Locus 7504

Sequence ID 2L_DroMel_CAF1
Location 20,809,241 – 20,809,382
Length 141
Max. P 0.929534
window12060 window12061

overview

Window 0

Location 20,809,241 – 20,809,345
Length 104
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 79.91
Mean single sequence MFE -28.67
Consensus MFE -23.05
Energy contribution -23.36
Covariance contribution 0.31
Combinations/Pair 1.19
Mean z-score -1.58
Structure conservation index 0.80
SVM decision value 0.39
SVM RNA-class probability 0.717348
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 20809241 104 + 22407834
ACAGAGGACGCACUGUACUUGCACAUAUGCAAGUGCACAUCAACUCCCACGCUCACCAACUCUACUUGUCUCU--------------CUCUCUUCUAGAGCUCGUGGUGGAGCUCACU--
...(((.......((((((((((....))))))))))......)))....((((((((.(((((.........--------------........)))))....)))).)))).....-- ( -28.95)
>DroSim_CAF1 36629 108 + 1
ACAGAGGACGCACUGUACUUGCACAUAUGCAAGUGUUCAUCAACUCCCACGCUCGCCAACUCUAUUUGUCUCU------C----UCUCUCUCUUCUGGAGCUCGUGGUGGAGCUCACU--
.(((((((.((.....(((((((....)))))))(((....)))......))..(.(((......))).)...------.----......)))))))((((((......))))))...-- ( -27.00)
>DroEre_CAF1 34763 107 + 1
ACAGAGGCCGCACUGUGCUUGCACAUAUGCAAGUGAUUAUCAACUCCCACGCUCGCCAACUCUACU-------------GUCUCUCUCUCUUUUGCGGAGCUGGUGGUGGAGCUCACUCC
...(((.((((.....(((((((....)))))))...................(((((.(((..(.-------------...............)..))).)))))))))..)))..... ( -28.59)
>DroYak_CAF1 33205 117 + 1
ACUGAGGACGGACUGUGCUUGCACAUAUGCAAGUGUUCAUAAACUCCCACG-UCGCCAACUCUACUUCUCUCUUCAUCUCUAUCUCUCUCUUUUGUGGAGCUUGUGGCGGAGCUCAUU--
..((((...((((...(((((((....))))))))))).....((((...(-((((...((((((.............................))))))...)))))))))))))..-- ( -30.15)
>consensus
ACAGAGGACGCACUGUACUUGCACAUAUGCAAGUGUUCAUCAACUCCCACGCUCGCCAACUCUACUUGUCUCU______C____UCUCUCUCUUCUGGAGCUCGUGGUGGAGCUCACU__
...(((........(((((((((....))))))))).......)))....((((((((.((((((.............................))))))....)))).))))....... (-23.05 = -23.36 +   0.31)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 1

Location 20,809,281 – 20,809,382
Length 101
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 78.48
Mean single sequence MFE -27.29
Consensus MFE -16.41
Energy contribution -16.47
Covariance contribution 0.06
Combinations/Pair 1.23
Mean z-score -2.25
Structure conservation index 0.60
SVM decision value 1.20
SVM RNA-class probability 0.929534
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 20809281 101 + 22407834
CAACUCCCACGCUCACCAACUCUACUUGUCUCU--------------CUCUCUUCUAGAGCUCGUGGUGGAGCUCACU-----CCCGCUCCCGCUCUCGUGCUCGUUAUAUUCAUAGAGC
..........((((..(((......))).....--------------..........((((.((.((((((((.....-----...))).)))))..)).))))............)))) ( -23.80)
>DroSim_CAF1 36669 105 + 1
CAACUCCCACGCUCGCCAACUCUAUUUGUCUCU------C----UCUCUCUCUUCUGGAGCUCGUGGUGGAGCUCACU-----CCCGCUACCGCUCUCGCGCUCGUUGUAUUCAUAGAGC
..........(((((.(((......))).)...------.----.............((((.((.((((((((.....-----...))).)))))..)).))))............)))) ( -23.50)
>DroEre_CAF1 34803 107 + 1
CAACUCCCACGCUCGCCAACUCUACU-------------GUCUCUCUCUCUUUUGCGGAGCUGGUGGUGGAGCUCACUCCGCUCCCGCUCCCGCUCUCGCGCUCGCUGUAUUCGUAGAGC
...................((((((.-------------...............(((((((.((..((((((....))))))..))))).))))....((....)).......)))))). ( -34.30)
>DroYak_CAF1 33245 112 + 1
AAACUCCCACG-UCGCCAACUCUACUUCUCUCUUCAUCUCUAUCUCUCUCUUUUGUGGAGCUUGUGGCGGAGCUCAUU-----CCCGCUC-CGCUCUCGCGC-CGUUUUAUUCAUAGAGC
........(((-.((((((((((((.............................)))))).))).((((((((.....-----...))))-))))...))).-))).............. ( -27.55)
>consensus
CAACUCCCACGCUCGCCAACUCUACUUGUCUCU______C____UCUCUCUCUUCUGGAGCUCGUGGUGGAGCUCACU_____CCCGCUCCCGCUCUCGCGCUCGUUGUAUUCAUAGAGC
...(((....((((((((.((((((.............................))))))....)))).)))).............((...(((....)))...))..........))). (-16.41 = -16.47 +   0.06)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:38:26 2006