Locus 1870

Sequence ID	X_DroMel_CAF1
Location	5,157,466 – 5,157,561
Length	95
Max. P	0.997012

overview

Window 7

Location	5,157,466 – 5,157,561
Length	95
Sequences	5
Columns	115
Reading direction	forward
Mean pairwise identity	71.76
Mean single sequence MFE	-33.87
Consensus MFE	-14.81
Energy contribution	-17.29
Covariance contribution	2.48
Combinations/Pair	1.21
Mean z-score	-2.52
Structure conservation index	0.44
SVM decision value	2.78
SVM RNA-class probability	0.997012
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5157466 95 + 22224390
CUCUCCAUGGGCCGCCAUUUUGUUUAGCGGCCACGCGAG--------------------AAUUCAGCAUGCAAAUUGGCGGGAAUUCCACUCUACACACCGCCACUUGGAGACCC
.((((((..((((((((.(((((...(((....)))(..--------------------....).....))))).)))))((....))............)))...))))))... ( -32.30)
>DroSec_CAF1 3498 93 + 1
NNNNNNNNNNNCGGCCAUUUUGUUUCGUGGCCACGCGAA--------------------AAUUUAGCGUCCAAAUCGGCGGGAAUUCCAGUCUAC--ACCGCCAUUUGGAGAGCC
............((((((........)))))).(((...--------------------......)))(((((((.(((((..............--.))))))))))))..... ( -30.06)
>DroSim_CAF1 3618 93 + 1
UUCUCCACUGGCGGCCAUUUUGUUUCGUGGCCACGCGAA--------------------AAUUUAGCGUCCAAAUUGGCGGGAAUUCCAGUCUAC--ACCGCCAUUUGGAGAGCC
(((((((.(((.((((((........))))))((((...--------------------......)))))))...((((((..............--.))))))..))))))).. ( -34.16)
>DroEre_CAF1 3193 108 + 1
CUCUCCACCGUCCGCCAUUUUGUUCUGCGCCCACGCGAGAGGCUCAAAAA----AUGCGAAUUCAGCGAACAAAUUGGCGCGAAUUCCAGUCUCC--GUCGCC-CUUGGAGAGCC
(((((((......((((.(((((((((.(((..(....).))).))....----..((.......))))))))).))))((((............--.)))).-..))))))).. ( -36.72)
>DroYak_CAF1 2724 113 + 1
CUCUCCACCGUCCGCCAUUUUGUAUUGCGCCCACGCGAAGAGCGCAAAAAAAAUAUGCGAAUUCAGCCAGCAAAUUGGCGCGAAUUCCAGUCUCC--GUCGCAAAUUGGAGAGCC
(((((((..(..(((.((.....)).)))..)..((((.(((((((.........)))((((((.(((((....)))))..))))))..).))).--.))))....))))))).. ( -36.10)
>consensus
CUCUCCACCGGCCGCCAUUUUGUUUCGCGGCCACGCGAA____________________AAUUCAGCGUCCAAAUUGGCGGGAAUUCCAGUCUAC__ACCGCCACUUGGAGAGCC
(((((((......((((.(((((((((((....))))))..............................))))).)))).((....))..................))))))).. (-14.81 = -17.29 +   2.48)

alignment

secondary structure

dotplot

Window 8

Location	5,157,466 – 5,157,561
Length	95
Sequences	5
Columns	115
Reading direction	reverse
Mean pairwise identity	71.76
Mean single sequence MFE	-36.72
Consensus MFE	-11.69
Energy contribution	-12.89
Covariance contribution	1.20
Combinations/Pair	1.10
Mean z-score	-2.04
Structure conservation index	0.32
SVM decision value	1.20
SVM RNA-class probability	0.929079
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5157466 95 - 22224390
GGGUCUCCAAGUGGCGGUGUGUAGAGUGGAAUUCCCGCCAAUUUGCAUGCUGAAUU--------------------CUCGCGUGGCCGCUAAACAAAAUGGCGGCCCAUGGAGAG
...((((((.(((((((((((((((((((.....))))...)))))))))))....--------------------.))))(.((((((((.......))))))))).)))))). ( -40.40)
>DroSec_CAF1 3498 93 - 1
GGCUCUCCAAAUGGCGGU--GUAGACUGGAAUUCCCGCCGAUUUGGACGCUAAAUU--------------------UUCGCGUGGCCACGAAACAAAAUGGCCGNNNNNNNNNNN
(((..((((((((((((.--(............)))))).))))))).))).....--------------------.......(((((..........)))))............ ( -26.10)
>DroSim_CAF1 3618 93 - 1
GGCUCUCCAAAUGGCGGU--GUAGACUGGAAUUCCCGCCAAUUUGGACGCUAAAUU--------------------UUCGCGUGGCCACGAAACAAAAUGGCCGCCAGUGGAGAA
(((..((((((((((((.--(............)))))).))))))).)))...((--------------------((((((((((((..........)))))))..))))))). ( -34.70)
>DroEre_CAF1 3193 108 - 1
GGCUCUCCAAG-GGCGAC--GGAGACUGGAAUUCGCGCCAAUUUGUUCGCUGAAUUCGCAU----UUUUUGAGCCUCUCGCGUGGGCGCAGAACAAAAUGGCGGACGGUGGAGAG
..(((((((..-((((.(--(((........))))))))...((((((((((....)....----.(((((.((((.......)))).)))))......)))))))))))))))) ( -38.80)
>DroYak_CAF1 2724 113 - 1
GGCUCUCCAAUUUGCGAC--GGAGACUGGAAUUCGCGCCAAUUUGCUGGCUGAAUUCGCAUAUUUUUUUUGCGCUCUUCGCGUGGGCGCAAUACAAAAUGGCGGACGGUGGAGAG
..(((((((.(((((...--(....)(((((((((.((((......))))))))))).))((((((..((((((((.......))))))))...)))))))))))...))))))) ( -43.60)
>consensus
GGCUCUCCAAAUGGCGGU__GUAGACUGGAAUUCCCGCCAAUUUGCACGCUGAAUU____________________UUCGCGUGGCCGCAAAACAAAAUGGCGGACGGUGGAGAG
...((((((..................((.....))((((.((((...((.............................))((....))....)))).))))......)))))). (-11.69 = -12.89 +   1.20)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:20:38 2006