Locus 1658

Sequence ID dm3.chr2L
Location 12,886,446 – 12,886,546
Length 100
Max. P 0.968552
window2270 window2271

overview

Window 0

Location 12,886,446 – 12,886,542
Length 96
Sequences 11
Columns 119
Reading direction forward
Mean pairwise identity 86.18
Shannon entropy 0.27458
G+C content 0.30032
Mean single sequence MFE -21.73
Consensus MFE -15.37
Energy contribution -15.69
Covariance contribution 0.32
Combinations/Pair 1.13
Mean z-score -2.56
Structure conservation index 0.71
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.80
SVM RNA-class probability 0.968552
Prediction RNA
WARNING Out of training range. z-scores are NOT reliable.

Download alignment: ClustalW | MAF

>dm3.chr2L 12886446 96 + 23011544
-----------------------CCCGCAUUGCAUUUUCUGUGCGAUUUAAUACGCAUUUAAAUGCAAAUUUAUAUACGAAAUUAUCUACGUGAAGAAAUCUUCGGGUUUUAAUAACAU
-----------------------(((...((((((((...(((((........)))))..))))))))........................((((....)))))))............ ( -22.70, z-score =  -3.01, R)
>droSim1.chr2L 12680522 96 + 22036055
-----------------------CCCGCAUUGCAUUUUCUGUGCGAUUUAAUACGCAUUUAAAUGCAAAUUUAUAUACGAAAUUAUCUACGUGAAGAAAUCUUCGGGUUUUAAUAACAU
-----------------------(((...((((((((...(((((........)))))..))))))))........................((((....)))))))............ ( -22.70, z-score =  -3.01, R)
>droSec1.super_16 1048363 96 + 1878335
-----------------------CCCGCAUUGCAUUUUCUGUGCGAUUUAAUACGCAUUUAAAUGCAAAUUUAUAUACGAAAUUAUCUACGUGAAGAAAUCUUCGGGUUUUAAUAACAU
-----------------------(((...((((((((...(((((........)))))..))))))))........................((((....)))))))............ ( -22.70, z-score =  -3.01, R)
>droYak2.chr2L 9308871 96 + 22324452
-----------------------UCCGCAUUGCAUUUUCUGUGCGAUUUAAUACGCAUUUAAAUGCAAAUUUAUAUACGAAAUUAUCUACGUGAAGAAAUCUUCGGGUUUUAAUAACAU
-----------------------......((((((((...(((((........)))))..)))))))).............((((...((.(((((....))))).))..))))..... ( -22.50, z-score =  -2.95, R)
>droEre2.scaffold_4929 14086079 96 - 26641161
-----------------------CCCGCAUUGCAUUUUCUGUGCGAUUUAAUACGCAUUUAAAUGCAAAUUUAUAUACGAAAUUAUCUACGUGAAGAAAUCUUCGGAUUUUAAUAACAU
-----------------------..(((.((((((((...(((((........)))))..))))))))..........((.....))...)))..((((((....))))))........ ( -22.10, z-score =  -3.14, R)
