Locus 5969

Sequence ID	3L_DroMel_CAF1
Location	15,980,904 – 15,981,059
Length	155
Max. P	0.954070

overview

Window 2

Location	15,980,904 – 15,981,019
Length	115
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	88.66
Mean single sequence MFE	-36.96
Consensus MFE	-29.08
Energy contribution	-29.56
Covariance contribution	0.48
Combinations/Pair	1.07
Mean z-score	-1.72
Structure conservation index	0.79
SVM decision value	0.53
SVM RNA-class probability	0.772067
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15980904 115 + 23771897
GUUGCGCUUAGUAGCUUAGAAUCAAAGUCGGAUCAGCGCAAAAUUCUGUGAUCUUCUCUGAUCUCCAGCGAUUGCUCUCUGCCGACGUCGCUGCCGCU-----GCCGCUGCUCUGCAGCU
((((((...((((((...........(((((...((.((((....(((.((((......))))..)))...)))).))...)))))((.((....)).-----)).)))))).)))))). ( -37.50)
>DroSec_CAF1 10060 109 + 1
GUUGCGCUUAGUAGCUUAGAAUCAAAGUCGGAUCAGCGCAAAAUUCUGUGAUCUUCUCUGAUCUCCAGCGAUUGCGCUCUGCCGACGUCGCUGC-----------CGCUGCUCUGCCGCU
...((((..((((((.(((.......(((((...(((((((....(((.((((......))))..)))...)))))))...)))))....))).-----------.))))))..).))). ( -39.60)
>DroSim_CAF1 10773 115 + 1
GUUGCGCUUAGUAGCUUAGAAUCAAAGUCGGAUCAGCGCAAAAUUCUGUGAUCUUCUCUGAUCUCCAGCGAUUGCGCUCUGCCGACGUCGCUGCCGCU-----GCCGCUGCUCUGCCGCU
...((((..((((((...........(((((...(((((((....(((.((((......))))..)))...)))))))...)))))((.((....)).-----)).))))))..).))). ( -41.90)
>DroEre_CAF1 10788 120 + 1
GUUGCGCUUAGUAGCUUAGAAUCAAAGUCGGAUCAGCGCAAAUUUCUGUGAUCUUCUCUGAUCUCCAGCGAUUGCUCUCUGCCGACGUCGCUGCCGCUGUUCUGCCGCUGCUCUGCCGCU
...((((..((((((.((((((....(((((...((.((((.((.(((.((((......))))..))).)))))).))...)))))...((....)).))))))..))))))..).))). ( -39.10)
>DroYak_CAF1 10313 97 + 1
GUUGCGUUUAGUAGCUUAGAAUCAAAGUCGGAUCAGCGCAAAUUUCUGUGAUCUUCUCAGAUCUCCAGCGAUUGCUCUCUGCCGGC-----------------------GCUCUGCCGCU
(((((.....)))))..........((.(((...(((((.((((.(((.(((((....)))))..))).))))((.....))..))-----------------------)))...))))) ( -26.70)
>consensus
GUUGCGCUUAGUAGCUUAGAAUCAAAGUCGGAUCAGCGCAAAAUUCUGUGAUCUUCUCUGAUCUCCAGCGAUUGCUCUCUGCCGACGUCGCUGCCGCU_____GCCGCUGCUCUGCCGCU
...((((..((((((...........(((((...((.((((....(((.((((......))))..)))...)))).))...))))).........((......)).))))))..)).)). (-29.08 = -29.56 +   0.48)

