Locus 4686

Sequence ID	2L_DroMel_CAF1
Location	13,467,786 – 13,467,922
Length	136
Max. P	0.947442

overview

Window 6

Location	13,467,786 – 13,467,890
Length	104
Sequences	3
Columns	104
Reading direction	forward
Mean pairwise identity	99.36
Mean single sequence MFE	-42.17
Consensus MFE	-39.20
Energy contribution	-42.53
Covariance contribution	3.33
Combinations/Pair	1.00
Mean z-score	-2.38
Structure conservation index	0.93
SVM decision value	0.98
SVM RNA-class probability	0.893227
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 13467786 104 + 22407834
UGCUCUUUCGAUUUCCACCUGGCCGGAUGGCUGAUUCAGCGACUGGGUGACUGGUUGACUGGCUGACCUGCCAGAGGCAGAGCCACCUGUCAUUGUCAUGGAAU
............(((((.(((((.((.((((.....(((((((..(....)..)))).))))))).)).))))).(((((......))))).......))))). ( -38.90)
>DroSec_CAF1 67292 104 + 1
UGCUCUUUCGAUUUCCACCUGGCCGGAUGGCUGAUUCAGCGACUGGGUGACUGGUUGACUGGCUGUCCUGCCAGAGGCAGAGCCACCUGUCAUUGUCAUGGAAU
............(((((.(((((.(((((((.....(((((((..(....)..)))).)))))))))).))))).(((((......))))).......))))). ( -43.80)
>DroSim_CAF1 68512 104 + 1
UGCUCUUUCGAUUUCCACCUGGCCGGAUGGCUGAUUCAGCGACUGGGUGACUGGUUGACUGGCUGUCCUGCCAGAGGCAGAGCCACCUGUCAUUGUCAUGGAAU
............(((((.(((((.(((((((.....(((((((..(....)..)))).)))))))))).))))).(((((......))))).......))))). ( -43.80)
>consensus
UGCUCUUUCGAUUUCCACCUGGCCGGAUGGCUGAUUCAGCGACUGGGUGACUGGUUGACUGGCUGUCCUGCCAGAGGCAGAGCCACCUGUCAUUGUCAUGGAAU
............(((((.(((((.(((((((.....(((((((..(....)..)))).)))))))))).))))).(((((......))))).......))))). (-39.20 = -42.53 +   3.33)

alignment

secondary structure

dotplot

Window 7

Location	13,467,786 – 13,467,890
Length	104
Sequences	3
Columns	104
Reading direction	reverse
Mean pairwise identity	99.36
Mean single sequence MFE	-36.80
Consensus MFE	-36.80
Energy contribution	-36.80
Covariance contribution	0.00
Combinations/Pair	1.00
Mean z-score	-2.23
Structure conservation index	1.00
SVM decision value	1.37
SVM RNA-class probability	0.947442
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 13467786 104 - 22407834
AUUCCAUGACAAUGACAGGUGGCUCUGCCUCUGGCAGGUCAGCCAGUCAACCAGUCACCCAGUCGCUGAAUCAGCCAUCCGGCCAGGUGGAAAUCGAAAGAGCA
.((((((..((.((((.(((((((......(((((......)))))......)))))))..)))).)).....(((....)))...)))))).((....))... ( -36.80)
>DroSec_CAF1 67292 104 - 1
AUUCCAUGACAAUGACAGGUGGCUCUGCCUCUGGCAGGACAGCCAGUCAACCAGUCACCCAGUCGCUGAAUCAGCCAUCCGGCCAGGUGGAAAUCGAAAGAGCA
.((((((..((.((((.(((((((......(((((......)))))......)))))))..)))).)).....(((....)))...)))))).((....))... ( -36.80)
>DroSim_CAF1 68512 104 - 1
AUUCCAUGACAAUGACAGGUGGCUCUGCCUCUGGCAGGACAGCCAGUCAACCAGUCACCCAGUCGCUGAAUCAGCCAUCCGGCCAGGUGGAAAUCGAAAGAGCA
.((((((..((.((((.(((((((......(((((......)))))......)))))))..)))).)).....(((....)))...)))))).((....))... ( -36.80)
>consensus
AUUCCAUGACAAUGACAGGUGGCUCUGCCUCUGGCAGGACAGCCAGUCAACCAGUCACCCAGUCGCUGAAUCAGCCAUCCGGCCAGGUGGAAAUCGAAAGAGCA
.((((((..((.((((.(((((((......(((((......)))))......)))))))..)))).)).....(((....)))...)))))).((....))... (-36.80 = -36.80 +   0.00)

