Locus 2368

Sequence ID	2R_DroMel_CAF1
Location	8,598,154 – 8,598,265
Length	111
Max. P	0.863379

overview

Window 0

Location	8,598,154 – 8,598,265
Length	111
Sequences	4
Columns	118
Reading direction	forward
Mean pairwise identity	89.08
Mean single sequence MFE	-41.42
Consensus MFE	-29.93
Energy contribution	-31.24
Covariance contribution	1.31
Combinations/Pair	1.03
Mean z-score	-2.48
Structure conservation index	0.72
SVM decision value	0.84
SVM RNA-class probability	0.863379
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 8598154 111 + 20766785
CAGGAGCUG-----GAUAAAGGAGCAC-GGGGUGGAUUCCCUGCUCUGGACAGCGGACUGUGGA-UGUGGAUGUGGAUGUGGCAAAAGUUGCCAACUGGCCAACAAAUUGCCGCAUGA
(((..((((-----......((((((.-((((.....))))))))))...))))...)))....-...........(((((((((..((((((....)).))))...))))))))).. ( -42.60)
>DroSec_CAF1 82456 105 + 1
CAGGAGCUG-----GAUAAAGGAGCAC-GGGGUGGAUUCCGAGCUCUGGACAGCGGACUGUGGA-UG------UGGAUGUGGCAAAAGUAGCCAACUGGCCAACAAAUUGCCGCAUGA
(((..((((-----......(((((.(-((((....))))).)))))...))))...)))....-..------...(((((((((..((.(((....)))..))...))))))))).. ( -38.50)
>DroSim_CAF1 74418 111 + 1
CAGGAGCUG-----GAUAAAGGAGCAC-GGGGUGGAUUCCCUGCUCUGGACAGCGGACUGUGGA-UGUGAAUGUGGAUGUGGCAAAAGUUGCCAACUGGCCAACAAAUUGCCGCAUGA
(((..((((-----......((((((.-((((.....))))))))))...))))...)))....-...........(((((((((..((((((....)).))))...))))))))).. ( -42.60)
>DroYak_CAF1 77488 118 + 1
CAGGAGUUGGCCAGGAUAAAGGAGCUCUGGGGUGGAUUCCCUGCCCUGGACAGCGGACAACAGACUGUGCAUGUGGAUGAGGCAAAAGUUGCCAACUGGCCAACAAAUUGCCGCAUGA
.....(((((((((.........((((..(((..(.....)..)))..))..))((.((((....(((.(((....)))..)))...))))))..))))))))).............. ( -42.00)
>consensus
CAGGAGCUG_____GAUAAAGGAGCAC_GGGGUGGAUUCCCUGCUCUGGACAGCGGACUGUGGA_UGUG_AUGUGGAUGUGGCAAAAGUUGCCAACUGGCCAACAAAUUGCCGCAUGA
(((..((((...........(((((...((((.....)))).)))))...))))...)))................(((((((((..((((((....)).))))...))))))))).. (-29.93 = -31.24 +   1.31)

alignment

secondary structure

dotplot

Window 1

Location	8,598,154 – 8,598,265
Length	111
Sequences	4
Columns	118
Reading direction	reverse
Mean pairwise identity	89.08
Mean single sequence MFE	-32.77
Consensus MFE	-23.11
Energy contribution	-23.30
Covariance contribution	0.19
Combinations/Pair	1.12
Mean z-score	-2.15
Structure conservation index	0.71
SVM decision value	0.46
SVM RNA-class probability	0.747008
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 8598154 111 - 20766785
UCAUGCGGCAAUUUGUUGGCCAGUUGGCAACUUUUGCCACAUCCACAUCCACA-UCCACAGUCCGCUGUCCAGAGCAGGGAAUCCACCCC-GUGCUCCUUUAUC-----CAGCUCCUG
..(((.(((((...((((.((....))))))..))))).)))...........-....(((...((((....((((((((.......)))-.))))).......-----))))..))) ( -32.30)
>DroSec_CAF1 82456 105 - 1
UCAUGCGGCAAUUUGUUGGCCAGUUGGCUACUUUUGCCACAUCCA------CA-UCCACAGUCCGCUGUCCAGAGCUCGGAAUCCACCCC-GUGCUCCUUUAUC-----CAGCUCCUG
..(((.(((((...((.((((....))))))..))))).)))...------..-....(((...((((....((((.(((........))-).)))).......-----))))..))) ( -31.70)
>DroSim_CAF1 74418 111 - 1
UCAUGCGGCAAUUUGUUGGCCAGUUGGCAACUUUUGCCACAUCCACAUUCACA-UCCACAGUCCGCUGUCCAGAGCAGGGAAUCCACCCC-GUGCUCCUUUAUC-----CAGCUCCUG
..(((.(((((...((((.((....))))))..))))).)))...........-....(((...((((....((((((((.......)))-.))))).......-----))))..))) ( -32.30)
>DroYak_CAF1 77488 118 - 1
UCAUGCGGCAAUUUGUUGGCCAGUUGGCAACUUUUGCCUCAUCCACAUGCACAGUCUGUUGUCCGCUGUCCAGGGCAGGGAAUCCACCCCAGAGCUCCUUUAUCCUGGCCAACUCCUG
..............(((((((((..((((.....))))................((((.(((((........)))))(((......)))))))...........)))))))))..... ( -34.80)
>consensus
UCAUGCGGCAAUUUGUUGGCCAGUUGGCAACUUUUGCCACAUCCACAU_CACA_UCCACAGUCCGCUGUCCAGAGCAGGGAAUCCACCCC_GUGCUCCUUUAUC_____CAGCUCCUG
..(((.(((((...((((.((....))))))..))))).)))...............((((....))))...((((.(((.......)))...))))..................... (-23.11 = -23.30 +   0.19)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:28:11 2006