Locus 11908

Sequence ID	dm3.chr3R
Location	24,498,073 – 24,498,256
Length	183
Max. P	0.924146

overview

Window 4

Location	24,498,073 – 24,498,256
Length	183
Sequences	6
Columns	192
Reading direction	forward
Mean pairwise identity	69.99
Shannon entropy	0.56485
G+C content	0.42232
Mean single sequence MFE	-47.10
Consensus MFE	-23.12
Energy contribution	-24.80
Covariance contribution	1.67
Combinations/Pair	1.35
Mean z-score	-1.63
Structure conservation index	0.49
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	1.31
SVM RNA-class probability	0.924146
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 24498073 183 + 27905053
UUUUCCGUCUAGAUGUCGCACGCGUGCGGUUUUGAAUUCUCAAUAGUGGGCGCCAAAAAGCAUCGACUAGCGCCAUCUAUUAACAAAAGUACAUAUA-GAAAGAGAAAGGAAUAAGAGCGACUGAAUAAGCAGCAAACGGAGAGCGAGACAAAUAUAGGCGUCAAGUGCGCAAAAUUCAAACAG--------
((((.(((((.(((((((((....))).((((((...(((((((((..(((((................)))))..)))))................-...................((..((.....))..)).....)))).)))))).......)))))).)).))).)))).........-------- ( -40.49, z-score =   0.41, R)
>droAna3.scaffold_12928 102877 186 - 771024
UCUUCUACUUCAUUAUCACUCUCAACUUAUUUUUAAAUUUCCCUAUACGGUCCCAGAAA--GUUCACUAAAAAUUUGAACUUUUGACACCCUAACUU--ACACGAAGUUUAAUGCAUAUGGCCGAAUAUUCCGUU--CGGCUGGCAGUACAAAAAUAGGGGUUAAGUUCGCAAAAUUCAAAAUUGACAGCAA
.......................((((((..........(((((((..(((....((((--(((((.........)))))))))...))).......--.......((....(((....((((((((.....)))--))))).)))..))....))))))).)))))).((.....(((....)))..)).. ( -35.30, z-score =  -1.38, R)
>droEre2.scaffold_4820 6941173 160 - 10470090
GUUUCUGUCUAGAUGUCGCUCAUGUGUACUUUCGAAUUCUCAAUAGUGGGCGCCAGGCAUCAUCGUCUGGCGCCAUCUAUUAUCAGAAA-------------GAGAAACGAAUAAGAGCGACUGAAUACGCAA----------GCGAGACAAAUAUAUGCA-CAAGUGCGCGAAAUUCAAAUAA--------
((((((((((....(((((((.(((....((((...((((.(((((..((((((((((......))))))))))..)))))...)))).-------------..))))...))).)))))))......((...----------.))))))).......(((-....)))..)))))........-------- ( -54.10, z-score =  -3.85, R)
>droYak2.chr3R 6840131 182 - 28832112
UUUUCCGCCUAGAUGUCGCACAUGUGCAGUUUCGAAUACUCAAUAGUGGGCGCCAGGCAUCAUCCACUGGCGCCAUCUAUUAUCAGAAGUACAUUUACGAACGAGAUAGGAAUAAGAGCGACUGAAUACGCAACAAACGGAAAGCGAGAUAAAUAUAUGCA-CAUAUGCGCGAAAUUUAAAAA---------
.........(((((.((((.((((((((((((((....((((((((..((((((((..........))))))))..))))).......(((....)))....)))............(((........))).............)))))).......))))-))..)).)))).)))))....--------- ( -48.61, z-score =  -2.03, R)
>droSec1.super_4 3380207 182 + 6179234
UUUUCCGUUUAGAUGUCGCACGCGUGCGGUUUCGAAUUCUCAAUAGUGGGCGCCAGACAUCAUCGACUGGCGCCAUCUAUUAUCAAAAGUACUUAUA-GAAAGAGAAAGGAAUA-GUGCGAAUGAAUACGCAGCAAACGGAAAGUGAGACAAAUAUAUGCGUCAAGUGCGCAAAAUUCAAACCG--------
((((((((((...(((..((..((..(.(((((...(((((.......((((((((.(......).)))))))).(((((..............)))-))..))))).))))).-)..))..)).....)))..)))))))))).............(((((.....)))))............-------- ( -52.84, z-score =  -2.15, R)
>droSim1.chr3R 24195554 183 + 27517382
UUGUCCGUCUAGAUGUCGCACGCGUGCGGUUUCGAAUUCUCAAUAGUGGGCGCCAGACAUCGUCGACUGGCGCCAUCUAUUGUCAAAAGUACUUAUA-GAAAGAGAAAGGAAUAAGAGCGACUGAAUACGCAGCAAACGGAAAGCGAGACAAAUAUAUGCGUCAAGUGCGCAAAAUUCAAACAG--------
((((.((.((.(((((((((....))))((((((..((((((((((..((((((((.(......).))))))))..))))))......((.(((((.-.............))))).(((........))).))....))))..))))))........))))).)))).))))...........-------- ( -51.24, z-score =  -0.80, R)
>consensus
UUUUCCGUCUAGAUGUCGCACGCGUGCGGUUUCGAAUUCUCAAUAGUGGGCGCCAGACAUCAUCGACUGGCGCCAUCUAUUAUCAAAAGUACAUAUA_GAAAGAGAAAGGAAUAAGAGCGACUGAAUACGCAGCAAACGGAAAGCGAGACAAAUAUAUGCGUCAAGUGCGCAAAAUUCAAACAG________
.............((.(((((...((((.........(((((((((..((((((((..........))))))))..)))))....................................(((........)))..............))))........))))....))))))).................... (-23.12 = -24.80 +   1.67)

