Locus 8770

Sequence ID 3R_DroMel_CAF1
Location 23,408,841 – 23,409,038
Length 197
Max. P 0.784992
window14092 window14093

overview

Window 2

Location 23,408,841 – 23,408,958
Length 117
Sequences 6
Columns 117
Reading direction reverse
Mean pairwise identity 77.89
Mean single sequence MFE -42.06
Consensus MFE -23.23
Energy contribution -26.20
Covariance contribution 2.97
Combinations/Pair 1.17
Mean z-score -1.93
Structure conservation index 0.55
SVM decision value 0.57
SVM RNA-class probability 0.784992
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 23408841 117 - 27905053
CCCUCGAGGGCCAGUUCCAGGCACAUACUGGAUCCUCCGUCGGAUCCGGAACCCUGCUGGGAGUUGCCGUCGUGGGAAGUAGUUCCUCCUCCGCCCGAUCCCAGUCCCAAACUGGAC
(((.(((.(((.(.((((((.((....((((((((......)))))))).....)))))))).).))).))).)))........................(((((.....))))).. ( -45.90)
>DroGri_CAF1 46105 93 - 1
CCCUCCAACGCCAGUUCCAGGCACAUGCUUGAGCCACCAUCGGAU------CCAUGAUGCGAAUUG---------GAAUCGGGUCCACU---GCC------AAUUCCCAUUGUGGAC
...(((.......((((.((((....)))))))).......)))(------(((..(((.((((((---------(...(((.....))---)))------))))).)))..)))). ( -30.24)
>DroSim_CAF1 23486 117 - 1
CCCUCGAGGGCCAGUUCCAGGCACAUACUGGAUCCUCCAUCGGAUCCGGAGCCCUGCUGGGAAUUGCCGUCGUGGGAAUUAGUUCCUCCUCCACCCGAUCCCAGUCCCAAACUGGAC
(((.(((.(((.((((((.((((....((((((((......)))))))).....)))).))))))))).))).)))........................(((((.....))))).. ( -48.00)
>DroEre_CAF1 26730 117 - 1
CCUUCGAGGGCCAGUUCCAGGCACAUACUGGAUCCUCCGUCGGAUCCGGAGCCCUGCUGGGAGUUGCCGUCGUGGGAAUUGGCUCCUCCUCCGCCCGUUCCCAGUCCCAAACUGGAC
.....(((((((((((((.(((((...((((((((......))))))))..(((....))).).))))......))))))))).))))............(((((.....))))).. ( -51.40)
>DroYak_CAF1 24661 117 - 1
CCUUCGAGUGCCAGUUCCAGGCACAUACUGGAUCCUCCGUCGGAUCCGGAACCCUGCUGGGAGUUGCCGUCGUGUGAAUUGGCUCCUCCUCCGCCCGUUCCCAGUCCCAAGCUGGAC
.....(((.(((((((((((((((...((((((((......))))))))..(((....))).).))))....)).))))))))..)))............(((((.....))))).. ( -44.20)
>DroAna_CAF1 21547 108 - 1
CCCUCCAAGGCCAGCUCCAAGCACAUACUGGAGCCACCGUCGGAUC------CCUGCUGGGAGUUUCCAUCGUGCGAGUUG---CCACCGCCACCUCCUCCCAGACCCAGGCUGGAC
...((((.(((.(((((...((((....((((((..(((.(((...------.))).)))..).)))))..))))))))))---))...(((...((......))....))))))). ( -32.60)
>consensus
CCCUCGAGGGCCAGUUCCAGGCACAUACUGGAUCCUCCGUCGGAUCCGGA_CCCUGCUGGGAGUUGCCGUCGUGGGAAUUGGCUCCUCCUCCGCCCGAUCCCAGUCCCAAACUGGAC
....(((.(((.((((((.((((....((((((((......)))))))).....)))).))))))))).)))............................(((((.....))))).. (-23.23 = -26.20 +   2.97)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 3