alignment

secondary structure

dotplot

Window 3

Location	15,980,904 – 15,981,019
Length	115
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	88.66
Mean single sequence MFE	-36.42
Consensus MFE	-29.60
Energy contribution	-30.30
Covariance contribution	0.70
Combinations/Pair	1.00
Mean z-score	-1.42
Structure conservation index	0.81
SVM decision value	0.07
SVM RNA-class probability	0.569474
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15980904 115 - 23771897
AGCUGCAGAGCAGCGGC-----AGCGGCAGCGACGUCGGCAGAGAGCAAUCGCUGGAGAUCAGAGAAGAUCACAGAAUUUUGCGCUGAUCCGACUUUGAUUCUAAGCUACUAAGCGCAAC
.(((((......)))))-----.((((...(((.((((((((...((((...(((..((((......)))).)))....)))).)))..))))).)))...))..(((....)))))... ( -38.00)
>DroSec_CAF1 10060 109 - 1
AGCGGCAGAGCAGCG-----------GCAGCGACGUCGGCAGAGCGCAAUCGCUGGAGAUCAGAGAAGAUCACAGAAUUUUGCGCUGAUCCGACUUUGAUUCUAAGCUACUAAGCGCAAC
.(((.(..((.(((.-----------....(((.(((((...(((((((...(((..((((......)))).)))....)))))))...))))).))).......))).))..))))... ( -38.60)
>DroSim_CAF1 10773 115 - 1
AGCGGCAGAGCAGCGGC-----AGCGGCAGCGACGUCGGCAGAGCGCAAUCGCUGGAGAUCAGAGAAGAUCACAGAAUUUUGCGCUGAUCCGACUUUGAUUCUAAGCUACUAAGCGCAAC
.((.((......)).))-----.((((...(((.(((((...(((((((...(((..((((......)))).)))....)))))))...))))).)))...))..(((....)))))... ( -40.20)
>DroEre_CAF1 10788 120 - 1
AGCGGCAGAGCAGCGGCAGAACAGCGGCAGCGACGUCGGCAGAGAGCAAUCGCUGGAGAUCAGAGAAGAUCACAGAAAUUUGCGCUGAUCCGACUUUGAUUCUAAGCUACUAAGCGCAAC
.(((..(((((.((.((......)).))..(((.((((((((...((((...(((..((((......)))).)))....)))).)))..))))).))).......))).))...)))... ( -38.70)
>DroYak_CAF1 10313 97 - 1
AGCGGCAGAGC-----------------------GCCGGCAGAGAGCAAUCGCUGGAGAUCUGAGAAGAUCACAGAAAUUUGCGCUGAUCCGACUUUGAUUCUAAGCUACUAAACGCAAC
.(((..(((((-----------------------..((((((...((((...(((..(((((....))))).)))....)))).)))..)))...(((....)))))).))...)))... ( -26.60)
>consensus
AGCGGCAGAGCAGCGGC_____AGCGGCAGCGACGUCGGCAGAGAGCAAUCGCUGGAGAUCAGAGAAGAUCACAGAAUUUUGCGCUGAUCCGACUUUGAUUCUAAGCUACUAAGCGCAAC
.(((..(((((.((.((......)).))......((((((((...((((...(((..((((......)))).)))....)))).)))..)))))...........))).))...)))... (-29.60 = -30.30 +   0.70)

alignment

secondary structure

dotplot

Window 4

Location	15,980,944 – 15,981,059
Length	115
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	88.66
Mean single sequence MFE	-33.16
Consensus MFE	-26.62
Energy contribution	-27.00
Covariance contribution	0.38
Combinations/Pair	1.04
Mean z-score	-2.12
Structure conservation index	0.80
SVM decision value	1.44
SVM RNA-class probability	0.954070
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15980944 115 - 23771897
AAGUAAUAAACCAAUUAGGACAUCAAAGUGUUCAGCCGGCAGCUGCAGAGCAGCGGC-----AGCGGCAGCGACGUCGGCAGAGAGCAAUCGCUGGAGAUCAGAGAAGAUCACAGAAUUU
.................((((((....)))))).((((((.(((((...((......-----.)).)))))...))))))...((....)).(((..((((......)))).)))..... ( -35.90)
>DroSec_CAF1 10100 109 - 1
AAGUAAUAAACCAAUUAGGACAUCAAAGUGUUCAGCCGACAGCGGCAGAGCAGCG-----------GCAGCGACGUCGGCAGAGCGCAAUCGCUGGAGAUCAGAGAAGAUCACAGAAUUU
..........((.....))........((((((.((((((.((......)).((.-----------...))...)))))).)))))).....(((..((((......)))).)))..... ( -32.80)
>DroSim_CAF1 10813 115 - 1
AAGUAAUAAACCAAUUAGGACAUCAAAGUGUUCAGCCGACAGCGGCAGAGCAGCGGC-----AGCGGCAGCGACGUCGGCAGAGCGCAAUCGCUGGAGAUCAGAGAAGAUCACAGAAUUU
..........((.....))........((((((.((((((.((.((......)).))-----.((....))...)))))).)))))).....(((..((((......)))).)))..... ( -36.90)
>DroEre_CAF1 10828 120 - 1
AAGUAAUAAACCAAUUAGGACAUCAAAGUGUUCAGCCGACAGCGGCAGAGCAGCGGCAGAACAGCGGCAGCGACGUCGGCAGAGAGCAAUCGCUGGAGAUCAGAGAAGAUCACAGAAAUU
.................((((((....)))))).((((((.((......)).((.((......)).))......))))))...((....)).(((..((((......)))).)))..... ( -34.30)
>DroYak_CAF1 10353 97 - 1
AAGUAAUAAACCAAUUAGGACAUCAAAGUGUUCAGCCGACAGCGGCAGAGC-----------------------GCCGGCAGAGAGCAAUCGCUGGAGAUCUGAGAAGAUCACAGAAAUU
..((.............((((((....)))))).((((....))))...))-----------------------.(((((.((......))))))).(((((....)))))......... ( -25.90)
>consensus
AAGUAAUAAACCAAUUAGGACAUCAAAGUGUUCAGCCGACAGCGGCAGAGCAGCGGC_____AGCGGCAGCGACGUCGGCAGAGAGCAAUCGCUGGAGAUCAGAGAAGAUCACAGAAUUU
..........(((....((((((....)))))).((((((.((......)).((.((......)).))......)))))).....((....))))).((((......))))......... (-26.62 = -27.00 +   0.38)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:05:26 2006