Locus 7212

Sequence ID	3R_DroMel_CAF1
Location	18,976,035 – 18,976,162
Length	127
Max. P	0.998524

overview

Window 1

Location	18,976,035 – 18,976,128
Length	93
Sequences	5
Columns	95
Reading direction	reverse
Mean pairwise identity	91.47
Mean single sequence MFE	-20.54
Consensus MFE	-16.92
Energy contribution	-17.92
Covariance contribution	1.00
Combinations/Pair	1.00
Mean z-score	-2.98
Structure conservation index	0.82
SVM decision value	3.13
SVM RNA-class probability	0.998524
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 18976035 93 - 27905053
GCGCGGAAACGCGGUCAUAGCAAUCAAUUUUAUCACUUGCUGUAUAAAUUAAAUUACAUC--CCCUGAUGUUAUAAAACUUAAAGACCAAAAACA
..(((....)))(((((((((((.............)))))))............(((((--....))))).............))))....... ( -22.52)
>DroSec_CAF1 87046 93 - 1
GCGCGGAAACGCGGUCAUAGCAAUCAAUUUUAUUACUUGCUGUAUAAAUUAAAGUACAUC--CCCUGAUGUUGUAAAACUUAAAGACCAAAAACA
..(((....)))(((((((((((.............)))))))........(((((((((--....)))))......))))...))))....... ( -23.02)
>DroSim_CAF1 88857 93 - 1
GCGCGGAAACGCGGUCAUAGCAAUCAAUUUUAUCACUUGCUGUAUAAAUUAAAGUACAUC--CCCUGAUGUCGUAAAACUUAAAGACCAAAAACA
..(((....)))(((((((((((.............)))))))..........(.(((((--....))))))............))))....... ( -23.22)
>DroEre_CAF1 87651 95 - 1
GCGCGGAAUCGCGGUCAUAGCCAUUAAAUUUAUCACUUGCAGUGUAAAUUAAAGUACAUCUCCUUUGAUAUUAUAAAACUUAAAGACCAAAAACA
..(((....)))((((..........((((((.(((.....))))))))).......(((......)))...............))))....... ( -15.60)
>DroYak_CAF1 90254 93 - 1
GCGCGGAAACGCGGUCAUAGCAAUUAAAUUUAUCACUUGCAGUAUACAUUAAAGUACAUC--CCUUGAUAUUAUAAAACCUAAAGACCAAAAACA
..(((....)))((((...((((.............)))).((((........))))...--......................))))....... ( -18.32)
>consensus
GCGCGGAAACGCGGUCAUAGCAAUCAAUUUUAUCACUUGCUGUAUAAAUUAAAGUACAUC__CCCUGAUGUUAUAAAACUUAAAGACCAAAAACA
..(((....)))(((((((((((.............)))))))............(((((......))))).............))))....... (-16.92 = -17.92 +   1.00)

alignment

secondary structure

dotplot

Window 2

Location	18,976,054 – 18,976,162
Length	108
Sequences	5
Columns	112
Reading direction	reverse
Mean pairwise identity	90.51
Mean single sequence MFE	-26.34
Consensus MFE	-22.08
Energy contribution	-22.04
Covariance contribution	-0.04
Combinations/Pair	1.14
Mean z-score	-2.05
Structure conservation index	0.84
SVM decision value	1.84
SVM RNA-class probability	0.979605
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 18976054 108 - 27905053
--UUGACUUAUACAAUUUCUUAUCGGGGAUUUAUUGGCGCGGAAACGCGGUCAUAGCAAUCAAUUUUAUCACUUGCUGUAUAAAUUAAAUUACAUC--CCCUGAUGUUAUAA
--..................((((((((((.((..((((((....))).)))(((((((.............)))))))...........)).)))--))).))))...... ( -26.92)
>DroSec_CAF1 87065 108 - 1
--UUGGCUUAUACAAUUUCUUAUCGGGGAUUUAUUGGCGCGGAAACGCGGUCAUAGCAAUCAAUUUUAUUACUUGCUGUAUAAAUUAAAGUACAUC--CCCUGAUGUUGUAA
--........((((((.((.....((((((.((((((((((....))).)))(((((((.............))))))).........)))).)))--))).)).)))))). ( -31.62)
>DroSim_CAF1 88876 108 - 1
--UUGGCUUAUACAAUUUCUUAUCGGGGAUUUAUUGGCGCGGAAACGCGGUCAUAGCAAUCAAUUUUAUCACUUGCUGUAUAAAUUAAAGUACAUC--CCCUGAUGUCGUAA
--..................((((((((((.((((((((((....))).)))(((((((.............))))))).........)))).)))--))).))))...... ( -29.12)
>DroEre_CAF1 87670 112 - 1
UCUUGACUCAUACAGUUUCUUAUCGGGGAUUUAUUGGCGCGGAAUCGCGGUCAUAGCCAUUAAAUUUAUCACUUGCAGUGUAAAUUAAAGUACAUCUCCUUUGAUAUUAUAA
....................((((((((((.((((((((((....))).)))..........((((((.(((.....)))))))))..)))).))))))...))))...... ( -19.90)
>DroYak_CAF1 90273 108 - 1
--UUAACUUAUACAGUUUCUUAUCGGGGAUUUAUUGGCGCGGAAACGCGGUCAUAGCAAUUAAAUUUAUCACUUGCAGUAUACAUUAAAGUACAUC--CCUUGAUAUUAUAA
--..................((((((((((.((((((((((....))).)))...((((.............))))............)))).)))--)).)))))...... ( -24.12)
>consensus
__UUGACUUAUACAAUUUCUUAUCGGGGAUUUAUUGGCGCGGAAACGCGGUCAUAGCAAUCAAUUUUAUCACUUGCUGUAUAAAUUAAAGUACAUC__CCCUGAUGUUAUAA
....................((((((((.......((((((....))).)))(((((((.............)))))))...................))))))))...... (-22.08 = -22.04 +  -0.04)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:40:18 2006