Locus 5364

Sequence ID 3R_DroMel_CAF1
Location 14,085,700 – 14,085,793
Length 93
Max. P 0.859288
window8741 window8742

overview

Window 1

Location 14,085,700 – 14,085,793
Length 93
Sequences 6
Columns 109
Reading direction forward
Mean pairwise identity 84.29
Mean single sequence MFE -18.43
Consensus MFE -15.67
Energy contribution -16.00
Covariance contribution 0.33
Combinations/Pair 1.00
Mean z-score -2.07
Structure conservation index 0.85
SVM decision value 0.82
SVM RNA-class probability 0.859288
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14085700 93 + 27905053
AAUUAAGUCACCCUUUUAAUACGCUAUUUAAUUUCCAGCGUAAUGUUGUCAUCCUUCUUGACAAAUGGUCACCCAAAACAACGAGG-------UCCUUCC---------
...........((((....((((((...........)))))).((((((((.......))))...(((....))).))))..))))-------.......--------- ( -15.30)
>DroPse_CAF1 11403 108 + 1
AAUUAAGUCACCCUUUUAUUACGCUAUUUCAUUUGCAGCGUAAUGUUGUCAACCUUCCUGACAAAUGGUCACCCGAAACAACGGAGCAGCCCAACCCUCCU-CAAACCU
......((.(((....(((((((((...........)))))))))((((((.......))))))..))).))..........((((..........)))).-....... ( -19.90)
>DroSec_CAF1 8383 102 + 1
AAUUAAGUCACCCUUUUAAUACGCUAUUUAAUUUCCAGCGUAAUGUUGUCAUCCUUCUUGACAAAUGGUCACCCAAAACAACGAGG-------ACCUUCCGCCGGAUUU
.((((((.......)))))).............(((.(((.....((((((.......))))))..((((..(.........)..)-------)))...))).)))... ( -18.20)
>DroEre_CAF1 8336 102 + 1
AAUUAAGUCACCCUUUUAUUACGCUAUUUAAUUUCCAGCGUAAUGUUGUCAUCCGUCUUGACAAAUGGUCACCCAAAACAACGAGG-------UCCUUCCCCCGGAUUC
......((.(((....(((((((((...........)))))))))((((((.......))))))..))).))............((-------(((.......))))). ( -20.00)
>DroAna_CAF1 8130 95 + 1
AAUUAAGUCACCCUUUUAUUACGCUAUUUAAUUUCCAGCGUAAUGUUGUCAACCUUCUUGACAAAUGGUCACCCAAAACAACGCAACU-----ACCCUCC---------
......((.(((....(((((((((...........)))))))))(((((((.....)))))))..))).))................-----.......--------- ( -17.30)
>DroPer_CAF1 11419 108 + 1
AAUUAAGUCACCCUUUUAUUACGCUAUUUCAUUUGCAGCGUAAUGUUGUCAACCUUCCUGACAAAUGGUCACCCAAAACAACGGAGCAGCCCAACCCUCCU-CAAACCU
......((.(((....(((((((((...........)))))))))((((((.......))))))..))).))..........((((..........)))).-....... ( -19.90)
>consensus
AAUUAAGUCACCCUUUUAUUACGCUAUUUAAUUUCCAGCGUAAUGUUGUCAACCUUCUUGACAAAUGGUCACCCAAAACAACGAAG_______ACCCUCC__C__A__U
......((.(((....(((((((((...........)))))))))((((((.......))))))..))).))..................................... (-15.67 = -16.00 +   0.33)

alignment

Postscript

secondary structure

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dotplot

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Window 2

Location 14,085,700 – 14,085,793
Length 93
Sequences 6
Columns 109
Reading direction reverse
Mean pairwise identity 84.29
Mean single sequence MFE -28.28
Consensus MFE -22.07
Energy contribution -22.02
Covariance contribution -0.06
Combinations/Pair 1.11
Mean z-score -2.22
Structure conservation index 0.78
SVM decision value 0.50
SVM RNA-class probability 0.759329
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14085700 93 - 27905053
---------GGAAGGA-------CCUCGUUGUUUUGGGUGACCAUUUGUCAAGAAGGAUGACAACAUUACGCUGGAAAUUAAAUAGCGUAUUAAAAGGGUGACUUAAUU
---------..(((.(-------(((.((((((.(((....)))...(((......)))))))))..(((((((.........)))))))......))))..))).... ( -23.70)
>DroPse_CAF1 11403 108 - 1
AGGUUUG-AGGAGGGUUGGGCUGCUCCGUUGUUUCGGGUGACCAUUUGUCAGGAAGGUUGACAACAUUACGCUGCAAAUGAAAUAGCGUAAUAAAAGGGUGACUUAAUU
.((..((-(((((((.....)).)))).)))..))((((.(((..(((((((.....))))))).(((((((((.........))))))))).....))).)))).... ( -28.40)
>DroSec_CAF1 8383 102 - 1
AAAUCCGGCGGAAGGU-------CCUCGUUGUUUUGGGUGACCAUUUGUCAAGAAGGAUGACAACAUUACGCUGGAAAUUAAAUAGCGUAUUAAAAGGGUGACUUAAUU
...(((((((...(((-------(((((......)))).))))..((((((.......)))))).....)))))))...................(((....))).... ( -30.10)
>DroEre_CAF1 8336 102 - 1
GAAUCCGGGGGAAGGA-------CCUCGUUGUUUUGGGUGACCAUUUGUCAAGACGGAUGACAACAUUACGCUGGAAAUUAAAUAGCGUAAUAAAAGGGUGACUUAAUU
..((((((((......-------))))((((((..((....))((((((....))))))))))))(((((((((.........)))))))))....))))......... ( -32.20)
>DroAna_CAF1 8130 95 - 1
---------GGAGGGU-----AGUUGCGUUGUUUUGGGUGACCAUUUGUCAAGAAGGUUGACAACAUUACGCUGGAAAUUAAAUAGCGUAAUAAAAGGGUGACUUAAUU
---------.......-----(((..(.((....(((....))).(((((((.....))))))).(((((((((.........)))))))))...)).)..)))..... ( -25.40)
>DroPer_CAF1 11419 108 - 1
AGGUUUG-AGGAGGGUUGGGCUGCUCCGUUGUUUUGGGUGACCAUUUGUCAGGAAGGUUGACAACAUUACGCUGCAAAUGAAAUAGCGUAAUAAAAGGGUGACUUAAUU
.......-.((((((.....)).))))......((((((.(((..(((((((.....))))))).(((((((((.........))))))))).....))).)))))).. ( -29.90)
>consensus
A__U__G__GGAAGGU_______CCUCGUUGUUUUGGGUGACCAUUUGUCAAGAAGGAUGACAACAUUACGCUGGAAAUUAAAUAGCGUAAUAAAAGGGUGACUUAAUU
............(((........))).......((((((.(((..((((((.......)))))).(((((((((.........))))))))).....))).)))))).. (-22.07 = -22.02 +  -0.06)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:52:57 2006