Locus 3418

Sequence ID dm3.chr2R
Location 5,116,850 – 5,117,002
Length 152
Max. P 0.999667
window4694 window4695 window4696 window4697

overview

Window 4

Location 5,116,850 – 5,116,970
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 72.65
Shannon entropy 0.48651
G+C content 0.38929
Mean single sequence MFE -27.52
Consensus MFE -15.17
Energy contribution -16.69
Covariance contribution 1.52
Combinations/Pair 1.29
Mean z-score -1.47
Structure conservation index 0.55
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.71
SVM RNA-class probability 0.795443
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 5116850 120 + 21146708
GAAAAGCACAGAUAUGCCAGGAGAAUUGGGAGCAACUUUAAAAGGUGUCGAAAAGUGGGCAAUACAAAAACGAGAUUCUUCAUUGCAUACUUUUAGACAGCUGUAUGGGGGAUUAAGUGA
......(((.(...(.((((.....)))).).)..(((((..((.((((.(((((((.(((((.(......).((....))))))).))))))).)))).))...)))))......))). ( -25.70, z-score =  -0.91, R)
>droSim1.chr2R 3781223 120 + 19596830
GAAAAGCACAGAUAUGCCAGGAGAAUGGGGAGCAACUUUAAAAGGUGUCGAAAAGUGUGCAAUACGAAAUCGAGAUUCUUCAUUGCAUACUUUUAGACAGCUGUAUGGGGGAUUAAGUGA
......(((.....(.(((......))).).....(((((..((.((((.(((((((((((((.((....)).((....))))))))))))))).)))).))...)))))......))). ( -32.80, z-score =  -2.79, R)
>droSec1.super_1 2748419 120 + 14215200
GAAAAGCAUAGAUAUGCCAGGAGAUUUGGGAGCAACUAUAAAAGGUGUCGAAAAGUGUGCAAUACCAAAUCGGGAUUCUUCAUUGCACACUUUUAGACAGCUGUAUGGGGGAUUAAGUGA
.....((((....))))......((((((...(..(((((..((.((((.(((((((((((((.((.....))((....))))))))))))))).)))).)).)))))..).)))))).. ( -36.30, z-score =  -3.45, R)
>droYak2.chr2L 17771735 105 + 22324452
---------GAAGACCACAGUGUAAUAGGAACAUGUUGUGAAUGGUGUCGAAAAGUAUGCAUU--UAAAUUGGGCUUC----GUGCAUAAUUGGAAACAGCUCUAUGAGAGAUUAUGCGA
---------((((.((.((((.(((((......)))))(((((((((.(.....)))).))))--)).))))))))))----.((((((((((....)).(((.....))))))))))). ( -23.60, z-score =  -0.68, R)
>droEre2.scaffold_4929 9099690 112 - 26641161
-------GAAAAUUAGUAAGCAGAAUUUGUAGCAAUUUGAAAUAGUGUCGAAAAGUAUGCAUU-CAAAAUCGGGAUUUCUGGUUGCAUAAGUUUAGACAGCUCCAUGAGAGAUUAUGUGA
-------...........(((.(((((......))))).......((((.(((..((((((..-((((((....)))).))..))))))..))).))))))).(((((....)))))... ( -19.20, z-score =   0.49, R)
>consensus
GAAAAGCACAGAUAUGCCAGGAGAAUUGGGAGCAACUUUAAAAGGUGUCGAAAAGUGUGCAAUACAAAAUCGGGAUUCUUCAUUGCAUACUUUUAGACAGCUGUAUGGGGGAUUAAGUGA
...................................(((((..((.((((.(((((((((((((..................))))))))))))).)))).))...))))).......... (-15.17 = -16.69 +   1.52)

