Locus 13429

Sequence ID dm3.chrX
Location 6,494,190 – 6,494,365
Length 175
Max. P 0.795255
window18493 window18494

overview

Window 3

Location 6,494,190 – 6,494,365
Length 175
Sequences 4
Columns 176
Reading direction forward
Mean pairwise identity 96.01
Shannon entropy 0.06314
G+C content 0.35478
Mean single sequence MFE -43.50
Consensus MFE -34.24
Energy contribution -33.55
Covariance contribution -0.69
Combinations/Pair 1.09
Mean z-score -2.21
Structure conservation index 0.79
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.27
SVM RNA-class probability 0.619825
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 6494190 175 + 22422827
UGCGGGAAAACGAUAUCACACGAUGAUAUUUGAUUUCUUUCAAGAGGAUAUAUUGUUAUAAUGAUUGCUAUAUAUACUCCUCACAACCCAAUCGAUUUUGGGCCGUGACGCGGGAUUUUUUGUUUAUGUUCUUUUGAAAGCAGUGUGCGAAAAGAAACCCUUUUUUUU-CGAAUAA
(((.(((((.((((((((.....))))).))).)))))((((((((((((((....((((........))))....((((((((..(((((......)))))..)))).).)))..........)))))))))))))).))).(((.(((((((((.....)))))))-)).))). ( -43.00, z-score =  -1.83, R)
>droYak2.chrX 2460946 174 + 21770863
UGUGGUGAAACAAUAUCACACGAUGAUAUUUGAUUUCUUUCAAGAGGAUAUAUUGUUAUAAUGAUUGCCAUAUAUACUCCUCACAACCCAAACGAUUUUGGGCCGUGACGCGGAAUUUUUUGUUUAUGUUCUUUUGAAACCAGUGUGCGAAAAGAAACCCUUUUUUU--CGAAUAU
..((((((((((((((((.....))))).))).)))).((((((((((((((....(((((((.....))).)))).(((((((..((((((....))))))..))))...)))..........))))))))))))))))))((((.(((((((((....)))))))--)).)))) ( -44.10, z-score =  -2.83, R)
>droSec1.super_4 5872074 176 - 6179234
UGCGGGGAAACGAUAUCACACGAUGAUAUUUGAUUUCUUUCAAGAGGAUAUAUUUUUAUAAUGCUUGCUAUAUAUACUCCUCACAACCCAAUCGAUUUUGGGCCGUGACGCGGGAUUUUUUGUUUAUGUUCUUUUGAAACCAGUGUGCGAAAAGAAACCCUUUUUUUUUCGAAUAA
...(((((((((((((((.....))))).))).)))))((((((((((((((.......(((.(((((............((((..(((((......)))))..)))).)))))))).......)))))))))))))).))..(((.((((((((((....)))))))))).))). ( -43.76, z-score =  -2.16, R)
>droSim1.chrX 5101464 174 + 17042790
UGCGGGGAAACGAUAUCACACGAUGAUAUUUGAUUUCUUUCAAGAGGAUAUAUUUUUAUAAUGCUUGCUAUAUAUACUCCUCACAACCCAAUCGAUUUUGGGCCGUGACGCGGGAUUUUUUGUUUAUGUUCUUUUGAAACCAGUGUGCGAAAAGAAACCCUUUUUUU--CGAAUAA
...(((((((((((((((.....))))).))).)))))((((((((((((((.......(((.(((((............((((..(((((......)))))..)))).)))))))).......)))))))))))))).))..(((.(((((((((....)))))))--)).))). ( -43.16, z-score =  -2.03, R)
>consensus
UGCGGGGAAACGAUAUCACACGAUGAUAUUUGAUUUCUUUCAAGAGGAUAUAUUGUUAUAAUGAUUGCUAUAUAUACUCCUCACAACCCAAUCGAUUUUGGGCCGUGACGCGGGAUUUUUUGUUUAUGUUCUUUUGAAACCAGUGUGCGAAAAGAAACCCUUUUUUU__CGAAUAA
.((((((((.((((((((.....))))).))).)))))((((((((((((((....(((((((.....))).)))).(((((((..(((((......)))))..))))...)))..........)))))))))))))).......)))((((((.....))))))........... (-34.24 = -33.55 +  -0.69)

