Locus 3874

Sequence ID	3L_DroMel_CAF1
Location	11,219,901 – 11,220,000
Length	99
Max. P	0.983940

overview

Window 7

Location	11,219,901 – 11,220,000
Length	99
Sequences	4
Columns	103
Reading direction	forward
Mean pairwise identity	92.74
Mean single sequence MFE	-35.23
Consensus MFE	-30.41
Energy contribution	-31.72
Covariance contribution	1.31
Combinations/Pair	1.03
Mean z-score	-2.99
Structure conservation index	0.86
SVM decision value	1.96
SVM RNA-class probability	0.983940
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 11219901 99 + 23771897
UUCUGCAGGCUAAGGAUUUAAGAAAAGUAUCUUUAAGAUGCAGCCAAGGCAGUUACACCUGUGUAGGUGCACGUA----CGUGUGGGUGCAGCUGUGUGCAGA
.((((((.(((((((((...........)))))))((.((((.(((..(((.(((((....))))).)))((...----.)).))).)))).)))).)))))) ( -34.50)
>DroSec_CAF1 28637 99 + 1
UUCUGCAGGCUAAGGAUUUAAGAAAAGUAUCUUUAAGAUGCAGCCUAGGCAGUUUCACCUGUGUAGGUGCACGUA----CGUGUGGGUGCAGCUGUGUGCAGA
.((((((.(((((((((...........)))))))....((.(((((.((((......)))).)))))((((.((----....)).)))).)).)).)))))) ( -35.90)
>DroSim_CAF1 28894 99 + 1
UUCUGCAGGCUAAGGAUUUAAGAAAAGUAUCUUUAAGAUGCAGCCUAGGCAGUUUCACCUGUGUAGGUCCACGUA----CGUGUGGGUGCAGCUGUGUGCAGA
.((((((.(((((((((...........)))))))((.(((((((((.((((......)))).)))))(((((..----..))))).)))).)))).)))))) ( -36.30)
>DroEre_CAF1 30134 99 + 1
UUCAGCAGGCUAAGGAUUUGAGAAAAGUAUCUUUAAGAUGCAGC----ACAGUUUCACCUGUGUAGGUGCACGUACGUACGUGUGGGUGCAUCUGUGUGCAGA
....(((.((................(((((.....))))).((----((((......))))))((((((((.((((....)))).)))))))))).)))... ( -34.20)
>consensus
UUCUGCAGGCUAAGGAUUUAAGAAAAGUAUCUUUAAGAUGCAGCCUAGGCAGUUUCACCUGUGUAGGUGCACGUA____CGUGUGGGUGCAGCUGUGUGCAGA
.((((((.(((((((((...........)))))))((.(((((((((.((((......)))).)))))(((((......)))))...)))).)))).)))))) (-30.41 = -31.72 +   1.31)

alignment

secondary structure

dotplot

Window 8

Location	11,219,901 – 11,220,000
Length	99
Sequences	4
Columns	103
Reading direction	reverse
Mean pairwise identity	92.74
Mean single sequence MFE	-26.21
Consensus MFE	-21.39
Energy contribution	-22.39
Covariance contribution	1.00
Combinations/Pair	1.00
Mean z-score	-2.88
Structure conservation index	0.82
SVM decision value	1.38
SVM RNA-class probability	0.947932
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 11219901 99 - 23771897
UCUGCACACAGCUGCACCCACACG----UACGUGCACCUACACAGGUGUAACUGCCUUGGCUGCAUCUUAAAGAUACUUUUCUUAAAUCCUUAGCCUGCAGAA
((((((....((((((.(((...(----((..(((((((....)))))))..)))..))).)))......((((......))))........))).)))))). ( -29.00)
>DroSec_CAF1 28637 99 - 1
UCUGCACACAGCUGCACCCACACG----UACGUGCACCUACACAGGUGAAACUGCCUAGGCUGCAUCUUAAAGAUACUUUUCUUAAAUCCUUAGCCUGCAGAA
((((((....((((..........----...(((((((((..(((......)))..)))).)))))....((((......)))).......)))).)))))). ( -25.70)
>DroSim_CAF1 28894 99 - 1
UCUGCACACAGCUGCACCCACACG----UACGUGGACCUACACAGGUGAAACUGCCUAGGCUGCAUCUUAAAGAUACUUUUCUUAAAUCCUUAGCCUGCAGAA
(((((........(((.((((...----...))))((((....)))).....)))..((((((.......((((......)))).......))))))))))). ( -26.34)
>DroEre_CAF1 30134 99 - 1
UCUGCACACAGAUGCACCCACACGUACGUACGUGCACCUACACAGGUGAAACUGU----GCUGCAUCUUAAAGAUACUUUUCUCAAAUCCUUAGCCUGCUGAA
..(((((((((.........(((((....)))))(((((....)))))...))))----).))))......(((......))).......((((....)))). ( -23.80)
>consensus
UCUGCACACAGCUGCACCCACACG____UACGUGCACCUACACAGGUGAAACUGCCUAGGCUGCAUCUUAAAGAUACUUUUCUUAAAUCCUUAGCCUGCAGAA
((((((..(((.........((((......))))(((((....)))))...)))....(((((.......((((......)))).......))))))))))). (-21.39 = -22.39 +   1.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:08:51 2006