Locus 4727

Sequence ID	2L_DroMel_CAF1
Location	13,548,781 – 13,548,877
Length	96
Max. P	0.982894

overview

Window 8

Location	13,548,781 – 13,548,877
Length	96
Sequences	4
Columns	106
Reading direction	forward
Mean pairwise identity	89.95
Mean single sequence MFE	-33.30
Consensus MFE	-27.88
Energy contribution	-28.00
Covariance contribution	0.13
Combinations/Pair	1.07
Mean z-score	-2.78
Structure conservation index	0.84
SVM decision value	1.93
SVM RNA-class probability	0.982894
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 13548781 96 + 22407834
AUCGAAUGAAAAGAAGAAGAAAACAAGUUCUGGGCGCACAGUGGGGCAAGCUUAGAACU---GUAGUGACCACUGUGCGGCAGCAGUUGAGCUUCUAGU-------
..............(((((....(((.(.((.(.((((((((((..((.((........---))..)).)))))))))).))).).)))..)))))...------- ( -30.30)
>DroSec_CAF1 7641 103 + 1
AUCGAAAGAAGAGAAGAAGAAAACAAGUUCUGGGCGCACAGUGGGGCAAGCUUAGAACU---GUAGUGACCACUGUGCGGCAGCAGUUGAGCUUCUAGUUUCGCAU
.((....)).(((((((((....(((.(.((.(.((((((((((..((.((........---))..)).)))))))))).))).).)))..)))))..)))).... ( -34.80)
>DroSim_CAF1 7868 103 + 1
AUCGAAAGAAGAGAAGAAGAAAACAAGUUCUGGGCGCACAGUGGGGCAAGCUUAGAACU---GUAGUGACCACUGUGCGGCAGCAGUUGAGCUUCUAGUUUCGCAU
.((....)).(((((((((....(((.(.((.(.((((((((((..((.((........---))..)).)))))))))).))).).)))..)))))..)))).... ( -34.80)
>DroEre_CAF1 9982 106 + 1
GUCAAAAGAAGAGAUGGAGAAAACAAGUUCUGGGCGCACAGUGGUGCAAGCUUAGAAGUCUAGUGGUGACCACUGUGCGGCAGCAGUUAAGCUUCUAGAUUCGCAU
.......(((....((((..............(.(((((((((((.((.(((.((....)))))..))))))))))))).)(((......)))))))..))).... ( -33.30)
>consensus
AUCGAAAGAAGAGAAGAAGAAAACAAGUUCUGGGCGCACAGUGGGGCAAGCUUAGAACU___GUAGUGACCACUGUGCGGCAGCAGUUGAGCUUCUAGUUUCGCAU
.((....)).....(((((....(((.(.((.(.((((((((((.....(((............)))..)))))))))).))).).)))..))))).......... (-27.88 = -28.00 +   0.13)

alignment

secondary structure

dotplot

Window 9

Location	13,548,781 – 13,548,877
Length	96
Sequences	4
Columns	106
Reading direction	reverse
Mean pairwise identity	89.95
Mean single sequence MFE	-26.80
Consensus MFE	-22.17
Energy contribution	-21.98
Covariance contribution	-0.19
Combinations/Pair	1.05
Mean z-score	-2.54
Structure conservation index	0.83
SVM decision value	1.63
SVM RNA-class probability	0.968891
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 13548781 96 - 22407834
-------ACUAGAAGCUCAACUGCUGCCGCACAGUGGUCACUAC---AGUUCUAAGCUUGCCCCACUGUGCGCCCAGAACUUGUUUUCUUCUUCUUUUCAUUCGAU
-------...(((((..(((...(((.((((((((((.((....---(((.....)))))..))))))))))..)))...)))....))))).............. ( -24.90)
>DroSec_CAF1 7641 103 - 1
AUGCGAAACUAGAAGCUCAACUGCUGCCGCACAGUGGUCACUAC---AGUUCUAAGCUUGCCCCACUGUGCGCCCAGAACUUGUUUUCUUCUUCUCUUCUUUCGAU
...(((((..(((((..(((...(((.((((((((((.((....---(((.....)))))..))))))))))..)))...)))....))))).......))))).. ( -27.40)
>DroSim_CAF1 7868 103 - 1
AUGCGAAACUAGAAGCUCAACUGCUGCCGCACAGUGGUCACUAC---AGUUCUAAGCUUGCCCCACUGUGCGCCCAGAACUUGUUUUCUUCUUCUCUUCUUUCGAU
...(((((..(((((..(((...(((.((((((((((.((....---(((.....)))))..))))))))))..)))...)))....))))).......))))).. ( -27.40)
>DroEre_CAF1 9982 106 - 1
AUGCGAAUCUAGAAGCUUAACUGCUGCCGCACAGUGGUCACCACUAGACUUCUAAGCUUGCACCACUGUGCGCCCAGAACUUGUUUUCUCCAUCUCUUCUUUUGAC
...((((...((((((......)))..(((((((((((((....(((....)))....)).)))))))))))......................)))...)))).. ( -27.50)
>consensus
AUGCGAAACUAGAAGCUCAACUGCUGCCGCACAGUGGUCACUAC___AGUUCUAAGCUUGCCCCACUGUGCGCCCAGAACUUGUUUUCUUCUUCUCUUCUUUCGAU
..........(((((..(((...(((.((((((((((.........................))))))))))..)))...))).)))))................. (-22.17 = -21.98 +  -0.19)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:25:42 2006