Locus 387

Sequence ID	2R_DroMel_CAF1
Location	2,364,306 – 2,364,462
Length	156
Max. P	0.999386

overview

Window 7

Location	2,364,306 – 2,364,422
Length	116
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	89.20
Mean single sequence MFE	-36.44
Consensus MFE	-29.20
Energy contribution	-28.36
Covariance contribution	-0.84
Combinations/Pair	1.25
Mean z-score	-1.56
Structure conservation index	0.80
SVM decision value	0.36
SVM RNA-class probability	0.702617
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 2364306 116 - 20766785
CACUCAUUUAUUACAAGCGCAGAGCGGUAUUUUCCAUCUUAUCUGCUCGGGGGCCAGCUUCCCCGCAAUUUGCGUUUGCAGUGGCCUCGGCUUUGGUGCU----CUCCAUACCCGAAAGU
.......(((((.((((((((((((((...............))))))(((((......)))))......)))))))).)))))..((((...(((....----..)))...)))).... ( -36.56)
>DroSec_CAF1 13842 116 - 1
CACUCAUUUAUUACGAGCGCAGAGCGGUAUUUUCCAUCUUAUCUGCUCGGGGGCCAGCUUCCCCGCAAUUUGCGUUUGCAGUGGCCUCGGCUUUGGUGCG----CUCCAUACCCGAAAGU
..............(((((((((((((...............)))))).(((((((((.....(((.....)))...))..)))))))........))))----)))......(....). ( -38.06)
>DroSim_CAF1 13936 116 - 1
CACUCAUUUAUUACGAGCGCAGAGCGGUAUUUUCCAUCUUAUCUGCUCGGGGGCCAGCUUCCCCGCAAUUUGCGUUUGCAGUGGCCUCGGCUUUGGUGCG----CUCCAUACCCGAAAGU
..............(((((((((((((...............)))))).(((((((((.....(((.....)))...))..)))))))........))))----)))......(....). ( -38.06)
>DroEre_CAF1 13540 119 - 1
CACUCAUUUGUUACAAGCGCAGAGCGAUAUUUUCCAUCUUAUCUGCUCGGGGGCCAGCUUCC-CGCAAUUUGCGUUUGCAUUGGCCCCAGCUCCCAGCUCCAAACUCCAGUCCCAAAAGU
......((((..((..(.(((((..(((.......)))...))))).).(((((((((....-(((.....)))...))..)))))))(((.....)))..........))..))))... ( -32.90)
>DroYak_CAF1 13288 116 - 1
CACUCAUUUAUUACGAGCGCAGAGUGAUAUUUUCCGUCUUAUCUGCUCGGGGGCCAGCUUCCUCGCAAUACGCGUUUGCAUUGGCCUCGGCUUGGGUGUC----CUCCAUGCCCAAAAGU
..............(((((((((..(((.......)))...)))))...(((((((((.....(((.....)))...))..))))))).))))((((((.----....))))))...... ( -36.60)
>consensus
CACUCAUUUAUUACGAGCGCAGAGCGGUAUUUUCCAUCUUAUCUGCUCGGGGGCCAGCUUCCCCGCAAUUUGCGUUUGCAGUGGCCUCGGCUUUGGUGCC____CUCCAUACCCGAAAGU
..............(((((((((..(((.......)))...)))))...(((((((((.....(((.....)))...))..))))))).)))).((((...........))))....... (-29.20 = -28.36 +  -0.84)

alignment

secondary structure

dotplot

Window 8

Location	2,364,342 – 2,364,462
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	95.25
Mean single sequence MFE	-33.72
Consensus MFE	-31.44
Energy contribution	-31.12
Covariance contribution	-0.32
Combinations/Pair	1.19
Mean z-score	-2.18
Structure conservation index	0.93
SVM decision value	3.56
SVM RNA-class probability	0.999386
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 2364342 120 - 20766785
AUGUCUGCCGAUAUGUAUUUACUUUCAAUUUUAGGCAGUACACUCAUUUAUUACAAGCGCAGAGCGGUAUUUUCCAUCUUAUCUGCUCGGGGGCCAGCUUCCCCGCAAUUUGCGUUUGCA
.((((((((........................))))).)))...........((((((((((((((...............))))))(((((......)))))......)))))))).. ( -35.72)
>DroSec_CAF1 13878 120 - 1
AUAUCUGCCGAUAUGUAUUUACUUUCAAUUUUAGGCAGAACACUCAUUUAUUACGAGCGCAGAGCGGUAUUUUCCAUCUUAUCUGCUCGGGGGCCAGCUUCCCCGCAAUUUGCGUUUGCA
...((((((........................))))))..............((((((((((((((...............))))))(((((......)))))......)))))))).. ( -35.22)
>DroSim_CAF1 13972 120 - 1
AUAUCUGCCGAUAUGUAUUUACUUUCAAUUUUAGGCAGAACACUCAUUUAUUACGAGCGCAGAGCGGUAUUUUCCAUCUUAUCUGCUCGGGGGCCAGCUUCCCCGCAAUUUGCGUUUGCA
...((((((........................))))))..............((((((((((((((...............))))))(((((......)))))......)))))))).. ( -35.22)
>DroEre_CAF1 13580 119 - 1
AUGUCUGCCGAUAUGUAUUUACUUUCAAUUUUAGGCGGAACACUCAUUUGUUACAAGCGCAGAGCGAUAUUUUCCAUCUUAUCUGCUCGGGGGCCAGCUUCC-CGCAAUUUGCGUUUGCA
.((((((((........................))))).)))...........((((((((((((((((..........)))).))))(((((....)))))-.......)))))))).. ( -32.06)
>DroYak_CAF1 13324 120 - 1
AUGUCUGCCGAUACGUAUUUACUUUCAAUUUUAGGCAGAACACUCAUUUAUUACGAGCGCAGAGUGAUAUUUUCCGUCUUAUCUGCUCGGGGGCCAGCUUCCUCGCAAUACGCGUUUGCA
.((((((((........................))))).)))...........(((((((.((((((((..........)))).))))(((((....))))).........))))))).. ( -30.36)
>consensus
AUGUCUGCCGAUAUGUAUUUACUUUCAAUUUUAGGCAGAACACUCAUUUAUUACGAGCGCAGAGCGGUAUUUUCCAUCUUAUCUGCUCGGGGGCCAGCUUCCCCGCAAUUUGCGUUUGCA
...((((((........................))))))..............((((((((((((((((..........)))).))))(((((......)))))......)))))))).. (-31.44 = -31.12 +  -0.32)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:37:10 2006