Locus 2822

Sequence ID 3L_DroMel_CAF1
Location 8,042,612 – 8,042,727
Length 115
Max. P 0.838636
window4407 window4408

overview

Window 7

Location 8,042,612 – 8,042,727
Length 115
Sequences 5
Columns 115
Reading direction forward
Mean pairwise identity 90.09
Mean single sequence MFE -25.54
Consensus MFE -19.22
Energy contribution -21.58
Covariance contribution 2.36
Combinations/Pair 1.05
Mean z-score -2.06
Structure conservation index 0.75
SVM decision value 0.74
SVM RNA-class probability 0.838636
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 8042612 115 + 23771897
UAUUUGCUGAAUAUUUCUUCUAUAUUUUCUGCGGAUAUGGAAUUGUUUAGAAUUUCAAAACAAAUAUUUUGAGCAUAGGGGUUAUGCAUAUUUGAAUAUCUCCAAUAUCCCGGAU
........((((((.......))))))((((.(((((((((..((((((((...((((((......))))))((((((...))))))...))))))))..))).)))))))))). ( -27.90)
>DroSec_CAF1 13754 115 + 1
UAUUUGCCGAAUAUUUCUUCUAUAUUUUCUGCGGUAAUGGAAGUGUUUAAUAUUUCAAAAGAAGUAUUUUGAGCAUAGGGGUUAUCCAUAUUUGAAUAUCUCCAAUAUCCCGGAU
........((((((.......))))))((((.((((.((((..(((((((((((((((((......))))))).)))(((....)))....)))))))..)))).)))).)))). ( -24.50)
>DroSim_CAF1 13764 115 + 1
UAUUUGUCGAAUAUUUCUUCUAUAUUUUCUGCGGUAAUGGAAGUGUUUAAUAUUUCAAAAGAAGUAUUUUGAGCAUAGGGGUUAUGCAUAUUUGAAUAUCUCCAAUAUCCCGGAU
........((((((.......))))))((((.((((.((((..(((((((....((((((......))))))((((((...))))))....)))))))..)))).)))).)))). ( -26.10)
>DroEre_CAF1 13640 107 + 1
UACUUGUUGAAUAUUUCUUCUAUAUUUUCUGCGGAUAUGGAAGUGUUUAAUAUUUCAAAACAUGUAUUUUGAGCAUAGGGAUUAUGCAU--------AUCUCCAAUAUCCCGAAU
....(((((((((...(((((((((((.....)))))))))))))))))))).(((((((......)))))))....(((((..((...--------.....))..))))).... ( -22.80)
>DroYak_CAF1 14124 115 + 1
UGUUUGUUGAAUAUUUCUUCUAUAUUUUCUGCGGAUAUUGAAGUGUUUAAUAUUUCAAAACAGGUAUUUUGAGCAUAGGGAUUAUGCAUAUUUAAAUAUCUCCAAUAUCCCGGAU
........((((((.......))))))((((.((((((((.(((((((((....((((((......))))))((((((...))))))....))))))).)).)))))))))))). ( -26.40)
>consensus
UAUUUGUUGAAUAUUUCUUCUAUAUUUUCUGCGGAUAUGGAAGUGUUUAAUAUUUCAAAACAAGUAUUUUGAGCAUAGGGGUUAUGCAUAUUUGAAUAUCUCCAAUAUCCCGGAU
........((((((.......))))))((((.(((((((((..(((((((....((((((......))))))((((((...))))))....)))))))..))).)))))))))). (-19.22 = -21.58 +   2.36)

alignment

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secondary structure

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dotplot

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Window 8

Location 8,042,612 – 8,042,727
Length 115
Sequences 5
Columns 115
Reading direction reverse
Mean pairwise identity 90.09
Mean single sequence MFE -19.52
Consensus MFE -14.48
Energy contribution -15.92
Covariance contribution 1.44
Combinations/Pair 1.04
Mean z-score -1.88
Structure conservation index 0.74
SVM decision value 0.38
SVM RNA-class probability 0.710987
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 8042612 115 - 23771897
AUCCGGGAUAUUGGAGAUAUUCAAAUAUGCAUAACCCCUAUGCUCAAAAUAUUUGUUUUGAAAUUCUAAACAAUUCCAUAUCCGCAGAAAAUAUAGAAGAAAUAUUCAGCAAAUA
.((.(((((((.((((............(((((.....)))))(((((((....)))))))............)))))))))).).)).......(((......)))........ ( -20.70)
>DroSec_CAF1 13754 115 - 1
AUCCGGGAUAUUGGAGAUAUUCAAAUAUGGAUAACCCCUAUGCUCAAAAUACUUCUUUUGAAAUAUUAAACACUUCCAUUACCGCAGAAAAUAUAGAAGAAAUAUUCGGCAAAUA
..((.((.((.(((((.((((((....)))))).....(((..((((((......)))))).)))........))))).))))............(((......)))))...... ( -15.00)
>DroSim_CAF1 13764 115 - 1
AUCCGGGAUAUUGGAGAUAUUCAAAUAUGCAUAACCCCUAUGCUCAAAAUACUUCUUUUGAAAUAUUAAACACUUCCAUUACCGCAGAAAAUAUAGAAGAAAUAUUCGACAAAUA
...(((.....(((((............(((((.....)))))((((((......))))))............)))))...)))...........(((......)))........ ( -15.80)
>DroEre_CAF1 13640 107 - 1
AUUCGGGAUAUUGGAGAU--------AUGCAUAAUCCCUAUGCUCAAAAUACAUGUUUUGAAAUAUUAAACACUUCCAUAUCCGCAGAAAAUAUAGAAGAAAUAUUCAACAAGUA
.(((.((((((.((((..--------..(((((.....)))))(((((((....)))))))...........)))).))))))...)))......(((......)))........ ( -21.10)
>DroYak_CAF1 14124 115 - 1
AUCCGGGAUAUUGGAGAUAUUUAAAUAUGCAUAAUCCCUAUGCUCAAAAUACCUGUUUUGAAAUAUUAAACACUUCAAUAUCCGCAGAAAAUAUAGAAGAAAUAUUCAACAAACA
.((.((((((((((((...(((((....(((((.....)))))(((((((....)))))))....)))))..))))))))))).).)).......(((......)))........ ( -25.00)
>consensus
AUCCGGGAUAUUGGAGAUAUUCAAAUAUGCAUAACCCCUAUGCUCAAAAUACUUGUUUUGAAAUAUUAAACACUUCCAUAUCCGCAGAAAAUAUAGAAGAAAUAUUCAACAAAUA
.((.(((((((.((((............(((((.....)))))(((((((....)))))))...........)))).)))))).).)).......(((......)))........ (-14.48 = -15.92 +   1.44)

alignment

Postscript

secondary structure

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dotplot

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Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:42:35 2006