Location 23,408,921 – 23,409,038
Length 117
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 83.73
Mean single sequence MFE -55.70
Consensus MFE -40.87
Energy contribution -39.85
Covariance contribution -1.02
Combinations/Pair 1.37
Mean z-score -1.68
Structure conservation index 0.73
SVM decision value 0.01
SVM RNA-class probability 0.539706
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 23408921 117 + 27905053
GA---GGAUCCAGUAUGUGCCUGGAACUGGCCCUCGAGGGUGAACGCCUCUGCAAGGCGGGUGACUGCCGGGCGGGCGUGGCCUUCUUCCAGGCGGCCAUUCAGGCCGGAACCGAGGAUC
..---((.(((.......((((((((..((((..((.((((....))))((((..(((((....)))))..)))).)).))))...))))))))((((.....))))))).))....... ( -62.30)
>DroVir_CAF1 45300 117 + 1
GC---AGUUCCAGCAUGUGUCUGGAGCUGGCUUUGGAGGGCGAACGUCUGUGCAAGGCAGGUGAUUGUCGGGCGGGCGUUGCCUUCUUCCAGGCAGCGAUACAGGCAGGCACCGACGAUC
.(---(((((((((....).)))))))))((((((..((((....))))...))))))....(((((((((((..(((((((((......))))))).......))..)).))))))))) ( -52.81)
>DroGri_CAF1 46161 117 + 1
GU---GGCUCAAGCAUGUGCCUGGAACUGGCGUUGGAGGGUGAGCGUCUCUGCAAAGCGGGCGAUUGUCGGGCGGGCGUUGCCUUCUUUCAGGCAGCCAUCCAAGCGGGCACCGACGAUC
..---.((((..((....(((.......))).(((.((((.......)))).))).))))))(((((((((((.(((..(((((......))))))))..((....)))).))))))))) ( -45.00)
>DroYak_CAF1 24741 117 + 1
GA---GGAUCCAGUAUGUGCCUGGAACUGGCACUCGAAGGCGAACGCCUUUGCAAGGCGGGCGAUUGCCGGGCGGGCGUGGCCUUCUUCCAGGCGGCCAUUCAGGCCGGAACCGAGGAUC
..---((.(((.......((((((((.........((((((..((((((..((..(((((....)))))..)))))))).))))))))))))))((((.....))))))).))....... ( -57.60)
>DroMoj_CAF1 44382 120 + 1
GCGGCGGCUCUAGCAUGUGUCUGGAGCUGGCCCUGGAAGGCGAACGCCUCUGCAAGGCAGGCGAUUGCCGAGCGGGCGUUGCCUUCUUCCAAGCAGCCAUCCAGGCGGGCACCGACGACC
.(((((((((((((....).)))))))))((((.(((((((.(((((((..((..(((((....)))))..))))))))))))))))........(((.....))))))).)))...... ( -61.40)
>DroAna_CAF1 21618 117 + 1
GU---GGCUCCAGUAUGUGCUUGGAGCUGGCCUUGGAGGGCGAACGGCUGUGCAAGGCGGGCGACUGUCGGGCGGGCGUGGCCUUCUUUCAAGCAGCCAUCCAGGCGGGCACCGAGGACC
..---(((((((((....)).)))))))(((((((((((((..(((.((((.(..(((((....)))))).)))).))).))))))......((.(((.....)))..))..))))).)) ( -55.10)
>consensus
GA___GGCUCCAGCAUGUGCCUGGAACUGGCCCUGGAGGGCGAACGCCUCUGCAAGGCGGGCGAUUGCCGGGCGGGCGUGGCCUUCUUCCAGGCAGCCAUCCAGGCGGGCACCGACGAUC
.....((..((......(((((((((.........((((((..((((((..((..(((((....)))))..)))))))).)))))))))))))))(((.....))).))..))....... (-40.87 = -39.85 +  -1.02)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:19:25 2006