Locus 2306

Sequence ID 2R_DroMel_CAF1
Location 8,490,116 – 8,490,235
Length 119
Max. P 0.682995
window3795 window3796

overview

Window 5

Location 8,490,116 – 8,490,235
Length 119
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 85.12
Mean single sequence MFE -34.20
Consensus MFE -25.16
Energy contribution -26.41
Covariance contribution 1.25
Combinations/Pair 1.11
Mean z-score -1.43
Structure conservation index 0.74
SVM decision value -0.02
SVM RNA-class probability 0.523872
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 8490116 119 + 20766785
UAUCCGCAAUCGCUGCUGUCUCCAUUAAAGAUCCAUCUGGGCUUGUCAGAA-UGGCUGGCUGGUUCCGCGGAGCAGCAGCUACCACUUACUUUCAGCCAGACAGCGACGAAUCGCAAUCU
.....((..(((.(((((((.(((((.(((.(((....)))))).....))-))).(((((((....(.(((((....))).)).)......)))))))))))))).)))...))..... ( -39.00)
>DroSec_CAF1 2402 114 + 1
NNNNNNNNNNNNNCGCUGUUCCCAUUAAAGAUCCAUCUGGGCUGGUCAGAAAAGGCUGGCUGGUU------GGCAGCAGCUACCACUUACUUUCAGCCAGACAGCGACGAAUCGCAAUCU
.............(((((((........(((....))).((((((((((......)))))((((.------(((....)))))))........))))).))))))).............. ( -30.60)
>DroSim_CAF1 2338 113 + 1
UAUCAGCCAUCGCUGCUGUUCCCAUUAAAGAUCCAUCUGGGCUUGUCAGAA-UGGCUGGCUGGUU------GGCAGCAGCUACCACUUACUUUCAGCCAGACAGCGACGAAUCGCAAUCU
.....((..(((.((((((..(((((.(((.(((....)))))).....))-)))((((((((.(------(((....))))..........)))))))))))))).)))...))..... ( -34.20)
>DroYak_CAF1 2416 108 + 1
UAUCAGCCAUCGCUGCUGUGCCCAUUAAAGAUCCAUCUGGGCCUGUCAGAA-UGGUUGGCUGG-----------AGCAGCUACCACUUACUUUCAGCCAGACAGCGACGAAUCGCAAUCU
.....((..(((.((((((..(((((..((..((....))..)).....))-)))((((((((-----------((.((......))...)))))))))))))))).)))...))..... ( -33.00)
>consensus
UAUCAGCCAUCGCUGCUGUUCCCAUUAAAGAUCCAUCUGGGCUUGUCAGAA_UGGCUGGCUGGUU______GGCAGCAGCUACCACUUACUUUCAGCCAGACAGCGACGAAUCGCAAUCU
.........(((.((((((.............((((((((.....)))))..)))((((((((........(((....)))...........)))))))))))))).))).......... (-25.16 = -26.41 +   1.25)

alignment

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secondary structure

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dotplot

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Window 6

Location 8,490,116 – 8,490,235
Length 119
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 85.12
Mean single sequence MFE -38.70
Consensus MFE -27.08
Energy contribution -27.45
Covariance contribution 0.37
Combinations/Pair 1.06
Mean z-score -1.72
Structure conservation index 0.70
SVM decision value 0.31
SVM RNA-class probability 0.682995
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 8490116 119 - 20766785
AGAUUGCGAUUCGUCGCUGUCUGGCUGAAAGUAAGUGGUAGCUGCUGCUCCGCGGAACCAGCCAGCCA-UUCUGACAAGCCCAGAUGGAUCUUUAAUGGAGACAGCAGCGAUUGCGGAUA
...(((((((.(((.((((((((((((....(..((((.(((....)))))))..)..)))))..(((-(.(((.......)))))))...........))))))).))))))))))... ( -46.30)
>DroSec_CAF1 2402 114 - 1
AGAUUGCGAUUCGUCGCUGUCUGGCUGAAAGUAAGUGGUAGCUGCUGCC------AACCAGCCAGCCUUUUCUGACCAGCCCAGAUGGAUCUUUAAUGGGAACAGCGNNNNNNNNNNNNN
.....((((((((((((((((.(((((........((((((...)))))------)......)))))......)).))))...)))))))).....((....)))).............. ( -31.04)
>DroSim_CAF1 2338 113 - 1
AGAUUGCGAUUCGUCGCUGUCUGGCUGAAAGUAAGUGGUAGCUGCUGCC------AACCAGCCAGCCA-UUCUGACAAGCCCAGAUGGAUCUUUAAUGGGAACAGCAGCGAUGGCUGAUA
((((.((((....)))).))))(((((........((((((...)))))------)..)))))(((((-(((((.....((((.............)))).....))).))))))).... ( -39.42)
>DroYak_CAF1 2416 108 - 1
AGAUUGCGAUUCGUCGCUGUCUGGCUGAAAGUAAGUGGUAGCUGCU-----------CCAGCCAACCA-UUCUGACAGGCCCAGAUGGAUCUUUAAUGGGCACAGCAGCGAUGGCUGAUA
..........(((((((((.(((.(((..((..((((((.((((..-----------.))))..))))-))))..)))(((((.............))))).))))))))))))...... ( -38.02)
>consensus
AGAUUGCGAUUCGUCGCUGUCUGGCUGAAAGUAAGUGGUAGCUGCUGCC______AACCAGCCAGCCA_UUCUGACAAGCCCAGAUGGAUCUUUAAUGGGAACAGCAGCGAUGGCUGAUA
....(((((((((((((((((((((((......(((....)))((((...........)))))))))).....))).)))...)))))))).....((....)))))............. (-27.08 = -27.45 +   0.37)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:26:22 2006