Locus 1186

Sequence ID 3L_DroMel_CAF1
Location 3,375,306 – 3,375,453
Length 147
Max. P 0.773328
window1858 window1859

overview

Window 8

Location 3,375,306 – 3,375,413
Length 107
Sequences 4
Columns 112
Reading direction reverse
Mean pairwise identity 89.79
Mean single sequence MFE -27.95
Consensus MFE -21.94
Energy contribution -22.00
Covariance contribution 0.06
Combinations/Pair 1.04
Mean z-score -1.52
Structure conservation index 0.78
SVM decision value 0.12
SVM RNA-class probability 0.592577
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 3375306 107 - 23771897
-GAGAUGUCUGGAGAACUCCGCCAGAGAAAAA-AAAAACGAAAGAAAAACCGGAGGGGG--GGUUGGCUGAAGUGUGCA-GGGGAAGCGGACUAGGGCAGUUGCUCAUAACU
-(((.((((((((....)))(((.........-.....(....)...((((........--)))))))...(((.(((.-......))).))).)))))....)))...... ( -26.10)
>DroSec_CAF1 42446 106 - 1
UGAGAUGUCUGGAGAACUCCGCCAGAGAAAAA-AAAAACGAGAGAAAAGCCGGAGGG-G--GG-UGGCUGAAGUGUGCA-GGGGAAGCGGACUAGGGCAGUUGCUCAUAACU
.....(.(((((....(((((...........-.....)).))).....))))).).-(--((-..((((.(((.(((.-......))).)))....))))..)))...... ( -26.99)
>DroSim_CAF1 40174 107 - 1
-GAGAUGUCUGGAGAACUCCGCCAGAGAAAAAAAAAAACGAGAGAAAAGUCGGAGGGGG--GG-UGGCUGCAGUGUGCG-GGGGAAGCGGACUAGGGCAGUUGCUCAUAACU
-..(((.(((((.(.....).)))))............(....)....))).......(--((-..((((((((.(((.-......))).)))...)))))..)))...... ( -29.60)
>DroEre_CAF1 41816 105 - 1
-GAGAUGUCUGGAGAACUCCGCCAGAGGAA-G-----AGGAGGGAAAAGCCGGAGGGGAGGGGUUGGCUGAAGUGUGCAGGGGGAAGCGGACUAGGGCAGUUGCUCAUAACU
-....(.(((((....((((.((...))..-.-----.)))).......))))).).(((.(..((.((..(((.(((........))).))).)).))..).)))...... ( -29.10)
>consensus
_GAGAUGUCUGGAGAACUCCGCCAGAGAAAAA_AAAAACGAGAGAAAAGCCGGAGGGGG__GG_UGGCUGAAGUGUGCA_GGGGAAGCGGACUAGGGCAGUUGCUCAUAACU
.(((.((((((((....)))((((..............(....).....((....)).......))))...(((.(((........))).))).)))))....)))...... (-21.94 = -22.00 +   0.06)

alignment

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secondary structure

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dotplot

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Window 9

Location 3,375,343 – 3,375,453
Length 110
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 87.29
Mean single sequence MFE -32.27
Consensus MFE -23.33
Energy contribution -23.05
Covariance contribution -0.28
Combinations/Pair 1.08
Mean z-score -2.02
Structure conservation index 0.72
SVM decision value 0.54
SVM RNA-class probability 0.773328
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 3375343 110 - 23771897
ACUUGAGAUUCUCGUACGUGCCCAGAUGCGUGGGAAUGAC-GAGAUGUCUGGAGAACUCCGCCAGAGAAAAA-AAAAACGAAAGAAAAACCGGAGGGGG--------GGUUGGCUGAAGU
.(((.((((((((((.(((.((((......)))).)))))-)))).)))).)))...((.(((.........-.....(....)...((((........--------))))))).))... ( -33.70)
>DroSec_CAF1 42483 109 - 1
ACUUGAGAUUCUCGUACGUGCCCAGAUGCGUGGGAAUGAUUGAGAUGUCUGGAGAACUCCGCCAGAGAAAAA-AAAAACGAGAGAAAAGCCGGAGGG-G--------GG-UGGCUGAAGU
.(((.(((((((((..(((.((((......)))).)))..))))).)))).)))....(((((.........-.....(....).....((....))-.--------))-)))....... ( -28.70)
>DroSim_CAF1 40211 110 - 1
ACUUGAGAUUCUCGUACGUGCCCAGAUGCGUGGGAAUGAC-GAGAUGUCUGGAGAACUCCGCCAGAGAAAAAAAAAAACGAGAGAAAAGUCGGAGGGGG--------GG-UGGCUGCAGU
.(((.((((((((((.(((.((((......)))).)))))-)))).)))).))).(((((.((...((..........(....).....))...)).))--------))-)......... ( -33.06)
>DroEre_CAF1 41854 107 - 1
ACUUGAGAUUCUCGUACGUGCCCAGAUGCGUGGGAAUGAC-GAGAUGUCUGGAGAACUCCGCCAGAGGAA-G-----AGGAGGGAAAAGCCGGAGGGGAGG------GGUUGGCUGAAGU
.(((.((((((((((.(((.((((......)))).)))))-)))).)))).)))..((((.((...))..-.-----.)))).....((((((........------..))))))..... ( -34.50)
>DroYak_CAF1 41343 114 - 1
ACUUGAGAUUCUCGUACGUGCCCAGAUGCGUGGGAAUGAC-GAGAUGUCUGGAGAACUCUGCCAGAGGAAAA-----AAGAGAGAAAAGCCAAAGGGGAGGGGAGUGGGUUGACUGAAGU
.(((.((((((((((.(((.((((......)))).)))))-)))).)))).)))..((((.((...((....-----............))....)).)))).(((......)))..... ( -31.39)
>consensus
ACUUGAGAUUCUCGUACGUGCCCAGAUGCGUGGGAAUGAC_GAGAUGUCUGGAGAACUCCGCCAGAGAAAAA_AAAAACGAGAGAAAAGCCGGAGGGGG________GGUUGGCUGAAGU
.(((.((((((((((.(((.((((......)))).))))).)))).)))).)))..(((((.............................)))))......................... (-23.33 = -23.05 +  -0.28)

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 10:01:33 2006