Locus 8182

Sequence ID	3R_DroMel_CAF1
Location	21,995,169 – 21,995,327
Length	158
Max. P	0.956736

overview

Window 1

Location	21,995,169 – 21,995,287
Length	118
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	81.98
Mean single sequence MFE	-31.39
Consensus MFE	-23.55
Energy contribution	-25.46
Covariance contribution	1.91
Combinations/Pair	1.18
Mean z-score	-1.66
Structure conservation index	0.75
SVM decision value	0.31
SVM RNA-class probability	0.683162
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 21995169 118 - 27905053
GCUGGCAACUUUACAACAGUGUGAAGU--GGUAAAGUGGUUCGCCAGGCUCAUUAAUUUUACUCAGCCAGAGAUGAAUAAUGAGUUGGGUUUAAGGGGGCUACUCAGACAUAAAAUAUAU
.(((((.((((((((....))))))))--.))..(((((((((((..((((((((..(((((((.....))).))))))))))))..)))......)))))))))))............. ( -34.10)
>DroSim_CAF1 31473 118 - 1
GCUGGCAACUUUACAACAGUGUGAAGU--GGUAAAGUGGUUCGCCAGGCUCAUUAAUUUUACUCAGCCAGAGAUGAAUAAUGAGUUGGGUUUAAGGGGGCUACUCAGACAUAAAAUAUAU
.(((((.((((((((....))))))))--.))..(((((((((((..((((((((..(((((((.....))).))))))))))))..)))......)))))))))))............. ( -34.10)
>DroEre_CAF1 37113 116 - 1
GCUGGCAACUUUACAACAGUGUGAAGU--GGUAAAGUGGUUCGCCAGGCUCAUUAAUUUUGCUCAGCCGGAGAUGAAUAAUGAGUUGGGCUUAAGGGGGCUACUCAGACAUAAAAU--AU
.(((((.((((((((....))))))))--.))..(((((((((((..((((((((.((...(((.....)))..)).))))))))..)))......))))))))))).........--.. ( -36.00)
>DroYak_CAF1 35747 116 - 1
GCUGGCAACUUUACAACAGUGUGAAGU--GGUAAAGUGGUUCGCCAGGCUCAUUAAUUUUACUCAGCCGGAGAUGAAUAAUGAGUUGGUUUUAAGGGGGCCACUCAGACAUAAAAU--AU
.(((((.((((((((....))))))))--.))..(((((((((((((.(((((((..(((((((.....))).)))))))))))))))).......))))))))))).........--.. ( -35.01)
>DroAna_CAF1 41825 95 - 1
----------------------CAAGUUGGUUACAGCGGUUGGCCAUGCAAAUUAAUUUUACUCAACCGGGGAUGAAUAAUGAGCUCGGUUUUU-GGGACAGCUCACACAGAGAAU--AU
----------------------...((((....))))((....))................((((((((((.............)))))))..(-(((....))))....)))...--.. ( -17.72)
>consensus
GCUGGCAACUUUACAACAGUGUGAAGU__GGUAAAGUGGUUCGCCAGGCUCAUUAAUUUUACUCAGCCGGAGAUGAAUAAUGAGUUGGGUUUAAGGGGGCUACUCAGACAUAAAAU__AU
.(((((.((((((((....))))))))...))..(((((((((((..((((((((..(((((((.....))).))))))))))))..)))......)))))))))))............. (-23.55 = -25.46 +   1.91)

alignment

secondary structure

dotplot

Window 2

Location	21,995,209 – 21,995,327
Length	118
Sequences	4
Columns	118
Reading direction	forward
Mean pairwise identity	99.01
Mean single sequence MFE	-31.78
Consensus MFE	-32.04
Energy contribution	-31.60
Covariance contribution	-0.44
Combinations/Pair	1.06
Mean z-score	-2.87
Structure conservation index	1.01
SVM decision value	1.47
SVM RNA-class probability	0.956736
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 21995209 118 + 27905053
UUAUUCAUCUCUGGCUGAGUAAAAUUAAUGAGCCUGGCGAACCACUUUACCACUUCACACUGUUGUAAAGUUGCCAGCAAAGCAUUAUUUCUUUGUUUGCAUUCAAGUAGCCGGAUUA
.........((((((((.(((((...(((((((((((((....(((((((.((........)).)))))))))))))....)).)))))......))))).......))))))))... ( -30.00)
>DroSim_CAF1 31513 118 + 1
UUAUUCAUCUCUGGCUGAGUAAAAUUAAUGAGCCUGGCGAACCACUUUACCACUUCACACUGUUGUAAAGUUGCCAGCAAAGCAUUAUUUCUUUGUUUGCAUUCAAGUAGCCGGAUUA
.........((((((((.(((((...(((((((((((((....(((((((.((........)).)))))))))))))....)).)))))......))))).......))))))))... ( -30.00)
>DroEre_CAF1 37151 118 + 1
UUAUUCAUCUCCGGCUGAGCAAAAUUAAUGAGCCUGGCGAACCACUUUACCACUUCACACUGUUGUAAAGUUGCCAGCAAAGCAUUAUUUCUUUGUUUGCAUUCAAGUAGCCGGAUUA
.........((((((((((((((..(((((...((((((....(((((((.((........)).))))))))))))).....)))))....)))))))((......)))))))))... ( -34.90)
>DroYak_CAF1 35785 118 + 1
UUAUUCAUCUCCGGCUGAGUAAAAUUAAUGAGCCUGGCGAACCACUUUACCACUUCACACUGUUGUAAAGUUGCCAGCAAAGCAUUAUUUCUUUGUUUGCAUUCAAGUAGCCGGAUUA
.........((((((((.(((((...(((((((((((((....(((((((.((........)).)))))))))))))....)).)))))......))))).......))))))))... ( -32.20)
>consensus
UUAUUCAUCUCCGGCUGAGUAAAAUUAAUGAGCCUGGCGAACCACUUUACCACUUCACACUGUUGUAAAGUUGCCAGCAAAGCAUUAUUUCUUUGUUUGCAUUCAAGUAGCCGGAUUA
.........((((((((.(((((...(((((((((((((....(((((((.((........)).)))))))))))))....)).)))))......))))).......))))))))... (-32.04 = -31.60 +  -0.44)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:04:35 2006