Locus 439

Sequence ID	dm3.chr2L
Location	3,079,749 – 3,079,839
Length	90
Max. P	0.997612

overview

Window 8

Location	3,079,749 – 3,079,839
Length	90
Sequences	7
Columns	115
Reading direction	forward
Mean pairwise identity	63.82
Shannon entropy	0.63116
G+C content	0.44171
Mean single sequence MFE	-25.35
Consensus MFE	-7.48
Energy contribution	-8.36
Covariance contribution	0.88
Combinations/Pair	1.06
Mean z-score	-1.89
Structure conservation index	0.30
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	0.34
SVM RNA-class probability	0.650298
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 3079749 90 + 23011544
UUGUGGUUGAGAAGUCAGCAGACAAACAUCAUCAUAAAUCGAUUUAUGAUGUGCGUA-GAUGAUGUCUGUAGAGAUGGUCCUUCUCCGCCA------------------------
...((((.((((((((.(((((((..((((((((((((....)))))))).......-)))).))))))).)).......)))))).))))------------------------ ( -27.82, z-score =  -2.39, R)
>droSim1.chr2L 3017852 90 + 22036055
UUGUGGUUGAGAAGUCAGCAGACAAACAUCAUCAUAAAUCGAUUUAUGAUGUGUGUA-GAUGAUGUCUGUAGAGGCGGUCCUUCUCCGCCA------------------------
...((((.((((((...((..(((.(((((((((((.((((.....))))...))).-)))))))).)))....))....)))))).))))------------------------ ( -30.60, z-score =  -3.13, R)
>droSec1.super_5 1231756 89 + 5866729
UUGUGGUUGAGAAGCCAGCAGACAAACAUCAUCAUAAAUCGAUUUAUGAUUUGCGUA-GAUGAUGUC-GUAGAGACGGUCCUUCUCCGCCA------------------------
...((((.((((((......(((..((((((((.(((((((.....)))))))....-))))))))(-((....)))))))))))).))))------------------------ ( -25.90, z-score =  -2.20, R)
>droEre2.scaffold_4929 3122288 83 + 26641161
UUGUGGUUGAGAAGUCAGCAGACGAACAUC---AUAAAUCGAUUUAUGGUGUACCUG-GUUGAUGUCUGGAGCGGU----CUUCUCCGCCA------------------------
...((((.((((((.(.((......(((((---(((((....))))))))))..(..-(.......)..).)).).----)))))).))))------------------------ ( -27.30, z-score =  -2.04, R)
>droYak2.chr2L 3070540 68 + 22324452
UUGUGGUCGAAAAGUCAGCAGACAAACAUCAUCAUAAAUCGAUUUAUGAUGUACCCAUACUCGUACUC-----------------------------------------------
.(((((.......(((....)))......(((((((((....)))))))))...))))).........----------------------------------------------- ( -14.00, z-score =  -1.69, R)
>dp4.chr4_group1 668564 111 - 5278887
UUGCGGUUGAAAAGUCAGCAGACAAACAACAUCAUAAAUCGAUUUACGAUGCCCGGA----GGCAACCGAGAAGGAUGUCUACUCCUCCCACAUUAACCUGACGCAUUCGUACGA
.((((..((....(((((...........((((.((((....)))).))))...(((----((((.((.....)).)))...))))............))))).))..))))... ( -24.10, z-score =  -0.54, R)
>droPer1.super_5 601502 111 + 6813705
UUGCGGUUGAAAAGUCAGCAGACAAACAACAUCAUAAAUCGAUUUACGAUGCCCGGA----GGCAACCGAGGAGGAUGUCUACUCCUCCCACAUUAACCUGACGCAUUCGUACGA
.((((..((....(((((...........((((.((((....)))).))))...((.----(....).((((((........))))))))........))))).))..))))... ( -27.70, z-score =  -1.25, R)
>consensus
UUGUGGUUGAGAAGUCAGCAGACAAACAUCAUCAUAAAUCGAUUUAUGAUGUGCGUA_GAUGAUGUCCGUAGAGGAGGUCCUUCUCCGCCA________________________
(((..((((......))))...)))....(((((((((....)))))))))................................................................ ( -7.48 =  -8.36 +   0.88)

