Locus 1918

Sequence ID X_DroMel_CAF1
Location 5,291,754 – 5,291,940
Length 186
Max. P 0.997631
window3118 window3119 window3120

overview

Window 8

Location 5,291,754 – 5,291,860
Length 106
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 87.57
Mean single sequence MFE -40.82
Consensus MFE -32.98
Energy contribution -32.90
Covariance contribution -0.08
Combinations/Pair 1.07
Mean z-score -3.07
Structure conservation index 0.81
SVM decision value 2.90
SVM RNA-class probability 0.997631
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5291754 106 + 22224390
AAAA----GCGGAUAUCCAGCAGCUGGGAACACUCCAUCGAGGUUUUUCC----------CGACGCUUUUCCGAACGCCAACGAGCGGCAAGCCGCUGCCGAAAUAUCCGCCAACACUUU
....----((((((((...(((((((((((..(((....)))....))))----------))..((((..(((..((....))..))).)))).)))))....))))))))......... ( -37.40)
>DroSec_CAF1 28976 106 + 1
AAAA----GCGGAUAUCCAGAAACUGGGAACACUCCAUCGAGGUUUUUCC----------CGACGCUUCUCCGAGCGCCAACGAACGGAAAGCCGCUUCCGAAAUAUCCGCCAACACUUU
....----((((((((...(((.(((((((..(((....)))....))))----------))..((((.((((..((....))..)))))))).).)))....))))))))......... ( -31.10)
>DroSim_CAF1 19782 106 + 1
AAAA----GCGGAUAUCCAGCAGCUGGGAACACUCCAUCGAGGUUUUUCC----------CGACGCUUUUCCGAGCGCCAACGAGCGGCAAGCCGCUGCCGAAAUAUCCGCCAACACUUU
....----((((((((...(((((((((((..(((....)))....))))----------))..((((..(((..((....))..))).)))).)))))....))))))))......... ( -38.80)
>DroEre_CAF1 30138 118 + 1
AAACG--GGUGGAUAUCCAGCAGCUGGGAACACUCCAUCGAGGUUUUUCCGAGGCUUUUCCGAGGCUUUUCCGAGCGGCAACGAGCGGCAAGCCGCUGCCGAAAUAUCCGCCAACACUUU
.....--(((((((((...(((((((((((....((.(((.((....)))))))..)))))).(((((..(((..((....))..))).))))))))))....)))))))))........ ( -47.90)
>DroYak_CAF1 30099 109 + 1
AGUAGGCGGCGGAUAUCCAGCAGCUGGGAACACUCCAUCGAGGUUUUUCCGAGG-----------CUUUUCCGAGCGGCAACGAGCGGCAAGCCGCUGCCGAAAUAUCCGCCAACACUUU
(((.(..(((((((((...(((((((((((..(((....)))...)))))).((-----------(((..(((..((....))..))).))))))))))....)))))))))..)))).. ( -48.90)
>consensus
AAAA____GCGGAUAUCCAGCAGCUGGGAACACUCCAUCGAGGUUUUUCC__________CGACGCUUUUCCGAGCGCCAACGAGCGGCAAGCCGCUGCCGAAAUAUCCGCCAACACUUU
........((((((((...(((((.(((((..(((....)))...)))))..............((((..(((..((....))..))).)))).)))))....))))))))......... (-32.98 = -32.90 +  -0.08)

alignment

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secondary structure

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dotplot

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Window 9

Location 5,291,754 – 5,291,860
Length 106
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 87.57
Mean single sequence MFE -46.66
Consensus MFE -36.82
Energy contribution -36.74
Covariance contribution -0.08
Combinations/Pair 1.06
Mean z-score -3.16
Structure conservation index 0.79
SVM decision value 2.75
SVM RNA-class probability 0.996778
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5291754 106 - 22224390
AAAGUGUUGGCGGAUAUUUCGGCAGCGGCUUGCCGCUCGUUGGCGUUCGGAAAAGCGUCG----------GGAAAAACCUCGAUGGAGUGUUCCCAGCUGCUGGAUAUCCGC----UUUU
........((((((((((.(((((((.((((.(((..((....))..)))..))))...(----------((((....(((....)))..))))).))))))))))))))))----)... ( -47.50)
>DroSec_CAF1 28976 106 - 1
AAAGUGUUGGCGGAUAUUUCGGAAGCGGCUUUCCGUUCGUUGGCGCUCGGAGAAGCGUCG----------GGAAAAACCUCGAUGGAGUGUUCCCAGUUUCUGGAUAUCCGC----UUUU
........((((((((((.(((((((.((((((((..((....))..))))).)))...(----------((((....(((....)))..))))).))))))))))))))))----)... ( -45.00)
>DroSim_CAF1 19782 106 - 1
AAAGUGUUGGCGGAUAUUUCGGCAGCGGCUUGCCGCUCGUUGGCGCUCGGAAAAGCGUCG----------GGAAAAACCUCGAUGGAGUGUUCCCAGCUGCUGGAUAUCCGC----UUUU
........((((((((((.(((((((((....)).......((((((......))))))(----------((((....(((....)))..))))).))))))))))))))))----)... ( -47.60)
>DroEre_CAF1 30138 118 - 1
AAAGUGUUGGCGGAUAUUUCGGCAGCGGCUUGCCGCUCGUUGCCGCUCGGAAAAGCCUCGGAAAAGCCUCGGAAAAACCUCGAUGGAGUGUUCCCAGCUGCUGGAUAUCCACC--CGUUU
........((.(((((((.((((((((((((.(((..((....))..)))..)))))..((((...((((((.......)))).))....))))..)))))))))))))).))--..... ( -44.60)
>DroYak_CAF1 30099 109 - 1
AAAGUGUUGGCGGAUAUUUCGGCAGCGGCUUGCCGCUCGUUGCCGCUCGGAAAAG-----------CCUCGGAAAAACCUCGAUGGAGUGUUCCCAGCUGCUGGAUAUCCGCCGCCUACU
..((((.(((((((((((.((((((((((((.(((..((....))..)))..)))-----------))..((((....(((....)))..))))..))))))))))))))))))..)))) ( -48.60)
>consensus
AAAGUGUUGGCGGAUAUUUCGGCAGCGGCUUGCCGCUCGUUGGCGCUCGGAAAAGCGUCG__________GGAAAAACCUCGAUGGAGUGUUCCCAGCUGCUGGAUAUCCGC____UUUU
.........(((((((((.(((((((.((((.(((..((....))..)))..))))..............((((....(((....)))..))))..))))))))))))))))........ (-36.82 = -36.74 +  -0.08)

