Locus 1845

Sequence ID 3R_DroMel_CAF1
Location 5,297,945 – 5,298,041
Length 96
Max. P 0.701522
window3035 window3036

overview

Window 5

Location 5,297,945 – 5,298,041
Length 96
Sequences 6
Columns 96
Reading direction forward
Mean pairwise identity 82.08
Mean single sequence MFE -38.65
Consensus MFE -24.08
Energy contribution -23.25
Covariance contribution -0.83
Combinations/Pair 1.47
Mean z-score -2.21
Structure conservation index 0.62
SVM decision value 0.35
SVM RNA-class probability 0.701522
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 5297945 96 + 27905053
CCCACAAGCUGUGAGCUGAGCUCCUCCUCCUUGACCUCCACGGGUGAGUUGGAGGAGGGAGUAACGAGCUCAGAGUUGUCCUCGACUGUGACAGUU
......((((((.(.((((((((...((((((..(((((((......).))))))))))))....))))))))(((((....))))).).)))))) ( -39.90)
>DroSim_CAF1 2179 96 + 1
CCCACAAGCUGUGGACUCAGCUCCUCCUCCUUGACCUCCACGGGUGAGUUGGAGGAGGGAGUAACGAGCUCAGAGUUGUCUUCGACUGUGACAGUC
.((((.....))))((((..(((((((..(((.((((....)))))))..))))))).)))).....(.(((.(((((....))))).)))).... ( -38.00)
>DroEre_CAF1 2416 96 + 1
CCCACCAGCUGUGGGCUCAGCUCCUCCUCCUUGACCUCCACGGGCGAGUUGGAGGAGGGGGUAACGAGCUCAGAGUUGUCCUCGACUGUGACAGUC
.....(((((.(((((((....((((((((((.(.((((....).))).).))))))))))....))))))).))))).....(((((...))))) ( -44.50)
>DroYak_CAF1 2171 96 + 1
CCCACUAACUGUGGGCUCAGCUCCUCCUCCUUGACCUCCACGGGUGAGUUCGAGGAGGGAGUGACGAGCUCAGAGUUGUCCUCGACUGUGACAGUC
.....(((((.(((((((.(((((..((((((((.((((....).))).)))))))))))))...))))))).))))).....(((((...))))) ( -42.70)
>DroMoj_CAF1 2509 96 + 1
GCCACCAGCUGUUGGCUCAGCUCAUCGUCUUUGACCUCGUCGGCUGAGCCUGACGAUGUGCCACCCAGCUCGGUGCCAUCCUCGACAGUUACAGUC
......((((((((((((((((.((.(((...)))...)).))))))))).((.((((.((.(((......))))))))).)))))))))...... ( -35.30)
>DroAna_CAF1 2674 96 + 1
GCCACAAGCUGUUGGUUCAGCUCCUCCUCCUUCAUCUCCACGGGGGAGUUGGAAGAGGGAGGCACCAUGUCAGUAUUAUCCUCAACGGUGACAGUC
(((...(((((......)))))..(((..((((..((((.....))))...))))..))))))....(((((.(.((......)).).)))))... ( -31.50)
>consensus
CCCACAAGCUGUGGGCUCAGCUCCUCCUCCUUGACCUCCACGGGUGAGUUGGAGGAGGGAGUAACGAGCUCAGAGUUGUCCUCGACUGUGACAGUC
.......(((((.((((..((((((((((((((.((.....)).))))...))))))).)))....))))((.(((((....))))).))))))). (-24.08 = -23.25 +  -0.83)

alignment

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secondary structure

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dotplot

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Window 6

Location 5,297,945 – 5,298,041
Length 96
Sequences 6
Columns 96
Reading direction reverse
Mean pairwise identity 82.08
Mean single sequence MFE -36.48
Consensus MFE -22.94
Energy contribution -22.83
Covariance contribution -0.11
Combinations/Pair 1.27
Mean z-score -1.66
Structure conservation index 0.63
SVM decision value -0.06
SVM RNA-class probability 0.500000
Prediction OTHER

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 5297945 96 - 27905053
AACUGUCACAGUCGAGGACAACUCUGAGCUCGUUACUCCCUCCUCCAACUCACCCGUGGAGGUCAAGGAGGAGGAGCUCAGCUCACAGCUUGUGGG
...((((.(......)))))...((((((((.((.((((..((((((.(......)))))))....)))))).))))))))(((((.....))))) ( -37.20)
>DroSim_CAF1 2179 96 - 1
GACUGUCACAGUCGAAGACAACUCUGAGCUCGUUACUCCCUCCUCCAACUCACCCGUGGAGGUCAAGGAGGAGGAGCUGAGUCCACAGCUUGUGGG
(((((...))))).......((((..(((((.((.((((..((((((.(......)))))))....)))))).)))))))))((((.....)))). ( -36.40)
>DroEre_CAF1 2416 96 - 1
GACUGUCACAGUCGAGGACAACUCUGAGCUCGUUACCCCCUCCUCCAACUCGCCCGUGGAGGUCAAGGAGGAGGAGCUGAGCCCACAGCUGGUGGG
(((((...)))))(((.....)))...(((((((.((.((((((....(((.......)))....)))))).))))).))))((((.....)))). ( -36.30)
>DroYak_CAF1 2171 96 - 1
GACUGUCACAGUCGAGGACAACUCUGAGCUCGUCACUCCCUCCUCGAACUCACCCGUGGAGGUCAAGGAGGAGGAGCUGAGCCCACAGUUAGUGGG
(((((...)))))(((.....)))(.(((((.((.((((((((.((........)).)))).....)))))).))))).).(((((.....))))) ( -38.50)
>DroMoj_CAF1 2509 96 - 1
GACUGUAACUGUCGAGGAUGGCACCGAGCUGGGUGGCACAUCGUCAGGCUCAGCCGACGAGGUCAAAGACGAUGAGCUGAGCCAACAGCUGGUGGC
(((.......)))......(.((((.(((((((((((.(((((((.(((...)))(((...)))...))))))).)))..)))..))))))))).) ( -38.10)
>DroAna_CAF1 2674 96 - 1
GACUGUCACCGUUGAGGAUAAUACUGACAUGGUGCCUCCCUCUUCCAACUCCCCCGUGGAGAUGAAGGAGGAGGAGCUGAACCAACAGCUUGUGGC
......(((((((.((.......)).).))))))(((((..((((...((((.....))))..))))..)))))(((((......)))))...... ( -32.40)
>consensus
GACUGUCACAGUCGAGGACAACUCUGAGCUCGUUACUCCCUCCUCCAACUCACCCGUGGAGGUCAAGGAGGAGGAGCUGAGCCCACAGCUUGUGGG
.....((((...((((..((....))..))))......((((((((..(((.......))).....))))))))(((((......))))).)))). (-22.94 = -22.83 +  -0.11)

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 10:20:57 2006