>droAna3.scaffold_12916 3638164 96 - 16180835
-----------------------CCCUCAUGGCAUUUUCUGUGCGAUUUAAUACGCAUUUAAAUGCAAAUUUAUAUUCGAAAUUAUCUACGUGAAGAAAUCUUCAGGUUUUAAUAACAU
-----------------------.....(((((((((...(((((........)))))..))))))...............((((...((.(((((....))))).))..))))..))) ( -21.50, z-score =  -3.12, R)
>dp4.chr4_group4 541771 96 + 6586962
-----------------------GUUUCGGUGCAUUUUCUGUGCGAUUUAAUACGCAUUUAAAUGCAAAUUUAUAUACGAAAUUAUCUACGUGAAGAAAUCUUCAGGUUUUAAUAACAU
-----------------------..((((.(((((((...(((((........)))))..)))))))..........))))((((...((.(((((....))))).))..))))..... ( -23.80, z-score =  -3.39, R)
>droPer1.super_46 76647 96 - 590583
-----------------------GUUUCGGUGCAUUUUCUGUGCGAUUUAAUACGCAUUUAAAUGCAAAUUUAUAUACGAAAUUAUCUACGUGAAGAAAUCUUCAGGUUUUAAUAACAU
-----------------------..((((.(((((((...(((((........)))))..)))))))..........))))((((...((.(((((....))))).))..))))..... ( -23.80, z-score =  -3.39, R)
>droWil1.scaffold_180708 5926918 96 + 12563649
-----------------------AUCGCAUUGCAUUUUCUGAGCGAUUUAAUACGCAUUUAAAUGCAAAUUUAAAUAUGAAAUUAUCUACGUGAAGAAAUCUUCAGAUUUUAAUAACAU
-----------------------.((((.((((((((.....(((........)))....)))))))).((((....)))).........)))).((((((....))))))........ ( -16.40, z-score =  -0.92, R)
>droMoj3.scaffold_6500 25925377 119 + 32352404
CCUUUCUGUGUAUGCGUGUGCAUCUCAUAUUGCAUUUUCUGUGCGAUUUAAUACCCAUUUAAAUGUAAAUUUGUAUACGAAAUUAUCUACGUGAAGAAAUCUUCAGCUUUUAAUAACAU
.......((((...((((((((........(((((.....)))))((((((.......)))))).......))))))))............(((((....)))))..........)))) ( -20.30, z-score =  -1.10, R)
>droGri2.scaffold_15252 9936292 118 + 17193109
-AACGAAGUUUGUGUGCGUGUUCCUCUUAUUGCAUUUUCUGUGCGAUUUAAUACCCAUUUAAAUUCAAAUUUGCAUACGAAAUUAUCUACGUGAAGAAAUCUCUAGGUUUUAAUAAAAU
-.(((.((((((((((((.(((.........((((.....))))(((((((.......)))))))..))).)))))))))).....)).)))...((((((....))))))........ ( -20.50, z-score =  -1.07, R)
>consensus
_______________________CCCGCAUUGCAUUUUCUGUGCGAUUUAAUACGCAUUUAAAUGCAAAUUUAUAUACGAAAUUAUCUACGUGAAGAAAUCUUCAGGUUUUAAUAACAU
.............................((((((((...(((((........)))))..)))))))).............((((....(.(((((....))))))....))))..... (-15.37 = -15.69 +   0.32)

