Locus 5726

Sequence ID	X_DroMel_CAF1
Location	14,814,864 – 14,815,009
Length	145
Max. P	0.610763

overview

Window 3

Location	14,814,864 – 14,814,982
Length	118
Sequences	4
Columns	118
Reading direction	reverse
Mean pairwise identity	92.23
Mean single sequence MFE	-33.83
Consensus MFE	-33.16
Energy contribution	-33.04
Covariance contribution	-0.12
Combinations/Pair	1.08
Mean z-score	-1.26
Structure conservation index	0.98
SVM decision value	0.11
SVM RNA-class probability	0.589852
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 14814864 118 - 22224390
GGCUCGGCCUACGACAGCAUUGCGAUUUAAUUACAUUAGCGACAGCUGGAGAAUGCACAAAAGUGGGUUGGCCAGCGGGGGGUUAAGCAAGAGUGUGUGGUGAAAGUGAAGUAAAGUA
(((...)))(((..((.(((..((...........(((((..(.(((((..(((.(((....))).)))..)))))..)..))))).........))..)))....))..)))..... ( -30.95)
>DroSim_CAF1 8093 111 - 1
GGCUCGGCCUCCGACAGCAUUGCGAUUUAAUUACAUUAGCGACAGCUGGAGAAUGCACAAAAGUGGGUUGGCCAGCGGGGGGCUAAGUGAGAGUGUGUGGUGAAAGUAAAG-------
...((((...))))...(((..((......((((.(((((..(.(((((..(((.(((....))).)))..)))))..)..))))))))).....))..))).........------- ( -35.60)
>DroEre_CAF1 13943 118 - 1
GGCUCGGCCUCCGACAGCAUUGCGAUUUAAUUACAUUAGCGACAGCUGGAGAAUGCACAAAAGUGGGUUGGCCAGCGGGGGGUUAAGUAAGAGUGGGCGGUGAAAGUGAAGUACAGUU
.(((..((((((.......((((...............))))..(((((..(((.(((....))).)))..))))).))))))..)))..((.((..(............)..)).)) ( -34.36)
>DroYak_CAF1 1514 118 - 1
GGCUCGGCCUCCGACAGCAUUGCGAUUUAAUUACAUUAGCGACAGCUGGAGAAUGCACAAAAGUGGGUUGGCCAGCGGGGGGUUAAGUAAGAGUGGGUGGUGAAAGUAAUAUAAAGUG
.(((..(((.((.((.((...)).......((((.(((((..(.(((((..(((.(((....))).)))..)))))..)..)))))))))..)).)).)))...)))........... ( -34.40)
>consensus
GGCUCGGCCUCCGACAGCAUUGCGAUUUAAUUACAUUAGCGACAGCUGGAGAAUGCACAAAAGUGGGUUGGCCAGCGGGGGGUUAAGUAAGAGUGGGUGGUGAAAGUAAAGUAAAGU_
.(((..((((((.......((((...............))))..(((((..(((.(((....))).)))..))))).))))))..))).............................. (-33.16 = -33.04 +  -0.12)

alignment

secondary structure

dotplot

Window 4

Location	14,814,904 – 14,815,009
Length	105
Sequences	5
Columns	105
Reading direction	reverse
Mean pairwise identity	99.62
Mean single sequence MFE	-27.80
Consensus MFE	-27.80
Energy contribution	-27.80
Covariance contribution	0.00
Combinations/Pair	1.00
Mean z-score	-1.26
Structure conservation index	1.00
SVM decision value	0.16
SVM RNA-class probability	0.610763
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 14814904 105 - 22224390
AAAUUUUAUUGUCCGAAAAGUAAAAAAGGCUCGGCCUACGACAGCAUUGCGAUUUAAUUACAUUAGCGACAGCUGGAGAAUGCACAAAAGUGGGUUGGCCAGCGG
...(((((((........)))))))...(((.((((..(..((((.((((...............))))..))))..)(((.(((....))).)))))))))).. ( -27.96)
>DroSec_CAF1 8878 105 - 1
AAAUUUUAUUGUCCGAAAAGUAAAAAAGGCUCGGCCUCCGACAGCAUUGCGAUUUAAUUACAUUAGCGACAGCUGGAGAAUGCACAAAAGUGGGUUGGCCAGCGG
...(((((((........)))))))...(((.((((..(..((((.((((...............))))..))))..)(((.(((....))).)))))))))).. ( -27.76)
>DroSim_CAF1 8126 105 - 1
AAAUUUUAUUGUCCGAAAAGUAAAAAAGGCUCGGCCUCCGACAGCAUUGCGAUUUAAUUACAUUAGCGACAGCUGGAGAAUGCACAAAAGUGGGUUGGCCAGCGG
...(((((((........)))))))...(((.((((..(..((((.((((...............))))..))))..)(((.(((....))).)))))))))).. ( -27.76)
>DroEre_CAF1 13983 105 - 1
AAAUUUUAUUGUCCGAAAAGUAAAAAAGGCUCGGCCUCCGACAGCAUUGCGAUUUAAUUACAUUAGCGACAGCUGGAGAAUGCACAAAAGUGGGUUGGCCAGCGG
...(((((((........)))))))...(((.((((..(..((((.((((...............))))..))))..)(((.(((....))).)))))))))).. ( -27.76)
>DroYak_CAF1 1554 105 - 1
AAAUUUUAUUGUCCGAAAAGUAAAAAAGGCUCGGCCUCCGACAGCAUUGCGAUUUAAUUACAUUAGCGACAGCUGGAGAAUGCACAAAAGUGGGUUGGCCAGCGG
...(((((((........)))))))...(((.((((..(..((((.((((...............))))..))))..)(((.(((....))).)))))))))).. ( -27.76)
>consensus
AAAUUUUAUUGUCCGAAAAGUAAAAAAGGCUCGGCCUCCGACAGCAUUGCGAUUUAAUUACAUUAGCGACAGCUGGAGAAUGCACAAAAGUGGGUUGGCCAGCGG
...(((((((........)))))))...(((.((((..(..((((.((((...............))))..))))..)(((.(((....))).)))))))))).. (-27.80 = -27.80 +   0.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:54:56 2006