Locus 5998

Sequence ID	3R_DroMel_CAF1
Location	15,787,898 – 15,788,067
Length	169
Max. P	0.891735

overview

Window 1

Location	15,787,898 – 15,788,001
Length	103
Sequences	5
Columns	106
Reading direction	reverse
Mean pairwise identity	94.29
Mean single sequence MFE	-27.26
Consensus MFE	-21.58
Energy contribution	-22.42
Covariance contribution	0.84
Combinations/Pair	1.04
Mean z-score	-1.58
Structure conservation index	0.79
SVM decision value	0.12
SVM RNA-class probability	0.594341
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 15787898 103 - 27905053
CCUGCUGCAAGGAAAAGGUUAAGAGGCAAAGAAACGCUAGGUAGUCCU---GCUAAAUCGGCGGAAAAACAAGCGGCAGGAAGCGAACAGCAUGCAAAUCAGUUCG
((((((((........(..((...(((........)))...))..)((---(((.....)))))........))))))))...(((((.............))))) ( -27.62)
>DroSec_CAF1 9161 106 - 1
CCUGCUGCAAGGAAAAGGUUAAUAGGCAAAGAAACGCUAGGUAGUCCUGCUGCUAAAUCGGCGGAAAAACAAGCGGCAGGAAGCGAACAGCAUGCAAAUCAGUUCG
((((((((.......((((((...(((........)))...))).))).(((((.....)))))........))))))))...(((((.............))))) ( -29.62)
>DroSim_CAF1 13628 106 - 1
CCUGCUGCAAGGAAAAGGUUAAGAGGCAAAGAAACGCUAGGUAGUCCUGCUGCUAAAUCGGCGGAAAAACAAGCGGCAGGAAGCGAACAGCAUGCAAAUCAGUUCG
((((((((.......((((((...(((........)))...))).))).(((((.....)))))........))))))))...(((((.............))))) ( -29.62)
>DroEre_CAF1 12969 103 - 1
CCCGCUGCAAGGAAAAGGUUAAGAGCCAAAGAAAAGCUAGGUAGUCCU---GCUAAAUCGGCGGAAAAACAAGCGGCAGAAAGCGAACGGCAUGCAAAUCAGUUCG
.((((((.........(((.....))).......(((.(((....)))---)))....))))))........((........))((((.............)))). ( -23.02)
>DroYak_CAF1 30329 103 - 1
CCUGCUGCAAAGAAAAAGUUAAGAGCCAAAGAAACGCCAGGUAGUCUU---GCUAAAUCGGCGGAAAAACAAGCGGCAGGAAGCGAACAGCAUGCAAAUCAGUUCG
((((((((.........((.....))........(((((..(((....---.)))..).)))).........))))))))...(((((.............))))) ( -26.42)
>consensus
CCUGCUGCAAGGAAAAGGUUAAGAGGCAAAGAAACGCUAGGUAGUCCU___GCUAAAUCGGCGGAAAAACAAGCGGCAGGAAGCGAACAGCAUGCAAAUCAGUUCG
((((((((.........(((....))).......((((...((((......))))....)))).........))))))))...(((((.............))))) (-21.58 = -22.42 +   0.84)

