Locus 3970

Sequence ID	3L_DroMel_CAF1
Location	11,534,411 – 11,534,568
Length	157
Max. P	0.999787

overview

Window 6

Location	11,534,411 – 11,534,528
Length	117
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	70.46
Mean single sequence MFE	-26.44
Consensus MFE	-15.89
Energy contribution	-18.01
Covariance contribution	2.12
Combinations/Pair	1.15
Mean z-score	-2.74
Structure conservation index	0.60
SVM decision value	4.08
SVM RNA-class probability	0.999787
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 11534411 117 + 23771897
ACAAAAAGGUUAAAGUCGAAAAUUAACUAAAAAGGUUACCUGGG---UAGCCAGGGUGGAAAUCUUAAUGUUGUUUCCAAAACUCCCAGAAAGGAACAAUUUGGGGAUUAUCAACCACCA
.......((((((.........)))))).....((((((....)---)))))..(((((.((((((...((((((((...............))))))))...)))))).....))))). ( -28.56)
>DroSec_CAF1 40801 117 + 1
ACAAAAAGGUUGAAGUCGCAAAUUAACUAAAAAGGUUACCUGGG---UAACCAGGGUGGAAAUCUUAAAGUUCUUUCCACAACUCACAUAAAGAAACAAUUUGGGGAUUUUCAACAACCA
.......(((((...........(((((.....)))))(((((.---...))))).(((((((((..(((((.((((...............)))).)))))..))))))))).))))). ( -30.46)
>DroEre_CAF1 35118 110 + 1
ACAAAAAGGGUGCAGUAGC------ACCAAAAAGGUUACCUGGAAGUUCUACAGGGUGGAAUUCUUAAAGUUGUUUCCCAAACUCCUAAAAGGGAACAUUUUGGAGAUAGUCAACC----
........(((((....))------))).....((((.((((.........))))...((..((((.(((.(((((((.............))))))).))).))))...))))))---- ( -28.02)
>DroYak_CAF1 39679 95 + 1
A-------------------------CCAAAAAGGUUACCUAAAAGUCCUACAGGGUGGAAAUCUCAAAAUUGUUUCCAAAACUUCCAAAAAGAAUCAUUUUGGAGAUAGUCAACCACCA
(-------------------------((.....)))..................(((((..........(((((((((((((.(((......)))...)))))))))))))...))))). ( -18.72)
>consensus
ACAAAAAGGUUGAAGUCGC______ACCAAAAAGGUUACCUGGA___UAUACAGGGUGGAAAUCUUAAAGUUGUUUCCAAAACUCCCAAAAAGAAACAAUUUGGAGAUAGUCAACCACCA
.................................((((.(((((.......)))))..((.((((((.((((((((((...............)))))))))).)))))).)))))).... (-15.89 = -18.01 +   2.12)

alignment

secondary structure

dotplot

Window 7

Location	11,534,451 – 11,534,568
Length	117
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	81.03
Mean single sequence MFE	-26.80
Consensus MFE	-18.41
Energy contribution	-19.04
Covariance contribution	0.63
Combinations/Pair	1.15
Mean z-score	-2.38
Structure conservation index	0.69
SVM decision value	1.64
SVM RNA-class probability	0.969560
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 11534451 117 + 23771897
UGGG---UAGCCAGGGUGGAAAUCUUAAUGUUGUUUCCAAAACUCCCAGAAAGGAACAAUUUGGGGAUUAUCAACCACCACCCCAACAUCUUGACCGGUUUUUACCUUCACAACCCUUAU
.(((---(.(..((((((((((((.....((((((((...............))))))))((((((..............))))))..........))))))))))))..).)))).... ( -31.10)
>DroSec_CAF1 40841 117 + 1
UGGG---UAACCAGGGUGGAAAUCUUAAAGUUCUUUCCACAACUCACAUAAAGAAACAAUUUGGGGAUUUUCAACAACCACCCCAACAUCUUGACCGGUUUUUACCUUCACAACCCUUAU
.(((---(....((((((((((((......((((((.............)))))).....((((((..............))))))..........))))))))))))....)))).... ( -27.16)
>DroEre_CAF1 35152 114 + 1
UGGAAGUUCUACAGGGUGGAAUUCUUAAAGUUGUUUCCCAAACUCCUAAAAGGGAACAUUUUGGAGAUAGUCAACC------CCAACUUCUUGUCCGGUUUUUACCUUCACAACCCUUAU
.(((((((.....((((.((..((((.(((.(((((((.............))))))).))).))))...)).)))------).)))))))(((..(((....)))...)))........ ( -25.82)
>DroYak_CAF1 39694 120 + 1
UAAAAGUCCUACAGGGUGGAAAUCUCAAAAUUGUUUCCAAAACUUCCAAAAAGAAUCAUUUUGGAGAUAGUCAACCACCAACCCAACAGCUUGUCCGGUUUUUACCUUCACAACCCUUAA
............(((((.(((........(((((((((((((.(((......)))...)))))))))))))........((((..((.....))..))))......)))...)))))... ( -23.10)
>consensus
UGGA___UAUACAGGGUGGAAAUCUUAAAGUUGUUUCCAAAACUCCCAAAAAGAAACAAUUUGGAGAUAGUCAACCACCACCCCAACAUCUUGACCGGUUUUUACCUUCACAACCCUUAU
............(((((.((((((((.((((((((((...............)))))))))).)))))............................(((....))))))...)))))... (-18.41 = -19.04 +   0.63)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:11:21 2006