Locus 2318

Sequence ID	2L_DroMel_CAF1
Location	6,286,872 – 6,287,026
Length	154
Max. P	0.999961

overview

Window 2

Location	6,286,872 – 6,286,992
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	97.67
Mean single sequence MFE	-32.02
Consensus MFE	-31.14
Energy contribution	-30.86
Covariance contribution	-0.28
Combinations/Pair	1.09
Mean z-score	-1.55
Structure conservation index	0.97
SVM decision value	1.65
SVM RNA-class probability	0.970024
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 6286872 120 + 22407834
GCUCAGUUGGUAAAAUAUUUUGGUAAGCUCGAAGUGUUGAGGCAGUCAAAGAACUGAGGGGCAAUCCUUUAACAAAUUAAUUUUUAGCCUCAAAUGAGCGCCAGCUGCCUUUAAUAGCUU
(((((((((((....(((....))).(((((.....((((((((((......)))(((((....))))).................))))))).)))))))))))))........))).. ( -32.20)
>DroSec_CAF1 123131 119 + 1
GCUCAGUUGGUAAAAUAUUUUGGUAAGCUCGAAGUGUUGGGGCAGUCAAAGAACUGAG-GGCAAUCCUUUAACAAAUUAAUUUUUAGCCUCAAAUGAGCGCCAGCUGCCUUUAAUAGCUU
(((((((((((....(((....))).(((((.....((((((((((......)))(((-((....)))))................))))))).)))))))))))))........))).. ( -30.60)
>DroSim_CAF1 137850 117 + 1
GCUCAGUUGGUAAAAUAUUUUGGUAAGCUCGAAGUGUUGAGGCAGUCAA---ACUGAGGGGCAAUCCUUUAACAAAUUAAUUUUUAGCCUCAAAUGAGCGCCAGCUGCCUUUAAUAGCUU
(((((((((((....(((....))).(((((.....(((((((......---..((((((.....))))))..(((......))).))))))).)))))))))))))........))).. ( -31.60)
>DroEre_CAF1 122800 120 + 1
GCUCAGUUGGUAAAAUAUUUUGGUAAGCUCGAAGUGUUGAGGCAGUCAAAGAACUGAGGGGCAAUCCUUUAACAAAUUAAUUUUUAGCCUCAAAUGAGCGCCAGCUGCCUUUAAUGGCUU
....(((((((....(((....))).(((((.....((((((((((......)))(((((....))))).................))))))).))))))))))))(((......))).. ( -33.60)
>DroYak_CAF1 136071 120 + 1
GCUCAGUUGGUAAAAUAUUUUGGUAAGCUCGAAGUGUUGAGGCAGUCAAAGAACUGAGGGGCAAUCCUUUAACAAAUUAAUUUUUAGCCUCAAAUGAGCGCCGGCUGCCUUUAAUAGCUU
(((..((((....((((((((((.....))))))))))(((((((((.......((((((.....))))))...............(((((....))).)).)))))))))))))))).. ( -32.10)
>consensus
GCUCAGUUGGUAAAAUAUUUUGGUAAGCUCGAAGUGUUGAGGCAGUCAAAGAACUGAGGGGCAAUCCUUUAACAAAUUAAUUUUUAGCCUCAAAUGAGCGCCAGCUGCCUUUAAUAGCUU
(((((((((((....(((....))).(((((.....((((((((((......)))(((((....))))).................))))))).)))))))))))))........))).. (-31.14 = -30.86 +  -0.28)

