Locus 5342

Sequence ID	3R_DroMel_CAF1
Location	14,020,100 – 14,020,247
Length	147
Max. P	0.999920

overview

Window 6

Location	14,020,100 – 14,020,207
Length	107
Sequences	5
Columns	107
Reading direction	reverse
Mean pairwise identity	82.08
Mean single sequence MFE	-31.35
Consensus MFE	-27.32
Energy contribution	-27.45
Covariance contribution	0.13
Combinations/Pair	1.22
Mean z-score	-2.69
Structure conservation index	0.87
SVM decision value	2.54
SVM RNA-class probability	0.995073
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14020100 107 - 27905053
GCGGUCGAAUAUUCGUAAGUCGGACUAGAUCUAUGUAACGAAUAUAGUUCGCCUUGCGGACAUUCGACUGUUUGCUUAAAGUAAUGUUAAACAUGUAUGCAACAAGU
((((((((((.((((((((.(((((((..((........))...))))))).)))))))).))))))))))((((.((.....(((.....))).)).))))..... ( -36.10)
>DroSec_CAF1 5249 93 - 1
GCGGUCGAACAUCAGUAAGUCGAACUAGAUCUA-----CGAAUAUAGUUCGCCUUGCGGAGGUUCGUCUGUGUGCUUAAAGUAAU---------GUAUGCAACAAGU
((((.(((((.((.(((((.(((((((......-----......))))))).))))).)).))))).)))).(((....(....)---------....)))...... ( -29.30)
>DroSim_CAF1 5228 102 - 1
GCGGUCGAGCAUCAGUAAGUCGAACUAGAUCUA-----CGAAUAUAGUUCGCCUUGCGGAGGUUCGUCUGUGUGCUUAAAGUAAUGUUAAACAUGUAUGCAACAAGU
((((.(((((.((.(((((.(((((((......-----......))))))).))))).)).))))).)))).(((.((.....(((.....))).)).)))...... ( -30.00)
>DroEre_CAF1 5241 100 - 1
GCGGUCGAGCUUCCGUAAGUCGGACCACAACUA-----G-AA-ACAGUUCGCGGUAUGGACGUUCGACUGUAUGCUUAAAGUAAUGUUAAACAUGUAUGCAACAAGU
((((((((((.((((((.(.(((((........-----.-..-...))))))..)))))).)))))))))).(((.((.....(((.....))).)).)))...... ( -29.94)
>DroYak_CAF1 5209 100 - 1
GCGGCCGAGCUUCUGUAAGUCGGACUAGAACUA-----G-AA-UUAGUUCGUCUUAUGGACGUUCGACUGUAUGCUUAAAGUAAUGUUAAACAUGUAUGCAACAAGA
((((.(((((.((((((((.((((((((.....-----.-..-)))))))).)))))))).))))).)))).(((.((.....(((.....))).)).)))...... ( -31.40)
>consensus
GCGGUCGAGCAUCAGUAAGUCGGACUAGAUCUA_____CGAAUAUAGUUCGCCUUGCGGACGUUCGACUGUAUGCUUAAAGUAAUGUUAAACAUGUAUGCAACAAGU
((((.(((((.((((((((.(((((((.................))))))).)))))))).))))).)))).(((.((.....(((.....))).)).)))...... (-27.32 = -27.45 +   0.13)

alignment

secondary structure

dotplot

Window 7

Location	14,020,127 – 14,020,247
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	86.82
Mean single sequence MFE	-33.79
Consensus MFE	-31.05
Energy contribution	-30.77
Covariance contribution	-0.28
Combinations/Pair	1.25
Mean z-score	-3.62
Structure conservation index	0.92
SVM decision value	4.56
SVM RNA-class probability	0.999920
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14020127 120 - 27905053
ACCAAGCAACAAAAACUGUAAUCGUAAUGAACAAACAAAUGCGGUCGAAUAUUCGUAAGUCGGACUAGAUCUAUGUAACGAAUAUAGUUCGCCUUGCGGACAUUCGACUGUUUGCUUAAA
...((((((..............((.....))........((((((((((.((((((((.(((((((..((........))...))))))).)))))))).))))))))))))))))... ( -37.80)
>DroSec_CAF1 5267 115 - 1
ACCAAGCAACAAAAACAGUAAUCGUAAUGAACAAACAAAUGCGGUCGAACAUCAGUAAGUCGAACUAGAUCUA-----CGAAUAUAGUUCGCCUUGCGGAGGUUCGUCUGUGUGCUUAAA
...((((................((.....))......((((((.(((((.((.(((((.(((((((......-----......))))))).))))).)).))))).))))))))))... ( -32.00)
>DroSim_CAF1 5255 115 - 1
ACCAAGCAACAAAAACAGUAAUCGUAAUGAACAAACAAAUGCGGUCGAGCAUCAGUAAGUCGAACUAGAUCUA-----CGAAUAUAGUUCGCCUUGCGGAGGUUCGUCUGUGUGCUUAAA
...((((................((.....))......((((((.(((((.((.(((((.(((((((......-----......))))))).))))).)).))))).))))))))))... ( -32.00)
>DroEre_CAF1 5268 113 - 1
ACCAAGCAACAAAAACAGUAAACGUAAUGAACAAACAAAUGCGGUCGAGCUUCCGUAAGUCGGACCACAACUA-----G-AA-ACAGUUCGCGGUAUGGACGUUCGACUGUAUGCUUAAA
...((((................((.....))......((((((((((((.((((((.(.(((((........-----.-..-...))))))..)))))).))))))))))))))))... ( -32.84)
>DroYak_CAF1 5236 113 - 1
ACCAAGCAACAAAAACAGUAAUCGUAAUGAACAAACAAAUGCGGCCGAGCUUCUGUAAGUCGGACUAGAACUA-----G-AA-UUAGUUCGUCUUAUGGACGUUCGACUGUAUGCUUAAA
...((((................((.....))......((((((.(((((.((((((((.((((((((.....-----.-..-)))))))).)))))))).))))).))))))))))... ( -34.30)
>consensus
ACCAAGCAACAAAAACAGUAAUCGUAAUGAACAAACAAAUGCGGUCGAGCAUCAGUAAGUCGGACUAGAUCUA_____CGAAUAUAGUUCGCCUUGCGGACGUUCGACUGUAUGCUUAAA
...((((................((.....))......((((((.(((((.((((((((.(((((((.................))))))).)))))))).))))).))))))))))... (-31.05 = -30.77 +  -0.28)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:52:24 2006