alignment

secondary structure

dotplot

Window 8

Location	13,467,818 – 13,467,922
Length	104
Sequences	3
Columns	104
Reading direction	forward
Mean pairwise identity	94.87
Mean single sequence MFE	-37.20
Consensus MFE	-30.49
Energy contribution	-33.50
Covariance contribution	3.01
Combinations/Pair	1.09
Mean z-score	-2.45
Structure conservation index	0.82
SVM decision value	0.33
SVM RNA-class probability	0.690316
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 13467818 104 + 22407834
GAUUCAGCGACUGGGUGACUGGUUGACUGGCUGACCUGCCAGAGGCAGAGCCACCUGUCAUUGUCAUGGAAUGGUAAUGGGAAGGAGAAGGGAAUCGGAAUGGG
(((((((((((..(....)..)))).))((((...(((((...))))))))).(((.(((((..(((...)))..)))))..)))......)))))........ ( -37.80)
>DroSec_CAF1 67324 104 + 1
GAUUCAGCGACUGGGUGACUGGUUGACUGGCUGUCCUGCCAGAGGCAGAGCCACCUGUCAUUGUCAUGGAAUGGGAAUGGGAAUGGGAAGGCAAUUGGAAUGGG
.((((((((((..(....)..)))).))((((...(((((...))))))))).(((.(((((.((((.........)))).)))))..)))......))))... ( -34.50)
>DroSim_CAF1 68544 104 + 1
GAUUCAGCGACUGGGUGACUGGUUGACUGGCUGUCCUGCCAGAGGCAGAGCCACCUGUCAUUGUCAUGGAAUGGGAAUGGGAAUGGUAGGGGAAUUGGAAUGGG
(((((((((((..(....)..)))).))((((...(((((...))))))))).(((..((((.((((.........)))).))))..))).)))))........ ( -39.30)
>consensus
GAUUCAGCGACUGGGUGACUGGUUGACUGGCUGUCCUGCCAGAGGCAGAGCCACCUGUCAUUGUCAUGGAAUGGGAAUGGGAAUGGGAAGGGAAUUGGAAUGGG
(((((((((((..(....)..)))).))((((...(((((...))))))))).(((.(((((.((((.........)))).)))))..))))))))........ (-30.49 = -33.50 +   3.01)

alignment

secondary structure

dotplot

Window 9

Location	13,467,818 – 13,467,922
Length	104
Sequences	3
Columns	104
Reading direction	reverse
Mean pairwise identity	94.87
Mean single sequence MFE	-23.90
Consensus MFE	-23.90
Energy contribution	-23.90
Covariance contribution	0.00
Combinations/Pair	1.00
Mean z-score	-2.01
Structure conservation index	1.00
SVM decision value	1.32
SVM RNA-class probability	0.942008
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 13467818 104 - 22407834
CCCAUUCCGAUUCCCUUCUCCUUCCCAUUACCAUUCCAUGACAAUGACAGGUGGCUCUGCCUCUGGCAGGUCAGCCAGUCAACCAGUCACCCAGUCGCUGAAUC
.........................................((.((((.(((((((......(((((......)))))......)))))))..)))).)).... ( -23.90)
>DroSec_CAF1 67324 104 - 1
CCCAUUCCAAUUGCCUUCCCAUUCCCAUUCCCAUUCCAUGACAAUGACAGGUGGCUCUGCCUCUGGCAGGACAGCCAGUCAACCAGUCACCCAGUCGCUGAAUC
.........................................((.((((.(((((((......(((((......)))))......)))))))..)))).)).... ( -23.90)
>DroSim_CAF1 68544 104 - 1
CCCAUUCCAAUUCCCCUACCAUUCCCAUUCCCAUUCCAUGACAAUGACAGGUGGCUCUGCCUCUGGCAGGACAGCCAGUCAACCAGUCACCCAGUCGCUGAAUC
.........................................((.((((.(((((((......(((((......)))))......)))))))..)))).)).... ( -23.90)
>consensus
CCCAUUCCAAUUCCCUUCCCAUUCCCAUUCCCAUUCCAUGACAAUGACAGGUGGCUCUGCCUCUGGCAGGACAGCCAGUCAACCAGUCACCCAGUCGCUGAAUC
.........................................((.((((.(((((((......(((((......)))))......)))))))..)))).)).... (-23.90 = -23.90 +   0.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:24:36 2006