Locus 3407

Sequence ID	2L_DroMel_CAF1
Location	9,862,701 – 9,862,793
Length	92
Max. P	0.994373

overview

Window 2

Location	9,862,701 – 9,862,793
Length	92
Sequences	5
Columns	98
Reading direction	forward
Mean pairwise identity	79.05
Mean single sequence MFE	-32.42
Consensus MFE	-23.92
Energy contribution	-25.16
Covariance contribution	1.24
Combinations/Pair	1.04
Mean z-score	-2.63
Structure conservation index	0.74
SVM decision value	2.47
SVM RNA-class probability	0.994373
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 9862701 92 + 22407834
CUCAUUGUUUGGCACUUAGUCAGGACGAUGUCGGCAGCAGAGGCUCCUGCUUCUGCUCCUGCU------CCUGCUCCUGCUCGUGCAUCUGCGCUGCC
..(((((((((((.....)))).)))))))..((((((((((((....))))))((...(((.------(..((....))..).)))...)))))))) ( -36.50)
>DroSec_CAF1 70754 74 + 1
CUCAUUGUUCGGCACUUAGUCAGGACGAUGUCGGCAGCAGACGCUCCUGCUUCUGCUCCU------------------------GCAUCUGCGCUGCC
..(((((((((((.....))).)))))))).((((.(((((.((....((....))....------------------------)).))))))))).. ( -27.30)
>DroSim_CAF1 77535 74 + 1
CUCAUUGUUCGGCACUUAGUCAGGACGAUGUCGGCAGCAGAGGCUCCUGCUUCUGCUCCU------------------------GCAUCUGCGCUGCC
..(((((((((((.....))).))))))))..((((((((((((....))))))((....------------------------))......)))))) ( -31.10)
>DroEre_CAF1 75469 92 + 1
CUCAUUGUUCGGCACUUAGUCAGGAGGAUGUCGGCAGCAGAGACUCCUGCUCCAGCUCCAGCU------CCUGCUCCUGCUCUUGCAUCUGCGCUGCC
.........((((....((.((((((((.((.((.(((((......))))))).))))).((.------...)))))))))...((....)))))).. ( -29.50)
>DroYak_CAF1 74336 98 + 1
CUCAUUGUUCGGCACUUAGUCAGGACGAUGUCGGCAGCAGAGACUUUAGCUACUGCUCCUUCUCCUGAUCCUGCAACUGCAACUGCAGCUGCGCUGCC
..(((((((((((.....))).))))))))..((((((.((((....(((....)))...))))........(((.((((....)))).))))))))) ( -37.70)
>consensus
CUCAUUGUUCGGCACUUAGUCAGGACGAUGUCGGCAGCAGAGGCUCCUGCUUCUGCUCCU_CU______CCUGC__CUGC___UGCAUCUGCGCUGCC
..(((((((((((.....))).))))))))..((((((((((((....))))))..............................((....)))))))) (-23.92 = -25.16 +   1.24)

alignment

secondary structure

dotplot

Window 3

Location	9,862,701 – 9,862,793
Length	92
Sequences	5
Columns	98
Reading direction	reverse
Mean pairwise identity	79.05
Mean single sequence MFE	-31.02
Consensus MFE	-19.28
Energy contribution	-19.32
Covariance contribution	0.04
Combinations/Pair	1.12
Mean z-score	-1.65
Structure conservation index	0.62
SVM decision value	0.04
SVM RNA-class probability	0.555189
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 9862701 92 - 22407834
GGCAGCGCAGAUGCACGAGCAGGAGCAGG------AGCAGGAGCAGAAGCAGGAGCCUCUGCUGCCGACAUCGUCCUGACUAAGUGCCAAACAAUGAG
(((((.((....)).).(((((((((...------.)).((((((((.((....)).)))))).)).......))))).))...)))).......... ( -31.70)
>DroSec_CAF1 70754 74 - 1
GGCAGCGCAGAUGC------------------------AGGAGCAGAAGCAGGAGCGUCUGCUGCCGACAUCGUCCUGACUAAGUGCCGAACAAUGAG
((((.....((((.------------------------.((((((((.((....)).)))))).))..))))((....))....)))).......... ( -25.80)
>DroSim_CAF1 77535 74 - 1
GGCAGCGCAGAUGC------------------------AGGAGCAGAAGCAGGAGCCUCUGCUGCCGACAUCGUCCUGACUAAGUGCCGAACAAUGAG
((((.....((((.------------------------.((((((((.((....)).)))))).))..))))((....))....)))).......... ( -25.80)
>DroEre_CAF1 75469 92 - 1
GGCAGCGCAGAUGCAAGAGCAGGAGCAGG------AGCUGGAGCUGGAGCAGGAGUCUCUGCUGCCGACAUCCUCCUGACUAAGUGCCGAACAAUGAG
((((..((....))...(((((((((...------.)).(((..(((((((((....)))))).)))...)))))))).))...)))).......... ( -30.40)
>DroYak_CAF1 74336 98 - 1
GGCAGCGCAGCUGCAGUUGCAGUUGCAGGAUCAGGAGAAGGAGCAGUAGCUAAAGUCUCUGCUGCCGACAUCGUCCUGACUAAGUGCCGAACAAUGAG
((((..((((((((....)))))))).((.((((((((.(((((((..((....))..))))).))....)).))))))))...)))).......... ( -41.40)
>consensus
GGCAGCGCAGAUGCA___GCAG__GCAGG______AG_AGGAGCAGAAGCAGGAGCCUCUGCUGCCGACAUCGUCCUGACUAAGUGCCGAACAAUGAG
((((..((....)).........................((((((((.((....)).)))))).))..................)))).......... (-19.28 = -19.32 +   0.04)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:51:44 2006