Locus 1950

Sequence ID dm3.chr2L
Location 15,039,296 – 15,039,402
Length 106
Max. P 0.627500
window2691 window2692

overview

Window 1

Location 15,039,296 – 15,039,402
Length 106
Sequences 7
Columns 106
Reading direction forward
Mean pairwise identity 56.55
Shannon entropy 0.87439
G+C content 0.28485
Mean single sequence MFE -14.40
Consensus MFE -5.68
Energy contribution -5.41
Covariance contribution -0.26
Combinations/Pair 1.50
Mean z-score -0.53
Structure conservation index 0.39
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.20
SVM RNA-class probability 0.589217
Prediction RNA
WARNING Out of training range. z-scores are NOT reliable.

Download alignment: ClustalW | MAF

>dm3.chr2L 15039296 106 + 23011544
CUUUAACAGUGAUGUGAUGGGAAUAAAUAUACAAAUGUAUUCAGAAACUGCAAAGUUAAAACAAAAUAUAUUAGCUACUCCAAAUUGGCUAUAAAAUAACCAAAUG
.....(((....)))..((((((((.((......)).)))))...((((....))))..............((((((........))))))........))).... ( -12.80, z-score =  -0.00, R)
>droPer1.super_5 2618256 101 + 6813705
CUUAUUCAGCGCCCUAUACUAAAUAAUU--AGAUUUGUAUU---AAAAUAUUCAGAAGUGACAGUAUAUCGCCACAAAAAACAUUUAGCUAUAAAAUAGCUGGCUC
.......(((((..((((((..((((..--....))))...---.......(((....))).))))))..)).............(((((((...)))))))))). ( -13.10, z-score =   0.12, R)
>dp4.chr4_group1 2691037 101 - 5278887
CUUAUUCAGCACCCUAUACUAAAUAGUU--AGAUUUGUAUU---AAAAUAUUCAGAAGUGACAGUAUAUCGCCACAAAAAACAUUUAGCUAUAAAAUAGCUGCCUC
......((((....((((((((((.(((--...((((.((.---.....)).)))).(((.(........).)))....))))))))).)))).....)))).... ( -11.90, z-score =  -0.00, R)
>droAna3.scaffold_12916 15358748 84 - 16180835
--------------------UUUUCGAUAAACAAGGGUUUAAAAAUGUAGUAAAAUAGUAACAUUUUGAUGAGAAUAUAAAUGAUGGGACCUAAAAUACCCUGG--
--------------------((((((.(((((....)))))(((((((............)))))))..))))))..........(((..........)))...-- (  -9.20, z-score =   0.87, R)
>droEre2.scaffold_4929 6779024 106 + 26641161
CUUUUACAGUAAUGUGAGGAGAUCAUAUAAAAAAAUGUAUUCAGAAUUUGCUAAAUAGAAACGAAAAAUAUUAGCUUAUCCAAUUUGGCUAUAAUAUAGCCAAGUG
...(((((....)))))(((((..((((......))))..)).......(((((................)))))...))).((((((((((...)))))))))). ( -21.59, z-score =  -2.57, R)
>droSec1.super_3 1301437 106 + 7220098
CUUUUACAGUAAUAUGCAAAGAAUAGAUGUAAAAGUGUAUUCAGAAACUACUAAAUAAAAACAAAAAAUAUUAGCUACGCCAAGUUGGCUAUAAAAUAGCCAAAUG
((((((((....(((.......)))..)))))))).................................................((((((((...))))))))... ( -15.20, z-score =  -0.90, R)
>droSim1.chr2L 14786368 106 + 22036055
CUUUCAUAUUAAUAUGAUAUGAAUAGAUGUACAAGUGUAUUCAGAAACUACUAAAUAAAAGCAAAAAAUAUUAGCUACGCCAAGUUGGCUAUAAAAUAGCCAAAUG
..((((((((.....))))))))..((.((((....)))))).................(((...........)))........((((((((...))))))))... ( -17.00, z-score =  -1.25, R)
>consensus
CUUUUACAGUAAUAUGAAAUGAAUAGAUAUACAAGUGUAUUCAGAAACUACUAAAUAGAAACAAAAUAUAUUAGCUAAACCAAUUUGGCUAUAAAAUAGCCAAAUG
....................................................................................((((((((...))))))))... ( -5.68 =  -5.41 +  -0.26)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 2

Location 15,039,296 – 15,039,402
Length 106
Sequences 7
Columns 106
Reading direction reverse
Mean pairwise identity 56.55
Shannon entropy 0.87439
G+C content 0.28485
Mean single sequence MFE -17.04
Consensus MFE -5.20
Energy contribution -4.47
Covariance contribution -0.73
Combinations/Pair 1.67
Mean z-score -1.04
Structure conservation index 0.31
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.28
SVM RNA-class probability 0.627500
Prediction RNA
WARNING Out of training range. z-scores are NOT reliable.

