Locus 4643

Sequence ID dm3.chr2R
Location 14,827,208 – 14,827,362
Length 154
Max. P 0.998502
window6374 window6375 window6376 window6377

overview

Window 4

Location 14,827,208 – 14,827,302
Length 94
Sequences 6
Columns 113
Reading direction forward
Mean pairwise identity 73.67
Shannon entropy 0.43820
G+C content 0.47401
Mean single sequence MFE -37.87
Consensus MFE -14.88
Energy contribution -16.60
Covariance contribution 1.73
Combinations/Pair 1.18
Mean z-score -3.25
Structure conservation index 0.39
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.20
SVM RNA-class probability 0.985265
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 14827208 94 + 21146708
AAAAACAAAUGAAGCCAAG-CCGAAUGCA---GAGGUCUGG-----GCAUGGCUAAUGCAAUGGCUAUGAC------CAUACCAUAGAUCUGGCUUUGGCUAUGGCUAU----
............(((((((-(((((.(((---(((((.(((-----.((((((((......)))))))).)------)).))).....))).))))))))).)))))..---- ( -37.40, z-score =  -3.93, R)
>droPer1.super_2 6104313 109 + 9036312
AAAAACAAAUGAAGCCAAAACCGAAUGUGUCCAAAGCCAAGUGGAUGUCUGGCCCAUACAGAGGCAAAGGCAGAGGCCAUGUCCGUGCCAUGGCUAAUGCAAUGGCAAU----
.............((((...((...(((((.....((((..(....)..))))..)))))..)).....(((..(((((((.......)))))))..)))..))))...---- ( -31.00, z-score =  -0.68, R)
>dp4.chr3 5903294 109 + 19779522
AAAAACAAAUGAAGCCAAAACCGAAUGUGUCCAAAGCCAAGUGGAUGUCUGGCCCAUACAGAGGCAAAGGCAGAGGCCAUGUCCGUGCCAUGGCUAAUGCAAUGGCAAU----
.............((((...((...(((((.....((((..(....)..))))..)))))..)).....(((..(((((((.......)))))))..)))..))))...---- ( -31.00, z-score =  -0.68, R)
>droYak2.chr2R 6771338 98 - 21139217
AAAAACAAAUGAAGCCAAA-CCGAAUGCA---GAGGUCUGG-----GCAUGGCUAAUGCAAUGGCUAUGAC------CAUACCAUAGCCAUGGCUAUGGCUAUGGAUCUGCCU
...................-......(((---(((((((((-----.(((.((....)).))).))).)))------)...((((((((((....)))))))))).))))).. ( -38.00, z-score =  -3.72, R)
>droSec1.super_1 12333503 99 + 14215200
AAAAACAAAUGAAGCCAAG-CCGAAUGCA---GAGGUCUGG-----GCAUGGCUAAUGCAAUGGCUAUGACCAUAGCCAUACCAUAGACCUGGCUUUGGCUAUGGCUA-----
............(((((((-(((((.((.---.((((((((-----((((.....)))).((((((((....)))))))).))..)))))).))))))))).))))).----- ( -44.90, z-score =  -5.24, R)
>droSim1.chr2R 13526370 100 + 19596830
AAAAACAAAUGAAGCCAAG-CCGAAUGCA---GAGGUCUGG-----GCAUGGCUAAUGCAAUGGCUAUGACCAUAGCCAUACCAUAGACCUGGCUUUGGCUAUGGCUAU----
............(((((((-(((((.((.---.((((((((-----((((.....)))).((((((((....)))))))).))..)))))).))))))))).)))))..---- ( -44.90, z-score =  -5.24, R)
>consensus
AAAAACAAAUGAAGCCAAA_CCGAAUGCA___GAGGUCUGG_____GCAUGGCUAAUGCAAUGGCUAUGAC____GCCAUACCAUAGACAUGGCUAUGGCUAUGGCUAU____
.............((((.................(((.(((......((((((((......)))))))).......))).))).......((((....))))))))....... (-14.88 = -16.60 +   1.73)