alignment

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secondary structure

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dotplot

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Window 5

Location 5,116,850 – 5,116,970
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 72.65
Shannon entropy 0.48651
G+C content 0.38929
Mean single sequence MFE -21.20
Consensus MFE -14.31
Energy contribution -16.72
Covariance contribution 2.41
Combinations/Pair 1.17
Mean z-score -2.36
Structure conservation index 0.68
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.95
SVM RNA-class probability 0.996582
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 5116850 120 - 21146708
UCACUUAAUCCCCCAUACAGCUGUCUAAAAGUAUGCAAUGAAGAAUCUCGUUUUUGUAUUGCCCACUUUUCGACACCUUUUAAAGUUGCUCCCAAUUCUCCUGGCAUAUCUGUGCUUUUC
.................(((.((((.((((((..((((((.((((......)))).))))))..)))))).))))........(((((....)))))...)))((((....))))..... ( -21.00, z-score =  -2.17, R)
>droSim1.chr2R 3781223 120 - 19596830
UCACUUAAUCCCCCAUACAGCUGUCUAAAAGUAUGCAAUGAAGAAUCUCGAUUUCGUAUUGCACACUUUUCGACACCUUUUAAAGUUGCUCCCCAUUCUCCUGGCAUAUCUGUGCUUUUC
...............(((((.((((.((((((.(((((((..((((....))))..))))))).)))))).))))...........((((............))))...)))))...... ( -24.20, z-score =  -3.08, R)
>droSec1.super_1 2748419 120 - 14215200
UCACUUAAUCCCCCAUACAGCUGUCUAAAAGUGUGCAAUGAAGAAUCCCGAUUUGGUAUUGCACACUUUUCGACACCUUUUAUAGUUGCUCCCAAAUCUCCUGGCAUAUCUAUGCUUUUC
..................(((((((.((((((((((((((..((((....))))..)))))))))))))).))))......((((.((((............))))...))))))).... ( -31.80, z-score =  -4.87, R)
>droYak2.chr2L 17771735 105 - 22324452
UCGCAUAAUCUCUCAUAGAGCUGUUUCCAAUUAUGCAC----GAAGCCCAAUUUA--AAUGCAUACUUUUCGACACCAUUCACAACAUGUUCCUAUUACACUGUGGUCUUC---------
..((((((((((.....))).........)))))))..----((((.((......--..............((......))...((((((.......))).))))).))))--------- ( -13.40, z-score =  -0.18, R)
>droEre2.scaffold_4929 9099690 112 + 26641161
UCACAUAAUCUCUCAUGGAGCUGUCUAAACUUAUGCAACCAGAAAUCCCGAUUUUG-AAUGCAUACUUUUCGACACUAUUUCAAAUUGCUACAAAUUCUGCUUACUAAUUUUC-------
.................((((((((.(((..((((((..(((((.......)))))-..))))))..))).))))........((((......))))..))))..........------- ( -15.60, z-score =  -1.50, R)
>consensus
UCACUUAAUCCCCCAUACAGCUGUCUAAAAGUAUGCAAUGAAGAAUCCCGAUUUUGUAUUGCACACUUUUCGACACCUUUUAAAGUUGCUCCCAAUUCUCCUGGCAUAUCUGUGCUUUUC
...................(.((((.((((((((((((((..((((....))))..)))))))))))))).)))).)........................................... (-14.31 = -16.72 +   2.41)

alignment

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secondary structure

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dotplot

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Window 6

Location 5,116,890 – 5,117,002
Length 112
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 72.27
Shannon entropy 0.47232
G+C content 0.35560
Mean single sequence MFE -29.58
Consensus MFE -17.90
Energy contribution -19.35
Covariance contribution 1.45
Combinations/Pair 1.25
Mean z-score -2.82
Structure conservation index 0.61
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 3.25
SVM RNA-class probability 0.998061
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 5116890 112 + 21146708
AAAGGUGUCGAAAAGUGGGCAAUACAAAAACGAGAUUCUUCAUUGCAUACUUUUAGACAGCUGUAUGGGGGAUUAAGUGAUUUGCAGAUGGCAAAUUUAUAGUACCCAUAAA--------
..((.((((.(((((((.(((((.(......).((....))))))).))))))).)))).)).((((((..((((...(((((((.....)))))))..)))).))))))..-------- ( -33.20, z-score =  -3.90, R)
>droSim1.chr2R 3781263 112 + 19596830
AAAGGUGUCGAAAAGUGUGCAAUACGAAAUCGAGAUUCUUCAUUGCAUACUUUUAGACAGCUGUAUGGGGGAUUAAGUGAUUUGCAGAUAGCAAAUUUAUAGUACCAAUAAA--------
..((.((((.(((((((((((((.((....)).((....))))))))))))))).)))).))...(((...((((...(((((((.....)))))))..)))).))).....-------- ( -35.10, z-score =  -4.80, R)
>droSec1.super_1 2748459 113 + 14215200
AAAGGUGUCGAAAAGUGUGCAAUACCAAAUCGGGAUUCUUCAUUGCACACUUUUAGACAGCUGUAUGGGGGAUUAAGUGAUUUGCAGAUAGCAAAUUUAUAGUACCAAUAAAA-------
..((.((((.(((((((((((((.((.....))((....))))))))))))))).)))).))...(((...((((...(((((((.....)))))))..)))).)))......------- ( -37.30, z-score =  -5.04, R)
>droYak2.chr2L 17771766 114 + 22324452
AAUGGUGUCGAAAAGUAUGCA-UUUAAAUU--GGGCUUCG---UGCAUAAUUGGAAACAGCUCUAUGAGAGAUUAUGCGAUCUUUGGAUAGCAAAACUGUAGAAUCCAUAAUUUUCAACA
.....(((.(((((.((((.(-(((.....--..(((...---((((((((((....)).(((.....)))))))))))(((....)))))).........)))).)))).))))).))) ( -21.89, z-score =   0.25, R)
>droEre2.scaffold_4929 9099723 100 - 26641161
AAUAGUGUCGAAAAGUAUGCA-UUCAAAAUCGGGAUUUCUGGUUGCAUAAGUUUAGACAGCUCCAUGAGAGAUUAUGUGAACUUUGGAUUCCAAAACAAAA-------------------
.....((((.(((..((((((-..((((((....)))).))..))))))..))).))))..(((((((....))))).))..(((((...)))))......------------------- ( -20.40, z-score =  -0.63, R)
>consensus
AAAGGUGUCGAAAAGUGUGCAAUACAAAAUCGGGAUUCUUCAUUGCAUACUUUUAGACAGCUGUAUGGGGGAUUAAGUGAUUUGCAGAUAGCAAAUUUAUAGUACCAAUAAA________
.....((((.(((((((((((((..................))))))))))))).))))(((((...(.(((((....))))).)..)))))............................ (-17.90 = -19.35 +   1.45)

