Locus 5545

Sequence ID	3R_DroMel_CAF1
Location	14,650,274 – 14,650,387
Length	113
Max. P	0.998897

overview

Window 1

Location	14,650,274 – 14,650,387
Length	113
Sequences	4
Columns	113
Reading direction	forward
Mean pairwise identity	78.67
Mean single sequence MFE	-29.80
Consensus MFE	-19.11
Energy contribution	-22.61
Covariance contribution	3.50
Combinations/Pair	1.04
Mean z-score	-2.20
Structure conservation index	0.64
SVM decision value	1.36
SVM RNA-class probability	0.946524
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14650274 113 + 27905053
UUAGCUUCCUUUUUCGACAGUGUGUGUGGUGUGGCUGGCACAAACAUGGGCCAGCUAUAAAUUAUGAUCACAGCUAAAGUUUAUGCCGUGCCCCCCCCCCCCCACACACACAC
...................((((((((((((((((((((.((....)).)))))))))).........(((.((..........)).)))...........)))))))))).. ( -38.70)
>DroSim_CAF1 72507 96 + 1
UUAGCUUCCUUUUUCGACUGUGUGU-----------GGCACAAACAUGGGCCAGCUAUAAAUUAUGAUCACAGCUAAAGUUUAUGCCAUGCCCCCC----CACACACAC--AC
..................(((((((-----------((.........((((..((.(((((((.((........)).)))))))))...))))..)----)))))))).--.. ( -22.60)
>DroEre_CAF1 63897 98 + 1
UUGGCUUC-GCUGUGGACUAUGUGU--GGUGUGGCUGGCACAGGCAUGGGCCAGCUAUAAAUUAUGAUCACAGCUAAAGUUUAUGCCAUGCCCCA-----CACACA-------
..(((...-((.(((((((..((((--((((((((((((.((....)).)))))))))........)))))).)...)))))))))...)))...-----......------- ( -31.40)
>DroYak_CAF1 62533 94 + 1
UUCGCUUC-GCUUUGGACUAUGUAU--GGUGUGGCUGGCACAAGCAUGGGCCAGCUAUAAAUUAUGAUCACAGCUAAAGUUUAUGCCAUGCCCCA-----CA-----------
...((...-(((((((.((.(((((--((((((((((((.((....)).)))))))))..))))))..)).)))))))))....)).........-----..----------- ( -26.50)
>consensus
UUAGCUUC_GCUUUCGACUAUGUGU__GGUGUGGCUGGCACAAACAUGGGCCAGCUAUAAAUUAUGAUCACAGCUAAAGUUUAUGCCAUGCCCCA_____CACACA_______
...((....(((((((.(((((.......((((((((((.((....)).)))))))))).........))))))))))))....))........................... (-19.11 = -22.61 +   3.50)

alignment

secondary structure

dotplot

Window 2

Location	14,650,274 – 14,650,387
Length	113
Sequences	4
Columns	113
Reading direction	reverse
Mean pairwise identity	78.67
Mean single sequence MFE	-35.80
Consensus MFE	-23.05
Energy contribution	-25.74
Covariance contribution	2.69
Combinations/Pair	1.07
Mean z-score	-3.08
Structure conservation index	0.64
SVM decision value	3.27
SVM RNA-class probability	0.998897
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14650274 113 - 27905053
GUGUGUGUGUGGGGGGGGGGGGGCACGGCAUAAACUUUAGCUGUGAUCAUAAUUUAUAGCUGGCCCAUGUUUGUGCCAGCCACACCACACACACUGUCGAAAAAGGAAGCUAA
..((((((((((....(....(((..(((((((((.((((((((((.......)))))))))).....))))))))).))).).))))))))))................... ( -44.20)
>DroSim_CAF1 72507 96 - 1
GU--GUGUGUGUG----GGGGGGCAUGGCAUAAACUUUAGCUGUGAUCAUAAUUUAUAGCUGGCCCAUGUUUGUGCC-----------ACACACAGUCGAAAAAGGAAGCUAA
..--.((((((((----((.(((((((((........(((((((((.......)))))))))).)))))))).).))-----------))))))).................. ( -31.90)
>DroEre_CAF1 63897 98 - 1
-------UGUGUG-----UGGGGCAUGGCAUAAACUUUAGCUGUGAUCAUAAUUUAUAGCUGGCCCAUGCCUGUGCCAGCCACACC--ACACAUAGUCCACAGC-GAAGCCAA
-------((((((-----((((((.(((((((......((((((((.......))))))))(((....)))))))))))))...))--))))))).........-........ ( -38.60)
>DroYak_CAF1 62533 94 - 1
-----------UG-----UGGGGCAUGGCAUAAACUUUAGCUGUGAUCAUAAUUUAUAGCUGGCCCAUGCUUGUGCCAGCCACACC--AUACAUAGUCCAAAGC-GAAGCGAA
-----------.(-----((.(((.((((((((....(((((((((.......)))))))))((....))))))))))))).))).--................-........ ( -28.50)
>consensus
_______UGUGUG_____GGGGGCAUGGCAUAAACUUUAGCUGUGAUCAUAAUUUAUAGCUGGCCCAUGCUUGUGCCAGCCACACC__ACACACAGUCCAAAAA_GAAGCUAA
........(((((........(((.((((((((((.((((((((((.......)))))))))).....)))))))))))))........)))))................... (-23.05 = -25.74 +   2.69)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:57:45 2006