Locus 1533

Sequence ID	X_DroMel_CAF1
Location	4,443,872 – 4,444,095
Length	223
Max. P	0.992909

overview

Window 0

Location	4,443,872 – 4,443,992
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	97.17
Mean single sequence MFE	-36.60
Consensus MFE	-34.62
Energy contribution	-34.34
Covariance contribution	-0.28
Combinations/Pair	1.09
Mean z-score	-1.60
Structure conservation index	0.95
SVM decision value	1.72
SVM RNA-class probability	0.973980
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4443872 120 + 22224390
GAUGAAAAUGGCCCAGAGUGGGUGGAAAGUCAUAUAACAAGGACAGCGAACAGGUAGGAACUGCCUGGACAUGGCAUGCUCAUUAGGCAAAUCCUUGGAGACCCUUAUCGAGUGUGCGGA
.((((...(.((((.....)))).)....))))..........((..(..(((((((...)))))))..).))((((((((..((((....((....))....))))..))))))))... ( -35.10)
>DroSec_CAF1 45497 120 + 1
GAUGAAAAUGGCCCAGAGUGGGUGGAAAGUCAUAUAACAAGGACAGCGAACAGGUAGGAACUGCCUGGACAUGGCAUACUCAUUAGGCAAAUCCUUGGAGACCCUUAUCGAGUGUGCGGG
.((((...(.((((.....)))).)....))))..........((..(..(((((((...)))))))..).))((((((((..((((....((....))....))))..))))))))... ( -36.10)
>DroSim_CAF1 46688 120 + 1
GAUGAAAAUGGCCCAGAGUGGGUGGAAAGUCAUAUAACAAGGACAGCGAACAGGUAGGAACUGCCUGGACAUGGCAUGCUCAUUAGGCAAAUCCUUGGAGACCCUUAUCGAGUGUGCGGG
.((((...(.((((.....)))).)....))))..........((..(..(((((((...)))))))..).))((((((((..((((....((....))....))))..))))))))... ( -35.10)
>DroEre_CAF1 47350 120 + 1
GAUGAAAAUGGCCCAGAGUGGGUGGAAAGUCAUAUAACAAGGACAGCGAACAAGUAGGAACUGCCUGGACAUGGCAUGCUCAUUAGGCAAAUCCUUGGAGAGCCUUAUCGAGUGUGCGGG
.((((...(.((((.....)))).)....))))....((.(..(((.(....(((....))).))))..).))((((((((((.((((...((....))..)))).)).))))))))... ( -34.90)
>DroYak_CAF1 46161 120 + 1
GAUGAAAAUGGCCCAGAGUGGGUGGAAAGUCAUAUAAAAAGGACAACGAACAGGCAGGAACUGCCUGGACACGGCAUGCUCAUUAGGCAAAUCCUUGGAGAGCCUUAUCGAGUGUGCGGG
.((((...(.((((.....)))).)....))))..............(..(((((((...)))))))..).(.((((((((((.((((...((....))..)))).)).)))))))).). ( -41.80)
>consensus
GAUGAAAAUGGCCCAGAGUGGGUGGAAAGUCAUAUAACAAGGACAGCGAACAGGUAGGAACUGCCUGGACAUGGCAUGCUCAUUAGGCAAAUCCUUGGAGACCCUUAUCGAGUGUGCGGG
.((((...(.((((.....)))).)....))))..............(..(((((((...)))))))..).(.((((((((..((((....((....))....))))..)))))))).). (-34.62 = -34.34 +  -0.28)

