Locus 4772

Sequence ID X_DroMel_CAF1
Location 12,402,664 – 12,402,775
Length 111
Max. P 0.933805
window7812 window7813

overview

Window 2

Location 12,402,664 – 12,402,775
Length 111
Sequences 4
Columns 113
Reading direction forward
Mean pairwise identity 75.04
Mean single sequence MFE -28.31
Consensus MFE -15.16
Energy contribution -14.85
Covariance contribution -0.31
Combinations/Pair 1.31
Mean z-score -2.27
Structure conservation index 0.54
SVM decision value 1.23
SVM RNA-class probability 0.933805
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 12402664 111 + 22224390
UCGGUGGUAAAUGCAUAGAAAAUUGAGAAUGAAUUUACCAAAACGAUAAGCCAAGAGCUUUCUUUGUGGGCAAAUCGCAAAGAACACCACCA--AUAGCGGGCGCUGUGGUAU
(((.((((((((.(((............))).))))))))...)))...((((..(((.((((((((((.....)))))))))).....((.--.....))..))).)))).. ( -31.30)
>DroSec_CAF1 5347 111 + 1
UCGGUGGUAAAUGCAUAGAAAAUUGAGAAUGAAUUUACCAUAACAAUAUGCUGAAAGCUUCCAUUAUGGACAAAUAGCAAAGAACGCCACCA--AUAGCGGGCGCUGUGGUAU
..((((((((((.(((............))).))))))).........(((((......(((.....)))....)))))......)))((((--.((((....)))))))).. ( -25.80)
>DroEre_CAF1 5780 102 + 1
UCGGUGGUAAAUGCA--AAAAAU-----UUAGAUU----AAAUAAAUAAGCUAAAAGCUUCUUUUAUGGACAAUUUGCUAAGAACUCCACCACCACAGCGGGUGCUGUGGUAU
..(((((.....(((--((..((-----(((....----...)))))((((.....)))).............)))))........)))))((((((((....)))))))).. ( -28.92)
>DroYak_CAF1 5650 100 + 1
UCGGUGGUAAAUUGA--GA---------UUAGAUUCUCAAAAAAAAUAAGCUGGAAGCUUCCCCUAUGAACAAAUCGCUUGGAACGCCACCA--AUAGCGGGCGCUGUGGUAU
..((((((...((((--((---------......))))))......(((((.(((....))).....((.....)))))))....)))))).--(((((....)))))..... ( -27.20)
>consensus
UCGGUGGUAAAUGCA__GAAAAU_____AUAAAUUUACCAAAAAAAUAAGCUAAAAGCUUCCUUUAUGGACAAAUCGCAAAGAACGCCACCA__AUAGCGGGCGCUGUGGUAU
..((((((.........................................((.....)).(((.....)))...............))))))...(((((....)))))..... (-15.16 = -14.85 +  -0.31)

alignment

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secondary structure

Postscript

dotplot

Postscript

Window 3

Location 12,402,664 – 12,402,775
Length 111
Sequences 4
Columns 113
Reading direction reverse
Mean pairwise identity 75.04
Mean single sequence MFE -25.35
Consensus MFE -13.48
Energy contribution -13.85
Covariance contribution 0.37
Combinations/Pair 1.30
Mean z-score -1.86
Structure conservation index 0.53
SVM decision value 0.02
SVM RNA-class probability 0.544518
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 12402664 111 - 22224390
AUACCACAGCGCCCGCUAU--UGGUGGUGUUCUUUGCGAUUUGCCCACAAAGAAAGCUCUUGGCUUAUCGUUUUGGUAAAUUCAUUCUCAAUUUUCUAUGCAUUUACCACCGA
((((((((((....)))..--..))))))).....(((((..(((....((((....)))))))..)))))..((((((((.(((............))).)))))))).... ( -28.60)
>DroSec_CAF1 5347 111 - 1
AUACCACAGCGCCCGCUAU--UGGUGGCGUUCUUUGCUAUUUGUCCAUAAUGGAAGCUUUCAGCAUAUUGUUAUGGUAAAUUCAUUCUCAAUUUUCUAUGCAUUUACCACCGA
.......((((((.((...--..))))))))...((((.....(((.....))).......))))........((((((((.(((............))).)))))))).... ( -22.50)
>DroEre_CAF1 5780 102 - 1
AUACCACAGCACCCGCUGUGGUGGUGGAGUUCUUAGCAAAUUGUCCAUAAAAGAAGCUUUUAGCUUAUUUAUUU----AAUCUAA-----AUUUUU--UGCAUUUACCACCGA
..((((((((....))))))))(((((..(((((................)))))((.(((((.(((......)----)).))))-----).....--.)).....))))).. ( -26.89)
>DroYak_CAF1 5650 100 - 1
AUACCACAGCGCCCGCUAU--UGGUGGCGUUCCAAGCGAUUUGUUCAUAGGGGAAGCUUCCAGCUUAUUUUUUUUGAGAAUCUAA---------UC--UCAAUUUACCACCGA
.......(((....))).(--((((((......((((((.....)).....(((....))).)))).......((((((......---------))--))))....))))))) ( -23.40)
>consensus
AUACCACAGCGCCCGCUAU__UGGUGGCGUUCUUAGCGAUUUGUCCAUAAAGGAAGCUUUCAGCUUAUUGUUUUGGUAAAUCCAA_____AUUUUC__UGCAUUUACCACCGA
.......(((....)))....((((((.((.....)).......(((.(((((((((.....)))).))))).)))..............................)))))). (-13.48 = -13.85 +   0.37)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:32:48 2006