Locus 6092

Sequence ID dm3.chr3L
Location 3,607,175 – 3,607,264
Length 89
Max. P 0.727548
window8383 window8384

overview

Window 3

Location 3,607,175 – 3,607,264
Length 89
Sequences 5
Columns 93
Reading direction forward
Mean pairwise identity 77.02
Shannon entropy 0.41146
G+C content 0.37391
Mean single sequence MFE -15.61
Consensus MFE -8.80
Energy contribution -9.24
Covariance contribution 0.44
Combinations/Pair 1.09
Mean z-score -1.72
Structure conservation index 0.56
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.52
SVM RNA-class probability 0.727548
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 3607175 89 + 24543557
----AUUUAAGUAAUAUAUGUGGCCUCAAAGUCUCUACCCAACCCAUUCUCAUUUCACAGUGUUCACUCACUAGAGCCACUACUGUACACAUU
----......(((......(((((.((...((....))....................((((......)))).))))))).....)))..... ( -13.00, z-score =  -1.34, R)
>droSim1.chr3L 3144647 91 + 22553184
AAUUCAUUCAGUUAUAUAUGUGGGCUCAAUAUUACUACCCA--UCAUUCUCAUUACACAGUGUUCAAUCAUUAGAGCGACUACUGUACACAUC
..........((.....(((((((.............))))--.))).......))((((((.((..((....))..)).))))))....... ( -13.02, z-score =  -0.74, R)
>droSec1.super_2 3593096 88 + 7591821
----AAUUCAGUAAUAUAUGUGGACUCAAUAUUACUACCCAA-CCAUUCUCAUUACACAGUGUUCACUCAUUAGAGCGACUACUGUACUCAUC
----.....((((((((.((......))))))))))......-.............((((((.((.(((....))).)).))))))....... ( -17.40, z-score =  -2.51, R)
>droYak2.chr3L 4155091 89 + 24197627
----UUUUCUGUAAUAUAUGCUGGUUCAAUCAUGUUGCCCAAUCUUUUCUCGUAACAUAGUGUUCACUCAUUAGAGCGUCUACUGUACACAUG
----............((((.((..........(((((.............)))))((((((..(.(((....))).)..)))))).)))))) ( -12.32, z-score =   0.04, R)
>droEre2.scaffold_4784 6300922 82 + 25762168
-----------UAAUAUAUGUGUGUUCAAUAAUUUUACCCACCCGUUUCUCAUUACACAGUGGUCACUCACUAGAGCGACUACUGUACACAUC
-----------......((((((.....................((........))(((((((((.(((....))).))))))))))))))). ( -22.30, z-score =  -4.02, R)
>consensus
____AAUUCAGUAAUAUAUGUGGGCUCAAUAUUACUACCCAA_CCAUUCUCAUUACACAGUGUUCACUCAUUAGAGCGACUACUGUACACAUC
........................................................((((((.((.(((....))).)).))))))....... ( -8.80 =  -9.24 +   0.44)

alignment

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secondary structure

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dotplot

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Window 4

Location 3,607,175 – 3,607,264
Length 89
Sequences 5
Columns 93
Reading direction reverse
Mean pairwise identity 77.02
Shannon entropy 0.41146
G+C content 0.37391
Mean single sequence MFE -20.26
Consensus MFE -12.76
Energy contribution -14.16
Covariance contribution 1.40
Combinations/Pair 1.14
Mean z-score -1.33
Structure conservation index 0.63
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.25
SVM RNA-class probability 0.614024
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 3607175 89 - 24543557
AAUGUGUACAGUAGUGGCUCUAGUGAGUGAACACUGUGAAAUGAGAAUGGGUUGGGUAGAGACUUUGAGGCCACAUAUAUUACUUAAAU----
.(((((((((((..(.((((....)))).)..)))))............((((.(((....)))....))))))))))...........---- ( -19.20, z-score =  -0.50, R)
>droSim1.chr3L 3144647 91 - 22553184
GAUGUGUACAGUAGUCGCUCUAAUGAUUGAACACUGUGUAAUGAGAAUGA--UGGGUAGUAAUAUUGAGCCCACAUAUAUAACUGAAUGAAUU
.(((((((((((..(((.((....)).)))..))))).............--.((((...........))))))))))............... ( -17.40, z-score =  -0.53, R)
>droSec1.super_2 3593096 88 - 7591821
GAUGAGUACAGUAGUCGCUCUAAUGAGUGAACACUGUGUAAUGAGAAUGG-UUGGGUAGUAAUAUUGAGUCCACAUAUAUUACUGAAUU----
.......(((((..((((((....))))))..)))))((((((....(((-((.((((....)))).)).)))....))))))......---- ( -24.00, z-score =  -2.31, R)
>droYak2.chr3L 4155091 89 - 24197627
CAUGUGUACAGUAGACGCUCUAAUGAGUGAACACUAUGUUACGAGAAAAGAUUGGGCAACAUGAUUGAACCAGCAUAUAUUACAGAAAA----
((((((..((((.....(((((((((((....))).))))).))).....))))..).)))))..........................---- ( -15.40, z-score =  -0.45, R)
>droEre2.scaffold_4784 6300922 82 - 25762168
GAUGUGUACAGUAGUCGCUCUAGUGAGUGACCACUGUGUAAUGAGAAACGGGUGGGUAAAAUUAUUGAACACACAUAUAUUA-----------
.(((((((((((.(((((((....))))))).)))))..............(((..(((.....)))..)))))))))....----------- ( -25.30, z-score =  -2.87, R)
>consensus
GAUGUGUACAGUAGUCGCUCUAAUGAGUGAACACUGUGUAAUGAGAAUGG_UUGGGUAGAAAUAUUGAGCCCACAUAUAUUACUGAAAU____
.(((((((((((..((((((....))))))..)))))................((((...........))))))))))............... (-12.76 = -14.16 +   1.40)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 23:01:08 2011