alignment

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secondary structure

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dotplot

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Window 0

Location 5,291,820 – 5,291,940
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 97.83
Mean single sequence MFE -32.72
Consensus MFE -27.88
Energy contribution -29.76
Covariance contribution 1.88
Combinations/Pair 1.03
Mean z-score -1.79
Structure conservation index 0.85
SVM decision value 0.81
SVM RNA-class probability 0.856353
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5291820 120 + 22224390
ACGAGCGGCAAGCCGCUGCCGAAAUAUCCGCCAACACUUUUGCGAAUAAAACUAAAGAAAUUUGUUUGUUUUGAUUCAGUCGUUGCGGGUUUUUUAAGGCGAACACACAGCCCUGAAAAC
.((.(((((.....)))))))....((((((.((((((....((((..((((.(((....)))))))..))))....))).)))))))))((((((.(((.........))).)))))). ( -33.00)
>DroSec_CAF1 29042 120 + 1
ACGAACGGAAAGCCGCUUCCGAAAUAUCCGCCAACACUUUUGCGAAUAAAACUAAAGAAAUUUGUUUGUUUUGAUUCAGUCGUUGCGGGUUUUUUAAGGCGAACACACAGCCCUGAAAAC
.....(((((......)))))....((((((.((((((....((((..((((.(((....)))))))..))))....))).)))))))))((((((.(((.........))).)))))). ( -29.00)
>DroSim_CAF1 19848 120 + 1
ACGAGCGGCAAGCCGCUGCCGAAAUAUCCGCCAACACUUUUGCGAAUAAAACUAAAGAAAUUUGUUUGUUUUGAUUCAGUCGUUGCGGGUUUUUUAAGGCGAACACACAGCCCUGAAAAC
.((.(((((.....)))))))....((((((.((((((....((((..((((.(((....)))))))..))))....))).)))))))))((((((.(((.........))).)))))). ( -33.00)
>DroEre_CAF1 30216 119 + 1
ACGAGCGGCAAGCCGCUGCCGAAAUAUCCGCCAACACUUUUUCGAAUAAAACUAAAGAAAUUUGUUUGUUUUGAUUCAGUCGUUGCGGGUUUUUUAAGGCGAACACACAGCCCUGAAA-G
.((.(((((.....)))))))....((((((.((((((...(((((..((((.(((....)))))))..)))))...))).))))))))).(((((.(((.........))).)))))-. ( -34.00)
>DroYak_CAF1 30168 120 + 1
ACGAGCGGCAAGCCGCUGCCGAAAUAUCCGCCAACACUUUUUCGAAUAAAACUAAAGAAAUUUGUUUGUUUUGAUUCAGUCGUUGCGGGUUUUUUAAGGCGAACACACAGCCCUGAAAAC
.((.(((((.....)))))))....((((((.((((((...(((((..((((.(((....)))))))..)))))...))).)))))))))((((((.(((.........))).)))))). ( -34.60)
>consensus
ACGAGCGGCAAGCCGCUGCCGAAAUAUCCGCCAACACUUUUGCGAAUAAAACUAAAGAAAUUUGUUUGUUUUGAUUCAGUCGUUGCGGGUUUUUUAAGGCGAACACACAGCCCUGAAAAC
.....(((((......)))))....((((((.((((((....((((..((((.(((....)))))))..))))....))).)))))))))((((((.(((.........))).)))))). (-27.88 = -29.76 +   1.88)

alignment

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secondary structure

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dotplot

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Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:21:51 2006