Locus 6605

Sequence ID 3L_DroMel_CAF1
Location 17,550,806 – 17,550,899
Length 93
Max. P 0.997583
window10751 window10752

overview

Window 1

Location 17,550,806 – 17,550,899
Length 93
Sequences 5
Columns 115
Reading direction forward
Mean pairwise identity 76.07
Mean single sequence MFE -23.78
Consensus MFE -9.42
Energy contribution -10.06
Covariance contribution 0.64
Combinations/Pair 1.08
Mean z-score -2.80
Structure conservation index 0.40
SVM decision value 2.89
SVM RNA-class probability 0.997583
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17550806 93 + 23771897
GAAAAGUGCACAAAAUAGUGCAACUGCAAUCAAGAAUUGAGGUAGGUUGCAAUCAAAACAU------------GUGAUAUAUUGUGC--------AUCAAAAUGUUG--UAGUUU
.....((((((((.....(((((((....(((.....)))....)))))))((((......------------.))))...))))))--------))..........--...... ( -21.60)
>DroSec_CAF1 36386 93 + 1
GAAAAAUGCACAAAAUAGUGCAACUGCAAUCAAGAAUUGAGGUAGGUUGCAUUCAAAACAU------------GUGAUAUAUUGUGC--------AUGAAAAUGUUG--UAGUUG
.....((((((((.(((((((((((....(((.....)))....))))))))(((......------------.)))))).))))))--------))..........--...... ( -22.10)
>DroSim_CAF1 39874 93 + 1
GAAAAAUGCACAAAAUAGUGCAACUGCAAUCAAGAAUUGAGGUAGGUUGCAUUCAAAACAA------------GUGAUAUAUUGUGC--------AUCAAAAUGUUG--UAGUCG
.....((((((((.(((((((((((....(((.....)))....))))))))(((......------------.)))))).))))))--------))..........--...... ( -21.50)
>DroEre_CAF1 36283 114 + 1
AAGAAACACACUAAAUAGUGGCACUGCAAUCACGAAUUGAGGCAGGUUGUAGGCAAAACAAAUUAAAUUGCUUGCGACAGCCUGUGAUAUCGCACAU-AAAAUGUAGUUUAGUUA
.........(((((((...(((.((((..(((.....))).))))(((((((((((...........))))))))))).)))((((....))))...-........))))))).. ( -31.30)
>DroYak_CAF1 40015 104 + 1
AAAAAAAACACGAAAUAGUGCAACUGCAAUCAAGAAUUGAGGUAGGUUGCAAUCAAAACAAAUUAAGUUGCCUGUGAUAUGCUGUAA--------AU-AAAGUGUUG--CAGUUG
........(((......)))((((((((((.....(((..((((.((..((.....(((.......)))...))..)).))))...)--------))-.....))))--)))))) ( -22.40)
>consensus
GAAAAAUGCACAAAAUAGUGCAACUGCAAUCAAGAAUUGAGGUAGGUUGCAAUCAAAACAA____________GUGAUAUAUUGUGC________AU_AAAAUGUUG__UAGUUG
......(((((......)))))..(((((((.............)))))))................................................................ ( -9.42 = -10.06 +   0.64)

alignment

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secondary structure

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dotplot

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Window 2

Location 17,550,806 – 17,550,899
Length 93
Sequences 5
Columns 115
Reading direction reverse
Mean pairwise identity 76.07
Mean single sequence MFE -18.66
Consensus MFE -7.14
Energy contribution -8.14
Covariance contribution 1.00
Combinations/Pair 1.15
Mean z-score -2.43
Structure conservation index 0.38
SVM decision value 1.96
SVM RNA-class probability 0.983903
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17550806 93 - 23771897
AAACUA--CAACAUUUUGAU--------GCACAAUAUAUCAC------------AUGUUUUGAUUGCAACCUACCUCAAUUCUUGAUUGCAGUUGCACUAUUUUGUGCACUUUUC
......--...........(--------((((((.(((...(------------(.....))..((((((.....(((.....))).....)))))).))).)))))))...... ( -15.70)
>DroSec_CAF1 36386 93 - 1
CAACUA--CAACAUUUUCAU--------GCACAAUAUAUCAC------------AUGUUUUGAAUGCAACCUACCUCAAUUCUUGAUUGCAGUUGCACUAUUUUGUGCAUUUUUC
......--..........((--------((((((.((((((.------------......))).((((((.....(((.....))).....)))))).))).))))))))..... ( -16.70)
>DroSim_CAF1 39874 93 - 1
CGACUA--CAACAUUUUGAU--------GCACAAUAUAUCAC------------UUGUUUUGAAUGCAACCUACCUCAAUUCUUGAUUGCAGUUGCACUAUUUUGUGCAUUUUUC
......--.........(((--------((((((.((((((.------------......))).((((((.....(((.....))).....)))))).))).))))))))).... ( -17.90)
>DroEre_CAF1 36283 114 - 1
UAACUAAACUACAUUUU-AUGUGCGAUAUCACAGGCUGUCGCAAGCAAUUUAAUUUGUUUUGCCUACAACCUGCCUCAAUUCGUGAUUGCAGUGCCACUAUUUAGUGUGUUUCUU
.....((((.(((((..-(((((((..((((((((((((.((((((((......))).)))))..)))....))))......))))).....)).))).))..)))))))))... ( -22.00)
>DroYak_CAF1 40015 104 - 1
CAACUG--CAACACUUU-AU--------UUACAGCAUAUCACAGGCAACUUAAUUUGUUUUGAUUGCAACCUACCUCAAUUCUUGAUUGCAGUUGCACUAUUUCGUGUUUUUUUU
((((((--(((......-..--------.....(((.((((.((((((......)))))))))))))........(((.....))))))))))))(((......)))........ ( -21.00)
>consensus
CAACUA__CAACAUUUU_AU________GCACAAUAUAUCAC____________UUGUUUUGAAUGCAACCUACCUCAAUUCUUGAUUGCAGUUGCACUAUUUUGUGCAUUUUUC
.............................................................((((((((.(.............).))))))))((((......))))....... ( -7.14 =  -8.14 +   1.00)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:25:30 2006