUCGGUUUUAUGGCUCUGUUUUAUGUCU----
.((((((.(((((((((.....(((-(((.......(((((......)))))(((......)))......)-)))))...)))))))))))))))....(((..........))).---- ( -34.30)
>DroYak_CAF1 3580 112 - 1
CGAUC--------GAUCCAUUAUGGGGGACACUUAUGCGGUUUAAUUAUCGCUGAUCGGGUUUAAUUAGUUGCCCCACUCGAUCGAUCGUUGAUUUUAUGGCUCUGUUUUAUGUCUUAUU
(((((--------((((.....((((((((......(((((......)))))(((......)))....))).)))))...)))))))))..........(((..........)))..... ( -28.10)
>consensus
CGAUCGA____UCGAUCCAUUAUGG_GGACACUUAUGCGGUUUAAUUAUCGCUGAUCGGGUUUAAUUAUUU_CCCCACUCGAUCGAUCGUCGGUUUUAUGGCUCUGUUUUAUGUCU____
.((((((....))))))........((((((.....(((((......)))))(((((((((...............)))))))))...((((......)))).........))))))... (-21.57 = -22.14 +   0.56)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:03:17 2006