Locus 5359

Sequence ID	X_DroMel_CAF1
Location	13,953,822 – 13,953,964
Length	142
Max. P	0.983984

overview

Window 5

Location	13,953,822 – 13,953,927
Length	105
Sequences	4
Columns	106
Reading direction	reverse
Mean pairwise identity	94.47
Mean single sequence MFE	-25.56
Consensus MFE	-22.31
Energy contribution	-22.88
Covariance contribution	0.56
Combinations/Pair	1.04
Mean z-score	-2.13
Structure conservation index	0.87
SVM decision value	1.05
SVM RNA-class probability	0.907053
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 13953822 105 - 22224390
GGUUGGAAAAUGUUAUCGCAACCUGUGGGCGAAGAAUCUUGAAAGAUGAUUUGCUAGACCAGCAGGGUGAUAA-AAUCAAGCACAAAUUAAGCAAAAGAUUAGAUA
(.((((......(((((((..(((((.((((((..((((....))))..))))))......))))))))))))-..)))).)........................ ( -24.40)
>DroSec_CAF1 5262 105 - 1
GGUUGGAAAAUGCUAUCGCAACCUGUGGGCGAAGAAUCUCGAAAGAUGAUUUGCUCGACCAGCAGGGUGAUAA-AAUCAAGCACAAAUUAGGCAAAAGAUUAGAUA
.(((......(((((((((..(((((.(((((.(((((((....)).)))))..))).)).))))))))))..-.....)))).......)))............. ( -28.23)
>DroSim_CAF1 5664 105 - 1
GGUUGGAAAACGCUAUCGCAACCUGUGGGCGAAGAAUCUCGAAAGAUGAUUUGCUCGACCAGCAGGGUGAUAA-AAUCAAGCACAAAUUAAGCAAAAGAUUAGAUA
.(((....)))..((((((..(((((.(((((.(((((((....)).)))))..))).)).))))))))))).-......((.........))............. ( -29.30)
>DroYak_CAF1 5703 106 - 1
GGAAGGAAAAUGCUAUCGCAACCUGUGGGCGAAGAAUCUCGAAAGAUGAUUUGCUGGACCAGCUGGGUGAUAAAAAUGAAGCACAAAUUUAGCAAAAGAUUAGAUA
..........(((((((((..((.((.(((.(.(((((((....)).)))))..).).)).)).))))))))....((((.......)))))))............ ( -20.30)
>consensus
GGUUGGAAAAUGCUAUCGCAACCUGUGGGCGAAGAAUCUCGAAAGAUGAUUUGCUCGACCAGCAGGGUGAUAA_AAUCAAGCACAAAUUAAGCAAAAGAUUAGAUA
.............((((((..(((((.(((((.(((((((....)).)))))..))).)).)))))))))))........((.........))............. (-22.31 = -22.88 +   0.56)

alignment

secondary structure

dotplot

Window 6

Location	13,953,855 – 13,953,964
Length	109
Sequences	4
Columns	112
Reading direction	reverse
Mean pairwise identity	86.38
Mean single sequence MFE	-28.32
Consensus MFE	-22.17
Energy contribution	-22.80
Covariance contribution	0.63
Combinations/Pair	1.11
Mean z-score	-2.84
Structure conservation index	0.78
SVM decision value	1.96
SVM RNA-class probability	0.983984
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 13953855 109 - 22224390
GUAAUGUGAAAAAUCCAGAA---AAAAAGGAUUGAAAAGUGGUUGGAAAAUGUUAUCGCAACCUGUGGGCGAAGAAUCUUGAAAGAUGAUUUGCUAGACCAGCAGGGUGAUA
....(((((..(((((....---.....)))))........(((....)))....))))).(((((.((((((..((((....))))..))))))......)))))...... ( -25.30)
>DroSec_CAF1 5295 107 - 1
GAAAUGUGAAAAAUCAGGAA-----AAAGCUUUGAAAAGCGGUUGGAAAAUGCUAUCGCAACCUGUGGGCGAAGAAUCUCGAAAGAUGAUUUGCUCGACCAGCAGGGUGAUA
....(((((....(((((..-----.....)))))..((((.((....)))))).))))).(((((.(((((.(((((((....)).)))))..))).)).)))))...... ( -31.30)
>DroSim_CAF1 5697 107 - 1
GAAAUGUGAAAAAUCAGGAA-----AAAGCAUUGAAAAGCGGUUGGAAAACGCUAUCGCAACCUGUGGGCGAAGAAUCUCGAAAGAUGAUUUGCUCGACCAGCAGGGUGAUA
....(((((....((((...-----......))))..((((.((....)))))).))))).(((((.(((((.(((((((....)).)))))..))).)).)))))...... ( -32.50)
>DroYak_CAF1 5737 109 - 1
---UUGUGAAAAAUCAGGCAAAAAAAAAUGUCUAGAGAGUGGAAGGAAAAUGCUAUCGCAACCUGUGGGCGAAGAAUCUCGAAAGAUGAUUUGCUGGACCAGCUGGGUGAUA
---.........(((((((.........((((((.((..((((.((......)).)).))..)).))))))..(((((((....)).))))))))...((....)).)))). ( -24.20)
>consensus
GAAAUGUGAAAAAUCAGGAA_____AAAGCAUUGAAAAGCGGUUGGAAAAUGCUAUCGCAACCUGUGGGCGAAGAAUCUCGAAAGAUGAUUUGCUCGACCAGCAGGGUGAUA
............((((......................(((((.((......)))))))..(((((.(((((.(((((((....)).)))))..))).)).))))).)))). (-22.17 = -22.80 +   0.63)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:46:03 2006