Locus 7818

Sequence ID	3R_DroMel_CAF1
Location	20,947,733 – 20,947,884
Length	151
Max. P	0.856488

overview

Window 7

Location	20,947,733 – 20,947,845
Length	112
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	82.24
Mean single sequence MFE	-27.53
Consensus MFE	-20.37
Energy contribution	-19.85
Covariance contribution	-0.52
Combinations/Pair	1.35
Mean z-score	-1.33
Structure conservation index	0.74
SVM decision value	-0.00
SVM RNA-class probability	0.531768
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 20947733 112 - 27905053
GGCUCCUAUUGCUUUUAUGCAUAUGU-----CGACUUUUGGUUUUUAU-CCGAGUUU-UCCAGGGGUGGUU-CUACCCCUUCUCAUAGAUAACGUCUGGCCUAACUGUUACUUUUGCACC
(((.......)))....((((...((-----.(((....((((.((((-(.(((...-...(((((((...-.))))))).)))...))))).....)))).....)))))...)))).. ( -24.30)
>DroSec_CAF1 11175 113 - 1
GGCUCCUAUUGUUUUUAUGCAUAUGU-----CGACUUUUGGUUUCUAU-CCGAGUUUUUCUGGGGGUGGUU-CUACCCCUACUCAUAGAUAACGUCUGGCCUAACUGUUAUUUUUGCACC
((((.....((((((((((.......-----.....(((((.......-)))))......((((((((...-.))))))))..)))))).))))...))))................... ( -24.20)
>DroSim_CAF1 11035 113 - 1
GGCUCCUAUUGCUUUUAUGCAUAUGU-----CGACUUUUGGUUUCUAU-CCGAGUUUUUCCGGGGGUGGUU-CUACCCCUACUCAUAGAUAACGUCUGGCCUAACUGUUAUUUUUGCACC
((((.....(((......))).....-----.(((.....((((((((-..((((......(((((((...-.)))))))))))))))).)))))).))))................... ( -25.50)
>DroEre_CAF1 11087 114 - 1
GGCUCCAAUUGCUUUUAUGCAUAUGU-----CGAUUCUUGGUUUCUAU-CCGAGUUUUUCCGGGGGUGGUUCCUACCCCUUCUCACAGAUAUCGUCUGGCCUAACAGUUAUUUUUGCACC
.((...(((.(((.(((.((....(.-----.((..(((((.......-)))))..))..)((((((((...)))))))).....(((((...))))))).))).))).)))...))... ( -28.40)
>DroYak_CAF1 11175 115 - 1
GGCUCCAAAUGCUUUUAUGCAUAUGU-----CGACUCUUGGUUUCUAUUCCGAGUUUUUCCAGGGGUGGUUCCUACCCCUUCUCAUAGAUAACGUCUGGCCUAACAGUUAUUUUUGCACC
((((.((.((((......)))).)).-----.(((.(((((........))))).......((((((((...)))))))).............))).))))................... ( -28.90)
>DroAna_CAF1 11843 114 - 1
GGUUUCCUUCGC--CUAUGCAUUUGGGUGGUGAGCCAGUUACUUCUAG-UCGAGUUUUU--AGGGGUUGUU-CUACCCUUACUGGCGUCAAACGGUAGGCCUAACUUUUAUUUCUACACC
(((((((.((((--(((......)))))))((((((((..((((....-..))))...(--((((((....-..)))))))))))).)))...)).)))))................... ( -33.90)
>consensus
GGCUCCUAUUGCUUUUAUGCAUAUGU_____CGACUUUUGGUUUCUAU_CCGAGUUUUUCCAGGGGUGGUU_CUACCCCUACUCAUAGAUAACGUCUGGCCUAACUGUUAUUUUUGCACC
((((.....(((......)))...........(((.(((((........))))).......((((((((...)))))))).............))).))))................... (-20.37 = -19.85 +  -0.52)

