Locus 8612

Sequence ID dm3.chr3RHet
Location 1,833,484 – 1,833,621
Length 137
Max. P 0.979060
window11826 window11827

overview

Window 6

Location 1,833,484 – 1,833,621
Length 137
Sequences 4
Columns 144
Reading direction forward
Mean pairwise identity 68.99
Shannon entropy 0.50300
G+C content 0.35072
Mean single sequence MFE -29.62
Consensus MFE -13.95
Energy contribution -18.45
Covariance contribution 4.50
Combinations/Pair 1.14
Mean z-score -2.41
Structure conservation index 0.47
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.01
SVM RNA-class probability 0.979060
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3RHet 1833484 137 + 2517507
CCGGAUUCUUAAGUUAGUUUUUAAUCAUACUCCGAGGCUUACGCCUUGUAAUUAUAAAUACCCA---AAUAUUGUGACCCUCGCCCUAACGGGAGAGUGGUAAAUAAAUAUCAUUAAAUUAACCAA---CGACUUA-UAAUUUC
..(((((..((((((.(((((((((.(((...((((((....))))))................---..((((...((((((.(((....))).))).))).))))..))).))))))......))---)))))))-.))))). ( -29.70, z-score =  -2.13, R)
>droSec1.super_59 92262 136 + 165940
CUGAAUUCUUAAGUUAGUUUUUAAUCAUACUCCGAGGCUUACGCCUUGUAAUUAUAAAUACCCA---AAUAUUGUGACCCUCGCCCUAACGGGAGAGUGGUAAAUAAAUAUAACCAAACUAAACAAA--CGACUUA-UAAUU--
.........((((((.((((............((((((....))))))................---.(((((...((((((.(((....))).))).))).....))))).............)))--)))))))-.....-- ( -29.60, z-score =  -3.05, R)
>droYak2.chr2h 314306 139 - 894407
UUAGAUUUUUAA-UCAGUUAUAAAUCAUACUCCGUGGCUUACGCCUCGUA-UUGUAAACCUACAUAAAAAAUUAAGACCCUCGCCCUAACGGGAGAGUGGUAA-UAAAUA-AAUCAACUUAAAACACCACGACUUA-UAAUUUA
...(((.....)-))((((((((.((.(((..((.(((....))).))..-..)))...............(((..((((((.(((....))).))).)))..-)))...-...................)).)))-))))).. ( -27.70, z-score =  -2.54, R)
>droEre2.scaffold_4784 24528783 120 + 25762168
--------UUAAGUUAGUCUAAAAUUGUACUCCGGGGUUUA------ACAGCCUCGAUAAUCUG-----AAUUAA-ACCCUCGCCCUAACGGGAGAACGGGGAAUAAA-GUUAUCAAAUUAUUAAC---CAACCGAGUGAUUUA
--------.(((((((.((.....((((.((((((((((((------((((..........)))-----..))))-))))((.(((....))).)).))))).)))).-((((.........))))---.....)).))))))) ( -31.50, z-score =  -1.91, R)
>consensus
CUGGAUUCUUAAGUUAGUUUUAAAUCAUACUCCGAGGCUUACGCCUUGUAAUUAUAAAUACCCA___AAAAUUAAGACCCUCGCCCUAACGGGAGAGUGGUAAAUAAAUAUAAUCAAAUUAAAAAA___CGACUUA_UAAUUUA
.........((((((.................((((((....))))))............................((((((.(((....))).))).))).............................))))))........ (-13.95 = -18.45 +   4.50)

alignment

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secondary structure

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dotplot

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Window 7

Location 1,833,484 – 1,833,621
Length 137
Sequences 4
Columns 144
Reading direction reverse
Mean pairwise identity 68.99
Shannon entropy 0.50300
G+C content 0.35072
Mean single sequence MFE -33.05
Consensus MFE -18.44
Energy contribution -20.75
Covariance contribution 2.31
Combinations/Pair 1.16
Mean z-score -1.84
Structure conservation index 0.56
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.66
SVM RNA-class probability 0.958967
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3RHet 1833484 137 - 2517507
GAAAUUA-UAAGUCG---UUGGUUAAUUUAAUGAUAUUUAUUUACCACUCUCCCGUUAGGGCGAGGGUCACAAUAUU---UGGGUAUUUAUAAUUACAAGGCGUAAGCCUCGGAGUAUGAUUAAAAACUAACUUAAGAAUCCGG
.......-......(---((((((..((((((.((((((....(((.(((.(((....))).)))))).........---................(.((((....)))).))))))).)))))))))))))............ ( -34.80, z-score =  -2.13, R)
>droSec1.super_59 92262 136 - 165940
--AAUUA-UAAGUCG--UUUGUUUAGUUUGGUUAUAUUUAUUUACCACUCUCCCGUUAGGGCGAGGGUCACAAUAUU---UGGGUAUUUAUAAUUACAAGGCGUAAGCCUCGGAGUAUGAUUAAAAACUAACUUAAGAAUUCAG
--.....-....((.--...(((...(((((((((((((....(((.(((.(((....))).)))))).........---................(.((((....)))).))))))))))))))....)))....))...... ( -32.50, z-score =  -1.94, R)
>droYak2.chr2h 314306 139 + 894407
UAAAUUA-UAAGUCGUGGUGUUUUAAGUUGAUU-UAUUUA-UUACCACUCUCCCGUUAGGGCGAGGGUCUUAAUUUUUUAUGUAGGUUUACAA-UACGAGGCGUAAGCCACGGAGUAUGAUUUAUAACUGA-UUAAAAAUCUAA
....(((-(((((((((.(.......((.((((-((((((-..(((.(((.(((....))).))))))..)))........))))))).))..-..((.(((....))).)).).))))))))))))....-............ ( -36.20, z-score =  -2.51, R)
>droEre2.scaffold_4784 24528783 120 - 25762168
UAAAUCACUCGGUUG---GUUAAUAAUUUGAUAAC-UUUAUUCCCCGUUCUCCCGUUAGGGCGAGGGU-UUAAUU-----CAGAUUAUCGAGGCUGU------UAAACCCCGGAGUACAAUUUUAGACUAACUUAA--------
......((((.(..(---(((((((.(((((((((-((((..(((((((((......)))))).))).-.)))..-----.)).))))))))..)))------).)))).).))))....................-------- ( -28.70, z-score =  -0.77, R)
>consensus
UAAAUUA_UAAGUCG___UUGUUUAAUUUGAUUAUAUUUAUUUACCACUCUCCCGUUAGGGCGAGGGUCACAAUAUU___UGGAUAUUUAUAAUUACAAGGCGUAAGCCUCGGAGUAUGAUUAAAAACUAACUUAAGAAUCCAG
..........................(((((((((((((....(((.(((.(((....))).))))))...............................(((....)))...)))))))))))))................... (-18.44 = -20.75 +   2.31)

alignment

Postscript

secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 23:48:51 2011