Locus 1484

Sequence ID 3L_DroMel_CAF1
Location 4,325,879 – 4,326,064
Length 185
Max. P 0.860451
window2310 window2311

overview

Window 0

Location 4,325,879 – 4,325,996
Length 117
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 76.06
Mean single sequence MFE -28.52
Consensus MFE -10.94
Energy contribution -12.24
Covariance contribution 1.30
Combinations/Pair 1.00
Mean z-score -2.05
Structure conservation index 0.38
SVM decision value 0.83
SVM RNA-class probability 0.860451
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 4325879 117 - 23771897
GUAACAAAAUCGU---UGGUAGCAAUACCAAUAGCAGUAGCAAUGGCAACCCAAAGCCAAAAGCCUCAACCCGUUGGUUGGUUGUUGCAGUUGGUGCUGCACCUGUUACCCAGUUUUAUU
((((((.....((---(((((....))))))).((((((.((((.(((((....((((((.(((........)))..))))))))))).)))).))))))...))))))........... ( -41.70)
>DroSec_CAF1 12560 90 - 1
GUAACAAAAUCGU---UGGUUGCAAUACCAAUAGCAGUAGCAAUGGCAACCCAAAGCCAAAAG------------------------CAGUUGGU---GCACCUGUUACCCAGUUUUAUU
((((((.....((---((((......)))))).(((.((((..((((........))))....------------------------..)))).)---))...))))))........... ( -22.70)
>DroSim_CAF1 11192 93 - 1
GUAACAAAAUCGUUGUUGGUUGCAAUACCAAUAGCAGUAGCAAUGGCAACCCAAAGCCAAAAG------------------------CAGUUGGU---GCACCUGUUACCCAGUUUUAUU
((((((.....(((((((((......))))))))).(((.(((((((........))))....------------------------...))).)---))...))))))........... ( -25.21)
>DroEre_CAF1 12428 98 - 1
GUAACAAAAUCGU---UGGUAGGAAAAGCAAUAGCAA------------CCCAAAGCCAAAAGCCCCAACCCGCUG----GUUGUUGCAGUUGGU---GCACCUGUUACCCAGUUUUAUU
((((((......(---((((.((....((....))..------------.))...)))))..((.(((((..((..----......)).))))).---))...))))))........... ( -22.50)
>DroYak_CAF1 11558 112 - 1
GUAACUAAAUCGUUGUUGGUGGCAACAGCAAUAGCAA-AGCAAAGCAAAGCCAAAGCCAAAAGCCCCAACCCGCUG----GCUGUUGCAGUUGGU---GCACCUGUUACCCAGUUUUAUU
(((((......(((((((.((....)).)))))))..-.(((.(((...((...(((((...((........))))----)))...)).)))..)---))....)))))........... ( -30.50)
>consensus
GUAACAAAAUCGU___UGGUAGCAAUACCAAUAGCAGUAGCAAUGGCAACCCAAAGCCAAAAGCC_CAACCCG_UG____G_UGUUGCAGUUGGU___GCACCUGUUACCCAGUUUUAUU
((((((.....((...((((......))))...))....................(((((..((..((((..........))))..))..)))))........))))))........... (-10.94 = -12.24 +   1.30)

alignment

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secondary structure

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dotplot

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Window 1

Location 4,325,959 – 4,326,064
Length 105
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 68.14
Mean single sequence MFE -21.78
Consensus MFE -8.62
Energy contribution -9.30
Covariance contribution 0.68
Combinations/Pair 1.18
Mean z-score -1.85
Structure conservation index 0.40
SVM decision value 0.48
SVM RNA-class probability 0.752185
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 4325959 105 - 23771897
GCCACUGUGAAUAUGGCUUCCAAAACCGCAGUACAG--AAACAAAACACAAA---AAAAA---AAAC----GCAACGGUGGUAACAAAAUCGU---UGGUAGCAAUACCAAUAGCAGUAG
((((((((.....(((...))).....((.......--..............---.....---....----)).)))))))).........((---(((((....)))))))........ ( -20.11)
>DroSec_CAF1 12613 97 - 1
GCCGCUGUGAAUAUGGCUUCCAAAACCGCAGCUCAG--AAACAAAACACG--------------AAC----GCGACGGUGGUAACAAAAUCGU---UGGUUGCAAUACCAAUAGCAGUAG
((.(((((...(((.((..((((.((((..((....--............--------------...----))..))))(((......))).)---)))..)).)))...))))).)).. ( -20.31)
>DroSim_CAF1 11245 100 - 1
GCCGCUGUGAAUAUGGCUUCCAAAACCGCAGCACAG--AAACAAAACACG--------------AAC----GCGACGGUGGUAACAAAAUCGUUGUUGGUUGCAAUACCAAUAGCAGUAG
(((((((((....(((...)))....))))))....--..........((--------------...----.))..)))............(((((((((......)))))))))..... ( -24.70)
>DroYak_CAF1 11631 96 - 1
GCCGCUGUGAGUAUGGCUUCCAAAACCGCAGCACUG--AAACAAAACAAAAU---AAAUA------------------UGGUAACUAAAUCGUUGUUGGUGGCAACAGCAAUAGCAA-AG
(((((((((.((.(((...)))..))))))))..((--........))....---.....------------------.))).........(((((((.((....)).)))))))..-.. ( -25.00)
>DroAna_CAF1 12658 104 - 1
UUCGUUG--CCUAUGGCUUCCAAAACCACAAAACACUAAAAAAAAAGGCUAAUAAACAAAGCCAAACAAAACAAAAAGUGGUAACUAAAUCGU---AGCUGCCACUGCC-----------
.......--.....(((.............................((((.........)))).............(((((((.(((.....)---)).))))))))))----------- ( -18.80)
>consensus
GCCGCUGUGAAUAUGGCUUCCAAAACCGCAGCACAG__AAACAAAACACAA____A_A_A____AAC____GCAACGGUGGUAACAAAAUCGU___UGGUGGCAAUACCAAUAGCAGUAG
...((((((....(((...)))....))))))..............................................(((((.....(((......))).....))))).......... ( -8.62 =  -9.30 +   0.68)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:08:51 2006