Locus 2125

Sequence ID	2L_DroMel_CAF1
Location	5,732,486 – 5,732,577
Length	91
Max. P	0.990230

overview

Window 3

Location	5,732,486 – 5,732,577
Length	91
Sequences	5
Columns	91
Reading direction	forward
Mean pairwise identity	95.49
Mean single sequence MFE	-19.82
Consensus MFE	-15.98
Energy contribution	-15.86
Covariance contribution	-0.12
Combinations/Pair	1.13
Mean z-score	-1.96
Structure conservation index	0.81
SVM decision value	0.90
SVM RNA-class probability	0.876647
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 5732486 91 + 22407834
UCAAUGGUCGAGAAAACUUUUCAGUUGCCUACUUUCGGGCACCUUGACCUACUCAUGCAACUUUGUUUGUUGUCAAAAAAGUUGUUUUUAU
.....(((((((..((((....))))((((......))))..))))))).......((((((((.((((....))))))))))))...... ( -24.60)
>DroSec_CAF1 8385 91 + 1
UCAACGCUCGAGAAAACUUUUCAGUUGCCUACUUUCGGGCACCUUGACCUACUCAUGCAACUUUGUUUGUUGUCAAAAACGUUGUUUUUAU
.((((((((((((.((((....))))......))))))))...(((((..((....(((....)))..)).)))))....))))....... ( -18.80)
>DroSim_CAF1 4147 91 + 1
UCAACGCUCGAGAAAACUUUUCAGUUGCCUACUUUCGGGCACCUUGACCUACUCAUGCAACUUUGUUUGUUGUCAAAAAUGUUGUUUUUAU
.((((((((((((.((((....))))......))))))))...(((((..((....(((....)))..)).)))))....))))....... ( -18.50)
>DroEre_CAF1 4988 91 + 1
UCAACGCUCGAGAAAACUUUUCAGUUGCCUUCUUUCAGGCACCUUGACCUACUCGUGCAACUUUGUUUGUUGUCAAAAACGUUGGUUUUAU
(((((((.((((..((((....))))((((......))))...........)))).))......((((........)))))))))...... ( -20.70)
>DroYak_CAF1 4575 91 + 1
UCAACGCUCGAGAAAACUUUUCAGUUGCCUACUUUCAGGCACCUUGACCUACUCAUGCAACUUUGUUUGUUAUCAAAAACGUUGUUUUAAU
.((((((..(((..((((....))))((((......))))...........)))..))......((((........))))))))....... ( -16.50)
>consensus
UCAACGCUCGAGAAAACUUUUCAGUUGCCUACUUUCGGGCACCUUGACCUACUCAUGCAACUUUGUUUGUUGUCAAAAACGUUGUUUUUAU
.(((((.(((((..((((....))))((((......))))..))))).........(((((.......)))))......)))))....... (-15.98 = -15.86 +  -0.12)

alignment

secondary structure

dotplot

Window 4

Location	5,732,486 – 5,732,577
Length	91
Sequences	5
Columns	91
Reading direction	reverse
Mean pairwise identity	95.49
Mean single sequence MFE	-23.26
Consensus MFE	-19.08
Energy contribution	-19.64
Covariance contribution	0.56
Combinations/Pair	1.04
Mean z-score	-2.64
Structure conservation index	0.82
SVM decision value	2.20
SVM RNA-class probability	0.990230
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 5732486 91 - 22407834
AUAAAAACAACUUUUUUGACAACAAACAAAGUUGCAUGAGUAGGUCAAGGUGCCCGAAAGUAGGCAACUGAAAAGUUUUCUCGACCAUUGA
.......(((((((((((....)))).)))))))........((((.(((.((((....)..)))((((....)))).))).))))..... ( -22.10)
>DroSec_CAF1 8385 91 - 1
AUAAAAACAACGUUUUUGACAACAAACAAAGUUGCAUGAGUAGGUCAAGGUGCCCGAAAGUAGGCAACUGAAAAGUUUUCUCGAGCGUUGA
.......((((((((..((.(((......((((((.......(((......)))(....)...)))))).....))).))..)))))))). ( -23.20)
>DroSim_CAF1 4147 91 - 1
AUAAAAACAACAUUUUUGACAACAAACAAAGUUGCAUGAGUAGGUCAAGGUGCCCGAAAGUAGGCAACUGAAAAGUUUUCUCGAGCGUUGA
.......((((((((.((.((((.......)))))).)))).(.((.(((.((((....)..)))((((....)))).))).)).))))). ( -19.90)
>DroEre_CAF1 4988 91 - 1
AUAAAACCAACGUUUUUGACAACAAACAAAGUUGCACGAGUAGGUCAAGGUGCCUGAAAGAAGGCAACUGAAAAGUUUUCUCGAGCGUUGA
.......((((((((..((.(((......((((((.(...(((((......)))))...)...)))))).....))).))..)))))))). ( -25.40)
>DroYak_CAF1 4575 91 - 1
AUUAAAACAACGUUUUUGAUAACAAACAAAGUUGCAUGAGUAGGUCAAGGUGCCUGAAAGUAGGCAACUGAAAAGUUUUCUCGAGCGUUGA
.......((((((((..((.(((......((((((.....(((((......))))).......)))))).....))).))..)))))))). ( -25.70)
>consensus
AUAAAAACAACGUUUUUGACAACAAACAAAGUUGCAUGAGUAGGUCAAGGUGCCCGAAAGUAGGCAACUGAAAAGUUUUCUCGAGCGUUGA
.......((((((((..((.(((......((((((.......(((......)))(....)...)))))).....))).))..)))))))). (-19.08 = -19.64 +   0.56)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:20:15 2006