Locus 775

Sequence ID 3R_DroMel_CAF1
Location 2,681,944 – 2,682,052
Length 108
Max. P 0.946500
window1235 window1236

overview

Window 5

Location 2,681,944 – 2,682,052
Length 108
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 85.49
Mean single sequence MFE -20.68
Consensus MFE -14.27
Energy contribution -14.97
Covariance contribution 0.70
Combinations/Pair 1.12
Mean z-score -2.84
Structure conservation index 0.69
SVM decision value 0.05
SVM RNA-class probability 0.559887
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 2681944 108 + 27905053
AAAAGC---CUGGCAACACAUAAUGAUAGCAAUACUUAUCUUGCCAUCAGAAAGUCGAAAAAGUUUAAGCACUUUUUCAAUUUUU--------U-UUGUAACAACCACCAAUGCUUCUAU
..((((---.(((..........((((.((((........)))).))))((((((.((((((((......)))))))).))))))--------.-............)))..)))).... ( -20.10)
>DroSec_CAF1 41520 106 + 1
AAAAGC---CUGGCAACACAUAAUGAUAGCAAUACUUAUCUUGCCAUCAGAAAGUUGAAAAAGUUUAAGCACUUUUUAAAUUU----------U-UUGUAACAACCACCAAUCCUUCUAU
......---.((((((........(((((......))))))))))).(((((((((.(((((((......))))))).)))))----------)-)))...................... ( -17.30)
>DroSim_CAF1 34681 106 + 1
AAAAGC---CUGGCAACACAUAAUGAUAGCAAUACUUAUCUUGCCAUCAGAAAGUUGAAAAAGUUUAAGCACUUUUUCAAUUU----------U-UUGUAACAACCACCAAUGCUUCUAU
..((((---.((((((........(((((......))))))))))).(((((((((((((((((......)))))))))))))----------)-)))..............)))).... ( -26.00)
>DroEre_CAF1 35384 107 + 1
AAAAGC---CUGGUAACACAUAAUGAUAGCAAUACUUAUCUUGCCAUCAGAAAGUUGAAAAAGUUUAAGCACUUUUUCAGUUU----------UAUUGUAACAACCACCAAUGCUACUAU
...(((---.((((.........((((.((((........)))).)))).(((..(((((((((......)))))))))..))----------)............))))..)))..... ( -22.30)
>DroYak_CAF1 41985 106 + 1
AAAAGC---CUGGCAACACAUAAUGAUAGCAAUACUUAUCUUGCCAUCAGAAAGUUGAAAAAGUUUAAGCACUUUUUCCAUUU----------U-UUGUAACAAUCACCAAUGCUUCUAU
..((((---.((((((........(((((......))))))))))).((((((((.((((((((......)))))))).))))----------)-)))..............)))).... ( -21.90)
>DroAna_CAF1 29038 109 + 1
AGAAACACACAGUCAACAAAUAAUGAUAGCAACACUUAUCUUGCCAUCAGAAAGUUGAAAAAGUUU-----CUUUUUCGCGUUUUAGGAAAUAU-UUUUAAUAACAAACAAUAAA-----
((((((......(((((......((((.((((........)))).))))....)))))....))))-----))(((((........)))))...-....................----- ( -16.50)
>consensus
AAAAGC___CUGGCAACACAUAAUGAUAGCAAUACUUAUCUUGCCAUCAGAAAGUUGAAAAAGUUUAAGCACUUUUUCAAUUU__________U_UUGUAACAACCACCAAUGCUUCUAU
..........(((..........((((.((((........)))).))))..(((((((((((((......)))))))))))))........................))).......... (-14.27 = -14.97 +   0.70)

alignment

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secondary structure

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dotplot

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Window 6

Location 2,681,944 – 2,682,052
Length 108
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 85.49
Mean single sequence MFE -28.83
Consensus MFE -23.42
Energy contribution -24.32
Covariance contribution 0.89
Combinations/Pair 1.15
Mean z-score -3.24
Structure conservation index 0.81
SVM decision value 1.36
SVM RNA-class probability 0.946500
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 2681944 108 - 27905053
AUAGAAGCAUUGGUGGUUGUUACAA-A--------AAAAAUUGAAAAAGUGCUUAAACUUUUUCGACUUUCUGAUGGCAAGAUAAGUAUUGCUAUCAUUAUGUGUUGCCAG---GCUUUU
..((((((.((((..(....((((.-.--------.....((((((((((......)))))))))).....(((((((((........)))))))))...)))))..))))---)))))) ( -33.00)
>DroSec_CAF1 41520 106 - 1
AUAGAAGGAUUGGUGGUUGUUACAA-A----------AAAUUUAAAAAGUGCUUAAACUUUUUCAACUUUCUGAUGGCAAGAUAAGUAUUGCUAUCAUUAUGUGUUGCCAG---GCUUUU
...(((((.((((..(....((((.-.----------......(((((((......)))))))........(((((((((........)))))))))...)))))..))))---.))))) ( -24.70)
>DroSim_CAF1 34681 106 - 1
AUAGAAGCAUUGGUGGUUGUUACAA-A----------AAAUUGAAAAAGUGCUUAAACUUUUUCAACUUUCUGAUGGCAAGAUAAGUAUUGCUAUCAUUAUGUGUUGCCAG---GCUUUU
..((((((.((((..(....((((.-.----------...((((((((((......)))))))))).....(((((((((........)))))))))...)))))..))))---)))))) ( -33.30)
>DroEre_CAF1 35384 107 - 1
AUAGUAGCAUUGGUGGUUGUUACAAUA----------AAACUGAAAAAGUGCUUAAACUUUUUCAACUUUCUGAUGGCAAGAUAAGUAUUGCUAUCAUUAUGUGUUACCAG---GCUUUU
.....(((.(((((((....((((...----------....(((((((((......)))))))))......(((((((((........)))))))))...)))))))))))---)))... ( -29.60)
>DroYak_CAF1 41985 106 - 1
AUAGAAGCAUUGGUGAUUGUUACAA-A----------AAAUGGAAAAAGUGCUUAAACUUUUUCAACUUUCUGAUGGCAAGAUAAGUAUUGCUAUCAUUAUGUGUUGCCAG---GCUUUU
..((((((.((((..((....(((.-.----------.....((((((((......)))))))).......(((((((((........)))))))))...)))))..))))---)))))) ( -32.10)
>DroAna_CAF1 29038 109 - 1
-----UUUAUUGUUUGUUAUUAAAA-AUAUUUCCUAAAACGCGAAAAAG-----AAACUUUUUCAACUUUCUGAUGGCAAGAUAAGUGUUGCUAUCAUUAUUUGUUGACUGUGUGUUUCU
-----.....(((((........))-))).......(((((((((((((-----...))))))).......(((((((((.(....).)))))))))...............)))))).. ( -20.30)
>consensus
AUAGAAGCAUUGGUGGUUGUUACAA_A__________AAAUUGAAAAAGUGCUUAAACUUUUUCAACUUUCUGAUGGCAAGAUAAGUAUUGCUAUCAUUAUGUGUUGCCAG___GCUUUU
..((((((.(((((((....((((..................((((((((......)))))))).......(((((((((........)))))))))...)))))))))))...)))))) (-23.42 = -24.32 +   0.89)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:51:49 2006