Locus 7320

Sequence ID	2L_DroMel_CAF1
Location	20,469,533 – 20,469,692
Length	159
Max. P	0.997994

overview

Window 9

Location	20,469,533 – 20,469,652
Length	119
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	95.24
Mean single sequence MFE	-25.64
Consensus MFE	-23.42
Energy contribution	-22.98
Covariance contribution	-0.44
Combinations/Pair	1.09
Mean z-score	-1.84
Structure conservation index	0.91
SVM decision value	2.40
SVM RNA-class probability	0.993492
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 20469533 119 + 22407834
UAAAUUCCUCGAAAU-GUUUGUCACGUUCCGCACAUAAAAGGAUUUCAAUUUUCCAAUGUGACGAAAAGGCAUUUGCAUACGGAAGAAACCGUAGCAAAUAAAAUAAAAUUUUAUGUAGG
......(((((....-.(((((((((((............(((.........)))))))))))))).....((((((.(((((......)))))))))))..............)).))) ( -25.10)
>DroSec_CAF1 22512 119 + 1
UAAAUUUCUUGAAAU-GUUUGUCACGUUCCGCACAUAAAAGGAUUUCAAUUUUCCAAUGUGACGAAAAGGCAUUUGCAUACGGAAGAAACCGUAGCAAAUAAAAUUAAAUUUUAUGUAGG
.........((((((-.(((((((((((............(((.........)))))))))))))).....((((((.(((((......)))))))))))........))))))...... ( -25.00)
>DroSim_CAF1 24464 119 + 1
UAAAUUUCUUGAAAU-GUUUGUCACGUUCCGCACAUAAAAGGAUUUCAAUUUUCCAAUGUGACGAAAAGGCAUUUGCAUACGGAAGAAACCGUAGCAAAUAAAAUCAAAUUUUAUGUAGG
........((((...-.(((((((((((............(((.........)))))))))))))).....((((((.(((((......)))))))))))....))))............ ( -25.40)
>DroEre_CAF1 24777 119 + 1
UAAAUUCCUUGAAAUCGCUUGUCACGUUUCGCACAUAA-AGGAUUUCAAUUUUCCAAUGUGACAAAAAGGCAUUUGCAUACGGAAGAAACCGUAGCAAAUAAAAUCAAAUUUUAUGUUGG
........((((....((((((((((((..........-.(((.........))))))))))))....)))((((((.(((((......)))))))))))....))))............ ( -26.40)
>DroYak_CAF1 21964 120 + 1
UAAAUUUCUUGAAAUCGCUUGUCACGUUUCGCACAUAAAAGGAUUUCAAUUUUCCAAUGUGACAAAAAGGCAUUUGCAUGCGGAAGAAACCGUAGCAAAUAAAAUCAAAUUUUAUCUAGG
........((((....((((((((((((............(((.........))))))))))))....)))((((((.(((((......)))))))))))....))))............ ( -26.30)
>consensus
UAAAUUUCUUGAAAU_GUUUGUCACGUUCCGCACAUAAAAGGAUUUCAAUUUUCCAAUGUGACGAAAAGGCAUUUGCAUACGGAAGAAACCGUAGCAAAUAAAAUCAAAUUUUAUGUAGG
.........((((((.((((((((((((............(((.........)))))))))))))....))((((((.(((((......)))))))))))........))))))...... (-23.42 = -22.98 +  -0.44)