alignment

secondary structure

dotplot

Window 9

Location	3,079,749 – 3,079,839
Length	90
Sequences	7
Columns	115
Reading direction	reverse
Mean pairwise identity	63.82
Shannon entropy	0.63116
G+C content	0.44171
Mean single sequence MFE	-26.57
Consensus MFE	-12.91
Energy contribution	-13.34
Covariance contribution	0.43
Combinations/Pair	1.32
Mean z-score	-2.34
Structure conservation index	0.49
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	3.14
SVM RNA-class probability	0.997612
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 3079749 90 - 23011544
------------------------UGGCGGAGAAGGACCAUCUCUACAGACAUCAUC-UACGCACAUCAUAAAUCGAUUUAUGAUGAUGUUUGUCUGCUGACUUCUCAACCACAA
------------------------(((..((((((...((.(...((((((((((((-.......(((.......)))....))))))))))))..).)).))))))..)))... ( -27.70, z-score =  -3.83, R)
>droSim1.chr2L 3017852 90 - 22036055
------------------------UGGCGGAGAAGGACCGCCUCUACAGACAUCAUC-UACACACAUCAUAAAUCGAUUUAUGAUGAUGUUUGUCUGCUGACUUCUCAACCACAA
------------------------(((..((((((..(.((....((((((((((((-.......(((.......)))....))))))))))))..)).).))))))..)))... ( -28.90, z-score =  -4.46, R)
>droSec1.super_5 1231756 89 - 5866729
------------------------UGGCGGAGAAGGACCGUCUCUAC-GACAUCAUC-UACGCAAAUCAUAAAUCGAUUUAUGAUGAUGUUUGUCUGCUGGCUUCUCAACCACAA
------------------------(((..((((((..(((.(...((-(((((((((-.....(((((.......)))))..))))))).))))..).)))))))))..)))... ( -26.20, z-score =  -2.87, R)
>droEre2.scaffold_4929 3122288 83 - 26641161
------------------------UGGCGGAGAAG----ACCGCUCCAGACAUCAAC-CAGGUACACCAUAAAUCGAUUUAU---GAUGUUCGUCUGCUGACUUCUCAACCACAA
------------------------(((..((((((----....(..((((((((...-..)))(((.((((((....)))))---).)))..)))))..).))))))..)))... ( -23.00, z-score =  -2.54, R)
>droYak2.chr2L 3070540 68 - 22324452
-----------------------------------------------GAGUACGAGUAUGGGUACAUCAUAAAUCGAUUUAUGAUGAUGUUUGUCUGCUGACUUUUCGACCACAA
-----------------------------------------------...........(((((.(((((((((....)))))))))......(((....)))......))).)). ( -14.10, z-score =  -0.47, R)
>dp4.chr4_group1 668564 111 + 5278887
UCGUACGAAUGCGUCAGGUUAAUGUGGGAGGAGUAGACAUCCUUCUCGGUUGCC----UCCGGGCAUCGUAAAUCGAUUUAUGAUGUUGUUUGUCUGCUGACUUUUCAACCGCAA
.........((((.((......))((..(((((((((((..(....(((.....----.)))(((((((((((....))))))))))))..))))))))..)))..))..)))). ( -33.00, z-score =  -1.17, R)
>droPer1.super_5 601502 111 - 6813705
UCGUACGAAUGCGUCAGGUUAAUGUGGGAGGAGUAGACAUCCUCCUCGGUUGCC----UCCGGGCAUCGUAAAUCGAUUUAUGAUGUUGUUUGUCUGCUGACUUUUCAACCGCAA
.........((((.((......))((..(((((((((((..(..(((((.....----.)))))(((((((((....)))))))))..)..))))))))..)))..))..)))). ( -33.10, z-score =  -1.06, R)
>consensus
________________________UGGCGGAGAAGGACCACCUCUACAGACAUCAUC_UACGCACAUCAUAAAUCGAUUUAUGAUGAUGUUUGUCUGCUGACUUCUCAACCACAA
........................(((..((((...............................(((((((((....)))))))))......(((....))).))))..)))... (-12.91 = -13.34 +   0.43)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 21:12:59 2011