Locus 13412

Sequence ID dm3.chrX
Location 6,410,494 – 6,410,594
Length 100
Max. P 0.864789
window18465 window18466

overview

Window 5

Location 6,410,494 – 6,410,594
Length 100
Sequences 5
Columns 106
Reading direction forward
Mean pairwise identity 71.43
Shannon entropy 0.47981
G+C content 0.61772
Mean single sequence MFE -16.00
Consensus MFE -7.34
Energy contribution -7.54
Covariance contribution 0.20
Combinations/Pair 1.15
Mean z-score -2.02
Structure conservation index 0.46
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.97
SVM RNA-class probability 0.864789
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 6410494 100 + 22422827
AGCUAACGCCCCUGACUUAAACCACCCCA----ACCCCCCCCCUACCCACU-UGCCCCCC-GCUGUUGGCCGCGAUCCCCACUGCGAACUUGAAGCUUUAGCGUUG
.(((((.((....................----.............(((..-.((.....-))...))).((((........))))........)).))))).... ( -14.60, z-score =  -1.54, R)
>droSim1.chrX 5027363 85 + 17042790
-------------AGCU--AACGCCCCUG----ACCCCACCGCCACUUUUC-CACCCCCC-GCUGUUCGCCGCGAUCCCCACUGCGAACUUGAAGCUUUAGCGUUG
-------------.(((--((.((.....----........((........-........-)).((((((.(.(.....).).)))))).....)).))))).... ( -15.49, z-score =  -1.97, R)
>droSec1.super_4 5797409 85 - 6179234
-------------AGCU--AACGCCCCUG----ACCCCACCACCACUUUUC-CACCCCCC-CCUGUUCACCGCGAUCCCCACUGCGAACUUGAAGCUUUAGCGUUG
-------------.(((--((.((...((----....))............-........-....((((.((((........))))....)))))).))))).... ( -10.40, z-score =  -1.62, R)
>droYak2.chrX 2382580 106 + 21770863
AGCUAACGCCCCUGACUUAACCACCCCCCUUUUACCGCGCCCCUUUUUGCCGCGCCCCCCUGCUGUUCGCCGCGAUCCCCACUGCGAACUUGAAGCUUUAGCGCUG
.(((((.((...........................((((..(.....)..)))).........((((((.(.(.....).).)))))).....)).))))).... ( -22.10, z-score =  -2.95, R)
>droEre2.scaffold_4690 15350426 98 + 18748788
AGCUAACGCCCCUGACUUAACCCGCCCCU--------GACUCCCCCUAACUCCGCGCCCCUGCUGUUCGCCGCGAUCCCCACUGCGAACUUGAAGCUAUAGCGUUG
.((....))....................--------................((((....(((((((((.(.(.....).).))))))....)))....)))).. ( -17.40, z-score =  -2.00, R)
>consensus
AGCUAACGCCCCUGACUUAAACCCCCCCG____ACCCCACCCCCACUUACC_CGCCCCCC_GCUGUUCGCCGCGAUCCCCACUGCGAACUUGAAGCUUUAGCGUUG
.............(((................................................((((((.(.(.....).).)))))).....((....))))). ( -7.34 =  -7.54 +   0.20)

alignment

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secondary structure

Postscript

dotplot

Postscript

Window 6

Location 6,410,494 – 6,410,594
Length 100
Sequences 5
Columns 106
Reading direction reverse
Mean pairwise identity 71.43
Shannon entropy 0.47981
G+C content 0.61772
Mean single sequence MFE -28.06
Consensus MFE -14.22
Energy contribution -14.70
Covariance contribution 0.48
Combinations/Pair 1.21
Mean z-score -1.36
Structure conservation index 0.51
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.08
SVM RNA-class probability 0.535666
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 6410494 100 - 22422827
CAACGCUAAAGCUUCAAGUUCGCAGUGGGGAUCGCGGCCAACAGC-GGGGGGCA-AGUGGGUAGGGGGGGGGU----UGGGGUGGUUUAAGUCAGGGGCGUUAGCU
....(((((.(((((..(..(((.(((.....))).(((..(...-.)..))).-.)))..).......((.(----((((....))))).)).))))).))))). ( -26.10, z-score =  -0.08, R)
>droSim1.chrX 5027363 85 - 17042790
CAACGCUAAAGCUUCAAGUUCGCAGUGGGGAUCGCGGCGAACAGC-GGGGGGUG-GAAAAGUGGCGGUGGGGU----CAGGGGCGUU--AGCU-------------
....(((((.(((((..((((((.(((.....))).))))))...-........-......((((......))----))))))).))--))).------------- ( -28.00, z-score =  -1.90, R)
>droSec1.super_4 5797409 85 + 6179234
CAACGCUAAAGCUUCAAGUUCGCAGUGGGGAUCGCGGUGAACAGG-GGGGGGUG-GAAAAGUGGUGGUGGGGU----CAGGGGCGUU--AGCU-------------
....(((((.(((((..((((((.(((.....))).))))))...-........-.........(((.....)----))))))).))--))).------------- ( -22.20, z-score =  -1.13, R)
>droYak2.chrX 2382580 106 - 21770863
CAGCGCUAAAGCUUCAAGUUCGCAGUGGGGAUCGCGGCGAACAGCAGGGGGGCGCGGCAAAAAGGGGCGCGGUAAAAGGGGGGUGGUUAAGUCAGGGGCGUUAGCU
....(((((.(((((..((((((.(((.....))).))))))........(.((((.(.......).)))).).....................))))).))))). ( -32.60, z-score =  -1.47, R)
>droEre2.scaffold_4690 15350426 98 - 18748788
CAACGCUAUAGCUUCAAGUUCGCAGUGGGGAUCGCGGCGAACAGCAGGGGCGCGGAGUUAGGGGGAGUC--------AGGGGCGGGUUAAGUCAGGGGCGUUAGCU
....(((((((((((..((((((.(((.....))).)))))).((......)))))))))......(((--------...(((.......)))...)))..)))). ( -31.40, z-score =  -2.22, R)
>consensus
CAACGCUAAAGCUUCAAGUUCGCAGUGGGGAUCGCGGCGAACAGC_GGGGGGCG_GGAAAGUGGGGGUGGGGU____CGGGGGCGUUUAAGUCAGGGGCGUUAGCU
....(((...(((((..((((((.(((.....))).)))))).((......))..........................))))).....))).............. (-14.22 = -14.70 +   0.48)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 01:20:52 2011