Locus 7877

Sequence ID	X_DroMel_CAF1
Location	19,613,253 – 19,613,392
Length	139
Max. P	0.971975

overview

Window 3

Location	19,613,253 – 19,613,364
Length	111
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	92.06
Mean single sequence MFE	-45.10
Consensus MFE	-36.33
Energy contribution	-37.08
Covariance contribution	0.75
Combinations/Pair	1.00
Mean z-score	-1.71
Structure conservation index	0.81
SVM decision value	0.28
SVM RNA-class probability	0.666815
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 19613253 111 + 22224390
CAUACUGGUGGUGAUGGUAGUAGCUAGCGGCGUGGUGCUGGUGCUGCUGCACUGCAGCAUAUU------GCUGU---GCAUGAGCGUGGGCAUGGGCAUGGGCAUAUCCAAAGCCAGCAU
.....((.((((..(((.....(((....((.(.(((((..((((..(((((.((((....))------)).))---)))..))))..))))).)))...)))....)))..)))).)). ( -41.90)
>DroPse_CAF1 22034 110 + 1
-AUACUGGUGGUGGUGAUAGUAGCUAGCGGCGUGGUGCUGGUGCUGCUGCACUGCAGCAUACU------GCUGG---GCAUGGGCAUGUGCAUGGGCAUGGGCAUAUCCAAAGCCAGCAU
-......(((.((((........(((((((..((.(((.(((((....)))))))).))..))------)))))---...(((..((((.(((....))).))))..)))..)))).))) ( -46.80)
>DroSec_CAF1 19125 111 + 1
CAUACUGGUGGUGAUGGUAGUAGCUAGCGGCGUGGUGCUGGUGCUGCUGCACUGCAGCAUAUU------GCUGU---GCAUGAGCGUGGGCAUGGGCAUGGGCAUAUCCAAAGCCAGCAU
.....((.((((..(((.....(((....((.(.(((((..((((..(((((.((((....))------)).))---)))..))))..))))).)))...)))....)))..)))).)). ( -41.90)
>DroAna_CAF1 20452 120 + 1
CAUACUGGUGGUGGUGGUAGUAGCUAGCGGCGUGGUGCUGGUGCUGCUGCACUGCAGCAUACUGGGCAUGCUGGGCGGCAUGAGCGUGUGCAUGGGCAUGGGCAUAUCCAAAGCCAGCAU
....(((((.(..(((.(((((((.(.((((.....)))).)))))))))))..).((((((.(..((((((....))))))..))))))).(((..((....))..)))..)))))... ( -49.80)
>consensus
CAUACUGGUGGUGAUGGUAGUAGCUAGCGGCGUGGUGCUGGUGCUGCUGCACUGCAGCAUACU______GCUGG___GCAUGAGCGUGGGCAUGGGCAUGGGCAUAUCCAAAGCCAGCAU
.....((.((((..(((.....((.....))...(((((.(((((..(((((..((((...........))))....((....))..)))))..))))).)))))..)))..)))).)). (-36.33 = -37.08 +   0.75)