alignment

Postscript

secondary structure

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dotplot

Postscript

Window 1

Location 12,886,446 – 12,886,546
Length 100
Sequences 11
Columns 119
Reading direction forward
Mean pairwise identity 86.83
Shannon entropy 0.26542
G+C content 0.30370
Mean single sequence MFE -21.65
Consensus MFE -15.37
Energy contribution -15.69
Covariance contribution 0.32
Combinations/Pair 1.13
Mean z-score -2.43
Structure conservation index 0.71
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.52
SVM RNA-class probability 0.946124
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 12886446 100 + 23011544
-------------------CCCGCAUUGCAUUUUCUGUGCGAUUUAAUACGCAUUUAAAUGCAAAUUUAUAUACGAAAUUAUCUACGUGAAGAAAUCUUCGGGUUUUAAUAACAUUUCC
-------------------(((...((((((((...(((((........)))))..))))))))........................((((....)))))))................ ( -22.70, z-score =  -2.96, R)
>droSim1.chr2L 12680522 100 + 22036055
-------------------CCCGCAUUGCAUUUUCUGUGCGAUUUAAUACGCAUUUAAAUGCAAAUUUAUAUACGAAAUUAUCUACGUGAAGAAAUCUUCGGGUUUUAAUAACAUUUCC
-------------------(((...((((((((...(((((........)))))..))))))))........................((((....)))))))................ ( -22.70, z-score =  -2.96, R)
>droSec1.super_16 1048363 100 + 1878335
-------------------CCCGCAUUGCAUUUUCUGUGCGAUUUAAUACGCAUUUAAAUGCAAAUUUAUAUACGAAAUUAUCUACGUGAAGAAAUCUUCGGGUUUUAAUAACAUUUCC
-------------------(((...((((((((...(((((........)))))..))))))))........................((((....)))))))................ ( -22.70, z-score =  -2.96, R)
>droYak2.chr2L 9308871 100 + 22324452
-------------------UCCGCAUUGCAUUUUCUGUGCGAUUUAAUACGCAUUUAAAUGCAAAUUUAUAUACGAAAUUAUCUACGUGAAGAAAUCUUCGGGUUUUAAUAACAUUUCC
-------------------......((((((((...(((((........)))))..)))))))).............((((...((.(((((....))))).))..))))......... ( -22.50, z-score =  -2.89, R)
>droEre2.scaffold_4929 14086079 100 - 26641161
-------------------CCCGCAUUGCAUUUUCUGUGCGAUUUAAUACGCAUUUAAAUGCAAAUUUAUAUACGAAAUUAUCUACGUGAAGAAAUCUUCGGAUUUUAAUAACAUUUCC
-------------------..(((.((((((((...(((((........)))))..))))))))..........((.....))...)))..((((((....))))))............ ( -22.10, z-score =  -3.12, R)
>droAna3.scaffold_12916 3638164 100 - 16180835
-------------------CCCUCAUGGCAUUUUCUGUGCGAUUUAAUACGCAUUUAAAUGCAAAUUUAUAUUCGAAAUUAUCUACGUGAAGAAAUCUUCAGGUUUUAAUAACAUUUAC
-------------------.....(((((((((...(((((........)))))..))))))...............((((...((.(((((....))))).))..))))..))).... ( -21.60, z-score =  -3.15, R)
>dp4.chr4_group4 541771 100 + 6586962
-------------------GUUUCGGUGCAUUUUCUGUGCGAUUUAAUACGCAUUUAAAUGCAAAUUUAUAUACGAAAUUAUCUACGUGAAGAAAUCUUCAGGUUUUAAUAACAUUUGC
-------------------..((((.(((((((...(((((........)))))..)))))))..........))))((((...((.(((((....))))).))..))))......... ( -23.80, z-score =  -2.95, R)
>droPer1.super_46 76647 100 - 590583
-------------------GUUUCGGUGCAUUUUCUGUGCGAUUUAAUACGCAUUUAAAUGCAAAUUUAUAUACGAAAUUAUCUACGUGAAGAAAUCUUCAGGUUUUAAUAACAUUUGC
-------------------..((((.(((((((...(((((........)))))..)))))))..........))))((((...((.(((((....))))).))..))))......... ( -23.80, z-score =  -2.95, R)
>droWil1.scaffold_180708 5926918 100 + 12563649
-------------------AUCGCAUUGCAUUUUCUGAGCGAUUUAAUACGCAUUUAAAUGCAAAUUUAAAUAUGAAAUUAUCUACGUGAAGAAAUCUUCAGAUUUUAAUAACAUUCAC
-------------------.((((.((((((((.....(((........)))....)))))))).((((....)))).........)))).((((((....))))))............ ( -16.40, z-score =  -0.87, R)
>droMoj3.scaffold_6500 25925381 119 + 32352404
UCUGUGUAUGCGUGUGCAUCUCAUAUUGCAUUUUCUGUGCGAUUUAAUACCCAUUUAAAUGUAAAUUUGUAUACGAAAUUAUCUACGUGAAGAAAUCUUCAGCUUUUAAUAACAUUUAC
...((((...((((((((........(((((.....)))))((((((.......)))))).......))))))))............(((((....)))))..........)))).... ( -20.40, z-score =  -0.84, R)
>droGri2.scaffold_15252 9936296 118 + 17193109
-AAGUUUGUGUGCGUGUUCCUCUUAUUGCAUUUUCUGUGCGAUUUAAUACCCAUUUAAAUUCAAAUUUGCAUACGAAAUUAUCUACGUGAAGAAAUCUCUAGGUUUUAAUAAAAUUUAU
-...((((((((((.(((.........((((.....))))(((((((.......)))))))..))).))))))))))..............((((((....))))))............ ( -19.40, z-score =  -1.09, R)
>consensus
___________________CCCGCAUUGCAUUUUCUGUGCGAUUUAAUACGCAUUUAAAUGCAAAUUUAUAUACGAAAUUAUCUACGUGAAGAAAUCUUCAGGUUUUAAUAACAUUUCC
.........................((((((((...(((((........)))))..)))))))).............((((....(.(((((....))))))....))))......... (-15.37 = -15.69 +   0.32)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 21:36:12 2011