Locus 255

Sequence ID dm3.chr2L
Location 1,845,823 – 1,845,978
Length 155
Max. P 0.960271
window346 window347 window348 window349

overview

Window 6

Location 1,845,823 – 1,845,923
Length 100
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 58.51
Shannon entropy 0.68646
G+C content 0.28313
Mean single sequence MFE -18.31
Consensus MFE -6.40
Energy contribution -5.68
Covariance contribution -0.72
Combinations/Pair 1.67
Mean z-score -1.58
Structure conservation index 0.35
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.78
SVM RNA-class probability 0.814875
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 1845823 100 + 23011544
--------------------CUUUUGAAAAAAGCAGUUGUAGCAGAUUUAAAAUCCAUAAAUAAUUUGUGGCCCUCUGAAAACCACAAAAGUGGUUAUUAAUUUAAGCUUAGAAAAAAAA
--------------------..........((((........((((........((((((.....))))))...))))..((((((....))))))..........)))).......... ( -16.80, z-score =  -1.09, R)
>droEre2.scaffold_4929 1892810 119 + 26641161
AUGUUUCUUUUGAAGUUUAAUUUUUAUAAUAAGCAAUAACGGGAGAUGCAAAAUGUAUAAAUAAUUUGCGGUCCUUUAAUAGCCACAGGAGUGGUUAUUUAAUUAAGUUUAGAAAAAAA-
...(((.(((((((.(((((((..................((((..((((((.(((....))).)))))).))))..(((((((((....))))))))).)))))))))))))).))).- ( -24.50, z-score =  -2.03, R)
>droSec1.super_14 1792558 99 + 2068291
--------------------UUUCUUAAAAAAUCAGUUGUAGCAGAUUUAAAAUCCAUUAAUAAUUUGUGGCCCUCUGAAAACCACAAAUGUGGUUAUUAAUUUAAGCUUAGAAAAAAA-
--------------------...((((((...((((..((.(((((((..............))))))).))...)))).((((((....)))))).....))))))............- ( -18.84, z-score =  -2.32, R)
>droSim1.chr2L 1832914 99 + 22036055
--------------------CUUCUUAAAAAAUCAGUUGUAGCUGAUUUAAAAUCCAUUAAUAAUUUGUGGCCUUCUAAAAACCACAAAAGUGGUUAUUAAUUUAAGCUUAGAAAAAAA-
--------------------...((((((((((((((....)))))))).....(((((.....(((((((...........)))))))))))).......))))))............- ( -19.20, z-score =  -2.75, R)
>dp4.chr4_group3 8578231 100 + 11692001
----------AUGAUUUCCUCCUUUUACCCAAGUGAUUAUGGGAUUCGUAAUAGUUUCAAAGAAGUCAGUCCUUCCUAUAGAUCGU---UUCUAUCAAUCAUUUCAACCCCAA-------
----------.(((((((..((..((((....))))....))((..(......)..))...))))))).........(((((....---.)))))..................------- ( -12.20, z-score =   0.27, R)
>consensus
____________________CUUUUUAAAAAAGCAGUUGUAGCAGAUUUAAAAUCCAUAAAUAAUUUGUGGCCCUCUAAAAACCACAAAAGUGGUUAUUAAUUUAAGCUUAGAAAAAAA_
................................................................................((((((....))))))........................ ( -6.40 =  -5.68 +  -0.72)

