Locus 8139

Sequence ID 3R_DroMel_CAF1
Location 21,859,026 – 21,859,158
Length 132
Max. P 0.993231
window13090 window13091 window13092

overview

Window 0

Location 21,859,026 – 21,859,128
Length 102
Sequences 3
Columns 103
Reading direction forward
Mean pairwise identity 82.01
Mean single sequence MFE -18.00
Consensus MFE -16.15
Energy contribution -16.27
Covariance contribution 0.11
Combinations/Pair 1.05
Mean z-score -2.62
Structure conservation index 0.90
SVM decision value 2.38
SVM RNA-class probability 0.993231
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 21859026 102 + 27905053
CAAUUAUAGUAAAUAGUGGAGCAAAACCACCUUCAAUGUUAGUUGCAACAUGAGGAACGCUA-CAAAACAUCAACAACUACUAUUAUUAGUAGCAUCUUCAAC
......((((.....((((.......))))(((((.((((......)))))))))...))))-..............((((((....)))))).......... ( -17.30)
>DroSec_CAF1 42572 83 + 1
CAAUUAUAGUAAAUAGUGGAGAAAAACCACC-------------------UGAGGAACGCUA-AAAAGCAUCAAUAACUACUAUUAUUAGUAGGAUCUUCAAC
...............((((.......)))).-------------------((((((.((((.-...)))........((((((....))))))).)))))).. ( -18.50)
>DroSim_CAF1 35686 84 + 1
CAAUUAUAGUAAAUAGUGGAGCAAAACCACC-------------------UGAGGAACGCUACAAAAGCAUCAAUAACUACUAUUAUUGGUAGGAUCUUCAAC
...............((((.......)))).-------------------((((((.((((.....)))........((((((....))))))).)))))).. ( -18.20)
>consensus
CAAUUAUAGUAAAUAGUGGAGCAAAACCACC___________________UGAGGAACGCUA_AAAAGCAUCAAUAACUACUAUUAUUAGUAGGAUCUUCAAC
...............((((.......))))....................((((((..(((.....)))........((((((....))))))..)))))).. (-16.15 = -16.27 +   0.11)

alignment

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secondary structure

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dotplot

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Window 1

Location 21,859,026 – 21,859,128
Length 102
Sequences 3
Columns 103
Reading direction reverse
Mean pairwise identity 82.01
Mean single sequence MFE -19.30
Consensus MFE -15.64
Energy contribution -15.20
Covariance contribution -0.44
Combinations/Pair 1.09
Mean z-score -1.46
Structure conservation index 0.81
SVM decision value 0.14
SVM RNA-class probability 0.603295
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 21859026 102 - 27905053
GUUGAAGAUGCUACUAAUAAUAGUAGUUGUUGAUGUUUUG-UAGCGUUCCUCAUGUUGCAACUAACAUUGAAGGUGGUUUUGCUCCACUAUUUACUAUAAUUG
.........(((((((....)))))))..(..((((((((-((((((.....)))))))))..)))))..).(((((.......))))).............. ( -24.60)
>DroSec_CAF1 42572 83 - 1
GUUGAAGAUCCUACUAAUAAUAGUAGUUAUUGAUGCUUUU-UAGCGUUCCUCA-------------------GGUGGUUUUUCUCCACUAUUUACUAUAAUUG
..(((.((..((((((....))))))......(((((...-.))))))).)))-------------------(((((.......))))).............. ( -15.90)
>DroSim_CAF1 35686 84 - 1
GUUGAAGAUCCUACCAAUAAUAGUAGUUAUUGAUGCUUUUGUAGCGUUCCUCA-------------------GGUGGUUUUGCUCCACUAUUUACUAUAAUUG
..............((((.(((((((.....((((((.....)))))).....-------------------(((((.......)))))..))))))).)))) ( -17.40)
>consensus
GUUGAAGAUCCUACUAAUAAUAGUAGUUAUUGAUGCUUUU_UAGCGUUCCUCA___________________GGUGGUUUUGCUCCACUAUUUACUAUAAUUG
..............((((.(((((((.....((((((.....))))))........................(((((.......)))))..))))))).)))) (-15.64 = -15.20 +  -0.44)

alignment

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secondary structure

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dotplot

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Window 2

Location 21,859,066 – 21,859,158
Length 92
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 68.28
Mean single sequence MFE -17.27
Consensus MFE -5.64
Energy contribution -5.48
Covariance contribution -0.16
Combinations/Pair 1.17
Mean z-score -1.98
Structure conservation index 0.33
SVM decision value 0.66
SVM RNA-class probability 0.813663
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 21859066 92 + 27905053
AGUUGCAACAUGAGGAA---CGCUA-CAAA--------------ACAUCAACAACUACUAUUAUUAGUAGCAUCUUCAACGUCGAUAACUAUA----------CAGCAAUACAAUAAGGA
.(((((....((((((.---.((((-(...--------------......................))))).))))))..((.....))....----------..))))).......... ( -14.11)
>DroSec_CAF1 42603 77 + 1
----------UGAGGAA---CGCUA-AAAA--------------GCAUCAAUAACUACUAUUAUUAGUAGGAUCUUCAACGUCGAUAACUAUA----------CAGCA-----AUAAGGA
----------((((((.---((((.-...)--------------))........((((((....))))))).))))))...............----------.....-----....... ( -14.60)
>DroSim_CAF1 35717 83 + 1
----------UGAGGAA---CGCUACAAAA--------------GCAUCAAUAACUACUAUUAUUGGUAGGAUCUUCAACGUCGAUAACUAUA----------CAGCAAUACAAUAAGGA
----------((((((.---((((.....)--------------))........((((((....))))))).))))))...............----------................. ( -14.30)
>DroEre_CAF1 36277 113 + 1
AGUUGCAACAGGAGUAA---CACUA-CAAAAGAUGAAGCGGCAAACGUCAAUAACUACUA---UUAGUAGCAUCUUCAACAUCAAUAACUAUAACAUUAAAUCCAACAAUACAAUUGGGA
.(((((.......))))---)....-...((((((....(((....))).....((((..---...)))))))))).........................(((((........))))). ( -16.70)
>DroYak_CAF1 40164 119 + 1
AGUUGCAACAGGAGGAGCUGCACUA-CAAAAGACGAAGCAGCUAACCUCAAUGACUACUAUUAUUAGUAGCAUCUUCAACAUCAAAAACUAUAACAUUAAAUCCAGCAAUAUAACAAGGA
.(((((.....((((((((((....-...........))))))..)))).(((.((((((....)))))))))................................))))).......... ( -26.66)
>consensus
AGUUGCAACAUGAGGAA___CGCUA_CAAA______________ACAUCAAUAACUACUAUUAUUAGUAGCAUCUUCAACGUCGAUAACUAUA__________CAGCAAUACAAUAAGGA
......................................................((((((....)))))).................................................. ( -5.64 =  -5.48 +  -0.16)

alignment

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secondary structure

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dotplot

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Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:03:28 2006