Locus 6545

Sequence ID 3L_DroMel_CAF1
Location 17,292,649 – 17,292,788
Length 139
Max. P 0.980008
window10646 window10647 window10648

overview

Window 6

Location 17,292,649 – 17,292,748
Length 99
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 78.06
Mean single sequence MFE -35.37
Consensus MFE -22.31
Energy contribution -22.87
Covariance contribution 0.56
Combinations/Pair 1.08
Mean z-score -2.43
Structure conservation index 0.63
SVM decision value 1.85
SVM RNA-class probability 0.980008
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17292649 99 - 23771897
CUGCAGCAGC---------------------AGCAACCACUGCAAAUGCAACUGCAACUGCAUGUGCCAGUCGGAGCAUCAUCAAUCCAGUGGUUCUCCACUCUCGACUCCUAAGCAGCG
((((.(((((---------------------((......))))..(((((........))))).))).(((((((..........)))(((((....)))))...)))).....)))).. ( -28.80)
>DroSec_CAF1 176443 111 - 1
CUGCAGCAGCAG------UAGCAGCG---GCAGCAUCCACUGCAAAUGCAACUGCAACUGCAUCUGCCAGUCGGAGCAUCAUCAAUCCAGUGGUUCUCCACUCUCGACUCCUAAGCAGCG
.(((((..((((------(.(((...---((((......))))...))).)))))..))))).((((.(((((((..........)))(((((....)))))...)))).....)))).. ( -41.10)
>DroYak_CAF1 185213 120 - 1
CUGCAUCAUCAGUAGCUGCAACUGCAAGUGCAACUGCAAGUGCAAGUGGAACUGCAACUGCAACUGCCAGUCGGAGCAUCAUCAAUCCAGUGGUCCUCCACUCUCGACUCCUAAGUAGGA
((((.......((((.((((..((((..(.((..(((....)))..)).)..))))..)))).)))).(((((((..........)))(((((....)))))...)))).....)))).. ( -36.20)
>consensus
CUGCAGCAGCAG_______A_C_GC____GCAGCAACCACUGCAAAUGCAACUGCAACUGCAUCUGCCAGUCGGAGCAUCAUCAAUCCAGUGGUUCUCCACUCUCGACUCCUAAGCAGCG
((((.................................(((((((..(((....)))..)))).)))..(((((((..........)))(((((....)))))...)))).....)))).. (-22.31 = -22.87 +   0.56)

alignment

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secondary structure

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dotplot

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Window 7

Location 17,292,689 – 17,292,788
Length 99
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 80.34
Mean single sequence MFE -39.87
Consensus MFE -26.40
Energy contribution -27.73
Covariance contribution 1.33
Combinations/Pair 1.00
Mean z-score -1.94
Structure conservation index 0.66
SVM decision value 0.58
SVM RNA-class probability 0.789527
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17292689 99 + 23771897
GAUGCUCCGACUGGCACAUGCAGUUGCAGUUGCAUUUGCAGUGGUUGCU---------------------GCUGCUGCAGUGGGGGGUGCAUAAAUCACAGUCAUGCACGUGUUAAUAUC
((((((((.((((.((((.(((((.((..((((....))))..)).)))---------------------)))).)))))).))))((((((...........)))))).......)))) ( -35.60)
>DroSec_CAF1 176483 111 + 1
GAUGCUCCGACUGGCAGAUGCAGUUGCAGUUGCAUUUGCAGUGGAUGCUGC---CGCUGCUA------CUGCUGCUGCAGUGGGGGGUGCAUAAAUCACAGUCAUGCACGUGUUAAUAUC
((((((((.((((.(((..(((((.(((((.(((...(((.....))))))---.))))).)------))))..))))))).))))((((((...........)))))).......)))) ( -45.20)
>DroYak_CAF1 185253 120 + 1
GAUGCUCCGACUGGCAGUUGCAGUUGCAGUUCCACUUGCACUUGCAGUUGCACUUGCAGUUGCAGCUACUGAUGAUGCAGUGGGGGGUGCAUAAAUCACAGUCAUGCACGUGUUAAUAUC
((((((((.((((..(((((((..(((((...((.((((....)))).))...)))))..))))))).(....)...)))).))))((((((...........)))))).......)))) ( -38.80)
>consensus
GAUGCUCCGACUGGCAGAUGCAGUUGCAGUUGCAUUUGCAGUGGAUGCUGC____GC_G_U_______CUGCUGCUGCAGUGGGGGGUGCAUAAAUCACAGUCAUGCACGUGUUAAUAUC
((((((((.((((((((((((((......))))))))))(((....)))............................)))).))))((((((...........)))))).......)))) (-26.40 = -27.73 +   1.33)

alignment

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secondary structure

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dotplot

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Window 8

Location 17,292,689 – 17,292,788
Length 99
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 80.34
Mean single sequence MFE -35.03
Consensus MFE -19.83
Energy contribution -20.33
Covariance contribution 0.50
Combinations/Pair 1.00
Mean z-score -2.46
Structure conservation index 0.57
SVM decision value 0.46
SVM RNA-class probability 0.745056
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17292689 99 - 23771897
GAUAUUAACACGUGCAUGACUGUGAUUUAUGCACCCCCCACUGCAGCAGC---------------------AGCAACCACUGCAAAUGCAACUGCAACUGCAUGUGCCAGUCGGAGCAUC
...........((((.((((((.(...((((((........((((...((---------------------((......))))...))))........))))))..)))))))..)))). ( -28.09)
>DroSec_CAF1 176483 111 - 1
GAUAUUAACACGUGCAUGACUGUGAUUUAUGCACCCCCCACUGCAGCAGCAG------UAGCAGCG---GCAGCAUCCACUGCAAAUGCAACUGCAACUGCAUCUGCCAGUCGGAGCAUC
...........((((((((.......))))))))..((.(((((((..((((------(.((((..---((((((.....)))...)))..)))).)))))..))).)))).))...... ( -39.60)
>DroYak_CAF1 185253 120 - 1
GAUAUUAACACGUGCAUGACUGUGAUUUAUGCACCCCCCACUGCAUCAUCAGUAGCUGCAACUGCAAGUGCAACUGCAAGUGCAAGUGGAACUGCAACUGCAACUGCCAGUCGGAGCAUC
...........((((.((((((((((..(((((........))))).))))((((.((((..((((..(.((..(((....)))..)).)..))))..)))).))))))))))..)))). ( -37.40)
>consensus
GAUAUUAACACGUGCAUGACUGUGAUUUAUGCACCCCCCACUGCAGCAGCAG_______A_C_GC____GCAGCAACCACUGCAAAUGCAACUGCAACUGCAUCUGCCAGUCGGAGCAUC
...........((((((((.......))))))))..((.((((((..................((....)).........((((..(((....)))..))))..)).)))).))...... (-19.83 = -20.33 +   0.50)

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 12:23:51 2006