alignment

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secondary structure

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dotplot

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Window 7

Location 1,845,843 – 1,845,953
Length 110
Sequences 6
Columns 110
Reading direction forward
Mean pairwise identity 69.09
Shannon entropy 0.58647
G+C content 0.30652
Mean single sequence MFE -19.12
Consensus MFE -8.69
Energy contribution -8.92
Covariance contribution 0.23
Combinations/Pair 1.53
Mean z-score -1.32
Structure conservation index 0.45
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.51
SVM RNA-class probability 0.724269
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 1845843 110 + 23011544
AGCAGAUUUAAAAUCCAUAAAUAAUUUGUGGCCCUCUGAAAACCACAAAAGUGGUUAUUAAUUUAAGCUUAGAAAAAAAAGAAUAAGCUGAUUACAACCUAUUAACCAUU
..((((........((((((.....))))))...))))..((((((....))))))..(((((..((((((............)))))))))))................ ( -17.80, z-score =  -1.68, R)
>droEre2.scaffold_4929 1892850 109 + 26641161
GGGAGAUGCAAAAUGUAUAAAUAAUUUGCGGUCCUUUAAUAGCCACAGGAGUGGUUAUUUAAUUAAGUUUAGAAAAAAA-GCACAAGCUGAUUAUAACCUAUUAACCAUU
((..((((((((.(((....))).)))))(((.(((.(((((((((....))))))))).....)))...........(-((....))).......))).)))..))... ( -21.70, z-score =  -1.29, R)
>droYak2.chr2L 1819496 109 + 22324452
AGGAGUUGUAAAGCGCUUAAAUUAUUUGUGGUCUUAUGAUAACCGCGAAAGUGGUAAUUAAUUUAAGUUUAGAAAAAAA-GCAUAAGCUGAUUAUAACCUAAUGCCCAUU
.((.(((((((...((((((((((......(((....))).(((((....)))))...))))))))))..........(-((....)))..))))))))).......... ( -25.50, z-score =  -2.45, R)
>droSec1.super_14 1792578 109 + 2068291
AGCAGAUUUAAAAUCCAUUAAUAAUUUGUGGCCCUCUGAAAACCACAAAUGUGGUUAUUAAUUUAAGCUUAGAAAAAAA-GAAUAAGCUGAUUACAACCUAUUAACCAUU
.................((((((..((((((.....(((.((((((....)))))).))).....((((((........-...))))))..))))))..))))))..... ( -18.60, z-score =  -1.75, R)
>droSim1.chr2L 1832934 109 + 22036055
AGCUGAUUUAAAAUCCAUUAAUAAUUUGUGGCCUUCUAAAAACCACAAAAGUGGUUAUUAAUUUAAGCUUAGAAAAAAA-GAAUAAGCUGAUUACAACCUAUUAACCAUU
.................((((((..((((((.....(((.((((((....)))))).))).....((((((........-...))))))..))))))..))))))..... ( -18.20, z-score =  -1.66, R)
>dp4.chr4_group3 8578261 94 + 11692001
GGGAUUCGUAAUAGUUUCAAAGAAGUCAGUCCUUCCUAUAGAUCGU---UUCUAUCAAUCAUUUCAACCC-------------CAACCUGAUAGGGUUCUGAAAAGCAUU
(((..................((((......))))..(((((....---.))))).............))-------------)(((((....)))))............ ( -12.90, z-score =   0.90, R)
>consensus
AGCAGAUGUAAAAUCCAUAAAUAAUUUGUGGCCCUCUAAAAACCACAAAAGUGGUUAUUAAUUUAAGCUUAGAAAAAAA_GAAUAAGCUGAUUACAACCUAUUAACCAUU
...........................((((.....(((.((((((....)))))).))).....((((((............))))))................)))). ( -8.69 =  -8.92 +   0.23)

alignment

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secondary structure

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dotplot

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Window 8

Location 1,845,843 – 1,845,953
Length 110
Sequences 6
Columns 110
Reading direction reverse
Mean pairwise identity 69.09
Shannon entropy 0.58647
G+C content 0.30652
Mean single sequence MFE -20.37
Consensus MFE -9.27
Energy contribution -9.25
Covariance contribution -0.02
Combinations/Pair 1.59
Mean z-score -1.27
Structure conservation index 0.46
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.51
SVM RNA-class probability 0.723653
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 1845843 110 - 23011544
AAUGGUUAAUAGGUUGUAAUCAGCUUAUUCUUUUUUUUCUAAGCUUAAAUUAAUAACCACUUUUGUGGUUUUCAGAGGGCCACAAAUUAUUUAUGGAUUUUAAAUCUGCU
..((((((((((((((....)))))))).(((........)))..........))))))..((((((((((.....))))))))))........((((.....))))... ( -21.90, z-score =  -1.45, R)
>droEre2.scaffold_4929 1892850 109 - 26641161
AAUGGUUAAUAGGUUAUAAUCAGCUUGUGC-UUUUUUUCUAAACUUAAUUAAAUAACCACUCCUGUGGCUAUUAAAGGACCGCAAAUUAUUUAUACAUUUUGCAUCUCCC
...((((..((((((..((..(((....))-)..)).....))))))....((((.((((....)))).))))....))))(((((............)))))....... ( -19.30, z-score =  -1.22, R)
>droYak2.chr2L 1819496 109 - 22324452
AAUGGGCAUUAGGUUAUAAUCAGCUUAUGC-UUUUUUUCUAAACUUAAAUUAAUUACCACUUUCGCGGUUAUCAUAAGACCACAAAUAAUUUAAGCGCUUUACAACUCCU
...(.((.(((((((((....(((....))-)................................(.((((.......)))).)..))))))))))).)............ ( -14.10, z-score =  -0.21, R)
>droSec1.super_14 1792578 109 - 2068291
AAUGGUUAAUAGGUUGUAAUCAGCUUAUUC-UUUUUUUCUAAGCUUAAAUUAAUAACCACAUUUGUGGUUUUCAGAGGGCCACAAAUUAUUAAUGGAUUUUAAAUCUGCU
....((((((((((((((((.((((((...-........))))))...))).))))))..(((((((((((.....))))))))))))))))))((((.....))))... ( -24.70, z-score =  -2.40, R)
>droSim1.chr2L 1832934 109 - 22036055
AAUGGUUAAUAGGUUGUAAUCAGCUUAUUC-UUUUUUUCUAAGCUUAAAUUAAUAACCACUUUUGUGGUUUUUAGAAGGCCACAAAUUAUUAAUGGAUUUUAAAUCAGCU
..(.((((((((((((((((.((((((...-........))))))...))).))))))...((((((((((.....)))))))))).))))))).).............. ( -23.50, z-score =  -2.19, R)
>dp4.chr4_group3 8578261 94 - 11692001
AAUGCUUUUCAGAACCCUAUCAGGUUG-------------GGGUUGAAAUGAUUGAUAGAA---ACGAUCUAUAGGAAGGACUGACUUCUUUGAAACUAUUACGAAUCCC
......(((((((((((((......))-------------))))).....(((((......---.)))))....(((((......))))))))))).............. ( -18.70, z-score =  -0.14, R)
>consensus
AAUGGUUAAUAGGUUGUAAUCAGCUUAUUC_UUUUUUUCUAAGCUUAAAUUAAUAACCACUUUUGUGGUUUUCAGAAGGCCACAAAUUAUUUAUGGAUUUUAAAUCUCCU
..(((((..((((((......))))))...........................((((((....)))))).......)))))............................ ( -9.27 =  -9.25 +  -0.02)

