Locus 6909

Sequence ID 3L_DroMel_CAF1
Location 18,646,205 – 18,646,340
Length 135
Max. P 0.993063
window11203 window11204

overview

Window 3

Location 18,646,205 – 18,646,301
Length 96
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 70.49
Mean single sequence MFE -28.46
Consensus MFE -10.78
Energy contribution -11.58
Covariance contribution 0.80
Combinations/Pair 1.00
Mean z-score -2.41
Structure conservation index 0.38
SVM decision value 2.37
SVM RNA-class probability 0.993063
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 18646205 96 - 23771897
UCAGUCACCAAUGUAUUCUAAACUAAUGGGAUUUUGGUGAUCGACCCCUACUCUUCUUUGAGAU---------------------CAUUUGAAUAGGACAGC---AGUUAGUGGCAAUAU
((.((((((((...((((((......)))))).)))))))).))..(((((((......))).(---------------------(....)).))))...((---........))..... ( -21.70)
>DroSec_CAF1 7932 120 - 1
UCAGUCACCAAAGUAUUCUAAACUAAUGGGAUUUUGGUGAUCGACUCCUGCUCUUAUUUUAGAUGAUUACUAGGUGUCUAGUAACCAUUUGAAUAGGAAUGAAGCAGUUAGUGGUAAUAU
...(((((((((..((((((......)))))))))))))))(.(((.((((((((((((.(((((.(((((((....))))))).))))))))))))).....))))..))).)...... ( -35.80)
>DroSim_CAF1 7937 117 - 1
UCAGUCACCAAUGUAUUCUAAACUAAUGGGAUUUUGGUGAUCAACUAGAGCUCUUAUUUCAGAUGAUUACUGGUUUUCUAGUAACCAUUUGAAUAGGAAAGA---AGUUAGUGGCAAUAU
...((((((((...((((((......)))))).))))))))..(((((..((((((((.((((((.(((((((....))))))).)))))))))))))..).---..)))))........ ( -34.70)
>DroEre_CAF1 7864 102 - 1
UCAGUCACCAAUGCUUACUAAACUAAUGGGACUUUGGUGAUUGACCGCUGUUCUUAC------------------CACUAGUGACCAUUUGCAUAAAAUAGAAGCAGUUACUAGAAGAUU
(((((((((((..((((.........))))...))))))))))).............------------------..((((((((....(((...........)))))))))))...... ( -25.70)
>DroYak_CAF1 8341 115 - 1
UCAGUCACCAAUGUUUUCUAAACAAAUGGCACUUUGGUGAUUAACCGCUGGUCUUAUUUCGGAUAAAAAU-----UACUAGUAACCUUUCGUAUAAGAUAAAAGCAGUUAAUGGGAAUCU
...((((((((.((...(((......))).)).))))))))((((.(((.(((((((..((((.......-----............)))).)))))))...))).)))).......... ( -24.41)
>consensus
UCAGUCACCAAUGUAUUCUAAACUAAUGGGAUUUUGGUGAUCGACCCCUGCUCUUAUUUCAGAU_A__A______UACUAGUAACCAUUUGAAUAGGAAAGAAGCAGUUAGUGGCAAUAU
...((((((((...((((((......)))))).))))))))............................................................................... (-10.78 = -11.58 +   0.80)

alignment

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secondary structure

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dotplot

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Window 4

Location 18,646,237 – 18,646,340
Length 103
Sequences 5
Columns 119
Reading direction reverse
Mean pairwise identity 77.25
Mean single sequence MFE -22.98
Consensus MFE -13.48
Energy contribution -14.68
Covariance contribution 1.20
Combinations/Pair 1.00
Mean z-score -1.79
Structure conservation index 0.59
SVM decision value 0.39
SVM RNA-class probability 0.718840
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 18646237 103 - 23771897
UUUUCGUAGUUUAUUCUGCCAUAAAAGUACACCUUUAAAUCAGUCACCAAUGUAUUCUAAACUAAUGGGAUUUUGGUGAUCGACCCCUACUCUUCUUUGAGAU----------------
.....((((......))))....................((.((((((((...((((((......)))))).)))))))).))......(((......)))..---------------- ( -20.70)
>DroSec_CAF1 7972 119 - 1
AUUUCGUAGCUUAUUCUGCCAUAAAAGAACACCUUUAAAUCAGUCACCAAAGUAUUCUAAACUAAUGGGAUUUUGGUGAUCGACUCCUGCUCUUAUUUUAGAUGAUUACUAGGUGUCUA
.....((((......))))......(((.(((((...((((((((((((((..((((((......)))))))))))))))..........(((......))))))))...)))))))). ( -28.10)
>DroSim_CAF1 7974 115 - 1
----CGUAGUUUAUUCUGCCAUAAAAGUACACCUUUAAAUCAGUCACCAAUGUAUUCUAAACUAAUGGGAUUUUGGUGAUCAACUAGAGCUCUUAUUUCAGAUGAUUACUGGUUUUCUA
----.((((((...((((..((((.((.....(((((.....((((((((...((((((......)))))).))))))))....))))))).))))..)))).)))))).......... ( -24.60)
>DroEre_CAF1 7904 101 - 1
UGUUCGUAGUUUAUUCUGCCAUAAAAGUACACUUUUAAAUCAGUCACCAAUGCUUACUAAACUAAUGGGACUUUGGUGAUUGACCGCUGUUCUUAC------------------CACUA
.....((((......))))..((((((....))))))..(((((((((((..((((.........))))...))))))))))).............------------------..... ( -21.70)
>DroYak_CAF1 8381 114 - 1
UUUUCGUAGUUUAUUCUGCCAUAAAAGUACACUCUUAAAUCAGUCACCAAUGUUUUCUAAACAAAUGGCACUUUGGUGAUUAACCGCUGGUCUUAUUUCGGAUAAAAAU-----UACUA
.....(((((((..((((..((((.................(((((((((.((...(((......))).)).))))))))).(((...))).))))..))))...))))-----))).. ( -19.80)
>consensus
UUUUCGUAGUUUAUUCUGCCAUAAAAGUACACCUUUAAAUCAGUCACCAAUGUAUUCUAAACUAAUGGGAUUUUGGUGAUCGACCCCUGCUCUUAUUUCAGAU_A__A______UACUA
.....((((......))))....................((.((((((((...((((((......)))))).)))))))).)).................................... (-13.48 = -14.68 +   1.20)

alignment

Postscript

secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:32:49 2006