alignment

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secondary structure

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dotplot

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Window 4

Location 6,494,190 – 6,494,365
Length 175
Sequences 4
Columns 176
Reading direction reverse
Mean pairwise identity 96.01
Shannon entropy 0.06314
G+C content 0.35478
Mean single sequence MFE -37.31
Consensus MFE -35.17
Energy contribution -35.66
Covariance contribution 0.50
Combinations/Pair 1.00
Mean z-score -1.55
Structure conservation index 0.94
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.71
SVM RNA-class probability 0.795255
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 6494190 175 - 22422827
UUAUUCG-AAAAAAAAGGGUUUCUUUUCGCACACUGCUUUCAAAAGAACAUAAACAAAAAAUCCCGCGUCACGGCCCAAAAUCGAUUGGGUUGUGAGGAGUAUAUAUAGCAAUCAUUAUAACAAUAUAUCCUCUUGAAAGAAAUCAAAUAUCAUCGUGUGAUAUCGUUUUCCCGCA
......(-((((.....((((((((((.((.....))...............................(((((((((((......)))))))))))((((.((((((................)))))).)))).))))))))))..(((((((...)))))))..)))))..... ( -35.99, z-score =  -1.42, R)
>droYak2.chrX 2460946 174 - 21770863
AUAUUCG--AAAAAAAGGGUUUCUUUUCGCACACUGGUUUCAAAAGAACAUAAACAAAAAAUUCCGCGUCACGGCCCAAAAUCGUUUGGGUUGUGAGGAGUAUAUAUGGCAAUCAUUAUAACAAUAUAUCCUCUUGAAAGAAAUCAAAUAUCAUCGUGUGAUAUUGUUUCACCACA
......(--(((.....(((((((((((((((....))(((....))).................)))((((((((((((....))))))))))))((((.((((((................)))))).)))).)))))))))).((((((((...)))))))).))))...... ( -39.19, z-score =  -2.01, R)
>droSec1.super_4 5872074 176 + 6179234
UUAUUCGAAAAAAAAAGGGUUUCUUUUCGCACACUGGUUUCAAAAGAACAUAAACAAAAAAUCCCGCGUCACGGCCCAAAAUCGAUUGGGUUGUGAGGAGUAUAUAUAGCAAGCAUUAUAAAAAUAUAUCCUCUUGAAAGAAAUCAAAUAUCAUCGUGUGAUAUCGUUUCCCCGCA
................(((..........((((((((((((...........................(((((((((((......)))))))))))((((.((((((................)))))).)))).....))))))).........)))))..........)))... ( -37.04, z-score =  -1.39, R)
>droSim1.chrX 5101464 174 - 17042790
UUAUUCG--AAAAAAAGGGUUUCUUUUCGCACACUGGUUUCAAAAGAACAUAAACAAAAAAUCCCGCGUCACGGCCCAAAAUCGAUUGGGUUGUGAGGAGUAUAUAUAGCAAGCAUUAUAAAAAUAUAUCCUCUUGAAAGAAAUCAAAUAUCAUCGUGUGAUAUCGUUUCCCCGCA
.......--.......(((..........((((((((((((...........................(((((((((((......)))))))))))((((.((((((................)))))).)))).....))))))).........)))))..........)))... ( -37.04, z-score =  -1.37, R)
>consensus
UUAUUCG__AAAAAAAGGGUUUCUUUUCGCACACUGGUUUCAAAAGAACAUAAACAAAAAAUCCCGCGUCACGGCCCAAAAUCGAUUGGGUUGUGAGGAGUAUAUAUAGCAAGCAUUAUAAAAAUAUAUCCUCUUGAAAGAAAUCAAAUAUCAUCGUGUGAUAUCGUUUCCCCGCA
................(((..........((((((((((((...........................(((((((((((......)))))))))))((((.((((((................)))))).)))).....))))))).........)))))..........)))... (-35.17 = -35.66 +   0.50)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 01:21:15 2011