alignment

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secondary structure

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dotplot

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Window 9

Location 1,845,883 – 1,845,978
Length 95
Sequences 6
Columns 96
Reading direction reverse
Mean pairwise identity 70.15
Shannon entropy 0.57100
G+C content 0.30260
Mean single sequence MFE -18.95
Consensus MFE -7.72
Energy contribution -10.32
Covariance contribution 2.60
Combinations/Pair 1.24
Mean z-score -2.19
Structure conservation index 0.41
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.68
SVM RNA-class probability 0.960271
Prediction RNA
WARNING Out of training range. z-scores are NOT reliable.

Download alignment: ClustalW | MAF

>dm3.chr2L 1845883 95 - 23011544
-AAGCCACAUUAUAGUAACCGCAAAUAAUGGUUAAUAGGUUGUAAUCAGCUUAUUCUUUUUUUUCUAAGCUUAAAUUAAUAACCACUUUUGUGGUU
-.(((((((....((((((((.......)))))....(((((((((.((((((............))))))...))).)))))))))..))))))) ( -21.70, z-score =  -2.93, R)
>droEre2.scaffold_4929 1892890 94 - 26641161
-AAGCCAGAUUUAAAUAACCGCAAAUAAUGGUUAAUAGGUUAUAAUCAGCUUGUGC-UUUUUUUCUAAACUUAAUUAAAUAACCACUCCUGUGGCU
-.(((((.(......((((((.......))))))...((((((....(((....))-).......(((......))).)))))).....).))))) ( -16.50, z-score =  -0.89, R)
>droYak2.chr2L 1819536 94 - 22324452
-AAACCACAUUUAAAUAACCGCAAAUAAUGGGCAUUAGGUUAUAAUCAGCUUAUGC-UUUUUUUCUAAACUUAAAUUAAUUACCACUUUCGCGGUU
-...............((((((.((...(((((((.(((((......)))))))))-(((......))).............)))..)).)))))) ( -14.60, z-score =  -1.30, R)
>droSec1.super_14 1792618 94 - 2068291
-AAACCACAUUAUAGUAACCGCAAAUAAUGGUUAAUAGGUUGUAAUCAGCUUAUUC-UUUUUUUCUAAGCUUAAAUUAAUAACCACAUUUGUGGUU
-.(((((((......((((((.......))))))...(((((((((.((((((...-........))))))...))).)))))).....))))))) ( -21.70, z-score =  -3.46, R)
>droSim1.chr2L 1832974 94 - 22036055
-AAACCAAAUUGUAGUAACCGCAAAUAAUGGUUAAUAGGUUGUAAUCAGCUUAUUC-UUUUUUUCUAAGCUUAAAUUAAUAACCACUUUUGUGGUU
-...............(((((((((...((((((((((((((....)))))))).(-((.......)))..........))))))..))))))))) ( -21.20, z-score =  -2.95, R)
>dp4.chr4_group3 8578299 78 - 11692001
AAAAUUGACAAGCAAUACCUCC----AAUGCUUUUCAGAACCCUAUCAGGUUGGGGUUGAAAUGAUUGAUAGAAACGAUCUA--------------
....((((.(((((........----..))))).))))(((((((......))))))).....(((((.......)))))..-------------- ( -18.00, z-score =  -1.62, R)
>consensus
_AAACCACAUUAUAAUAACCGCAAAUAAUGGUUAAUAGGUUGUAAUCAGCUUAUGC_UUUUUUUCUAAACUUAAAUUAAUAACCACUUUUGUGGUU
................(((((((((...(((((((((((((......)))))))...........(((.......))).))))))..))))))))) ( -7.72 = -10.32 +   2.60)

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 21:09:30 2011