alignment

secondary structure

dotplot

Window 0

Location	20,469,533 – 20,469,652
Length	119
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	95.24
Mean single sequence MFE	-26.86
Consensus MFE	-24.02
Energy contribution	-23.50
Covariance contribution	-0.52
Combinations/Pair	1.10
Mean z-score	-2.18
Structure conservation index	0.89
SVM decision value	2.98
SVM RNA-class probability	0.997994
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 20469533 119 - 22407834
CCUACAUAAAAUUUUAUUUUAUUUGCUACGGUUUCUUCCGUAUGCAAAUGCCUUUUCGUCACAUUGGAAAAUUGAAAUCCUUUUAUGUGCGGAACGUGACAAAC-AUUUCGAGGAAUUUA
((((((((((((((((...((((((((((((......))))).)))))))..((((((......))))))..))))))...))))))).(((((.((.....))-.))))))))...... ( -27.70)
>DroSec_CAF1 22512 119 - 1
CCUACAUAAAAUUUAAUUUUAUUUGCUACGGUUUCUUCCGUAUGCAAAUGCCUUUUCGUCACAUUGGAAAAUUGAAAUCCUUUUAUGUGCGGAACGUGACAAAC-AUUUCAAGAAAUUUA
........((((((.....((((((((((((......))))).)))))))...(((((.(((((.(((.........)))....))))))))))..........-........)))))). ( -24.80)
>DroSim_CAF1 24464 119 - 1
CCUACAUAAAAUUUGAUUUUAUUUGCUACGGUUUCUUCCGUAUGCAAAUGCCUUUUCGUCACAUUGGAAAAUUGAAAUCCUUUUAUGUGCGGAACGUGACAAAC-AUUUCAAGAAAUUUA
(((((((((((...(((((((((((((((((......))))).))))))...((((((......))))))...)))))).))))))))).))............-............... ( -26.60)
>DroEre_CAF1 24777 119 - 1
CCAACAUAAAAUUUGAUUUUAUUUGCUACGGUUUCUUCCGUAUGCAAAUGCCUUUUUGUCACAUUGGAAAAUUGAAAUCCU-UUAUGUGCGAAACGUGACAAGCGAUUUCAAGGAAUUUA
((.......(((.((((..((((((((((((......))))).))))))).......)))).)))......((((((((((-((((((.....))))))..)).))))))))))...... ( -28.00)
>DroYak_CAF1 21964 120 - 1
CCUAGAUAAAAUUUGAUUUUAUUUGCUACGGUUUCUUCCGCAUGCAAAUGCCUUUUUGUCACAUUGGAAAAUUGAAAUCCUUUUAUGUGCGAAACGUGACAAGCGAUUUCAAGAAAUUUA
....(((((((........(((((((..(((......)))...)))))))...)))))))...........(((((((((((((((((.....)))))).))).))))))))........ ( -27.20)
>consensus
CCUACAUAAAAUUUGAUUUUAUUUGCUACGGUUUCUUCCGUAUGCAAAUGCCUUUUCGUCACAUUGGAAAAUUGAAAUCCUUUUAUGUGCGGAACGUGACAAAC_AUUUCAAGAAAUUUA
........((((((.....((((((((((((......))))).)))))))...(((((.(((((.(((.........)))....))))))))))...................)))))). (-24.02 = -23.50 +  -0.52)

alignment

secondary structure

dotplot

Window 1

Location	20,469,572 – 20,469,692
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	88.17
Mean single sequence MFE	-21.03
Consensus MFE	-17.33
Energy contribution	-18.37
Covariance contribution	1.04
Combinations/Pair	1.03
Mean z-score	-2.30
Structure conservation index	0.82
SVM decision value	1.98
SVM RNA-class probability	0.984528
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 20469572 120 + 22407834
GGAUUUCAAUUUUCCAAUGUGACGAAAAGGCAUUUGCAUACGGAAGAAACCGUAGCAAAUAAAAUAAAAUUUUAUGUAGGACUCAAAAAGUGUCAAUCCCAAAAAAAGAAGGAAAAAUCG
.........((((((................((((((.(((((......)))))))))))...................(((.(.....).)))................)))))).... ( -20.90)
>DroSec_CAF1 22551 109 + 1
GGAUUUCAAUUUUCCAAUGUGACGAAAAGGCAUUUGCAUACGGAAGAAACCGUAGCAAAUAAAAUUAAAUUUUAUGUAGGAUUC----------AAUCCAAAAAAAA-AAAAAAAAACAG
(((((.......(((.(((((((.....)..((((((.(((((......)))))))))))...........)))))).)))...----------)))))........-............ ( -19.70)
>DroSim_CAF1 24503 118 + 1
GGAUUUCAAUUUUCCAAUGUGACGAAAAGGCAUUUGCAUACGGAAGAAACCGUAGCAAAUAAAAUCAAAUUUUAUGUAGGACUCAAAAAGUGUCAAUCCAAAAAAAA--AAAGAAAACCG
((.((((..(((((.........)))))((.((((((.(((((......)))))))))))...................(((.(.....).)))...))........--...)))).)). ( -21.30)
>DroEre_CAF1 24816 117 + 1
GGAUUUCAAUUUUCCAAUGUGACAAAAAGGCAUUUGCAUACGGAAGAAACCGUAGCAAAUAAAAUCAAAUUUUAUGUUGGCCUCAAAAAGUGUGAAUCCAAAACAAA-AUA--AAAAUCC
((((((..((((((((((((((.........((((((.(((((......)))))))))))...........)))))))))......)))))..))))))........-...--....... ( -24.25)
>DroYak_CAF1 22004 115 + 1
GGAUUUCAAUUUUCCAAUGUGACAAAAAGGCAUUUGCAUGCGGAAGAAACCGUAGCAAAUAAAAUCAAAUUUUAUCUAGGACUCAAAAAGUGUGAAUCCAAAAAAAA-AAG--AAAA--A
(((.........)))................((((((.(((((......)))))))))))..................(((.(((.......))).)))........-...--....--. ( -19.00)
>consensus
GGAUUUCAAUUUUCCAAUGUGACGAAAAGGCAUUUGCAUACGGAAGAAACCGUAGCAAAUAAAAUCAAAUUUUAUGUAGGACUCAAAAAGUGUCAAUCCAAAAAAAA_AAA__AAAACCG
(((((...(((((((.((((((.........((((((.(((((......)))))))))))...........)))))).)))......))))...)))))..................... (-17.33 = -18.37 +   1.04)

