Locus 894

Sequence ID	dm3.chr2L
Location	6,514,964 – 6,515,058
Length	94
Max. P	0.954324

overview

Window 9

Location	6,514,964 – 6,515,058
Length	94
Sequences	6
Columns	94
Reading direction	forward
Mean pairwise identity	67.10
Shannon entropy	0.60595
G+C content	0.54820
Mean single sequence MFE	-27.07
Consensus MFE	-17.08
Energy contribution	-17.83
Covariance contribution	0.76
Combinations/Pair	1.48
Mean z-score	-0.75
Structure conservation index	0.63
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	1.00
SVM RNA-class probability	0.872064
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 6514964 94 + 23011544
CUCUGGUUUUGCACCAGAUGCAGAUGGGUGUCUCUGUGUGGGCAGCGGAAUCUGAAAUCUGGAGCUGGAAUACUGGGGAGCUUGGCUUGGCUGG
(((..((...((.((((((.(((((.(.(((((......))))).)...)))))..)))))).))......))..)))((((......)))).. ( -32.20, z-score =  -1.15, R)
>droSim1.chr2L 6306292 82 + 22036055
CUCUGGUUUUGCACCAGAUGCAGAUGGGUGUCUCUGUGUGGGCAGUGGAAUCUGAAAUCUGGAGCUGGGC-ACUGGGUACUGC-----------
(((..(((..((.((((((.(((((.(.(((((......))))).)...)))))..)))))).))..)))-...)))......----------- ( -25.90, z-score =  -0.41, R)
>droSec1.super_3 2055389 82 + 7220098
CUCUGGUUUUGCACCAGAUGCAGAUGGGUGUCUCUGUGUGGGCAGUGGAAUCUGAAAUCUGGAGCUGGGC-ACUGGGUACUGC-----------
(((..(((..((.((((((.(((((.(.(((((......))))).)...)))))..)))))).))..)))-...)))......----------- ( -25.90, z-score =  -0.41, R)
>droYak2.chr2L 15923252 81 - 22324452
CUCUGGUUUUGCACCAGAUGCAGAUGGGUGUCUCUGUGUGGGCAGCGGAUUCUGAAAUCUGGAGCUGGAA-GCUGGG-AGCUU-----------
.((..(((((((.((((((.(((((.(.(((((......))))).).)..))))..)))))).))..)))-))..))-.....----------- ( -27.20, z-score =  -0.63, R)
>droEre2.scaffold_4929 15423397 74 + 26641161
CUCUGGGUUUGCGCCAGAUGCAGAUGGGUGUCUCUGUGUGGGCAGUGGAAUCUGAAAUCUGGAGCUGGGAGCUU--------------------
((((.((((....((((((.(((((.(.(((((......))))).)...)))))..)))))))))).))))...-------------------- ( -24.90, z-score =  -1.10, R)
>dp4.chr4_group1 1576506 85 + 5278887
GCCCCGUGCCUUCUCGCAUGUACACAAGUACACAUGUA---GUACCUUCUCCUGCCACAUGCAGAUGUGUCUGUGGGGCACUCUGUGU------
(((((((((......)))))..((((..(((((((((.---(((........))).)))))....))))..)))))))).........------ ( -26.30, z-score =  -0.78, R)
>consensus
CUCUGGUUUUGCACCAGAUGCAGAUGGGUGUCUCUGUGUGGGCAGCGGAAUCUGAAAUCUGGAGCUGGGA_ACUGGG_ACCUC___________
.((((((...((.((((((.(((((.(.(((((......))))).)...)))))..)))))).))......))))))................. (-17.08 = -17.83 +   0.76)

alignment

secondary structure

dotplot

Window 0

Location	6,514,964 – 6,515,058
Length	94
Sequences	6
Columns	94
Reading direction	reverse
Mean pairwise identity	67.10
Shannon entropy	0.60595
G+C content	0.54820
Mean single sequence MFE	-19.18
Consensus MFE	-10.80
Energy contribution	-10.75
Covariance contribution	-0.05
Combinations/Pair	1.35
Mean z-score	-1.30
Structure conservation index	0.56
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	1.60
SVM RNA-class probability	0.954324
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 6514964 94 - 23011544
CCAGCCAAGCCAAGCUCCCCAGUAUUCCAGCUCCAGAUUUCAGAUUCCGCUGCCCACACAGAGACACCCAUCUGCAUCUGGUGCAAAACCAGAG
..(((........))).............((.((((((..(((((((..(((......))).)).....))))).)))))).)).......... ( -17.80, z-score =  -0.99, R)
>droSim1.chr2L 6306292 82 - 22036055
-----------GCAGUACCCAGU-GCCCAGCUCCAGAUUUCAGAUUCCACUGCCCACACAGAGACACCCAUCUGCAUCUGGUGCAAAACCAGAG
-----------(((.(....).)-))...((.((((((..(((((((..(((......))).)).....))))).)))))).)).......... ( -17.90, z-score =  -1.40, R)
>droSec1.super_3 2055389 82 - 7220098
-----------GCAGUACCCAGU-GCCCAGCUCCAGAUUUCAGAUUCCACUGCCCACACAGAGACACCCAUCUGCAUCUGGUGCAAAACCAGAG
-----------(((.(....).)-))...((.((((((..(((((((..(((......))).)).....))))).)))))).)).......... ( -17.90, z-score =  -1.40, R)
>droYak2.chr2L 15923252 81 + 22324452
-----------AAGCU-CCCAGC-UUCCAGCUCCAGAUUUCAGAAUCCGCUGCCCACACAGAGACACCCAUCUGCAUCUGGUGCAAAACCAGAG
-----------((((.-....))-)).((((....((((....)))).))))......((((........))))..((((((.....)))))). ( -17.90, z-score =  -1.26, R)
>droEre2.scaffold_4929 15423397 74 - 26641161
--------------------AAGCUCCCAGCUCCAGAUUUCAGAUUCCACUGCCCACACAGAGACACCCAUCUGCAUCUGGCGCAAACCCAGAG
--------------------.........((.((((((..(((((((..(((......))).)).....))))).)))))).)).......... ( -16.20, z-score =  -2.09, R)
>dp4.chr4_group1 1576506 85 - 5278887
------ACACAGAGUGCCCCACAGACACAUCUGCAUGUGGCAGGAGAAGGUAC---UACAUGUGUACUUGUGUACAUGCGAGAAGGCACGGGGC
------.........(((((....(((((..((((((((..((.........)---).))))))))..)))))...(((......))).))))) ( -27.40, z-score =  -0.67, R)
>consensus
___________GAGCU_CCCAGU_UCCCAGCUCCAGAUUUCAGAUUCCACUGCCCACACAGAGACACCCAUCUGCAUCUGGUGCAAAACCAGAG
.............................((.((((((..(((((..(.(((......))).)......))))).)))))).)).......... (-10.80 = -10.75 +  -0.05)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 21:21:31 2011