alignment

secondary structure

dotplot

Window 3

Location	6,286,872 – 6,286,992
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	97.67
Mean single sequence MFE	-26.98
Consensus MFE	-25.44
Energy contribution	-26.08
Covariance contribution	0.64
Combinations/Pair	1.04
Mean z-score	-1.43
Structure conservation index	0.94
SVM decision value	0.99
SVM RNA-class probability	0.896362
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 6286872 120 - 22407834
AAGCUAUUAAAGGCAGCUGGCGCUCAUUUGAGGCUAAAAAUUAAUUUGUUAAAGGAUUGCCCCUCAGUUCUUUGACUGCCUCAACACUUCGAGCUUACCAAAAUAUUUUACCAACUGAGC
..(((......)))...(((.((((..(((((((.............((((((((((((.....)))))))))))).)))))))......))))...))).................... ( -28.44)
>DroSec_CAF1 123131 119 - 1
AAGCUAUUAAAGGCAGCUGGCGCUCAUUUGAGGCUAAAAAUUAAUUUGUUAAAGGAUUGCC-CUCAGUUCUUUGACUGCCCCAACACUUCGAGCUUACCAAAAUAUUUUACCAACUGAGC
(((((......((((..((((.(((....)))))))...........((((((((((((..-..))))))))))))))))...........)))))........................ ( -26.63)
>DroSim_CAF1 137850 117 - 1
AAGCUAUUAAAGGCAGCUGGCGCUCAUUUGAGGCUAAAAAUUAAUUUGUUAAAGGAUUGCCCCUCAGU---UUGACUGCCUCAACACUUCGAGCUUACCAAAAUAUUUUACCAACUGAGC
(((((.....((((((.((((.(((....)))))))....((((.(((....(((......)))))).---))))))))))..........)))))........................ ( -21.26)
>DroEre_CAF1 122800 120 - 1
AAGCCAUUAAAGGCAGCUGGCGCUCAUUUGAGGCUAAAAAUUAAUUUGUUAAAGGAUUGCCCCUCAGUUCUUUGACUGCCUCAACACUUCGAGCUUACCAAAAUAUUUUACCAACUGAGC
..(((......)))...(((.((((..(((((((.............((((((((((((.....)))))))))))).)))))))......))))...))).................... ( -30.64)
>DroYak_CAF1 136071 120 - 1
AAGCUAUUAAAGGCAGCCGGCGCUCAUUUGAGGCUAAAAAUUAAUUUGUUAAAGGAUUGCCCCUCAGUUCUUUGACUGCCUCAACACUUCGAGCUUACCAAAAUAUUUUACCAACUGAGC
..(((......)))....((.((((..(((((((.............((((((((((((.....)))))))))))).)))))))......))))...))..................... ( -27.94)
>consensus
AAGCUAUUAAAGGCAGCUGGCGCUCAUUUGAGGCUAAAAAUUAAUUUGUUAAAGGAUUGCCCCUCAGUUCUUUGACUGCCUCAACACUUCGAGCUUACCAAAAUAUUUUACCAACUGAGC
..(((......)))....((.((((..(((((((.............((((((((((((.....)))))))))))).)))))))......))))...))..................... (-25.44 = -26.08 +   0.64)

alignment

secondary structure

dotplot

Window 4

Location	6,286,912 – 6,287,026
Length	114
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	92.01
Mean single sequence MFE	-37.44
Consensus MFE	-32.44
Energy contribution	-33.64
Covariance contribution	1.20
Combinations/Pair	1.06
Mean z-score	-3.05
Structure conservation index	0.87
SVM decision value	4.02
SVM RNA-class probability	0.999761
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 6286912 114 + 22407834
GGCAGUCAAAGAACUGAGGGGCAAUCCUUUAACAAAUUAAUUUUUAGCCUCAAAUGAGCGCCAGCUGCCUUUAAUAGCUUGUUUCCACCUACUU------AAGUGGGCGGAGGAAAGCCU
((((((........((((((.....))))))...............(((((....))).))..)))))).......((((.(((((.(((((..------..))))).))))).)))).. ( -36.40)
>DroSec_CAF1 123171 113 + 1
GGCAGUCAAAGAACUGAG-GGCAAUCCUUUAACAAAUUAAUUUUUAGCCUCAAAUGAGCGCCAGCUGCCUUUAAUAGCUUGUUUCCACCUACUU------AAGUGGGUGGAGGAGAGCCU
((((((........((((-((....))))))...............(((((....))).))..)))))).......((((.(((((((((((..------..))))))))))).)))).. ( -40.00)
>DroSim_CAF1 137890 111 + 1
GGCAGUCAA---ACUGAGGGGCAAUCCUUUAACAAAUUAAUUUUUAGCCUCAAAUGAGCGCCAGCUGCCUUUAAUAGCUUGUUUCCACCUACUU------AAGUGGGUGGAGGAGAGCCU
((((((...---..((((((.....))))))...............(((((....))).))..)))))).......((((.(((((((((((..------..))))))))))).)))).. ( -40.70)
>DroEre_CAF1 122840 120 + 1
GGCAGUCAAAGAACUGAGGGGCAAUCCUUUAACAAAUUAAUUUUUAGCCUCAAAUGAGCGCCAGCUGCCUUUAAUGGCUUGUUUCCACCUACUUACAAGUAAGUGGGAAAGGGGAAGCCU
((((((........((((((.....))))))...............(((((....))).))..))))))......((((..(..((.((((((((....))))))))...))..))))). ( -37.90)
>DroYak_CAF1 136111 114 + 1
GGCAGUCAAAGAACUGAGGGGCAAUCCUUUAACAAAUUAAUUUUUAGCCUCAAAUGAGCGCCGGCUGCCUUUAAUAGCUUGUUUCCACCUACUU------AAGUGCGGAAAUGGAAGCCU
(((((((.......((((((.....))))))...............(((((....))).)).)))))))...........((((((((((((..------..))).))...))))))).. ( -32.20)
>consensus
GGCAGUCAAAGAACUGAGGGGCAAUCCUUUAACAAAUUAAUUUUUAGCCUCAAAUGAGCGCCAGCUGCCUUUAAUAGCUUGUUUCCACCUACUU______AAGUGGGUGGAGGAAAGCCU
((((((........((((((.....))))))...............(((((....))).))..)))))).......((((.(((((.((((((((....)))))))).))))).)))).. (-32.44 = -33.64 +   1.20)

