Locus 2469

Sequence ID 2R_DroMel_CAF1
Location 8,861,984 – 8,862,132
Length 148
Max. P 0.851679
window4077 window4078

overview

Window 7

Location 8,861,984 – 8,862,103
Length 119
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 75.58
Mean single sequence MFE -25.82
Consensus MFE -12.46
Energy contribution -12.70
Covariance contribution 0.24
Combinations/Pair 1.06
Mean z-score -1.99
Structure conservation index 0.48
SVM decision value 0.79
SVM RNA-class probability 0.851679
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 8861984 119 - 20766785
GGAAA-AAGGGCGCUGGAAAAACAAGGUCGGACAAUUAGUCAGGUAAUUGACUGAUUAGAAAGCAAUGCCAGAAAUAAAAUGGCUAAUGUUUGAUGUAAUGUUUAAUUUUCAUUUAACAG
(((((-..(((((.((......))(.(((((((((((((((((....))))))))))..........((((.........))))....))))))).)..)))))..)))))......... ( -25.00)
>DroSec_CAF1 106866 99 - 1
GGAA--AAGGGCGCUGGAAAAACAAGGUCGGACAAUUAGUCAGGUAAUUGACUGAUUAGAAAGCAAUGCCACAAAUAAAA-------------------UGUUUGAUUUUCAUUUAAGCG
....--.....((((..(((...((((((((((((((((((((....)))))))))).....((...))...........-------------------.))))))))))..))).)))) ( -20.80)
>DroSim_CAF1 106777 99 - 1
GGAA--AAGGGCGCUGGAAAAACAAGGUCGGACAAUUAGUCAGGUAAUUGACUGAUUAGAAAGCAAUGCCACAAAUGAAA-------------------UGUUUAAUUUCCAUUUAAUCG
((((--(..((((.((.........(......)((((((((((....))))))))))......)).))))..((((....-------------------.))))..)))))......... ( -19.50)
>DroEre_CAF1 108533 105 - 1
----------GGGUUGGAAAAACCAGCUCGG-CAAUUAGUCAGGUAAUUGACUGAUUGCAAAGCAAUGCCACAAAUUAAAGUGCCAAUGUUUGCUGUAAUAGUUAAUUCUCACUUC----
----------(((((((.....))))))).(-(((((((((((....)))))))))))).(((((.((.(((........))).)).)))))........................---- ( -32.30)
>DroYak_CAF1 110969 119 - 1
GGAAAAAGGGGCGCUGGAAAAACAAGCUCGG-CAAUUAGUCAGGUAAUUGACUGAUUAGAAAGCAAUGCCACAAAUAAAAGUGCCAAUGUUUACAGCCAUGGUUAAUUGUCACUCUAGUG
...........(((((((...(((((((.((-(((((((((((....)))))))))).(.(((((.((.(((........))).)).))))).).)))..)))...))))...))))))) ( -31.50)
>consensus
GGAA__AAGGGCGCUGGAAAAACAAGGUCGGACAAUUAGUCAGGUAAUUGACUGAUUAGAAAGCAAUGCCACAAAUAAAA__GC_AAUGUUU___G__AUGUUUAAUUUUCAUUUAAGCG
.........((((((((..........)))).)((((((((((....))))))))))..........))).................................................. (-12.46 = -12.70 +   0.24)

alignment

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secondary structure

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dotplot

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Window 8

Location 8,862,024 – 8,862,132
Length 108
Sequences 5
Columns 117
Reading direction reverse
Mean pairwise identity 82.51
Mean single sequence MFE -26.96
Consensus MFE -13.58
Energy contribution -13.94
Covariance contribution 0.36
Combinations/Pair 1.05
Mean z-score -2.46
Structure conservation index 0.50
SVM decision value 0.46
SVM RNA-class probability 0.744476
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 8862024 108 - 20766785
-----GCAAGCUAGUUUCCCGUGAAAAGCGGGUU---GGAAA-AAGGGCGCUGGAAAAACAAGGUCGGACAAUUAGUCAGGUAAUUGACUGAUUAGAAAGCAAUGCCAGAAAUAAAA
-----(((.(((.(((((((((.....)))))..---.....-...(((..((......))..)))))))((((((((((....))))))))))....)))..)))........... ( -25.80)
>DroSec_CAF1 106887 106 - 1
-----GCAAGCAAGUCGCCCGGAA-AAGGGGGUU---GGAA--AAGGGCGCUGGAAAAACAAGGUCGGACAAUUAGUCAGGUAAUUGACUGAUUAGAAAGCAAUGCCACAAAUAAAA
-----(((.((..(((((((....-....)))).---....--...(((..((......))..))).)))((((((((((....)))))))))).....))..)))........... ( -25.10)
>DroSim_CAF1 106798 107 - 1
-----GCAAGCAAGUUCCGCGGAAAAAGGGGGUU---GGAA--AAGGGCGCUGGAAAAACAAGGUCGGACAAUUAGUCAGGUAAUUGACUGAUUAGAAAGCAAUGCCACAAAUGAAA
-----.....(((.((((.........)))).))---)...--...((((.((.........(......)((((((((((....))))))))))......)).)))).......... ( -21.50)
>DroEre_CAF1 108569 95 - 1
GCAAUGCAAGCAAGUG-CUCGGAA-AAG-------------------GGGUUGGAAAAACCAGCUCGG-CAAUUAGUCAGGUAAUUGACUGAUUGCAAAGCAAUGCCACAAAUUAAA
(((.(((.(((....)-)).....-...-------------------(((((((.....))))))).(-(((((((((((....))))))))))))...))).)))........... ( -34.10)
>DroYak_CAF1 111009 110 - 1
-----GCAAGCAAGUCCCUCGGAA-AAGCGGGCUGUCGGAAAAAGGGGCGCUGGAAAAACAAGCUCGG-CAAUUAGUCAGGUAAUUGACUGAUUAGAAAGCAAUGCCACAAAUAAAA
-----(((.((..(((((((((..-.((....)).))).....))))))(((((..........))))-)((((((((((....)))))))))).....))..)))........... ( -28.30)
>consensus
_____GCAAGCAAGUCCCCCGGAA_AAGCGGGUU___GGAA__AAGGGCGCUGGAAAAACAAGGUCGGACAAUUAGUCAGGUAAUUGACUGAUUAGAAAGCAAUGCCACAAAUAAAA
.....(((.((...................................(((..((......))..)))....((((((((((....)))))))))).....))..)))........... (-13.58 = -13.94 +   0.36)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:30:50 2006