Download alignment: ClustalW | MAF

>dm3.chr2L 15039296 106 - 23011544
CAUUUGGUUAUUUUAUAGCCAAUUUGGAGUAGCUAAUAUAUUUUGUUUUAACUUUGCAGUUUCUGAAUACAUUUGUAUAUUUAUUCCCAUCACAUCACUGUUAAAG
...((((((((...))))))))...((((((...(((((((..(((...((((....)))).......)))...)))))))))))))................... ( -15.80, z-score =  -0.68, R)
>droPer1.super_5 2618256 101 - 6813705
GAGCCAGCUAUUUUAUAGCUAAAUGUUUUUUGUGGCGAUAUACUGUCACUUCUGAAUAUUUU---AAUACAAAUCU--AAUUAUUUAGUAUAGGGCGCUGAAUAAG
..(((((((((...))))))((((((((...((((((......))))))....)))))))).---.((((((((..--....)))).))))..))).......... ( -20.60, z-score =  -1.06, R)
>dp4.chr4_group1 2691037 101 + 5278887
GAGGCAGCUAUUUUAUAGCUAAAUGUUUUUUGUGGCGAUAUACUGUCACUUCUGAAUAUUUU---AAUACAAAUCU--AACUAUUUAGUAUAGGGUGCUGAAUAAG
....((((.((((((((.(((((((((.((((((..((.(((...(((....))).))).))---..))))))...--))).))))))))))))))))))...... ( -21.20, z-score =  -1.23, R)
>droAna3.scaffold_12916 15358748 84 + 16180835
--CCAGGGUAUUUUAGGUCCCAUCAUUUAUAUUCUCAUCAAAAUGUUACUAUUUUACUACAUUUUUAAACCCUUGUUUAUCGAAAA--------------------
--..(((((......(....)..................(((((((............)))))))...))))).............-------------------- (  -8.00, z-score =   0.23, R)
>droEre2.scaffold_4929 6779024 106 - 26641161
CACUUGGCUAUAUUAUAGCCAAAUUGGAUAAGCUAAUAUUUUUCGUUUCUAUUUAGCAAAUUCUGAAUACAUUUUUUUAUAUGAUCUCCUCACAUUACUGUAAAAG
...((((((((...)))))))).(..((...(((((................)))))....))..)........(((((((((((........)))).))))))). ( -16.09, z-score =  -1.37, R)
>droSec1.super_3 1301437 106 - 7220098
CAUUUGGCUAUUUUAUAGCCAACUUGGCGUAGCUAAUAUUUUUUGUUUUUAUUUAGUAGUUUCUGAAUACACUUUUACAUCUAUUCUUUGCAUAUUACUGUAAAAG
...((((((((......(((.....))))))))))).............(((((((......)))))))..((((((((...................)))))))) ( -18.51, z-score =  -1.61, R)
>droSim1.chr2L 14786368 106 - 22036055
CAUUUGGCUAUUUUAUAGCCAACUUGGCGUAGCUAAUAUUUUUUGCUUUUAUUUAGUAGUUUCUGAAUACACUUGUACAUCUAUUCAUAUCAUAUUAAUAUGAAAG
...((((((((......(((.....))))))))))).........(((((((((((((.....((((((............)))))).....)))))).))))))) ( -19.10, z-score =  -1.52, R)
>consensus
CAUUUGGCUAUUUUAUAGCCAAAUUGGUGUAGCUAAUAUAUUUUGUUUCUAUUUAGUAGUUUCUGAAUACACUUGUAUAUCUAUUCACUUCACAUUACUGUAAAAG
.....((((((...))))))...................................................................................... ( -5.20 =  -4.47 +  -0.73)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 21:42:01 2011