alignment

secondary structure

dotplot

Window 5

Location	6,286,912 – 6,287,026
Length	114
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	92.01
Mean single sequence MFE	-37.44
Consensus MFE	-33.88
Energy contribution	-35.36
Covariance contribution	1.48
Combinations/Pair	1.10
Mean z-score	-3.29
Structure conservation index	0.90
SVM decision value	4.91
SVM RNA-class probability	0.999961
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 6286912 114 - 22407834
AGGCUUUCCUCCGCCCACUU------AAGUAGGUGGAAACAAGCUAUUAAAGGCAGCUGGCGCUCAUUUGAGGCUAAAAAUUAAUUUGUUAAAGGAUUGCCCCUCAGUUCUUUGACUGCC
.(((((...((((((.((..------..)).))))))...)))))......((((..((((.(((....)))))))...........((((((((((((.....)))))))))))))))) ( -39.00)
>DroSec_CAF1 123171 113 - 1
AGGCUCUCCUCCACCCACUU------AAGUAGGUGGAAACAAGCUAUUAAAGGCAGCUGGCGCUCAUUUGAGGCUAAAAAUUAAUUUGUUAAAGGAUUGCC-CUCAGUUCUUUGACUGCC
.((((....((((((.((..------..)).))))))....))))......((((..((((.(((....)))))))...........((((((((((((..-..)))))))))))))))) ( -38.20)
>DroSim_CAF1 137890 111 - 1
AGGCUCUCCUCCACCCACUU------AAGUAGGUGGAAACAAGCUAUUAAAGGCAGCUGGCGCUCAUUUGAGGCUAAAAAUUAAUUUGUUAAAGGAUUGCCCCUCAGU---UUGACUGCC
.(((..(((((((((.((..------..)).))))))((((((((......)))...((((.(((....))))))).........)))))...)))..)))...(((.---....))).. ( -33.30)
>DroEre_CAF1 122840 120 - 1
AGGCUUCCCCUUUCCCACUUACUUGUAAGUAGGUGGAAACAAGCCAUUAAAGGCAGCUGGCGCUCAUUUGAGGCUAAAAAUUAAUUUGUUAAAGGAUUGCCCCUCAGUUCUUUGACUGCC
.(((((....(((((.(((((((....)))))))))))).)))))......((((..((((.(((....)))))))...........((((((((((((.....)))))))))))))))) ( -41.20)
>DroYak_CAF1 136111 114 - 1
AGGCUUCCAUUUCCGCACUU------AAGUAGGUGGAAACAAGCUAUUAAAGGCAGCCGGCGCUCAUUUGAGGCUAAAAAUUAAUUUGUUAAAGGAUUGCCCCUCAGUUCUUUGACUGCC
.(((((...(((((((.((.------....))))))))).)))))......((((...(((.(((....))))))............((((((((((((.....)))))))))))))))) ( -35.50)
>consensus
AGGCUUUCCUCCACCCACUU______AAGUAGGUGGAAACAAGCUAUUAAAGGCAGCUGGCGCUCAUUUGAGGCUAAAAAUUAAUUUGUUAAAGGAUUGCCCCUCAGUUCUUUGACUGCC
.(((((...((((((.(((((....))))).))))))...)))))......((((..((((.(((....)))))))...........((((((((((((.....)))))))))))))))) (-33.88 = -35.36 +   1.48)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:25:05 2006