Locus 261

Sequence ID dm3.chr2L
Location 1,898,201 – 1,898,332
Length 131
Max. P 0.841104
window356 window357 window358

overview

Window 6

Location 1,898,201 – 1,898,291
Length 90
Sequences 7
Columns 100
Reading direction forward
Mean pairwise identity 75.42
Shannon entropy 0.48634
G+C content 0.43262
Mean single sequence MFE -23.70
Consensus MFE -13.49
Energy contribution -12.99
Covariance contribution -0.50
Combinations/Pair 1.62
Mean z-score -1.38
Structure conservation index 0.57
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.69
SVM RNA-class probability 0.786542
Prediction RNA
WARNING Out of training range. z-scores are NOT reliable.

Download alignment: ClustalW | MAF

>dm3.chr2L 1898201 90 + 23011544
GAUUUCAUAAUCCUAAAUUCGCUGGCAGUUGUUG--------AUGGUGCGAAUUCGCCAACAAAAGUGGGUUAAUUCGCACGGGCAGAAAGAGACAGC--
((((....))))........((((.......(((--------.(.(((((((((.(((.((....)).))).))))))))).).))).......))))-- ( -26.04, z-score =  -1.89, R)
>droAna3.scaffold_12916 489838 86 - 16180835
GAUUUCAUAAUCACAACAUGGUUGGCAGUUGUUGGCAGUUGGAUGGUGUGAAUGGGCCAACAAAAGUGGGUUAAUUCGCACAGGCA--------------
.........(((.((((...((..((....))..)).))))))).((((((((..(((.((....)).)))..)))))))).....-------------- ( -27.60, z-score =  -2.40, R)
>droEre2.scaffold_4929 1941837 89 + 26641161
GAUUUCAUAAUCCUAAAUUCGCUGCCAGUUGUUG--------AUGGUGCGAAUG-GCCAGCAAAAGUGGGUUAAUUCGCACGGACAGAUAGAGAUAAC--
.(((((((..(((...(((.((........)).)--------)).(((((((((-(((.((....)).)))).)))))))))))...)).)))))...-- ( -22.50, z-score =  -1.08, R)
>droYak2.chr2L 1877550 89 + 22324452
GAUUUCAUAAUCCCAAAUUCGCUGGCAGUUGUUG--------AUGGUGCGAAUGG-CCAGCAAAAGUGGGUUAAUUCGCACCGGCAGAAAGAGAUAGG--
.(((((.(((.((((..((.((((((..((((..--------.....))))...)-))))).))..))))))).(((((....)).))).)))))...-- ( -26.80, z-score =  -1.72, R)
>droSec1.super_14 1841802 89 + 2068291
GAUUUCAUAAUCCUAAAUUCGCUGGCAGUUGUUA--------AUGGUGCGAAUG-GCCAGCAAAAGUGGGUUAAUUCGCACGGGCAGAAAGAGACAGC--
((((....))))........((((.(..(((((.--------...(((((((((-(((.((....)).)))).)))))))).)))))...)...))))-- ( -24.00, z-score =  -1.20, R)
>droSim1.chr2L_random 106023 89 + 909653
GAUUUCAUAAUCCUAAAUUCGCUGGCAGUUGUUG--------AUGGUGCGAAUG-GCCAGCAAAAGUGGGUUAAUUCGCACGGGCAGAAAGAGACAGC--
((((....))))........((((.......(((--------.(.(((((((((-(((.((....)).)))).)))))))).).))).......))))-- ( -24.84, z-score =  -1.15, R)
>droGri2.scaffold_14978 939834 94 + 1124632
AAUUUCAUAACA--AAAUUAACUUGUUGUUAUGACUGCU--AAUGGUGUAAACG--GUAUUAAAAGUAGGUUAAUUUAUAUGAACGAUGACAGAGAUAGA
...((((((...--((((((((((.........(((..(--((((.((....))--.)))))..))))))))))))).))))))................ ( -14.10, z-score =  -0.19, R)
>consensus
GAUUUCAUAAUCCUAAAUUCGCUGGCAGUUGUUG________AUGGUGCGAAUG_GCCAGCAAAAGUGGGUUAAUUCGCACGGGCAGAAAGAGACAGC__
.............................................((((((((..(((.((....)).)))..))))))))................... (-13.49 = -12.99 +  -0.50)

