Locus 1753

Sequence ID	2L_DroMel_CAF1
Location	4,794,080 – 4,794,210
Length	130
Max. P	0.995237

overview

Window 4

Location	4,794,080 – 4,794,174
Length	94
Sequences	5
Columns	111
Reading direction	forward
Mean pairwise identity	68.51
Mean single sequence MFE	-25.14
Consensus MFE	-10.78
Energy contribution	-12.10
Covariance contribution	1.32
Combinations/Pair	1.24
Mean z-score	-2.48
Structure conservation index	0.43
SVM decision value	2.56
SVM RNA-class probability	0.995237
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 4794080 94 + 22407834
CAAUGUUGCUGGCAACAU----------------UGUUGCAGAGGGGAAUUUUCGAGUUCGAAAGUUUCUGGUUCGAUGGAAGGGGGAAUUGA-GAAAAAGCUUGAAUAAA
((((((((....))))))----------------))..((....(((((((((((....)))))))))))..((((((..........)))))-).....))......... ( -24.40)
>DroSec_CAF1 242166 95 + 1
CAAUGUUGCUGGCAACAU----------------UGUCGAAGAGGGGAAUUUUCGAGUUCGAAAGUUUCUGAUUCGAAGGAAGGGGGAAAAGGCAAAAAAGCUUGAAUAAA
((((((((....))))))----------------))(((((...(((((((((((....)))))))))))..))))).............((((......))))....... ( -28.40)
>DroSim_CAF1 219401 95 + 1
CAAUGUUGCUGGCAACAU----------------UGUCGAAGAGGGGAAUUUUCGAGUUCGAAAGUUUCUGAUUCGUAAGAAGGGGGAAAAGGCAAAAAAGCUUGAAUAAA
((((((((....))))))----------------))(((((((......)))))))((((.....(((((..(((....)))..))))).((((......))))))))... ( -27.30)
>DroWil_CAF1 242357 101 + 1
CAAC--CGUUAGCAACAUGCGGGGGUUACUGUUAUUUCGAAAAGCGGGGUUCUAGACUUCGAAAGCUUUUACCUAAAAUC-AGGGGUAAA-------CCAGAUCAAUUAAA
...(--(((.........))))((.(((((.........((((((((((((...))))))....)))))).(((......-)))))))).-------))............ ( -19.50)
>DroYak_CAF1 230426 89 + 1
CAAUGUUGCUGGCAACAU----------------GGCCGAAAAGGGGCAUUUUCGAGAUCGAAAACUGCUGCUUCGAAUGAAGGGG-AAAGUGCGAAAAAGCUCCG-----
..((((((....))))))----------------.........(((((.((((((.........(((.((.((((....)))).))-..))).)))))).))))).----- ( -26.10)
>consensus
CAAUGUUGCUGGCAACAU________________UGUCGAAGAGGGGAAUUUUCGAGUUCGAAAGUUUCUGAUUCGAAGGAAGGGGGAAAAGGCAAAAAAGCUUGAAUAAA
..((((((....))))))..........................(((((((((((....)))))))))))......................................... (-10.78 = -12.10 +   1.32)

alignment

secondary structure

dotplot

Window 5

Location	4,794,099 – 4,794,210
Length	111
Sequences	4
Columns	112
Reading direction	forward
Mean pairwise identity	74.85
Mean single sequence MFE	-23.78
Consensus MFE	-11.50
Energy contribution	-12.12
Covariance contribution	0.62
Combinations/Pair	1.13
Mean z-score	-2.03
Structure conservation index	0.48
SVM decision value	-0.03
SVM RNA-class probability	0.516813
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 4794099 111 + 22407834
GUUGCAGAGGGGAAUUUUCGAGUUCGAAAGUUUCUGGUUCGAUGGAAGGGGGAAUUGA-GAAAAAGCUUGAAUAAACGGUUCAAUUCAAAAUAUACAAAUCUGAUAAACAAG
(((.((((.(((((((((((....)))))))))))................(((((((-(...................))))))))............))))...)))... ( -22.91)
>DroSec_CAF1 242185 112 + 1
GUCGAAGAGGGGAAUUUUCGAGUUCGAAAGUUUCUGAUUCGAAGGAAGGGGGAAAAGGCAAAAAAGCUUGAAUAAACGGACUAAUACAAAAUAUACAAAUCUAAUAAAUAAG
.(((((((......)))))))(((((....(((((..(((....)))..))))).((((......)))).......)))))............................... ( -21.90)
>DroSim_CAF1 219420 112 + 1
GUCGAAGAGGGGAAUUUUCGAGUUCGAAAGUUUCUGAUUCGUAAGAAGGGGGAAAAGGCAAAAAAGCUUGAAUAAACGGACUAAUACAAAAUAUACAAAUCUAAUAAAUAAG
.(((((((......)))))))(((((....(((((..(((....)))..))))).((((......)))).......)))))............................... ( -22.00)
>DroYak_CAF1 230445 98 + 1
GCCGAAAAGGGGCAUUUUCGAGAUCGAAAACUGCUGCUUCGAAUGAAGGGG-AAAGUGCGAAAAAGCUCCG--------AUUGUUGCAAAGCGUGUG-CUGU----AGCAAG
........(((((.((((((.........(((.((.((((....)))).))-..))).)))))).))))).--------.((((((((..((....)-))))----))))). ( -28.30)
>consensus
GUCGAAGAGGGGAAUUUUCGAGUUCGAAAGUUUCUGAUUCGAAGGAAGGGGGAAAAGGCAAAAAAGCUUGAAUAAACGGACUAAUACAAAAUAUACAAAUCUAAUAAACAAG
..((((...(((((((((((....)))))))))))..))))....................................................................... (-11.50 = -12.12 +   0.62)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:10:17 2006