alignment

secondary structure

dotplot

Window 2

Location	15,787,937 – 15,788,041
Length	104
Sequences	5
Columns	107
Reading direction	reverse
Mean pairwise identity	93.59
Mean single sequence MFE	-26.94
Consensus MFE	-23.82
Energy contribution	-23.74
Covariance contribution	-0.08
Combinations/Pair	1.10
Mean z-score	-1.21
Structure conservation index	0.88
SVM decision value	0.18
SVM RNA-class probability	0.622851
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 15787937 104 - 27905053
UGAACUCAAUUUUCGGGCAGCAGAGCAAAUUCGUUAGAGUCCUGCUGCAAGGAAAAGGUUAAGAGGCAAAGAAACGCUAGGUAGUCCU---GCUAAAUCGGCGGAAA
.........(((((..(((((((..(....((....)))..)))))))..))))).(..((...(((........)))...))..)((---(((.....)))))... ( -26.60)
>DroSec_CAF1 9200 107 - 1
UGAACUCAAUUUUCGGGCAGCAGAGCAAAUUCGUUAGAGUCCUGCUGCAAGGAAAAGGUUAAUAGGCAAAGAAACGCUAGGUAGUCCUGCUGCUAAAUCGGCGGAAA
.........(((((..(((((((..(....((....)))..)))))))..)))))((((((...(((........)))...))).))).(((((.....)))))... ( -28.60)
>DroSim_CAF1 13667 107 - 1
UGAACUCAAUUUUCGGGCAGCAGAGCAAAUUCGUUAGAGUCCUGCUGCAAGGAAAAGGUUAAGAGGCAAAGAAACGCUAGGUAGUCCUGCUGCUAAAUCGGCGGAAA
.........(((((..(((((((..(....((....)))..)))))))..)))))((((((...(((........)))...))).))).(((((.....)))))... ( -28.60)
>DroEre_CAF1 13008 104 - 1
UGAACUCAAUUUUCAGGCAGCAGAGCAAAUUCGUUAGAGUCCCGCUGCAAGGAAAAGGUUAAGAGCCAAAGAAAAGCUAGGUAGUCCU---GCUAAAUCGGCGGAAA
..((((...(((((..(((((.(..(....((....)))..).)))))...)))))))))....(((.......(((.(((....)))---))).....)))..... ( -23.40)
>DroYak_CAF1 30368 104 - 1
UGAACUACAUUUUCGGGCAGCAGAGCAAAUUCGUUAGAAUCCUGCUGCAAAGAAAAAGUUAAGAGCCAAAGAAACGCCAGGUAGUCUU---GCUAAAUCGGCGGAAA
..((((...(((((..(((((((.(...((((....))))))))))))...)))))))))..............(((((..(((....---.)))..).)))).... ( -27.50)
>consensus
UGAACUCAAUUUUCGGGCAGCAGAGCAAAUUCGUUAGAGUCCUGCUGCAAGGAAAAGGUUAAGAGGCAAAGAAACGCUAGGUAGUCCU___GCUAAAUCGGCGGAAA
..((((...(((((..(((((((.(...((((....))))))))))))...)))))))))..............((((...((((......))))....)))).... (-23.82 = -23.74 +  -0.08)

alignment

secondary structure

dotplot

Window 3

Location	15,787,973 – 15,788,067
Length	94
Sequences	5
Columns	94
Reading direction	reverse
Mean pairwise identity	93.62
Mean single sequence MFE	-22.72
Consensus MFE	-19.46
Energy contribution	-19.38
Covariance contribution	-0.08
Combinations/Pair	1.12
Mean z-score	-1.56
Structure conservation index	0.86
SVM decision value	0.97
SVM RNA-class probability	0.891735
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 15787973 94 - 27905053
CAGAUACUAAAACGAUGGAAACGAGUUGAACUCAAUUUUCGGGCAGCAGAGCAAAUUCGUUAGAGUCCUGCUGCAAGGAAAAGGUUAAGAGGCA
......((..(((...(....)(((.....)))..(((((..(((((((..(....((....)))..)))))))..)))))..)))...))... ( -23.40)
>DroSec_CAF1 9239 94 - 1
CAGAUACUAAAACGAUGGAAACGAGUUGAACUCAAUUUUCGGGCAGCAGAGCAAAUUCGUUAGAGUCCUGCUGCAAGGAAAAGGUUAAUAGGCA
......(((.(((...(....)(((.....)))..(((((..(((((((..(....((....)))..)))))))..)))))..)))..)))... ( -23.40)
>DroSim_CAF1 13706 94 - 1
CAGAUACUAAAACGAUGGAAACGAGUUGAACUCAAUUUUCGGGCAGCAGAGCAAAUUCGUUAGAGUCCUGCUGCAAGGAAAAGGUUAAGAGGCA
......((..(((...(....)(((.....)))..(((((..(((((((..(....((....)))..)))))))..)))))..)))...))... ( -23.40)
>DroEre_CAF1 13044 94 - 1
CGGAUACCAAAAGGAUGGAAACGAGCUGAACUCAAUUUUCAGGCAGCAGAGCAAAUUCGUUAGAGUCCCGCUGCAAGGAAAAGGUUAAGAGCCA
.((..(((........(....)(((.....)))..(((((..(((((.(..(....((....)))..).)))))...))))))))......)). ( -21.10)
>DroYak_CAF1 30404 94 - 1
CAGUUACUAAAAGGAUGGAAACGAGUUGAACUACAUUUUCGGGCAGCAGAGCAAAUUCGUUAGAAUCCUGCUGCAAAGAAAAAGUUAAGAGCCA
............((.((....)).....((((...(((((..(((((((.(...((((....))))))))))))...))))))))).....)). ( -22.30)
>consensus
CAGAUACUAAAACGAUGGAAACGAGUUGAACUCAAUUUUCGGGCAGCAGAGCAAAUUCGUUAGAGUCCUGCUGCAAGGAAAAGGUUAAGAGGCA
.....(((........(....)(((.....)))..(((((..(((((((.(...((((....))))))))))))...))))))))......... (-19.46 = -19.38 +  -0.08)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:10:08 2006