Locus 7346

Sequence ID 3L_DroMel_CAF1
Location 19,712,458 – 19,712,578
Length 120
Max. P 0.538655
window11931 window11932

overview

Window 1

Location 19,712,458 – 19,712,578
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 90.13
Mean single sequence MFE -32.98
Consensus MFE -23.32
Energy contribution -23.36
Covariance contribution 0.04
Combinations/Pair 1.20
Mean z-score -1.90
Structure conservation index 0.71
SVM decision value 0.01
SVM RNA-class probability 0.538655
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 19712458 120 + 23771897
AAAGAUCUCGUCUAUUUUUAGAUUGCUCAGAUUUGUCUGUUUGCCUAGACUAAUCCGAGUGGUAUAGGUCUGCCAACACCUUCGGCUUAAUCGAACAAAAGUCUGUAUUUCAGGCUUUAU
..((((((...(((....)))((..(((.((((.(((((......))))).)))).)))..))..))))))(((.........)))...........((((((((.....)))))))).. ( -32.70)
>DroSec_CAF1 21722 120 + 1
AAAGAUGCCGGCUAUUUUUAGACUGCUCAGAUUUGACUGUUUGCCUAGACUAAUCCGAGAGGUAUAGGUCUGCCAACACCUUCGGCUUAAUCGGACAAAAGUCUGUAUUUCAGGCUUUAU
.....(((((((.((..(((((((....)).)))))..))..)))..((.(((.((((.((((...((....))...)))))))).))).)))).))((((((((.....)))))))).. ( -31.50)
>DroSim_CAF1 23905 120 + 1
AAAGGUGCCGGCUAUUUUUAGACUGCUCAGAUUUGACUGUUUGCCUAGACUAAUCCGAGAGGUAUAGGUCUGCCAACACCUUUGGCUUAAUCGGACAAAAGUCUGUAUUUCAGGCUUUAU
(((((((..(((............((.(((......)))...))..(((((.((((....)).)).))))))))..)))))))(((((((((((((....))))).)))..))))).... ( -34.20)
>DroEre_CAF1 24383 116 + 1
AAAGUUCCCGGCUAUUUUUAGGCUGCUCAGAUUACACUGUUUGCCUAGACUAAUCCGGGAGGUAUAGGUCUGCUAACACCUUCGGCUUAAUC----AGAAGUCUGUAUUUCAGGCUGAAA
..(.(((((((.....(((((((....(((......)))...))))))).....))))))).)...(((........)))((((((((((((----((....))).)))..)))))))). ( -35.80)
>DroYak_CAF1 22205 116 + 1
AAAGUUCUCGUCUAUUUUUAGGCUGCUCAGAUUUGACUGUUUGCCUAGACUAAUCCGAGAGGUAUAGGUCUGCUAACACCUUCGGCUUAUUC----AGAAGUCUGUAUUUCGGGCUUUAU
((((((((((......(((((((....(((......)))...)))))))......)))((((((((((((((.......(....)......)----)))..))))))))))))))))).. ( -30.72)
>consensus
AAAGAUCCCGGCUAUUUUUAGACUGCUCAGAUUUGACUGUUUGCCUAGACUAAUCCGAGAGGUAUAGGUCUGCCAACACCUUCGGCUUAAUCG_ACAAAAGUCUGUAUUUCAGGCUUUAU
.......(((..((...((((.(((..(((((......)))))..))).)))).(((((.(((...((....))...))))))))..))..)))...((((((((.....)))))))).. (-23.32 = -23.36 +   0.04)

alignment

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secondary structure

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dotplot

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Window 2

Location 19,712,458 – 19,712,578
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 90.13
Mean single sequence MFE -29.58
Consensus MFE -21.42
Energy contribution -23.38
Covariance contribution 1.96
Combinations/Pair 1.03
Mean z-score -1.66
Structure conservation index 0.72
SVM decision value -0.07
SVM RNA-class probability 0.500000
Prediction OTHER

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 19712458 120 - 23771897
AUAAAGCCUGAAAUACAGACUUUUGUUCGAUUAAGCCGAAGGUGUUGGCAGACCUAUACCACUCGGAUUAGUCUAGGCAAACAGACAAAUCUGAGCAAUCUAAAAAUAGACGAGAUCUUU
.....(((((.......(((....))).((((((.((((.(((((.((....)).)))))..)))).)))))))))))...((((....)))).....((((....)))).......... ( -28.50)
>DroSec_CAF1 21722 120 - 1
AUAAAGCCUGAAAUACAGACUUUUGUCCGAUUAAGCCGAAGGUGUUGGCAGACCUAUACCUCUCGGAUUAGUCUAGGCAAACAGUCAAAUCUGAGCAGUCUAAAAAUAGCCGGCAUCUUU
.....(((.(......(((((((((((.((((((.((((((((((.((....)).)))))).)))).))))))..))))))(((......)))...)))))........).)))...... ( -34.74)
>DroSim_CAF1 23905 120 - 1
AUAAAGCCUGAAAUACAGACUUUUGUCCGAUUAAGCCAAAGGUGUUGGCAGACCUAUACCUCUCGGAUUAGUCUAGGCAAACAGUCAAAUCUGAGCAGUCUAAAAAUAGCCGGCACCUUU
..((((.(((.....))).))))..............((((((((((((..........((((((((((.(.((.(.....))).).)))))))).))..........)))))))))))) ( -32.05)
>DroEre_CAF1 24383 116 - 1
UUUCAGCCUGAAAUACAGACUUCU----GAUUAAGCCGAAGGUGUUAGCAGACCUAUACCUCCCGGAUUAGUCUAGGCAAACAGUGUAAUCUGAGCAGCCUAAAAAUAGCCGGGAACUUU
.(((.((.(((....(((....))----).))).)).)))(((((.((.....)))))))((((((.(((...(((((...(((......)))....)))))....)))))))))..... ( -29.10)
>DroYak_CAF1 22205 116 - 1
AUAAAGCCCGAAAUACAGACUUCU----GAAUAAGCCGAAGGUGUUAGCAGACCUAUACCUCUCGGAUUAGUCUAGGCAAACAGUCAAAUCUGAGCAGCCUAAAAAUAGACGAGAACUUU
...............(((....))----)..(((.((((((((((.((.....)))))))).)))).)))((((((((...(((......)))....))))......))))......... ( -23.50)
>consensus
AUAAAGCCUGAAAUACAGACUUUUGU_CGAUUAAGCCGAAGGUGUUGGCAGACCUAUACCUCUCGGAUUAGUCUAGGCAAACAGUCAAAUCUGAGCAGUCUAAAAAUAGCCGGGAACUUU
.....(((((....((((....))))..((((((.((((((((((.((....)).)))))).)))).)))))))))))...(((......)))........................... (-21.42 = -23.38 +   1.96)

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 12:44:35 2006