Locus 938

Sequence ID 2R_DroMel_CAF1
Location 4,071,006 – 4,071,159
Length 153
Max. P 0.994876
window1658 window1659

overview

Window 8

Location 4,071,006 – 4,071,119
Length 113
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 91.28
Mean single sequence MFE -26.62
Consensus MFE -23.01
Energy contribution -23.17
Covariance contribution 0.16
Combinations/Pair 1.04
Mean z-score -1.26
Structure conservation index 0.86
SVM decision value 0.13
SVM RNA-class probability 0.599833
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4071006 113 + 20766785
UCGCUCAUAAAUUCAUGUCAAACAGGGCCAAGGUUGCCACUUUCC-------AUUUCGCACUUUCCAUAGGCGGAAGCCACAGGUGUGACAGCAACAAAUUAAGUUGCACAUAUAACUCA
...............(((((.((..(((.(((((....)))))..-------.((((((.((......)))))))))))....)).)))))(((((.......)))))............ ( -25.60)
>DroSec_CAF1 53684 113 + 1
GCGCUCAUAAAUUCAUGUCAAACAGGGCCAAGGUUGACACUUUCC-------AUUUCGCACUUUCCAUAGGCGGAAGCCACAGGUGUGACAGCAACAAAUUAAGUUGCACAUAUAACUCA
...............((((((.(........).))))))......-------...((((((((......(((....)))..))))))))..(((((.......)))))............ ( -25.70)
>DroSim_CAF1 61863 113 + 1
UCGCUCAUAAAUUCAUGUCAAACAGGGCCAAGGUUGCCACUUUCC-------GUUUCGCACUUUCCAUAGGCGGAAGCCACAGGUGUGACAGCAACAAAUUAAGUUGCACAUAUAACUCA
...............(((((.((..(((.(((((....)))))..-------.((((((.((......)))))))))))....)).)))))(((((.......)))))............ ( -25.50)
>DroEre_CAF1 55035 106 + 1
UCGCUCAUAAAUUCAUGUCAAACAGGGCCAAGGUUGCC--------------ACUUUCCACUUUCCCUAGGCGGAAGCCACAGGUGUGACAGCAACAAAUUAAGUUGCACAUAUAACUCA
...............(((((.((((((..(((((....--------------.......))))))))).(((....)))....)).)))))(((((.......)))))............ ( -26.50)
>DroYak_CAF1 57654 120 + 1
UUGCUCAUAAAUUCAUGUCAAACAGGGCCAAGGUUGCCACUUGCCACUUGCCACUUUCCACUUUCCAUUGGCGGAAGCCACAGGUGUGACAGCAACAAAUUAAGUUGCACAUAUAACUCA
...............(((((.....(((..((((.((.....)).)))))))......(((((.....((((....)))).))))))))))(((((.......)))))............ ( -29.80)
>consensus
UCGCUCAUAAAUUCAUGUCAAACAGGGCCAAGGUUGCCACUUUCC_______AUUUCGCACUUUCCAUAGGCGGAAGCCACAGGUGUGACAGCAACAAAUUAAGUUGCACAUAUAACUCA
..((((..................))))...(((((...................((((((((......(((....)))..))))))))..(((((.......))))).....))))).. (-23.01 = -23.17 +   0.16)

alignment

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secondary structure

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dotplot

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Window 9

Location 4,071,046 – 4,071,159
Length 113
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 90.07
Mean single sequence MFE -28.48
Consensus MFE -24.68
Energy contribution -25.08
Covariance contribution 0.40
Combinations/Pair 1.00
Mean z-score -2.21
Structure conservation index 0.87
SVM decision value 2.52
SVM RNA-class probability 0.994876
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4071046 113 + 20766785
UUUCC-------AUUUCGCACUUUCCAUAGGCGGAAGCCACAGGUGUGACAGCAACAAAUUAAGUUGCACAUAUAACUCACAACCCCAAGACGAUGCCUUCAAGGAAAUUGCCCCGACUA
.....-------.....(((.(((((...(((....)))...(((((((..(((((.......))))).........)))).)))..................))))).)))........ ( -27.30)
>DroSec_CAF1 53724 113 + 1
UUUCC-------AUUUCGCACUUUCCAUAGGCGGAAGCCACAGGUGUGACAGCAACAAAUUAAGUUGCACAUAUAACUCACAACCCCAAGUCGAUGCCUUCAAGGAAAUUGCCCCGACUA
.....-------.....(((.(((((...(((....)))..(((((((((.(((((.......))))).....(........)......))).))))))....))))).)))........ ( -28.30)
>DroSim_CAF1 61903 113 + 1
UUUCC-------GUUUCGCACUUUCCAUAGGCGGAAGCCACAGGUGUGACAGCAACAAAUUAAGUUGCACAUAUAACUCACAACCCCAAGACGAUGCCUUCAAGGAAAUUGCCCCGACUA
.....-------(((..(((.(((((...(((....)))...(((((((..(((((.......))))).........)))).)))..................))))).)))...))).. ( -28.20)
>DroEre_CAF1 55073 108 + 1
------------ACUUUCCACUUUCCCUAGGCGGAAGCCACAGGUGUGACAGCAACAAAUUAAGUUGCACAUAUAACUCACAACCCCAAGACGACGCCUUCAAGGAAAUUGCCCAGAAUA
------------.((...((.(((((...(((....)))..((((((....(((((.......)))))............(........)...))))))....))))).))...)).... ( -24.50)
>DroYak_CAF1 57694 119 + 1
UUGCCACUUGCCACUUUCCACUUUCCAUUGGCGGAAGCCACAGGUGUGACAGCAACAAAUUAAGUUGCACAUAUAACUCACAACCCCAAGACAGGGCCUUCAAGGAAAUUGCCCGG-CUA
..(((.((((........(((...((..((((....))))..)).)))...(((((.......)))))..................))))...((((.(((...)))...))))))-).. ( -34.10)
>consensus
UUUCC_______AUUUCGCACUUUCCAUAGGCGGAAGCCACAGGUGUGACAGCAACAAAUUAAGUUGCACAUAUAACUCACAACCCCAAGACGAUGCCUUCAAGGAAAUUGCCCCGACUA
.................(((.(((((...(((....)))...(((((((..(((((.......))))).........)))).)))..................))))).)))........ (-24.68 = -25.08 +   0.40)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:51:57 2006