Locus 12920

Sequence ID	dm3.chrX
Location	3,274,420 – 3,274,538
Length	118
Max. P	0.788681

overview

Window 6

Location	3,274,420 – 3,274,538
Length	118
Sequences	4
Columns	119
Reading direction	forward
Mean pairwise identity	73.14
Shannon entropy	0.43584
G+C content	0.53935
Mean single sequence MFE	-45.92
Consensus MFE	-25.09
Energy contribution	-28.40
Covariance contribution	3.31
Combinations/Pair	1.17
Mean z-score	-1.72
Structure conservation index	0.55
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	0.69
SVM RNA-class probability	0.788681
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chrX 3274420 118 + 22422827
GGGUGUGUGACCUAUUUCGCUGGCCGUUGGUGUGGCAAGUUGCGGUUGAGCGACAUGUUGCCAGCAGAUGUUGCAUCUGCGGCU-GCAAUUUCUGUUGCAGUUAUCGCUGUAGAUGCAA
.(((..((((......))))..)))((((((..((((.(((((......))))).)))))))))).....((((((((((((((-(((((....))))))......))))))))))))) ( -49.80, z-score =  -2.56, R)
>droSim1.chrX 2360484 118 + 17042790
GGGUGUGUGACCUAUUUCGCUGGCCGGCGGUGUGGCAAGUUGCGGUUGAGCGACAUGUUGCCAGCAGAUGUUGCAUCUGCGGCG-GCAAUUUCUGUUGCAGCUAUCGCUGGAGAUGCAA
((((.....)))).....((...((((((((((.(((((((((......))))).(((((((.(((((((...)))))))))))-))).......)))).)).))))))))....)).. ( -51.80, z-score =  -2.05, R)
>droSec1.super_10 2979438 118 + 3036183
GGGUGUGUGACCUAUUUCGCUGGCCGGCGGUGUGGCAAGUUGCGGUUGAGCGACAUGUUGCCAGCAGAUGUUGCAUCUGCGGCG-GCAAUUUCUGUUGCAGUUAUCGCUGGAGAUGCAA
((((.....)))).....((...(((((((((..(((((((((......))))).(((((((.(((((((...)))))))))))-))).......))))...)))))))))....)).. ( -51.90, z-score =  -2.40, R)
>dp4.chrXL_group1a 7390155 103 + 9151740
------------AGUGUCUGGGGCUGCUGGCU--ACCGGCUGAGA--GAGCGACAUGUUGCCGACACAUGUUGCUAGUGCAACGAGGGGCGUCUUUUGACCUUUUUGCAAAAAAAAAAA
------------...(.(((((((.....)))--.))))).....--.((((((((((.......))))))))))..(((((.((((..((.....)).)))).))))).......... ( -30.20, z-score =   0.12, R)
>consensus
GGGUGUGUGACCUAUUUCGCUGGCCGGCGGUGUGGCAAGUUGCGGUUGAGCGACAUGUUGCCAGCAGAUGUUGCAUCUGCGGCG_GCAAUUUCUGUUGCAGUUAUCGCUGGAGAUGCAA
((((.....))))((((.((((((.........((((.(((((......))))).)))))))))))))).((((((((.(((((.(((((....)))))......))))).)))))))) (-25.09 = -28.40 +   3.31)

alignment

secondary structure

dotplot

Window 7

Location	3,274,420 – 3,274,538
Length	118
Sequences	4
Columns	119
Reading direction	reverse
Mean pairwise identity	73.14
Shannon entropy	0.43584
G+C content	0.53935
Mean single sequence MFE	-31.77
Consensus MFE	-20.02
Energy contribution	-21.03
Covariance contribution	1.00
Combinations/Pair	1.22
Mean z-score	-1.36
Structure conservation index	0.63
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	0.56
SVM RNA-class probability	0.742578
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chrX 3274420 118 - 22422827
UUGCAUCUACAGCGAUAACUGCAACAGAAAUUGC-AGCCGCAGAUGCAACAUCUGCUGGCAACAUGUCGCUCAACCGCAACUUGCCACACCAACGGCCAGCGAAAUAGGUCACACACCC
.((.(((((.(((((((..(((((......))))-)((((((((((...))))))).)))....)))))))....(((.....(((........)))..)))...)))))))....... ( -35.90, z-score =  -2.79, R)
>droSim1.chrX 2360484 118 - 17042790
UUGCAUCUCCAGCGAUAGCUGCAACAGAAAUUGC-CGCCGCAGAUGCAACAUCUGCUGGCAACAUGUCGCUCAACCGCAACUUGCCACACCGCCGGCCAGCGAAAUAGGUCACACACCC
((((.(((.((((....))))....)))....((-((.((((((((...)))))))((((((...((.((......)).))))))))....).))))..))))....(((.....))). ( -34.60, z-score =  -1.24, R)
>droSec1.super_10 2979438 118 - 3036183
UUGCAUCUCCAGCGAUAACUGCAACAGAAAUUGC-CGCCGCAGAUGCAACAUCUGCUGGCAACAUGUCGCUCAACCGCAACUUGCCACACCGCCGGCCAGCGAAAUAGGUCACACACCC
((((......(((((((...((((......))))-.((((((((((...))))))).)))....))))))).....))))((.(((........))).)).......(((.....))). ( -33.50, z-score =  -1.45, R)
>dp4.chrXL_group1a 7390155 103 - 9151740
UUUUUUUUUUUGCAAAAAGGUCAAAAGACGCCCCUCGUUGCACUAGCAACAUGUGUCGGCAACAUGUCGCUC--UCUCAGCCGGU--AGCCAGCAGCCCCAGACACU------------
.........((((......(((....)))((..((.((((....(((.((((((.......)))))).))).--...)))).)).--.))..))))...........------------ ( -23.10, z-score =   0.04, R)
>consensus
UUGCAUCUCCAGCGAUAACUGCAACAGAAAUUGC_CGCCGCAGAUGCAACAUCUGCUGGCAACAUGUCGCUCAACCGCAACUUGCCACACCACCGGCCAGCGAAAUAGGUCACACACCC
((((.......((((((...((((......))))..((((((((((...))))))).)))....)))))).............(((........)))..))))................ (-20.02 = -21.03 +   1.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 01:11:21 2011