alignment

secondary structure

dotplot

Window 8

Location	20,947,773 – 20,947,884
Length	111
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	81.09
Mean single sequence MFE	-32.47
Consensus MFE	-23.54
Energy contribution	-23.10
Covariance contribution	-0.44
Combinations/Pair	1.44
Mean z-score	-2.03
Structure conservation index	0.73
SVM decision value	0.81
SVM RNA-class probability	0.856488
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 20947773 111 - 27905053
CAGAAAUCGACAAUAUUAUCAUAUUC-GGUCAGGCAAUGCGGCUCCUAUUGCUUUUAUGCAUAUGU-----CGACUUUUGGUUUUUAU-CCGAGUUU-UCCAGGGGUGGUU-CUACCCCU
(((((.((((((....(((((((...-....((((((((.(....))))))))).)))).))))))-----))).)))))........-........-...(((((((...-.))))))) ( -28.20)
>DroSec_CAF1 11215 112 - 1
CAGAAAUCGACAAUAUUAUCAUAUUC-GGUCAGGCAAUGGGGCUCCUAUUGUUUUUAUGCAUAUGU-----CGACUUUUGGUUUCUAU-CCGAGUUUUUCUGGGGGUGGUU-CUACCCCU
((((((((((((....(((((((...-....((((((((((...)))))))))).)))).))))))-----)))..(((((.......-)))))..))))))((((((...-.)))))). ( -32.80)
>DroSim_CAF1 11075 112 - 1
CAGAAAUCGACAAUAUUAUCAUAUUC-GGUGAGGCAAUGGGGCUCCUAUUGCUUUUAUGCAUAUGU-----CGACUUUUGGUUUCUAU-CCGAGUUUUUCCGGGGGUGGUU-CUACCCCU
(((((.((((((...(((((......-)))))(((((((((...)))))))))..........)))-----))).)))))........-............(((((((...-.))))))) ( -34.60)
>DroEre_CAF1 11127 113 - 1
CGGAAAUCGACCAUAUUAUCAUAUUC-GGUCAGGCAAUGGGGCUCCAAUUGCUUUUAUGCAUAUGU-----CGAUUCUUGGUUUCUAU-CCGAGUUUUUCCGGGGGUGGUUCCUACCCCU
(((((((((((.((((...((((...-....(((((((((....)).))))))).)))).))))))-----)))..(((((.......-)))))..))))))(((((((...))))))). ( -36.10)
>DroYak_CAF1 11215 114 - 1
CGGAAAUCGACAAUAUUAUCAUAUUC-GGUCAGGCAAUGGGGCUCCAAAUGCUUUUAUGCAUAUGU-----CGACUCUUGGUUUCUAUUCCGAGUUUUUCCAGGGGUGGUUCCUACCCCU
.(((((((((((..............-((...(((......)))))..((((......)))).)))-----)))..(((((........)))))..)))))((((((((...)))))))) ( -35.90)
>DroAna_CAF1 11883 114 - 1
UGUAAGAGAAAUAUCUUCUUAAAUUCAGGUCAUAUAUGGGGGUUUCCUUCGC--CUAUGCAUUUGGGUGGUGAGCCAGUUACUUCUAG-UCGAGUUUUU--AGGGGUUGUU-CUACCCUU
..(((((((....)).)))))................((((((((...((((--(((......))))))).)))))((..((((((((-........))--))))))....-)).))).. ( -27.20)
>consensus
CAGAAAUCGACAAUAUUAUCAUAUUC_GGUCAGGCAAUGGGGCUCCUAUUGCUUUUAUGCAUAUGU_____CGACUUUUGGUUUCUAU_CCGAGUUUUUCCAGGGGUGGUU_CUACCCCU
.(((((((((.........(((((.......((((((((((...))))))))))......)))))............)))))))))...............((((((((...)))))))) (-23.54 = -23.10 +  -0.44)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:55:30 2006