alignment

secondary structure

dotplot

Window 4

Location	19,613,293 – 19,613,392
Length	99
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	86.76
Mean single sequence MFE	-45.28
Consensus MFE	-34.71
Energy contribution	-34.52
Covariance contribution	-0.19
Combinations/Pair	1.03
Mean z-score	-2.71
Structure conservation index	0.77
SVM decision value	1.68
SVM RNA-class probability	0.971975
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 19613293 99 + 22224390
GUGCUGCUGCACUGCAGCAUAUU------GCUGU---GCAUGAGCGUGGGCAUGGGCAUGGGCAUAUCCAAAGCCAGCAUGUUGUAGUCCAUUGCCAUAGGCGGCAGC------------
..((((((((.(((((((.....------)))))---..(((.((((((((...(((((((((.........)))..))))))...))))).))))))))))))))))------------ ( -41.60)
>DroPse_CAF1 22073 111 + 1
GUGCUGCUGCACUGCAGCAUACU------GCUGG---GCAUGGGCAUGUGCAUGGGCAUGGGCAUAUCCAAAGCCAGCAUGUUGUAGUCCAUUCCCAUAGGCGGCAGCAGCGACUGCUGC
(((((((......))))))).((------(.(((---(.((((((....((((((((.((((....))))..)))..)))))....)))))).)))))))(((((((......))))))) ( -49.70)
>DroSec_CAF1 19165 99 + 1
GUGCUGCUGCACUGCAGCAUAUU------GCUGU---GCAUGAGCGUGGGCAUGGGCAUGGGCAUAUCCAAAGCCAGCAUGUUGUAGUCCAUUGCCAUAGGCGGCAGC------------
..((((((((.(((((((.....------)))))---..(((.((((((((...(((((((((.........)))..))))))...))))).))))))))))))))))------------ ( -41.60)
>DroAna_CAF1 20492 108 + 1
GUGCUGCUGCACUGCAGCAUACUGGGCAUGCUGGGCGGCAUGAGCGUGUGCAUGGGCAUGGGCAUAUCCAAAGCCAGCAUGUUGUAGUCCAUUGCCAUAUGCGGCAGC------------
..((((((((((((((((((.((((.((((((....)))))).((.(((((....))))).))..........)))).))))))))))............))))))))------------ ( -48.20)
>consensus
GUGCUGCUGCACUGCAGCAUACU______GCUGG___GCAUGAGCGUGGGCAUGGGCAUGGGCAUAUCCAAAGCCAGCAUGUUGUAGUCCAUUGCCAUAGGCGGCAGC____________
..((((((((((((((((((.........(((..........)))....((...(((.((((....))))..))).))))))))))))............))))))))............ (-34.71 = -34.52 +  -0.19)

alignment

secondary structure

dotplot

Window 5

Location	19,613,293 – 19,613,392
Length	99
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	86.76
Mean single sequence MFE	-38.42
Consensus MFE	-27.23
Energy contribution	-27.97
Covariance contribution	0.75
Combinations/Pair	1.00
Mean z-score	-2.35
Structure conservation index	0.71
SVM decision value	0.96
SVM RNA-class probability	0.890083
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 19613293 99 - 22224390
------------GCUGCCGCCUAUGGCAAUGGACUACAACAUGCUGGCUUUGGAUAUGCCCAUGCCCAUGCCCACGCUCAUGC---ACAGC------AAUAUGCUGCAGUGCAGCAGCAC
------------(((((.((....(((((((........)))...(((..(((......))).)))..))))...))...(((---((.((------(......))).)))))))))).. ( -33.50)
>DroPse_CAF1 22073 111 - 1
GCAGCAGUCGCUGCUGCCGCCUAUGGGAAUGGACUACAACAUGCUGGCUUUGGAUAUGCCCAUGCCCAUGCACAUGCCCAUGC---CCAGC------AGUAUGCUGCAGUGCAGCAGCAC
.........(((((((((.....((((.((((.(.....((((..(((..(((......))).))))))).....).)))).)---)))((------((....)))).).)))))))).. ( -44.70)
>DroSec_CAF1 19165 99 - 1
------------GCUGCCGCCUAUGGCAAUGGACUACAACAUGCUGGCUUUGGAUAUGCCCAUGCCCAUGCCCACGCUCAUGC---ACAGC------AAUAUGCUGCAGUGCAGCAGCAC
------------(((((.((....(((((((........)))...(((..(((......))).)))..))))...))...(((---((.((------(......))).)))))))))).. ( -33.50)
>DroAna_CAF1 20492 108 - 1
------------GCUGCCGCAUAUGGCAAUGGACUACAACAUGCUGGCUUUGGAUAUGCCCAUGCCCAUGCACACGCUCAUGCCGCCCAGCAUGCCCAGUAUGCUGCAGUGCAGCAGCAC
------------(((((.((((..((((.((..(.....((((..(((..(((......))).))))))).....)..))))))...((((((((...))))))))..)))).))))).. ( -42.00)
>consensus
____________GCUGCCGCCUAUGGCAAUGGACUACAACAUGCUGGCUUUGGAUAUGCCCAUGCCCAUGCACACGCUCAUGC___ACAGC______AAUAUGCUGCAGUGCAGCAGCAC
............(((((.((.....))..((.(((.((.(((((((((..(((......))).)))((((........))))...............)))))).)).))).))))))).. (-27.23 = -27.97 +   0.75)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:49:48 2006