alignment

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secondary structure

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dotplot

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Window 7

Location 1,898,234 – 1,898,330
Length 96
Sequences 5
Columns 97
Reading direction forward
Mean pairwise identity 92.72
Shannon entropy 0.13015
G+C content 0.52509
Mean single sequence MFE -25.22
Consensus MFE -20.04
Energy contribution -20.00
Covariance contribution -0.04
Combinations/Pair 1.14
Mean z-score -2.21
Structure conservation index 0.79
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.73
SVM RNA-class probability 0.800589
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 1898234 96 + 23011544
GAUGGUGCGAAUUCGCCAACAAAAGUGGGUUAAUUCGCACGGGCAGAAAGAGACAGCAGAUG-GUCGGGCGAAAGAGAUGGCAACAGAUGUGAAUAG
....(((((((((.(((.((....)).))).)))))))))...............(((..((-((((..(....)...))))..))..)))...... ( -26.50, z-score =  -2.57, R)
>droEre2.scaffold_4929 1941870 95 + 26641161
GAUGGUGCGAAUG-GCCAGCAAAAGUGGGUUAAUUCGCACGGACAGAUAGAGAUAACCGAUG-GGCGGGCGAGAGAGAUGGCAACAGAUGUGAAUAG
....(((((((((-(((.((....)).)))).))))))))...((.((........(((...-..)))..........((....)).)).))..... ( -23.40, z-score =  -1.94, R)
>droYak2.chr2L 1877583 95 + 22324452
GAUGGUGCGAAUG-GCCAGCAAAAGUGGGUUAAUUCGCACCGGCAGAAAGAGAUAGGUGAUG-GGCGGGCGAGAGAGAUGGCAACAGAUGUGAAUAG
..(((((((((((-(((.((....)).)))).))))))))))..........(((..((...-(.((..(....)...)).)..))..)))...... ( -25.00, z-score =  -2.39, R)
>droSec1.super_14 1841835 96 + 2068291
AAUGGUGCGAAUG-GCCAGCAAAAGUGGGUUAAUUCGCACGGGCAGAAAGAGACAGCCGAAGAGGCGGGCGAGAGAGAUGGCAACAGAUGUGAAUAG
....(((((((((-(((.((....)).)))).))))))))..(((......(...(((.....)))...)........((....))..)))...... ( -25.60, z-score =  -2.29, R)
>droSim1.chr2L_random 106056 96 + 909653
GAUGGUGCGAAUG-GCCAGCAAAAGUGGGUUAAUUCGCACGGGCAGAAAGAGACAGCCGACGAGGCGGGCGAGAGAGAUGGCAACAGAUGUGAAUAG
....(((((((((-(((.((....)).)))).))))))))..(((......(...(((.....)))...)........((....))..)))...... ( -25.60, z-score =  -1.87, R)
>consensus
GAUGGUGCGAAUG_GCCAGCAAAAGUGGGUUAAUUCGCACGGGCAGAAAGAGACAGCCGAUG_GGCGGGCGAGAGAGAUGGCAACAGAUGUGAAUAG
....((((((((..(((.((....)).)))..))))))))..(((...........(((......)))..........((....))..)))...... (-20.04 = -20.00 +  -0.04)

alignment

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secondary structure

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dotplot

Postscript

Window 8

Location 1,898,234 – 1,898,332
Length 98
Sequences 6
Columns 104
Reading direction forward
Mean pairwise identity 83.38
Shannon entropy 0.31642
G+C content 0.51122
Mean single sequence MFE -24.94
Consensus MFE -18.45
Energy contribution -18.29
Covariance contribution -0.16
Combinations/Pair 1.17
Mean z-score -1.73
Structure conservation index 0.74
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.87
SVM RNA-class probability 0.841104
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 1898234 98 + 23011544
-----GAUGGUGCGAAUUCGCCAACAAAAGUGGGUUAAUUCGCACGGGCAGAAAGAGACAGCAGAUG-GUCGGGCGAAAGAGAUGGCAACAGAUGUGAAUAGCU
-----....(((((((((.(((.((....)).))).)))))))))...............(((..((-((((..(....)...))))..))..)))........ ( -26.50, z-score =  -1.88, R)
>droAna3.scaffold_12916 489874 90 - 16180835
AGUUGGAUGGUGUGAAUGGGCCAACAAAAGUGGGUUAAUUCGCACAGGCAAGUGG--------------CUAAGAGAGAGAAAUAGAGACAGAUGUGAAUAGCU
(((((....((((((((..(((.((....)).)))..)))))))).(((.....)--------------))............................))))) ( -19.90, z-score =  -1.97, R)
>droEre2.scaffold_4929 1941870 97 + 26641161
-----GAUGGUGCGAAUG-GCCAGCAAAAGUGGGUUAAUUCGCACGGACAGAUAGAGAUAACCGAUG-GGCGGGCGAGAGAGAUGGCAACAGAUGUGAAUAGCU
-----....(((((((((-(((.((....)).)))).))))))))................(((...-..)))((........((....))..........)). ( -23.57, z-score =  -1.26, R)
>droYak2.chr2L 1877583 97 + 22324452
-----GAUGGUGCGAAUG-GCCAGCAAAAGUGGGUUAAUUCGCACCGGCAGAAAGAGAUAGGUGAUG-GGCGGGCGAGAGAGAUGGCAACAGAUGUGAAUAGCU
-----...((((((((((-(((.((....)).)))).)))))))))(((..................-.((.(.(....)...).)).((....)).....))) ( -25.30, z-score =  -1.59, R)
>droSec1.super_14 1841835 98 + 2068291
-----AAUGGUGCGAAUG-GCCAGCAAAAGUGGGUUAAUUCGCACGGGCAGAAAGAGACAGCCGAAGAGGCGGGCGAGAGAGAUGGCAACAGAUGUGAAUAGCU
-----....(((((((((-(((.((....)).)))).)))))))).(((.......(...(((.....)))...)...(.(..((....))..).).....))) ( -27.20, z-score =  -2.00, R)
>droSim1.chr2L_random 106056 98 + 909653
-----GAUGGUGCGAAUG-GCCAGCAAAAGUGGGUUAAUUCGCACGGGCAGAAAGAGACAGCCGACGAGGCGGGCGAGAGAGAUGGCAACAGAUGUGAAUAGCU
-----....(((((((((-(((.((....)).)))).)))))))).(((.......(...(((.....)))...)...(.(..((....))..).).....))) ( -27.20, z-score =  -1.67, R)
>consensus
_____GAUGGUGCGAAUG_GCCAGCAAAAGUGGGUUAAUUCGCACGGGCAGAAAGAGACAGCCGAUG_GGCGGGCGAGAGAGAUGGCAACAGAUGUGAAUAGCU
.........((((((((..(((.((....)).)))..))))))))...........................(((........((....))..........))) (-18.45 = -18.29 +  -0.16)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 21:09:37 2011