Locus 5613

Sequence ID 3L_DroMel_CAF1
Location 15,397,920 – 15,398,014
Length 94
Max. P 0.983066
window8870 window8871

overview

Window 0

Location 15,397,920 – 15,398,014
Length 94
Sequences 6
Columns 100
Reading direction forward
Mean pairwise identity 77.65
Mean single sequence MFE -22.87
Consensus MFE -15.04
Energy contribution -16.35
Covariance contribution 1.31
Combinations/Pair 1.14
Mean z-score -2.62
Structure conservation index 0.66
SVM decision value 1.93
SVM RNA-class probability 0.983066
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15397920 94 + 23771897
AUUUCU------AGUUUUUAUUUUUUUUCAUUCUCUUUUCCCACUUUCGGUGUCUCGAUCAGAUACCAAAAGGAUGGCCUCGGAAAAAAUAGAGUGCAGA
......------................((((((.((((((..((((.(((((((.....))))))).))))((.....))))))))...)))))).... ( -20.20)
>DroSec_CAF1 126832 94 + 1
AUUUCU------AGUUUUUAUUUUUUUUCAUUCUCUUUUCCCACUUUCGGUGUCUCGAUCAGAUACCAAAAGGAUGGCCUCGGAAAAAAUAGAGUGCAGA
......------................((((((.((((((..((((.(((((((.....))))))).))))((.....))))))))...)))))).... ( -20.20)
>DroSim_CAF1 129098 94 + 1
NNNNNN------NNNNNNNNNNNNNNUUCAUUCUCUUUUCCCACUUUCGGUGUCUCGUUUAGAUACCGAAAGGAUGGCCUCGGAAAAAAUAGAGUGCAGA
......------................((((((.((((((..((((((((((((.....))))))))))))((.....))))))))...)))))).... ( -26.00)
>DroEre_CAF1 127651 90 + 1
UUCUCU------AGUUUUUAU---UUUUCAUUCUGUUUUCCCACUUUCGGUGUCUCGAUCAGAUACCA-AAGGAUGGCCUCGGAAAAAAUAGAGAGCAGA
...(((------..(((((((---((((...((((.....(((((((.(((((((.....))))))).-)))).)))...)))))))))))))))..))) ( -24.10)
>DroYak_CAF1 130837 90 + 1
UUUUCU------AGUUUUUAU---UUUUCAUUCUGUUUUCCCACUUUCGGUGUCUCGAUCAGAUACCA-AAGGAUGGCCUCGGAAAAAAUAGAGAGCAGA
...(((------..(((((((---((((...((((.....(((((((.(((((((.....))))))).-)))).)))...)))))))))))))))..))) ( -24.20)
>DroAna_CAF1 272354 89 + 1
UUUUUUUUUGACAUUUUUUUUUUUUGUCCGUUCUAUUUUUCCACUUUUGGUGUCUCAAUCAGAUACCAAACGGAUGGCUU-----------GAAUGGGGA
..........................(((((((......(((...((((((((((.....)))))))))).)))......-----------))))))).. ( -22.50)
>consensus
UUUUCU______AGUUUUUAU___UUUUCAUUCUCUUUUCCCACUUUCGGUGUCUCGAUCAGAUACCAAAAGGAUGGCCUCGGAAAAAAUAGAGUGCAGA
............................((((((.((((((.......(((((((.....)))))))...(((....))).))))))...)))))).... (-15.04 = -16.35 +   1.31)

alignment

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secondary structure

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dotplot

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Window 1

Location 15,397,920 – 15,398,014
Length 94
Sequences 6
Columns 100
Reading direction reverse
Mean pairwise identity 77.65
Mean single sequence MFE -18.50
Consensus MFE -12.70
Energy contribution -12.98
Covariance contribution 0.28
Combinations/Pair 1.15
Mean z-score -1.63
Structure conservation index 0.69
SVM decision value 0.95
SVM RNA-class probability 0.887257
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15397920 94 - 23771897
UCUGCACUCUAUUUUUUCCGAGGCCAUCCUUUUGGUAUCUGAUCGAGACACCGAAAGUGGGAAAAGAGAAUGAAAAAAAAUAAAAACU------AGAAAU
....((.(((.((((((((((.....))((((((((.(((.....))).)))))))).))))))))))).))................------...... ( -20.10)
>DroSec_CAF1 126832 94 - 1
UCUGCACUCUAUUUUUUCCGAGGCCAUCCUUUUGGUAUCUGAUCGAGACACCGAAAGUGGGAAAAGAGAAUGAAAAAAAAUAAAAACU------AGAAAU
....((.(((.((((((((((.....))((((((((.(((.....))).)))))))).))))))))))).))................------...... ( -20.10)
>DroSim_CAF1 129098 94 - 1
UCUGCACUCUAUUUUUUCCGAGGCCAUCCUUUCGGUAUCUAAACGAGACACCGAAAGUGGGAAAAGAGAAUGAANNNNNNNNNNNNNN------NNNNNN
....((.(((.((((((((((.....))((((((((.(((.....))).)))))))).))))))))))).))................------...... ( -22.10)
>DroEre_CAF1 127651 90 - 1
UCUGCUCUCUAUUUUUUCCGAGGCCAUCCUU-UGGUAUCUGAUCGAGACACCGAAAGUGGGAAAACAGAAUGAAAA---AUAAAAACU------AGAGAA
.....((((((.(((((......((((..((-((((.(((.....))).)))))).))))..........(....)---..))))).)------))))). ( -17.80)
>DroYak_CAF1 130837 90 - 1
UCUGCUCUCUAUUUUUUCCGAGGCCAUCCUU-UGGUAUCUGAUCGAGACACCGAAAGUGGGAAAACAGAAUGAAAA---AUAAAAACU------AGAAAA
((((.((((..........))))((((..((-((((.(((.....))).)))))).)))).....)))).......---.........------...... ( -16.30)
>DroAna_CAF1 272354 89 - 1
UCCCCAUUC-----------AAGCCAUCCGUUUGGUAUCUGAUUGAGACACCAAAAGUGGAAAAAUAGAACGGACAAAAAAAAAAAAUGUCAAAAAAAAA
...((.(((-----------...((((...((((((.(((.....))).)))))).)))).......))).))........................... ( -14.60)
>consensus
UCUGCACUCUAUUUUUUCCGAGGCCAUCCUUUUGGUAUCUGAUCGAGACACCGAAAGUGGGAAAAGAGAAUGAAAA___AUAAAAACU______AGAAAA
(((...(((..........))).(((..((((((((.(((.....))).)))))))))))......)))............................... (-12.70 = -12.98 +   0.28)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:54:39 2006