alignment

secondary structure

dotplot

Window 5

Location	24,498,073 – 24,498,256
Length	183
Sequences	6
Columns	192
Reading direction	reverse
Mean pairwise identity	69.99
Shannon entropy	0.56485
G+C content	0.42232
Mean single sequence MFE	-48.07
Consensus MFE	-23.11
Energy contribution	-24.79
Covariance contribution	1.68
Combinations/Pair	1.41
Mean z-score	-1.66
Structure conservation index	0.48
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	1.27
SVM RNA-class probability	0.919913
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 24498073 183 - 27905053
--------CUGUUUGAAUUUUGCGCACUUGACGCCUAUAUUUGUCUCGCUCUCCGUUUGCUGCUUAUUCAGUCGCUCUUAUUCCUUUCUCUUUC-UAUAUGUACUUUUGUUAAUAGAUGGCGCUAGUCGAUGCUUUUUGGCGCCCACUAUUGAGAAUUCAAAACCGCACGCGUGCGACAUCUAGACGGAAAA
--------......((((...(((.(((.((((........))))..((.........)).........))))))....)))).....(((.((-((.((((....((.(((((((..((((((((..........))))))))..))))))).))........((((....)))))))).)))).)))... ( -41.50, z-score =  -0.42, R)
>droAna3.scaffold_12928 102877 186 + 771024
UUGCUGUCAAUUUUGAAUUUUGCGAACUUAACCCCUAUUUUUGUACUGCCAGCCG--AACGGAAUAUUCGGCCAUAUGCAUUAAACUUCGUGU--AAGUUAGGGUGUCAAAAGUUCAAAUUUUUAGUGAAC--UUUCUGGGACCGUAUAGGGAAAUUUAAAAAUAAGUUGAGAGUGAUAAUGAAGUAGAAGA
(..((.((((((((((((((((((((..((.....))..)))))....((.((((--((.......))))))..(((((....(((((.....--)))))..(((.(((((((((((.........)))))--))).))).)))))))))))))))))))).....))))).))..)............... ( -43.10, z-score =  -0.93, R)
>droEre2.scaffold_4820 6941173 160 + 10470090
--------UUAUUUGAAUUUCGCGCACUUG-UGCAUAUAUUUGUCUCGC----------UUGCGUAUUCAGUCGCUCUUAUUCGUUUCUC-------------UUUCUGAUAAUAGAUGGCGCCAGACGAUGAUGCCUGGCGCCCACUAUUGAGAAUUCGAAAGUACACAUGAGCGACAUCUAGACAGAAAC
--------.............((((....)-))).....(((((((((.----------...))......(((((((...((((.(((((-------------........(((((..((((((((.(......).))))))))..))))))))))..)))).(....)..)))))))....)))))))... ( -49.10, z-score =  -2.75, R)
>droYak2.chr3R 6840131 182 + 28832112
---------UUUUUAAAUUUCGCGCAUAUG-UGCAUAUAUUUAUCUCGCUUUCCGUUUGUUGCGUAUUCAGUCGCUCUUAUUCCUAUCUCGUUCGUAAAUGUACUUCUGAUAAUAGAUGGCGCCAGUGGAUGAUGCCUGGCGCCCACUAUUGAGUAUUCGAAACUGCACAUGUGCGACAUCUAGGCGGAAAA
---------........(((((((((((((-(((((((((((((..((......(..((..(((........)))...))..)......))...))))))))).......((((((..((((((((.(.......)))))))))..))))))............)))))))))))(....)...)))))).. ( -51.80, z-score =  -1.82, R)
>droSec1.super_4 3380207 182 - 6179234
--------CGGUUUGAAUUUUGCGCACUUGACGCAUAUAUUUGUCUCACUUUCCGUUUGCUGCGUAUUCAUUCGCAC-UAUUCCUUUCUCUUUC-UAUAAGUACUUUUGAUAAUAGAUGGCGCCAGUCGAUGAUGUCUGGCGCCCACUAUUGAGAAUUCGAAACCGCACGCGUGCGACAUCUAAACGGAAAA
--------.((..(((((..(((((....).))))...)))))..))..((((((((((.((((........)))).-..(((..(((((....-..((((....))))..(((((..((((((((.(......).))))))))..))))))))))...)))..((((....)))).....)))))))))). ( -50.80, z-score =  -2.25, R)
>droSim1.chr3R 24195554 183 - 27517382
--------CUGUUUGAAUUUUGCGCACUUGACGCAUAUAUUUGUCUCGCUUUCCGUUUGCUGCGUAUUCAGUCGCUCUUAUUCCUUUCUCUUUC-UAUAAGUACUUUUGACAAUAGAUGGCGCCAGUCGACGAUGUCUGGCGCCCACUAUUGAGAAUUCGAAACCGCACGCGUGCGACAUCUAGACGGACAA
--------(((((((.((.((((((....((.(((......))).))...........((((((..(((....(..(((((.............-.)))))..)......((((((..((((((((.(......).))))))))..)))))).......)))..)))).)))))))).)).))))))).... ( -52.14, z-score =  -1.77, R)
>consensus
________CUGUUUGAAUUUUGCGCACUUGACGCAUAUAUUUGUCUCGCUUUCCGUUUGCUGCGUAUUCAGUCGCUCUUAUUCCUUUCUCUUUC_UAUAUGUACUUUUGAUAAUAGAUGGCGCCAGUCGAUGAUGUCUGGCGCCCACUAUUGAGAAUUCGAAACCGCACGCGUGCGACAUCUAGACGGAAAA
...........(((((((((((((.(((..(((((.........................)))))....))))))...................................((((((..((((((((..........))))))))..))))))))))))))))..((((....))))................ (-23.11 = -24.79 +   1.68)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 00:51:58 2011