Locus 1939

Sequence ID	3R_DroMel_CAF1
Location	5,483,544 – 5,483,656
Length	112
Max. P	0.980468

overview

Window 7

Location	5,483,544 – 5,483,656
Length	112
Sequences	5
Columns	116
Reading direction	forward
Mean pairwise identity	83.10
Mean single sequence MFE	-27.80
Consensus MFE	-18.76
Energy contribution	-18.64
Covariance contribution	-0.12
Combinations/Pair	1.13
Mean z-score	-1.62
Structure conservation index	0.67
SVM decision value	-0.03
SVM RNA-class probability	0.520260
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 5483544 112 + 27905053
AGUUAAGAAAUAAAUUACAAAUUAAGCAGUGGAGGAAGUUAUUCAAUAUAGUAAGUUGUGCGAUCGCACAGGAGCAUUGCUCCUGGAUCAUACUAC-AUUUAGACUAU---CCUCC
..............................((((((((((....(((.(((((....((((....))))((((((...))))))......))))).-)))..)))).)---))))) ( -28.90)
>DroSec_CAF1 14419 112 + 1
AGUUAAGAAAUAAAUUACAAAUUAAGCAGUGGAGGAAGUUUUUCCAUAUAGUAAGUUGUGCGAUCGUACAGGAGCAUUGCUCCUGGAUCAUACUAC-AUUUGGACUAU---CCUCC
..............................((((((((....((((..(((((.(.....)((((...(((((((...))))))))))).))))).-...)))))).)---))))) ( -28.50)
>DroSim_CAF1 16645 115 + 1
AGUUAAGAAAUAAAUUACAAAUUAAGCAGUGGAGGAAGUUUUUCAAUAUAGUAAGUUGUGCGAAAGUACAGGAGCAUUGCUCCUGGAUCAUACUAC-AUUUAGUCAAUAUGGCUCC
..............................((((..............(((((....((((....))))((((((...))))))......)))))(-((.........))).)))) ( -22.40)
>DroEre_CAF1 14381 96 + 1
AGUUGGGAAAUGAGUUACAGAUUAAGCAGUGGAGGA-----------------AGAUGUGGGAUCCUAGAGGAGCAUUGCUCCUGGAUCAUACUACCAUUUAGACUAG---CCUCC
.(((((.(((((..(((((..((...(....)...)-----------------)..)))))(((((...((((((...))))))))))).......)))))...))))---).... ( -24.80)
>DroYak_CAF1 12877 112 + 1
AGUUAAGGAAUGAAUUGCAUAUUAAGCAGUGGAGGAAGUUUGUCAAUAUAGUAAGAUGUGGGAUCCCACUGGAGCAUUGCUCCUGGGUCAUACUAC-AUUUAGACUAG---CCUCC
.............(((((.......)))))(((((.((((((..(((.(((((.(((((((....)))).(((((...)))))...))).))))).-)))))))))..---))))) ( -34.40)
>consensus
AGUUAAGAAAUAAAUUACAAAUUAAGCAGUGGAGGAAGUUUUUCAAUAUAGUAAGUUGUGCGAUCGUACAGGAGCAUUGCUCCUGGAUCAUACUAC_AUUUAGACUAU___CCUCC
..............................(((((......................((((....))))((((((...))))))...........................))))) (-18.76 = -18.64 +  -0.12)

alignment

secondary structure

dotplot

Window 8

Location	5,483,544 – 5,483,656
Length	112
Sequences	5
Columns	116
Reading direction	reverse
Mean pairwise identity	83.10
Mean single sequence MFE	-29.45
Consensus MFE	-16.55
Energy contribution	-18.04
Covariance contribution	1.49
Combinations/Pair	1.04
Mean z-score	-3.41
Structure conservation index	0.56
SVM decision value	1.86
SVM RNA-class probability	0.980468
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 5483544 112 - 27905053
GGAGG---AUAGUCUAAAU-GUAGUAUGAUCCAGGAGCAAUGCUCCUGUGCGAUCGCACAACUUACUAUAUUGAAUAACUUCCUCCACUGCUUAAUUUGUAAUUUAUUUCUUAACU
(((((---(.(((...(((-((((((.(....((((((...))))))((((....))))..).))))))))).....))))))))).............................. ( -34.10)
>DroSec_CAF1 14419 112 - 1
GGAGG---AUAGUCCAAAU-GUAGUAUGAUCCAGGAGCAAUGCUCCUGUACGAUCGCACAACUUACUAUAUGGAAAAACUUCCUCCACUGCUUAAUUUGUAAUUUAUUUCUUAACU
(((((---(...((((..(-((((((((((((((((((...)))))))...))))).......)))))))))))......)))))).............................. ( -33.21)
>DroSim_CAF1 16645 115 - 1
GGAGCCAUAUUGACUAAAU-GUAGUAUGAUCCAGGAGCAAUGCUCCUGUACUUUCGCACAACUUACUAUAUUGAAAAACUUCCUCCACUGCUUAAUUUGUAAUUUAUUUCUUAACU
((((............(((-(((((((((..(((((((...))))))).....))).......)))))))))..........)))).............................. ( -21.06)
>DroEre_CAF1 14381 96 - 1
GGAGG---CUAGUCUAAAUGGUAGUAUGAUCCAGGAGCAAUGCUCCUCUAGGAUCCCACAUCU-----------------UCCUCCACUGCUUAAUCUGUAACUCAUUUCCCAACU
(((((---..((......(((......(((((((((((...))))))...))))))))...))-----------------.))))).............................. ( -23.00)
>DroYak_CAF1 12877 112 - 1
GGAGG---CUAGUCUAAAU-GUAGUAUGACCCAGGAGCAAUGCUCCAGUGGGAUCCCACAUCUUACUAUAUUGACAAACUUCCUCCACUGCUUAAUAUGCAAUUCAUUCCUUAACU
(((((---..(((...(((-((((((.((....(((((...))))).((((....)))).)).))))))))).....))).)))))..(((.......)))............... ( -35.90)
>consensus
GGAGG___AUAGUCUAAAU_GUAGUAUGAUCCAGGAGCAAUGCUCCUGUACGAUCGCACAACUUACUAUAUUGAAAAACUUCCUCCACUGCUUAAUUUGUAAUUUAUUUCUUAACU
(((((..................((.((((((((((((...)))))))...))))).))......(......)........)))))..(((.......)))............... (-16.55 = -18.04 +   1.49)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:23:22 2006