alignment

secondary structure

dotplot

Window 2

Location	20,469,572 – 20,469,692
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	88.17
Mean single sequence MFE	-25.05
Consensus MFE	-17.18
Energy contribution	-17.50
Covariance contribution	0.32
Combinations/Pair	1.07
Mean z-score	-3.02
Structure conservation index	0.69
SVM decision value	1.10
SVM RNA-class probability	0.915755
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 20469572 120 - 22407834
CGAUUUUUCCUUCUUUUUUUGGGAUUGACACUUUUUGAGUCCUACAUAAAAUUUUAUUUUAUUUGCUACGGUUUCUUCCGUAUGCAAAUGCCUUUUCGUCACAUUGGAAAAUUGAAAUCC
(((((((((..........(((((((.(.......).)))))))...............((((((((((((......))))).)))))))...............)))))))))...... ( -25.50)
>DroSec_CAF1 22551 109 - 1
CUGUUUUUUUUU-UUUUUUUUGGAUU----------GAAUCCUACAUAAAAUUUAAUUUUAUUUGCUACGGUUUCUUCCGUAUGCAAAUGCCUUUUCGUCACAUUGGAAAAUUGAAAUCC
.....((((..(-(((((..((((((----------((((..........)))))))).((((((((((((......))))).)))))))...........))..))))))..))))... ( -20.10)
>DroSim_CAF1 24503 118 - 1
CGGUUUUCUUU--UUUUUUUUGGAUUGACACUUUUUGAGUCCUACAUAAAAUUUGAUUUUAUUUGCUACGGUUUCUUCCGUAUGCAAAUGCCUUUUCGUCACAUUGGAAAAUUGAAAUCC
.((.((((..(--(((((..(((((.((((..(((((.(.....).)))))..))....((((((((((((......))))).))))))).....))))).))..))))))..)))).)) ( -25.80)
>DroEre_CAF1 24816 117 - 1
GGAUUUU--UAU-UUUGUUUUGGAUUCACACUUUUUGAGGCCAACAUAAAAUUUGAUUUUAUUUGCUACGGUUUCUUCCGUAUGCAAAUGCCUUUUUGUCACAUUGGAAAAUUGAAAUCC
(((((((--.((-(((.(..(((((...........((((((((........))).....(((((((((((......))))).)))))))))))...))).))..).))))).))))))) ( -28.84)
>DroYak_CAF1 22004 115 - 1
U--UUUU--CUU-UUUUUUUUGGAUUCACACUUUUUGAGUCCUAGAUAAAAUUUGAUUUUAUUUGCUACGGUUUCUUCCGCAUGCAAAUGCCUUUUUGUCACAUUGGAAAAUUGAAAUCC
.--.(((--(..-((((((..(((((((.......)))))))..(((((((........(((((((..(((......)))...)))))))...))))))).....))))))..))))... ( -25.00)
>consensus
CGAUUUU__UUU_UUUUUUUUGGAUUCACACUUUUUGAGUCCUACAUAAAAUUUGAUUUUAUUUGCUACGGUUUCUUCCGUAUGCAAAUGCCUUUUCGUCACAUUGGAAAAUUGAAAUCC
.....................(((((...........))))).........((((((((((((((((((((......))))).)))))).((.............))))))))))).... (-17.18 = -17.50 +   0.32)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:33:27 2006