Locus 4740

Sequence ID 3R_DroMel_CAF1
Location 12,433,319 – 12,433,456
Length 137
Max. P 0.822523
window7781 window7782 window7783

overview

Window 1

Location 12,433,319 – 12,433,416
Length 97
Sequences 3
Columns 97
Reading direction forward
Mean pairwise identity 95.88
Mean single sequence MFE -27.57
Consensus MFE -24.29
Energy contribution -24.40
Covariance contribution 0.11
Combinations/Pair 1.05
Mean z-score -1.89
Structure conservation index 0.88
SVM decision value 0.09
SVM RNA-class probability 0.580876
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12433319 97 + 27905053
UGUCCUUGAACCAGUGCAGGGGUUCCCCGGCUAACUACAAACUUGCACAGCAGGAAACUGUUGCAGCUACUUACUACGUAUAGGUUAACCUAUACUA
.((..(((.....((((((((....)))(........).....)))))(((((....))))).)))..)).......(((((((....))))))).. ( -29.50)
>DroSec_CAF1 9132 97 + 1
UGUCCUUGAACCAGUGCAGGGGUUCCCCGGCUAACUACUAACUUGCACAGUAGGAAACUGUUGCAGCUACUUACUGCGAAUAGGUUAACCCAUACUA
........((((.((((((((....)))(.....)........)))))..(((....)))((((((.......))))))...))))........... ( -24.80)
>DroSim_CAF1 9253 97 + 1
UGUCCUUGAACCAGUGCAGGGGUUCCCCGGCUAACUACUAACUUGCACAGCAGGAAACUGUUGCAGCUACUUACUGCGAAUAGGUUAACCUAUACCA
.............((((((((....)))(.....)........)))))(((((....)))))((((.......))))..(((((....))))).... ( -28.40)
>consensus
UGUCCUUGAACCAGUGCAGGGGUUCCCCGGCUAACUACUAACUUGCACAGCAGGAAACUGUUGCAGCUACUUACUGCGAAUAGGUUAACCUAUACUA
........((((.((((((((....)))(........).....)))))(((((....)))))((((.......)))).....))))........... (-24.29 = -24.40 +   0.11)

alignment

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secondary structure

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dotplot

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Window 2

Location 12,433,319 – 12,433,416
Length 97
Sequences 3
Columns 97
Reading direction reverse
Mean pairwise identity 95.88
Mean single sequence MFE -31.34
Consensus MFE -29.40
Energy contribution -28.30
Covariance contribution -1.10
Combinations/Pair 1.13
Mean z-score -1.99
Structure conservation index 0.94
SVM decision value 0.69
SVM RNA-class probability 0.822523
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12433319 97 - 27905053
UAGUAUAGGUUAACCUAUACGUAGUAAGUAGCUGCAACAGUUUCCUGCUGUGCAAGUUUGUAGUUAGCCGGGGAACCCCUGCACUGGUUCAAGGACA
..(((((((....))))))).((((...(((((((((((((.....))))).......))))))))((.(((....))).))))))(((....))). ( -32.41)
>DroSec_CAF1 9132 97 - 1
UAGUAUGGGUUAACCUAUUCGCAGUAAGUAGCUGCAACAGUUUCCUACUGUGCAAGUUAGUAGUUAGCCGGGGAACCCCUGCACUGGUUCAAGGACA
..(((.(((((..((.....(((((.....)))))....(((..((((((.......))))))..))).))..))))).)))....(((....))). ( -31.40)
>DroSim_CAF1 9253 97 - 1
UGGUAUAGGUUAACCUAUUCGCAGUAAGUAGCUGCAACAGUUUCCUGCUGUGCAAGUUAGUAGUUAGCCGGGGAACCCCUGCACUGGUUCAAGGACA
.((.(((((....)))))))(((((.....)))))..((((...((((((.......))))))...((.(((....))).))))))(((....))). ( -30.20)
>consensus
UAGUAUAGGUUAACCUAUUCGCAGUAAGUAGCUGCAACAGUUUCCUGCUGUGCAAGUUAGUAGUUAGCCGGGGAACCCCUGCACUGGUUCAAGGACA
((((...(((((((.((((.(((((.....))))).(((((.....))))).......)))))))))))(((....)))...))))(((....))). (-29.40 = -28.30 +  -1.10)

alignment

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secondary structure

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dotplot

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Window 3

Location 12,433,343 – 12,433,456
Length 113
Sequences 3
Columns 113
Reading direction forward
Mean pairwise identity 93.51
Mean single sequence MFE -26.50
Consensus MFE -21.12
Energy contribution -20.90
Covariance contribution -0.22
Combinations/Pair 1.10
Mean z-score -2.27
Structure conservation index 0.80
SVM decision value 0.07
SVM RNA-class probability 0.569456
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12433343 113 + 27905053
CCCCGGCUAACUACAAACUUGCACAGCAGGAAACUGUUGCAGCUACUUACUACGUAUAGGUUAACCUAUACUAGCUCUUGCUAAGUGUAUGUAAAUAGGAACACCUAAGUAAA
.....(((...((((.(((((((((((((....)))))).(((((........(((((((....))))))))))))..))).))))...))))..((((....)))))))... ( -32.80)
>DroSec_CAF1 9156 113 + 1
CCCCGGCUAACUACUAACUUGCACAGUAGGAAACUGUUGCAGCUACUUACUGCGAAUAGGUUAACCCAUACUAACUCUUGUUAAGUGUAUGUAAAUAUUAAUACCUAAGUAAA
....((.(((((.......((((((((.....)))).))))((........)).....))))).))(((((((((....))))...)))))...................... ( -19.90)
>DroSim_CAF1 9277 113 + 1
CCCCGGCUAACUACUAACUUGCACAGCAGGAAACUGUUGCAGCUACUUACUGCGAAUAGGUUAACCUAUACCAGCUCUUGCUAAGUGUAUGUAAAUAUUAAUACCUAAGUAAA
................((.((((((((((((..(((((((((.......))))))(((((....)))))..))).)))))))..))))).))..................... ( -26.80)
>consensus
CCCCGGCUAACUACUAACUUGCACAGCAGGAAACUGUUGCAGCUACUUACUGCGAAUAGGUUAACCUAUACUAGCUCUUGCUAAGUGUAUGUAAAUAUUAAUACCUAAGUAAA
................((((((.((((((....))))))..))(((.(((.((..(((((....)))))..((((....)))).))))).))).............))))... (-21.12 = -20.90 +  -0.22)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:37:48 2006