Locus 4556

Sequence ID	3L_DroMel_CAF1
Location	13,109,621 – 13,109,723
Length	102
Max. P	0.999483

overview

Window 4

Location	13,109,621 – 13,109,723
Length	102
Sequences	5
Columns	102
Reading direction	forward
Mean pairwise identity	98.14
Mean single sequence MFE	-33.32
Consensus MFE	-32.00
Energy contribution	-31.92
Covariance contribution	-0.08
Combinations/Pair	1.07
Mean z-score	-2.43
Structure conservation index	0.96
SVM decision value	3.64
SVM RNA-class probability	0.999483
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13109621 102 + 23771897
ACUGCUGCACACACAUGUUUGUCCUGCGCCUAAUUUUGGGUUGCGUGCACCAUGCGUCGCGUCACGUUGAAUACGAAUUGCGUGCAGCAAAAUAACUACUUC
..((((((((((.((((..((..(.(((((((....)))).))))..)).)))).)).(((...(((.....)))...)))))))))))............. ( -31.80)
>DroSec_CAF1 97288 102 + 1
ACUGCUGCACACACAUGUUUGUCCUGCGCCUAAUUUUGGGUUGCGUGCAUCAUGCGUCGCGUCACGUUGAAUACGACUUGCGUGCAGCAAAAUAACUACUUC
..((((((((((.((((..((..(.(((((((....)))).))))..)).)))).)).(((...(((.....)))...)))))))))))............. ( -32.80)
>DroSim_CAF1 95083 102 + 1
ACUGCUGCACACACAUGUUUGUCCUGCGCCUAAUUUUGGGUUGCGUGCACCAUGCGUCGCGUCACGUUGAAUGCGACUUGCGUGCAGCAAAAUAACUACUUC
..((((((((.((((((..((..(.(((((((....)))).))))..)).)))).((((((((.....).))))))).)).))))))))............. ( -35.80)
>DroEre_CAF1 93930 102 + 1
ACUGCUGCACACACAUGUUUGUCCUGCGCCCAAUUUUGGGUUGCGUGCACCAUGCGUCGCGUCACGUUGAAUACGACUUGCGUGCAGCAAAAUAACUACUUC
..((((((((((.((((..((..(.(((((((....)))).))))..)).)))).)).(((...(((.....)))...)))))))))))............. ( -34.10)
>DroYak_CAF1 97253 102 + 1
ACUGCUGCACACACAUGUUUGUCCUGCGCCUAAUUUUGGGUUGCGUGCACCAUGCGUCGCGUCACGUUGAAUUCGACUUGCGUGCAGCAAAAUAACUACUUC
..((((((((((.((((..((..(.(((((((....)))).))))..)).)))).)).(((....((((....)))).)))))))))))............. ( -32.10)
>consensus
ACUGCUGCACACACAUGUUUGUCCUGCGCCUAAUUUUGGGUUGCGUGCACCAUGCGUCGCGUCACGUUGAAUACGACUUGCGUGCAGCAAAAUAACUACUUC
..((((((((((.((((..((..(.(((((((....)))).))))..)).)))).)).(((...(((.....)))...)))))))))))............. (-32.00 = -31.92 +  -0.08)

alignment

secondary structure

dotplot

Window 5

Location	13,109,621 – 13,109,723
Length	102
Sequences	5
Columns	102
Reading direction	reverse
Mean pairwise identity	98.14
Mean single sequence MFE	-33.04
Consensus MFE	-31.20
Energy contribution	-31.48
Covariance contribution	0.28
Combinations/Pair	1.03
Mean z-score	-1.85
Structure conservation index	0.94
SVM decision value	2.15
SVM RNA-class probability	0.989118
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13109621 102 - 23771897
GAAGUAGUUAUUUUGCUGCACGCAAUUCGUAUUCAACGUGACGCGACGCAUGGUGCACGCAACCCAAAAUUAGGCGCAGGACAAACAUGUGUGUGCAGCAGU
............(((((((((((....(((.....)))....)).(((((((.((..(((..((........)).)).)..))..)))))))))))))))). ( -29.50)
>DroSec_CAF1 97288 102 - 1
GAAGUAGUUAUUUUGCUGCACGCAAGUCGUAUUCAACGUGACGCGACGCAUGAUGCACGCAACCCAAAAUUAGGCGCAGGACAAACAUGUGUGUGCAGCAGU
............(((((((((((..(((((..((.....)).)))))(((((.((..(((..((........)).)).)..))..)))))))))))))))). ( -32.00)
>DroSim_CAF1 95083 102 - 1
GAAGUAGUUAUUUUGCUGCACGCAAGUCGCAUUCAACGUGACGCGACGCAUGGUGCACGCAACCCAAAAUUAGGCGCAGGACAAACAUGUGUGUGCAGCAGU
............(((((((((((..(((((..((.....)).)))))(((((.((..(((..((........)).)).)..))..)))))))))))))))). ( -34.30)
>DroEre_CAF1 93930 102 - 1
GAAGUAGUUAUUUUGCUGCACGCAAGUCGUAUUCAACGUGACGCGACGCAUGGUGCACGCAACCCAAAAUUGGGCGCAGGACAAACAUGUGUGUGCAGCAGU
............(((((((((((..(((((..((.....)).)))))(((((.((..(((..((((....)))).)).)..))..)))))))))))))))). ( -37.40)
>DroYak_CAF1 97253 102 - 1
GAAGUAGUUAUUUUGCUGCACGCAAGUCGAAUUCAACGUGACGCGACGCAUGGUGCACGCAACCCAAAAUUAGGCGCAGGACAAACAUGUGUGUGCAGCAGU
............(((((((((((..((((...((.....))..))))(((((.((..(((..((........)).)).)..))..)))))))))))))))). ( -32.00)
>consensus
GAAGUAGUUAUUUUGCUGCACGCAAGUCGUAUUCAACGUGACGCGACGCAUGGUGCACGCAACCCAAAAUUAGGCGCAGGACAAACAUGUGUGUGCAGCAGU
............(((((((((((..(((((..((.....)).)))))(((((.((..(((..((........)).)).)..))..)))))))))))))))). (-31.20 = -31.48 +   0.28)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:26:28 2006