Locus 4161

Sequence ID 2L_DroMel_CAF1
Location 11,960,912 – 11,961,012
Length 100
Max. P 0.992205
window6568 window6569

overview

Window 8

Location 11,960,912 – 11,961,012
Length 100
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 75.34
Mean single sequence MFE -25.05
Consensus MFE -15.20
Energy contribution -15.28
Covariance contribution 0.08
Combinations/Pair 1.10
Mean z-score -1.30
Structure conservation index 0.61
SVM decision value -0.01
SVM RNA-class probability 0.527981
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 11960912 100 + 22407834
UCCACUUUUGGUGGUG----GU----------GGUGGUUGGU------CGGGGGAAAUUGGUUUGGAAAAUGUCAUUCAAGUUGCCAGGCAAGUUGACAAAUUUGUCAACUGAUAUGGAA
.(((((......))))----).----------........((------(..((.((.((((..(((......))).)))).)).)).))).((((((((....))))))))......... ( -24.10)
>DroVir_CAF1 165256 76 + 1
UACACGCAU-----------------------------------------AUGUAUGUAUGUAUAGAAAAUGUCAUUCAAGUCGCAA--CCAGUUGACAAAU-UGUCAACUGAUAUGGGA
((((..(((-----------------------------------------....)))..))))..................((.((.--.((((((((....-.))))))))...)).)) ( -18.20)
>DroSec_CAF1 180322 106 + 1
UCCACUUUUGGUGAUG----GUGGUGC----UGGUGGUUGGU------CGGGGGAAAUUGGUUUUGAAAAUGUCAUUCAAGUUGCCAGGCAAGUUGACAAAUUUGUCAACUGAUAUGGAA
((((..(((((..((.----.(((...----((..(.....(------(((((........))))))...)..)).))).))..)))))..((((((((....))))))))....)))). ( -25.10)
>DroSim_CAF1 146706 97 + 1
UCCACUUUUGGUGGU-----------------GGUGGUUGGU------CGGGGGAAAUUGGUUUGGAAAAUGUCAUUCAAGUUGCCAGGCAAGUUGACAAAUUUGUCAACUGAUAUGGAA
.(((((......)))-----------------))......((------(..((.((.((((..(((......))).)))).)).)).))).((((((((....))))))))......... ( -24.10)
>DroEre_CAF1 155238 84 + 1
UCCACUUUUGGUG------------------------------------GGGGGAAAUUGGUUUGGAAAAUGUCAUUCAAGUUGCCAGGCAAGUUGACAAAUUUGUCAACUGAUAUGGAA
(((((.....)))------------------------------------)).......(..((((((........))))))..)(((....((((((((....))))))))....))).. ( -22.00)
>DroYak_CAF1 151109 120 + 1
UCCACUUUUGGUGGUGCCUCAUGGUGCGGCAUGGUGGAAGGGAGGGCAGGGGGGAAAUUGGUUUGGAAAAUGUCAUUCAAGUUGCCAGGCAAGUUGACAAAUUUGUCAACUGAUAUGGAA
((((((....((.(..((....))..).))..)))))).......((..((.((...((((..(((......))).)))).)).))..)).((((((((....))))))))......... ( -36.80)
>consensus
UCCACUUUUGGUGGU_________________GGUGGUUGGU______CGGGGGAAAUUGGUUUGGAAAAUGUCAUUCAAGUUGCCAGGCAAGUUGACAAAUUUGUCAACUGAUAUGGAA
((((.....................................................(((((...(((.......))).....)))))...((((((((....))))))))....)))). (-15.20 = -15.28 +   0.08)

alignment

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secondary structure

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dotplot

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Window 9

Location 11,960,912 – 11,961,012
Length 100
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 75.34
Mean single sequence MFE -18.22
Consensus MFE -12.46
Energy contribution -12.68
Covariance contribution 0.22
Combinations/Pair 1.05
Mean z-score -2.60
Structure conservation index 0.68
SVM decision value 2.31
SVM RNA-class probability 0.992205
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 11960912 100 - 22407834
UUCCAUAUCAGUUGACAAAUUUGUCAACUUGCCUGGCAACUUGAAUGACAUUUUCCAAACCAAUUUCCCCCG------ACCAACCACC----------AC----CACCACCAAAAGUGGA
..(((....((((((((....))))))))....)))....................................------..........----------..----..((((.....)))). ( -15.50)
>DroVir_CAF1 165256 76 - 1
UCCCAUAUCAGUUGACA-AUUUGUCAACUGG--UUGCGACUUGAAUGACAUUUUCUAUACAUACAUACAU-----------------------------------------AUGCGUGUA
((.((.((((((((((.-....)))))))))--))).))..................((((..(((....-----------------------------------------)))..)))) ( -18.20)
>DroSec_CAF1 180322 106 - 1
UUCCAUAUCAGUUGACAAAUUUGUCAACUUGCCUGGCAACUUGAAUGACAUUUUCAAAACCAAUUUCCCCCG------ACCAACCACCA----GCACCAC----CAUCACCAAAAGUGGA
.(((((...((((((((....))))))))(((.(((....(((((.......)))))..............(------......).)))----)))....----...........))))) ( -19.10)
>DroSim_CAF1 146706 97 - 1
UUCCAUAUCAGUUGACAAAUUUGUCAACUUGCCUGGCAACUUGAAUGACAUUUUCCAAACCAAUUUCCCCCG------ACCAACCACC-----------------ACCACCAAAAGUGGA
..(((....((((((((....))))))))....)))....................................------..........-----------------.((((.....)))). ( -15.50)
>DroEre_CAF1 155238 84 - 1
UUCCAUAUCAGUUGACAAAUUUGUCAACUUGCCUGGCAACUUGAAUGACAUUUUCCAAACCAAUUUCCCCC------------------------------------CACCAAAAGUGGA
..(((....((((((((....))))))))....)))..................................(------------------------------------(((.....)))). ( -15.30)
>DroYak_CAF1 151109 120 - 1
UUCCAUAUCAGUUGACAAAUUUGUCAACUUGCCUGGCAACUUGAAUGACAUUUUCCAAACCAAUUUCCCCCCUGCCCUCCCUUCCACCAUGCCGCACCAUGAGGCACCACCAAAAGUGGA
.(((((...((((((((....))))))))(((((((((....(((...................))).....))))...........((((......))))))))).........))))) ( -25.71)
>consensus
UUCCAUAUCAGUUGACAAAUUUGUCAACUUGCCUGGCAACUUGAAUGACAUUUUCCAAACCAAUUUCCCCCG______ACCAACCACC_________________ACCACCAAAAGUGGA
.(((((...((((((((....))))))))....(((......(((.......)))....))).....................................................))))) (-12.46 = -12.68 +   0.22)

alignment

Postscript

secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:11:10 2006