Locus 5105

Sequence ID	X_DroMel_CAF1
Location	13,330,699 – 13,330,822
Length	123
Max. P	0.886637

overview

Window 3

Location	13,330,699 – 13,330,790
Length	91
Sequences	6
Columns	110
Reading direction	forward
Mean pairwise identity	82.65
Mean single sequence MFE	-28.12
Consensus MFE	-23.64
Energy contribution	-23.50
Covariance contribution	-0.14
Combinations/Pair	1.04
Mean z-score	-2.11
Structure conservation index	0.84
SVM decision value	0.94
SVM RNA-class probability	0.886637
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 13330699 91 + 22224390
UCACGUGUGA------------------GUGGAGUGGAGUGCAGGCCUCGUAAAAGUUUAUAUGGCAAGCACUUGGCGACGA-GCGAGCUACUGCAAAUAAUUGCAAAGU
....((.((.------------------.((..((.((((((..(((..((((....))))..)))..)))))).))..)).-.)).))...(((((....))))).... ( -28.40)
>DroPse_CAF1 93933 76 + 1
---------------------------------GUGGAGUGCAGGCCUCGUAAAAGUUUAUAUGGCAGGCACUUGGCGACGA-GCAAGCUACUGCAAAUAAUUGCAAAGU
---------------------------------((.((((((..(((..((((....))))..)))..)))))).)).....-....(((..(((((....))))).))) ( -24.10)
>DroSim_CAF1 35080 91 + 1
UCACGUGUGA------------------GUGGAGUGGAGUGCAGGCCUCGUAAAAGUUUAUAUGGCAAGCACUUGGCGACGA-GCGAGCUACUGCAAAUAAUUGCAAAGU
....((.((.------------------.((..((.((((((..(((..((((....))))..)))..)))))).))..)).-.)).))...(((((....))))).... ( -28.40)
>DroEre_CAF1 34666 91 + 1
UCACGUGUGA------------------GUGGAGUGGAGUGCAGGCCUCGUAAAAGUUUAUAUGGCAAGCACUUGGCGACGA-GCGAGCUACUGCAAAUAAUUGCAAAGU
....((.((.------------------.((..((.((((((..(((..((((....))))..)))..)))))).))..)).-.)).))...(((((....))))).... ( -28.40)
>DroAna_CAF1 19437 110 + 1
CCCCUUGUGACUAAGCCACUGGAUACUGGUUGAGUGAAGUGCAGGCCUCGUAAAAGUUUAUAUGGCAAGCACUUGGCGACGGGGCGAGCUACUGCAAAUAAUUGCAAAGU
((((((((.(((.(((((........))))).))).((((((..(((..((((....))))..)))..)))))).)))).))))...(((..(((((....))))).))) ( -34.80)
>DroPer_CAF1 94330 78 + 1
-------------------------------GUGUGGAGUGCAGGCCUCGUAAAAGUUUAUAUGGCAGGCACUUGGCGACGA-GCAAGCUACUGCAAAUAAUUGCAAAGU
-------------------------------((((.((((((..(((..((((....))))..)))..)))))).)).))..-....(((..(((((....))))).))) ( -24.60)
>consensus
UCACGUGUGA__________________GUGGAGUGGAGUGCAGGCCUCGUAAAAGUUUAUAUGGCAAGCACUUGGCGACGA_GCGAGCUACUGCAAAUAAUUGCAAAGU
.................................((.((((((..(((..((((....))))..)))..)))))).))..........(((..(((((....))))).))) (-23.64 = -23.50 +  -0.14)

alignment

secondary structure

dotplot

Window 4

Location	13,330,714 – 13,330,822
Length	108
Sequences	6
Columns	111
Reading direction	forward
Mean pairwise identity	90.31
Mean single sequence MFE	-34.52
Consensus MFE	-29.78
Energy contribution	-29.28
Covariance contribution	-0.50
Combinations/Pair	1.10
Mean z-score	-1.77
Structure conservation index	0.86
SVM decision value	0.59
SVM RNA-class probability	0.792282
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 13330714 108 + 22224390
GUGGAGUGCAGGCCUCGUAAAAGUUUAUAUGGCAAGCACUUGGCGACGA-GCGAGCUACUGCAAAUAAUUGCAAAGUCUU-UGGCCAAGUCUUGG-CAGCCACUGCUGCUG
((.((((((..(((..((((....))))..)))..)))))).))(((..-((.((..(((((((....))))..)))..)-).))...)))..((-((((....)))))). ( -37.70)
>DroPse_CAF1 93933 97 + 1
GUGGAGUGCAGGCCUCGUAAAAGUUUAUAUGGCAGGCACUUGGCGACGA-GCAAGCUACUGCAAAUAAUUGCAAAGUCUUUUGGCCAAGUCUUGG-------------CUG
((.((((((..(((..((((....))))..)))..)))))).))(((.(-(....))..(((((....)))))..)))....(((((.....)))-------------)). ( -32.70)
>DroEre_CAF1 34681 105 + 1
GUGGAGUGCAGGCCUCGUAAAAGUUUAUAUGGCAAGCACUUGGCGACGA-GCGAGCUACUGCAAAUAAUUGCAAAGUCUU-UGGCCAAGUCUUGG-CAGCCGCU---GCUG
((.((((((..(((..((((....))))..)))..)))))).))....(-(((.(((..(((((....))))).......-..((((.....)))-))))))))---.... ( -37.40)
>DroYak_CAF1 34693 105 + 1
GUGGAGUGCAGGCCUCGUAAAAGUUUAUAUGGCAAGCACUUGGCGACGA-GCGAGCUACUGCAAAUAAUUGCAAAGUCUU-UGGCCAAGUCUUGA-CAGCCACU---GCUG
((.((((((..(((..((((....))))..)))..)))))).))(((..-((.((..(((((((....))))..)))..)-).))...)))....-((((....---)))) ( -32.30)
>DroAna_CAF1 19470 107 + 1
GUGAAGUGCAGGCCUCGUAAAAGUUUAUAUGGCAAGCACUUGGCGACGGGGCGAGCUACUGCAAAUAAUUGCAAAGUCUC-UGGCAAAGUCUUGGGCUUCCACU---GCUG
((.((((((..(((..((((....))))..)))..)))))).))(((...((.((..(((((((....))))..)))..)-).))...)))...(((.......---))). ( -34.30)
>DroPer_CAF1 94332 97 + 1
GUGGAGUGCAGGCCUCGUAAAAGUUUAUAUGGCAGGCACUUGGCGACGA-GCAAGCUACUGCAAAUAAUUGCAAAGUCUUUUGGCCAAGUCUUGG-------------CUG
((.((((((..(((..((((....))))..)))..)))))).))(((.(-(....))..(((((....)))))..)))....(((((.....)))-------------)). ( -32.70)
>consensus
GUGGAGUGCAGGCCUCGUAAAAGUUUAUAUGGCAAGCACUUGGCGACGA_GCGAGCUACUGCAAAUAAUUGCAAAGUCUU_UGGCCAAGUCUUGG_CAGCCACU___GCUG
((.((((((..(((..((((....))))..)))..)))))).))(((...(((((((..(((((....))))).)).)))...))...))).................... (-29.78 = -29.28 +  -0.50)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:40:16 2006