Locus 4089

Sequence ID 3L_DroMel_CAF1
Location 11,916,176 – 11,916,296
Length 120
Max. P 0.750367
window6362 window6363

overview

Window 2

Location 11,916,176 – 11,916,296
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 94.08
Mean single sequence MFE -43.72
Consensus MFE -35.12
Energy contribution -35.28
Covariance contribution 0.16
Combinations/Pair 1.06
Mean z-score -1.59
Structure conservation index 0.80
SVM decision value 0.33
SVM RNA-class probability 0.693594
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 11916176 120 + 23771897
AAGGUCGUGAAUGCCGAGUACGAAAAGUCCGAGGACGAUCUGAAGGCUCUCCAGAGUGUGGGUCAGAUGGUCGGGGAAAUCCUGAAGCAGCUCACACCGGACAACUUCAUCGUGAAGGCC
............(((...(((((...(((....)))....(((((....(((.(.((((((((....((.(((((.....)))))..))))))))))))))...))))))))))..))). ( -39.10)
>DroSec_CAF1 91978 120 + 1
AAGGUCGUGAAUGCCCAGUACGAGAAGUCCGAGGACGAUCUGAAAGCUCUCCAGAGUGUGGGUCAGAUGGUCGGGGAAGUUCUGAAGCAGCUCACCCCGGACAAUUUCAUCGUGAAGGCC
............(((...(((((((((((((..(((.((((((..((((....)))).....)))))).)))(((..(((((....).))))..))))))))...))).)))))..))). ( -44.10)
>DroSim_CAF1 92238 120 + 1
AAGGUCGUGAAUGCCCAGUAUGAGAAGUCCGAGGACGAUCUGAAGGCUCUCCAGAGUGUGGGUCAGAUGGUCGGGGAAGUUCUGAAGCAGCUCACCCCGGACAACUUCAUCGUGAAGGCA
...........((((...(((((((((((((..(((.(((((((.((((....)))).)...)))))).)))(((..(((((....).))))..))))))))...))).)))))..)))) ( -42.50)
>DroEre_CAF1 94428 120 + 1
AAGGUCGUGAAUGCCCAGUACGAGAAGUCCGAGGAGGACCUGAAGGCCCUCCAGAGUGUGGGUCAGAUGCUCGGGGAAAUCCUGAAGCAGCUCACCCCGGACAACUUCAUCGUGAAGGCC
............(((...(((((((((((((.(((((.((....)).))))).......((((.((.((((((((.....)))).)))).)).)))))))))...))).)))))..))). ( -48.10)
>DroYak_CAF1 96529 120 + 1
AAGGUCGUGAAUGCCCAGUACGAGAAGUCCGAGGAGGAUCUGAAGGCGCUCCAGAGUGUGGGUCAGAUGCUCGGUGAAAUUCUGAAGCAGCUGACCCCGGACAACUUCAUCGUGAAGGCC
............(((...(((((((((((((.((((..((....))..)))).......(((((((.(((((((.......))).)))).))))))))))))...))).)))))..))). ( -44.80)
>consensus
AAGGUCGUGAAUGCCCAGUACGAGAAGUCCGAGGACGAUCUGAAGGCUCUCCAGAGUGUGGGUCAGAUGGUCGGGGAAAUUCUGAAGCAGCUCACCCCGGACAACUUCAUCGUGAAGGCC
............(((...((((((((((((...(((.((((((..((.((....)).))...)))))).)))((((.....(((...)))....))))))))...))).)))))..))). (-35.12 = -35.28 +   0.16)

alignment

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secondary structure

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dotplot

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Window 3

Location 11,916,176 – 11,916,296
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 94.08
Mean single sequence MFE -40.62
Consensus MFE -31.56
Energy contribution -31.56
Covariance contribution 0.00
Combinations/Pair 1.09
Mean z-score -1.88
Structure conservation index 0.78
SVM decision value 0.47
SVM RNA-class probability 0.750367
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 11916176 120 - 23771897
GGCCUUCACGAUGAAGUUGUCCGGUGUGAGCUGCUUCAGGAUUUCCCCGACCAUCUGACCCACACUCUGGAGAGCCUUCAGAUCGUCCUCGGACUUUUCGUACUCGGCAUUCACGACCUU
.(((...(((((((((((.(((((.(((...((..(((((...((...))...)))))..))))).))))).)).)))))....(((....)))...))))....)))............ ( -30.90)
>DroSec_CAF1 91978 120 - 1
GGCCUUCACGAUGAAAUUGUCCGGGGUGAGCUGCUUCAGAACUUCCCCGACCAUCUGACCCACACUCUGGAGAGCUUUCAGAUCGUCCUCGGACUUCUCGUACUGGGCAUUCACGACCUU
.((((..((((.(((...((((((((....(((...))).....))))(((.((((((......(((....)))...)))))).)))...)))))))))))...))))............ ( -37.70)
>DroSim_CAF1 92238 120 - 1
UGCCUUCACGAUGAAGUUGUCCGGGGUGAGCUGCUUCAGAACUUCCCCGACCAUCUGACCCACACUCUGGAGAGCCUUCAGAUCGUCCUCGGACUUCUCAUACUGGGCAUUCACGACCUU
(((((.....((((.(..((((((((....(((...))).....))))(((.((((((......(((....)))...)))))).)))...))))..)))))...)))))........... ( -36.70)
>DroEre_CAF1 94428 120 - 1
GGCCUUCACGAUGAAGUUGUCCGGGGUGAGCUGCUUCAGGAUUUCCCCGAGCAUCUGACCCACACUCUGGAGGGCCUUCAGGUCCUCCUCGGACUUCUCGUACUGGGCAUUCACGACCUU
.((((..((((.(((...(((((((((.((.(((((..((....))..))))).)).)))).......((((((((....)))))))).))))))))))))...))))............ ( -53.90)
>DroYak_CAF1 96529 120 - 1
GGCCUUCACGAUGAAGUUGUCCGGGGUCAGCUGCUUCAGAAUUUCACCGAGCAUCUGACCCACACUCUGGAGCGCCUUCAGAUCCUCCUCGGACUUCUCGUACUGGGCAUUCACGACCUU
.((((..((((.(((...((((((((((((.(((((..(.....)...))))).)))))))....(((((((...))))))).......))))))))))))...))))............ ( -43.90)
>consensus
GGCCUUCACGAUGAAGUUGUCCGGGGUGAGCUGCUUCAGAAUUUCCCCGACCAUCUGACCCACACUCUGGAGAGCCUUCAGAUCGUCCUCGGACUUCUCGUACUGGGCAUUCACGACCUU
.((((..((((.(((...((((((((....(((...))).....))))(((.((((((((((.....))).).....)))))).)))...)))))))))))...))))............ (-31.56 = -31.56 +   0.00)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:14:13 2006