Locus 14943

Sequence ID	dm3.chrX
Location	16,481,973 – 16,482,138
Length	165
Max. P	0.952391

overview

Window 7

Location	16,481,973 – 16,482,138
Length	165
Sequences	5
Columns	166
Reading direction	forward
Mean pairwise identity	82.86
Shannon entropy	0.30364
G+C content	0.45349
Mean single sequence MFE	-45.86
Consensus MFE	-33.12
Energy contribution	-34.36
Covariance contribution	1.24
Combinations/Pair	1.22
Mean z-score	-2.26
Structure conservation index	0.72
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	1.58
SVM RNA-class probability	0.952391
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chrX 16481973 165 + 22422827
AUGCAACAAAUAUUUAAUAAAGUUUAACUAAAGAUCAUUUAUCCGCCGUUACAUCGGCAACAAACUUGGUCGAGGAAUC-AAGUCGCCCGUCCGCAAACUGGACGGAAGAUUUGCCACCUUGAGGUGGAAUCACCGGCAACCGGCGUGAUCGCUCUCAAGUCAAAA
..((.........((((......)))).....((((((...((((((........(....)........((((((...(-(((((..(((((((.....)))))))..))))))...))))))))))))....((((...)))).))))))))............. ( -49.20, z-score =  -2.51, R)
>droEre2.scaffold_4690 6840231 166 + 18748788
AUUCAACAAUUAAUAAAUAUAAUUUAACUAUUGACCCUUUAUCCGCCGUUGUAUCGGCACUGGACUUGGCCGAGCAAUAAAAGUCGCCCGUCCCCAAAAUAGACAGAAGAUUCUCAACUUCGAAGUGGAACCACCGGCGACCGGUGUGACCGCUAUCAAGUCAAAA
......((((...(((((...)))))...))))...........((((......))))....(((((((...(((.......((((((.(((.........))).((((........))))...(((....))).)))))).((.....))))).))))))).... ( -40.00, z-score =  -1.64, R)
>droYak2.chrX 10588115 166 + 21770863
AUUCAACAAAUAAUUAAUAGAAUUUGACUAAAGACCCUUUAACUGCCGUUACAUUGGCACUGGACUUGGCAGAGGAUUAGAAGUCGGGUGUCCAGAACGUGGACAAAAGAUUCAUUACAUUGAGGUGGAACAACCGGCAACCGGCGUGACCGCUAUCAAGUCAAAA
......................(((((((....((((.....((((((...((.......))....))))))..(((.....)))))))(((((.....)))))....((((((......)))(((((.((..((((...)))).))..)))))))).))))))). ( -41.10, z-score =  -0.71, R)
>droSec1.super_17 305231 165 + 1527944
AUCCAACAAAUAUUUAAUAAAGUUUAACUAAAGAUCAAUUAUCUGCCGUUACAUCGGCAUCAGACUUGGUCGAGGAACC-AAGUCGCCCGUCCGCAAACUGGACGGAACAUUCGCCACCUUGAGGUGAAACCACCGCCAACCGGCGUGAUCGCUCUCAAGUCAAAA
........................((((...((((.....))))...))))....(((....((((((((......)))-)))))..(((((((.....))))))).......)))..((((((((((...(((.(((....)))))).)))).))))))...... ( -50.40, z-score =  -3.78, R)
>droSim1.chrX 12677111 165 + 17042790
AUCCAACAAAUAUUUAAUAAAGUUUAACUAAAAAUCAAUUGUCUGCCGUUACAUCGGCACCAGACUUGGUCGAGGAACC-AAGUCGCCCGUCCGCAAACUGGACGGAACAUUCGCCACCUUGAGGUGGAACCACCGCCAACCGGCGUGAUCGCUCUCAAGUCAAAA
......................................(((...((.(((((...(((....((((((((......)))-)))))..(((((((.....))))))).......))).......((((....))))(((....)))))))).))...)))....... ( -48.60, z-score =  -2.67, R)
>consensus
AUCCAACAAAUAUUUAAUAAAGUUUAACUAAAGAUCAUUUAUCUGCCGUUACAUCGGCACCAGACUUGGUCGAGGAAUC_AAGUCGCCCGUCCGCAAACUGGACGGAAGAUUCGCCACCUUGAGGUGGAACCACCGGCAACCGGCGUGAUCGCUCUCAAGUCAAAA
............................................((((......))))....(((((((((((((......((((..(((((((.....)))))))..)))).....))))))(((((...(.(((.....))).)...))))).))))))).... (-33.12 = -34.36 +   1.24)