alignment

secondary structure

dotplot

Window 1

Location	4,443,912 – 4,444,024
Length	112
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	91.25
Mean single sequence MFE	-29.52
Consensus MFE	-26.12
Energy contribution	-26.24
Covariance contribution	0.12
Combinations/Pair	1.12
Mean z-score	-1.98
Structure conservation index	0.88
SVM decision value	2.36
SVM RNA-class probability	0.992909
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4443912 112 + 22224390
GGACAGCGAACAGGUAGGAACUGCCUGGACAUGGCAUGCUCAUUAGGCAAAUCCUUGGAGACCCUUAUCGAGUGUGCGGAGUAUAUAAAAAAAAAAAAC--------AGAAGGCGAAUAA
.....((...(((((((...))))))).((.(.((((((((..((((....((....))....))))..)))))))).).)).................--------.....))...... ( -28.40)
>DroSec_CAF1 45537 112 + 1
GGACAGCGAACAGGUAGGAACUGCCUGGACAUGGCAUACUCAUUAGGCAAAUCCUUGGAGACCCUUAUCGAGUGUGCGGGGGAUAUAAAAAAAAAAAAC--------AGAAGGCGAAUAA
.....(((..(((((((...)))))))..)...((((((((..((((....((....))....))))..))))))))......................--------.....))...... ( -29.10)
>DroSim_CAF1 46728 109 + 1
GGACAGCGAACAGGUAGGAACUGCCUGGACAUGGCAUGCUCAUUAGGCAAAUCCUUGGAGACCCUUAUCGAGUGUGCGGGGGAUAUAAAAA---AAAAC--------AGAAGGCGAAUAA
.....(((..(((((((...)))))))..)...((((((((..((((....((....))....))))..))))))))..............---.....--------.....))...... ( -28.10)
>DroEre_CAF1 47390 117 + 1
GGACAGCGAACAAGUAGGAACUGCCUGGACAUGGCAUGCUCAUUAGGCAAAUCCUUGGAGAGCCUUAUCGAGUGUGCGGGGGAUAUAAAAA---AAAAACAAAAAGAAAAAGGCGAAUAA
.....(((..((.((((...)))).))..)...((((((((((.((((...((....))..)))).)).))))))))..............---..................))...... ( -25.30)
>DroYak_CAF1 46201 109 + 1
GGACAACGAACAGGCAGGAACUGCCUGGACACGGCAUGCUCAUUAGGCAAAUCCUUGGAGAGCCUUAUCGAGUGUGCGGGGGAUAUAAAAA---AAAAC--------GGAAGUCGAAUAA
.(((..((..(((((((...)))))))....(.((((((((((.((((...((....))..)))).)).)))))))).)............---....)--------)...)))...... ( -36.70)
>consensus
GGACAGCGAACAGGUAGGAACUGCCUGGACAUGGCAUGCUCAUUAGGCAAAUCCUUGGAGACCCUUAUCGAGUGUGCGGGGGAUAUAAAAA___AAAAC________AGAAGGCGAAUAA
.....(((..(((((((...)))))))..).(.((((((((..((((....((....))....))))..)))))))).).................................))...... (-26.12 = -26.24 +   0.12)

alignment

secondary structure

dotplot

Window 2

Location	4,443,992 – 4,444,095
Length	103
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	85.93
Mean single sequence MFE	-23.96
Consensus MFE	-19.35
Energy contribution	-19.63
Covariance contribution	0.28
Combinations/Pair	1.08
Mean z-score	-1.69
Structure conservation index	0.81
SVM decision value	0.45
SVM RNA-class probability	0.739933
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4443992 103 + 22224390
GUAUAUAAAAAAAAAAAAC--------AGAAGGCGAAUAAAACACCGAUGGGGUUGUAUUGUCACUGUCAUUGCCAGCGGAUGAGUAAUGUAGCCCCUCAUU---------CACCUUAUA
...................--------..((((.((((........((.(((((((((((((((((((........)))).))).)))))))))))))))))---------).))))... ( -25.00)
>DroSec_CAF1 45617 103 + 1
GGAUAUAAAAAAAAAAAAC--------AGAAGGCGAAUAAAACAACGAUGGGGUUGUAAUGUCACUGUCAUUGCCAGCGGAUGAGUAAUGUAGCCCCUCAUU---------CGCCUUAUA
...................--------..(((((((((........((.(((((((((.(((((((((........)))).))).)).))))))))))))))---------))))))... ( -26.70)
>DroSim_CAF1 46808 100 + 1
GGAUAUAAAAA---AAAAC--------AGAAGGCGAAUAAAACACCGAUGGGGUUGUAUUGUCACUGUCAUUGCCAGCGGAUGAGUAAUGUAGCCCCUCAUU---------CACCUUAUA
...........---.....--------..((((.((((........((.(((((((((((((((((((........)))).))).)))))))))))))))))---------).))))... ( -25.00)
>DroEre_CAF1 47470 117 + 1
GGAUAUAAAAA---AAAAACAAAAAGAAAAAGGCGAAUAAAACACCAAUGGGGUUGUAUUGUCACUGUCAUUGCCAGCGGAUGAGUAAUGUAGACCCUCAUUUAGAAGAGACACCUUAUA
((.........---.................(((.((((.(((.((....))))).))))))).(((.((((((((.....)).))))))))).))(((........))).......... ( -18.50)
>DroYak_CAF1 46281 109 + 1
GGAUAUAAAAA---AAAAC--------GGAAGUCGAAUAAAACACCGAUGGGGUUGUAUUGUCACUGUCAUUGCCAGCAGAUGAAUAAUGUAACCCCUCAUUUAGAAGAGCCACCUUAUA
((...((((..---...((--------....)).............((.(((((((((((((((((((........)))).)).))))))))))))))).))))......))........ ( -24.60)
>consensus
GGAUAUAAAAA___AAAAC________AGAAGGCGAAUAAAACACCGAUGGGGUUGUAUUGUCACUGUCAUUGCCAGCGGAUGAGUAAUGUAGCCCCUCAUU_________CACCUUAUA
.............................((((.(..............(((((((((((((((((((........)))).))).))))))))))))..............).))))... (-19.35 = -19.63 +   0.28)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:12:34 2006