alignment

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secondary structure

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dotplot

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Window 7

Location 5,116,890 – 5,117,002
Length 112
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 72.27
Shannon entropy 0.47232
G+C content 0.35560
Mean single sequence MFE -25.93
Consensus MFE -14.63
Energy contribution -17.48
Covariance contribution 2.85
Combinations/Pair 1.21
Mean z-score -3.76
Structure conservation index 0.56
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 4.16
SVM RNA-class probability 0.999667
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 5116890 112 - 21146708
--------UUUAUGGGUACUAUAAAUUUGCCAUCUGCAAAUCACUUAAUCCCCCAUACAGCUGUCUAAAAGUAUGCAAUGAAGAAUCUCGUUUUUGUAUUGCCCACUUUUCGACACCUUU
--------..((((((........((((((.....))))))..........)))))).((.((((.((((((..((((((.((((......)))).))))))..)))))).)))).)).. ( -26.77, z-score =  -4.18, R)
>droSim1.chr2R 3781263 112 - 19596830
--------UUUAUUGGUACUAUAAAUUUGCUAUCUGCAAAUCACUUAAUCCCCCAUACAGCUGUCUAAAAGUAUGCAAUGAAGAAUCUCGAUUUCGUAUUGCACACUUUUCGACACCUUU
--------......(((.......((((((.....)))))).....................(((.((((((.(((((((..((((....))))..))))))).)))))).))))))... ( -26.20, z-score =  -4.56, R)
>droSec1.super_1 2748459 113 - 14215200
-------UUUUAUUGGUACUAUAAAUUUGCUAUCUGCAAAUCACUUAAUCCCCCAUACAGCUGUCUAAAAGUGUGCAAUGAAGAAUCCCGAUUUGGUAUUGCACACUUUUCGACACCUUU
-------.......(((.......((((((.....)))))).....................(((.((((((((((((((..((((....))))..)))))))))))))).))))))... ( -32.80, z-score =  -5.70, R)
>droYak2.chr2L 17771766 114 - 22324452
UGUUGAAAAUUAUGGAUUCUACAGUUUUGCUAUCCAAAGAUCGCAUAAUCUCUCAUAGAGCUGUUUCCAAUUAUGCA---CGAAGCCC--AAUUUAAA-UGCAUACUUUUCGACACCAUU
(((((((((...((((....((((((((((.(((....))).)))............))))))).))))..((((((---.(((....--..)))...-)))))).)))))))))..... ( -24.80, z-score =  -2.68, R)
>droEre2.scaffold_4929 9099723 100 + 26641161
-------------------UUUUGUUUUGGAAUCCAAAGUUCACAUAAUCUCUCAUGGAGCUGUCUAAACUUAUGCAACCAGAAAUCCCGAUUUUGAA-UGCAUACUUUUCGACACUAUU
-------------------......(((((...)))))((((.(((........)))))))((((.(((..((((((..(((((.......)))))..-))))))..))).))))..... ( -19.10, z-score =  -1.69, R)
>consensus
________UUUAUGGGUACUAUAAAUUUGCUAUCUGCAAAUCACUUAAUCCCCCAUACAGCUGUCUAAAAGUAUGCAAUGAAGAAUCCCGAUUUUGUAUUGCACACUUUUCGACACCUUU
...........................................................(.((((.((((((((((((((.(((((....))))).)))))))))))))).)))).)... (-14.63 = -17.48 +   2.85)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:09:51 2011