alignment

secondary structure

dotplot

Window 8

Location	16,481,973 – 16,482,138
Length	165
Sequences	5
Columns	166
Reading direction	reverse
Mean pairwise identity	82.86
Shannon entropy	0.30364
G+C content	0.45349
Mean single sequence MFE	-51.44
Consensus MFE	-35.58
Energy contribution	-36.62
Covariance contribution	1.04
Combinations/Pair	1.28
Mean z-score	-1.88
Structure conservation index	0.69
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	0.72
SVM RNA-class probability	0.796010
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chrX 16481973 165 - 22422827
UUUUGACUUGAGAGCGAUCACGCCGGUUGCCGGUGAUUCCACCUCAAGGUGGCAAAUCUUCCGUCCAGUUUGCGGACGGGCGACUU-GAUUCCUCGACCAAGUUUGUUGCCGAUGUAACGGCGGAUAAAUGAUCUUUAGUUAAACUUUAUUAAAUAUUUGUUGCAU
.(((((((.((((...(((.(((((.((((.((((....))))....((..(((((((.(((((((.......))))))).))(((-(..........)))))))))..))...))))))))))))......)))).)))))))...................... ( -52.80, z-score =  -2.22, R)
>droEre2.scaffold_4690 6840231 166 - 18748788
UUUUGACUUGAUAGCGGUCACACCGGUCGCCGGUGGUUCCACUUCGAAGUUGAGAAUCUUCUGUCUAUUUUGGGGACGGGCGACUUUUAUUGCUCGGCCAAGUCCAGUGCCGAUACAACGGCGGAUAAAGGGUCAAUAGUUAAAUUAUAUUUAUUAAUUGUUGAAU
(((..((((((.((.((...((((((...))))))...)).)))).))))..))).((((.(((((..(((((...(((((((......))))))).)))))......((((......))))))))).))))(((((((((((..........))))))))))).. ( -53.10, z-score =  -2.32, R)
>droYak2.chrX 10588115 166 - 21770863
UUUUGACUUGAUAGCGGUCACGCCGGUUGCCGGUUGUUCCACCUCAAUGUAAUGAAUCUUUUGUCCACGUUCUGGACACCCGACUUCUAAUCCUCUGCCAAGUCCAGUGCCAAUGUAACGGCAGUUAAAGGGUCUUUAGUCAAAUUCUAUUAAUUAUUUGUUGAAU
.((..((..(((((.((.((.(((((...)))))))..)).........((((((((....((((((.....))))))...((((....((((((((((.....((.......))....)))))....)))))....))))..)))).)))).))))).))..)). ( -37.00, z-score =  -0.06, R)
>droSec1.super_17 305231 165 - 1527944
UUUUGACUUGAGAGCGAUCACGCCGGUUGGCGGUGGUUUCACCUCAAGGUGGCGAAUGUUCCGUCCAGUUUGCGGACGGGCGACUU-GGUUCCUCGACCAAGUCUGAUGCCGAUGUAACGGCAGAUAAUUGAUCUUUAGUUAAACUUUAUUAAAUAUUUGUUGGAU
......((((((.(.((...(((((.....)))))...)).))))))).(((((...((.((((((.......))))))))(((((-((((....)))))))))...)))))......(((((((((.(((((....((.....))..))))).)))))))))... ( -57.70, z-score =  -2.75, R)
>droSim1.chrX 12677111 165 - 17042790
UUUUGACUUGAGAGCGAUCACGCCGGUUGGCGGUGGUUCCACCUCAAGGUGGCGAAUGUUCCGUCCAGUUUGCGGACGGGCGACUU-GGUUCCUCGACCAAGUCUGGUGCCGAUGUAACGGCAGACAAUUGAUUUUUAGUUAAACUUUAUUAAAUAUUUGUUGGAU
.(((((((.((((.((((..(((((.((.(.((((....)))).).)).)))))..((((((((((.......))))))..(((((-((((....)))))))))...(((((......))))))))))))).)))).)))))))...................... ( -56.60, z-score =  -2.07, R)
>consensus
UUUUGACUUGAGAGCGAUCACGCCGGUUGCCGGUGGUUCCACCUCAAGGUGGCGAAUCUUCCGUCCAGUUUGCGGACGGGCGACUU_GAUUCCUCGACCAAGUCUGGUGCCGAUGUAACGGCAGAUAAAUGAUCUUUAGUUAAACUUUAUUAAAUAUUUGUUGAAU
....((((((.(((.((((.(((((.....)))))...(((((....))))).......(((((((.......))))))).......)))).)))...))))))...(((((......)))))..(((..(((.((((((........)))))).)))..)))... (-35.58 = -36.62 +   1.04)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 01:49:59 2011