Locus 9092

Sequence ID	3R_DroMel_CAF1
Location	24,267,427 – 24,267,558
Length	131
Max. P	0.791737

overview

Window 3

Location	24,267,427 – 24,267,530
Length	103
Sequences	6
Columns	105
Reading direction	forward
Mean pairwise identity	82.89
Mean single sequence MFE	-43.00
Consensus MFE	-29.33
Energy contribution	-30.63
Covariance contribution	1.31
Combinations/Pair	1.20
Mean z-score	-2.28
Structure conservation index	0.68
SVM decision value	0.41
SVM RNA-class probability	0.723884
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 24267427 103 + 27905053
CCACUAAUAGCCGUAAUUAGUGGCUGAUCCCUCUGCUGGGGGAUGAGUCCGUG-UCCGCAAGGAUGAGUCGGA-GAGUGGGGGCUCCGGCCUAAGGGCUGGGCUU
(((((.....(((......(.((((.(((((((....))))))).)))))..(-(((....))))....))).-.)))))((((.((((((....)))))))))) ( -50.80)
>DroSec_CAF1 90197 103 + 1
CCACUAAUAGCCGUAAUUAGUGGCUGAUCCCUCUGCUGGGGGAUGAGUCCGUG-UCCGCAAGGAUGAGUUGGA-GAGUGGGGGCUCCGGCCUAAGGGCUGGGAUC
(((((..(((((.......(.((((.(((((((....))))))).)))))..(-(((....))))).))))..-.))))).((..((((((....))))))..)) ( -47.40)
>DroSim_CAF1 94887 103 + 1
CCACUAAUAGCCGUAAUUAGUGGCUGAUCCCUCUGCUGGGGGAUGAGUCCGUG-UCCGCAAGGCUGAGUUGGA-GAGUGGGGGCUCUGGCCUAAGGGCUGGGAUC
(((((.....(((...(((((((((.(((((((....))))))).))))....-..(....))))))..))).-.))))).((..(..(((....)))..)..)) ( -42.60)
>DroEre_CAF1 97452 103 + 1
CCACUAAUAGCCGUAAUUAGUGGCUGAUCCCUCAGCUGGGGGAUGAGUUCGCG-UCCGCAGGGAUGAGUAGGU-GGGCUUGGGCUCCGGCCUAAGGGCUGGGAUC
........((((.......((((((.(((((((....))))))).)).))))(-(((((..(......)..))-))))...))))((((((....)))))).... ( -42.80)
>DroYak_CAF1 94321 104 + 1
CCACUAAUAGCCGUAAUUAGUGGCUGAUCCCGCUGCUGGGGGAUGAGUCCGUG-UCCGCAAGGAUGAGUAGGUUGGGAUUGGGCUACGGCCCAAGGGCUGGGAUC
((((((((.......))))))))..((((((.(((((...(((....)))..(-(((....)))).)))))....((.((((((....))))))...)))))))) ( -45.50)
>DroAna_CAF1 87636 92 + 1
CCACUAAUAGCCGUAAUUAGUGGCUGAUCCCU-UGACGGGGGAUGAGCCUACCCCCCGCA--GCUGAGU--------CUUGAGCCCCACC--AGCUCCCGAGCUC
........(((.((.....((((((.((((((-.....)))))).)))).)).....)).--)))(((.--------(((((((......--.))))..)))))) ( -28.90)
>consensus
CCACUAAUAGCCGUAAUUAGUGGCUGAUCCCUCUGCUGGGGGAUGAGUCCGUG_UCCGCAAGGAUGAGUAGGA_GAGUGGGGGCUCCGGCCUAAGGGCUGGGAUC
.........(((.......(.((((.(((((((....))))))).)))))....(((....))).................)))(((((((....)))))))... (-29.33 = -30.63 +   1.31)

alignment

secondary structure

dotplot

Window 4

Location	24,267,465 – 24,267,558
Length	93
Sequences	5
Columns	100
Reading direction	forward
Mean pairwise identity	88.03
Mean single sequence MFE	-38.02
Consensus MFE	-27.20
Energy contribution	-27.12
Covariance contribution	-0.08
Combinations/Pair	1.19
Mean z-score	-2.16
Structure conservation index	0.72
SVM decision value	0.59
SVM RNA-class probability	0.791737
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 24267465 93 + 27905053
GGGGAUGAGUCCGUGUCCGCAAGGAUGAGUCGGA-GAGUGGGGGCUCCGGCCUAAGGGCUGGGCUUUGAGAACUCUUG------GGGCCUCUGACUUUAA
..(((....)))..((((....))))((((((((-(..........((((((....))))))((((..((....))..------)))))))))))))... ( -41.50)
>DroSec_CAF1 90235 93 + 1
GGGGAUGAGUCCGUGUCCGCAAGGAUGAGUUGGA-GAGUGGGGGCUCCGGCCUAAGGGCUGGGAUCUGAGAACUCUUG------GGGCCUCUGACUUUAA
..(((....)))..((((....)))).......(-(((((((((((((((((....))))))).((..((....))..------)))))))).))))).. ( -38.30)
>DroSim_CAF1 94925 93 + 1
GGGGAUGAGUCCGUGUCCGCAAGGCUGAGUUGGA-GAGUGGGGGCUCUGGCCUAAGGGCUGGGAUCUGAGAACUCUUG------GGGCCUCUGACUUUAA
..(((....)))..(.((....)))........(-((((((((((((..(((....)))..)).((..((....))..------)))))))).))))).. ( -32.30)
>DroEre_CAF1 97490 99 + 1
GGGGAUGAGUUCGCGUCCGCAGGGAUGAGUAGGU-GGGCUUGGGCUCCGGCCUAAGGGCUGGGAUCUGAGAACUCCUGGGGUUGGGGGCUCUGACUUUAA
(((...((((((.((.((.(((((..........-(..((..((..((((((....))))))..))..))..)))))).)).)).))))))...)))... ( -41.20)
>DroYak_CAF1 94359 95 + 1
GGGGAUGAGUCCGUGUCCGCAAGGAUGAGUAGGUUGGGAUUGGGCUACGGCCCAAGGGCUGGGAUCUGAGAACUCUUGG-----GGGGCUCUGACUUUAA
(((...((((((..((((....))))(((((((((.((.((((((....))))))...)).).))))....))))....-----.))))))...)))... ( -36.80)
>consensus
GGGGAUGAGUCCGUGUCCGCAAGGAUGAGUAGGA_GAGUGGGGGCUCCGGCCUAAGGGCUGGGAUCUGAGAACUCUUG______GGGCCUCUGACUUUAA
(((...((((((.(((((....)))))........((((..((..(((((((....)))))))..))....)))).........))).)))...)))... (-27.20 = -27.12 +  -0.08)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:26:26 2006