alignment

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secondary structure

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Window 5

Location 14,827,208 – 14,827,302
Length 94
Sequences 6
Columns 113
Reading direction reverse
Mean pairwise identity 73.67
Shannon entropy 0.43820
G+C content 0.47401
Mean single sequence MFE -35.30
Consensus MFE -12.04
Energy contribution -11.72
Covariance contribution -0.33
Combinations/Pair 1.32
Mean z-score -2.48
Structure conservation index 0.34
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.28
SVM RNA-class probability 0.625109
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 14827208 94 - 21146708
----AUAGCCAUAGCCAAAGCCAGAUCUAUGGUAUG------GUCAUAGCCAUUGCAUUAGCCAUGC-----CCAGACCUC---UGCAUUCGG-CUUGGCUUCAUUUGUUUUU
----..(((((.((((.((..(((((((..((((((------((....((....))....)))))))-----).)))..))---))..)).))-)))))))............ ( -30.50, z-score =  -2.45, R)
>droPer1.super_2 6104313 109 - 9036312
----AUUGCCAUUGCAUUAGCCAUGGCACGGACAUGGCCUCUGCCUUUGCCUCUGUAUGGGCCAGACAUCCACUUGGCUUUGGACACAUUCGGUUUUGGCUUCAUUUGUUUUU
----...(((((.((....)).)))))(((((...((((...(((..((..(((....(((((((........))))))).)))..))...)))...))))...))))).... ( -31.30, z-score =  -0.52, R)
>dp4.chr3 5903294 109 - 19779522
----AUUGCCAUUGCAUUAGCCAUGGCACGGACAUGGCCUCUGCCUUUGCCUCUGUAUGGGCCAGACAUCCACUUGGCUUUGGACACAUUCGGUUUUGGCUUCAUUUGUUUUU
----...(((((.((....)).)))))(((((...((((...(((..((..(((....(((((((........))))))).)))..))...)))...))))...))))).... ( -31.30, z-score =  -0.52, R)
>droYak2.chr2R 6771338 98 + 21139217
AGGCAGAUCCAUAGCCAUAGCCAUGGCUAUGGUAUG------GUCAUAGCCAUUGCAUUAGCCAUGC-----CCAGACCUC---UGCAUUCGG-UUUGGCUUCAUUUGUUUUU
.(((.((.(((((.(((((((....)))))))))))------)))...)))...(((..(((((.((-----((((....)---)).....))-).))))).....))).... ( -35.90, z-score =  -2.91, R)
>droSec1.super_1 12333503 99 - 14215200
-----UAGCCAUAGCCAAAGCCAGGUCUAUGGUAUGGCUAUGGUCAUAGCCAUUGCAUUAGCCAUGC-----CCAGACCUC---UGCAUUCGG-CUUGGCUUCAUUUGUUUUU
-----.(((((.((((((.((.((((((..((((((((((((((....))))......)))))))))-----).)))))).---.)).)).))-)))))))............ ( -41.40, z-score =  -4.27, R)
>droSim1.chr2R 13526370 100 - 19596830
----AUAGCCAUAGCCAAAGCCAGGUCUAUGGUAUGGCUAUGGUCAUAGCCAUUGCAUUAGCCAUGC-----CCAGACCUC---UGCAUUCGG-CUUGGCUUCAUUUGUUUUU
----..(((((.((((((.((.((((((..((((((((((((((....))))......)))))))))-----).)))))).---.)).)).))-)))))))............ ( -41.40, z-score =  -4.23, R)
>consensus
____AUAGCCAUAGCCAAAGCCAGGGCUAUGGUAUGGC____GUCAUAGCCAUUGCAUUAGCCAUGC_____CCAGACCUC___UGCAUUCGG_CUUGGCUUCAUUUGUUUUU
.......(((((.((((.((......)).)))))))))....((((...((..((((..((...((.......))...))....))))...))...))))............. (-12.04 = -11.72 +  -0.33)

alignment

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secondary structure

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dotplot

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Window 6

Location 14,827,239 – 14,827,330
Length 91
Sequences 4
Columns 113
Reading direction forward
Mean pairwise identity 79.49
Shannon entropy 0.30663
G+C content 0.52012
Mean single sequence MFE -42.55
Consensus MFE -27.71
Energy contribution -30.53
Covariance contribution 2.81
Combinations/Pair 1.03
Mean z-score -3.76
Structure conservation index 0.65
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 3.38
SVM RNA-class probability 0.998502
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 14827239 91 + 21146708
GUCUGGGCAUGGCUAAUGCAAUGGCUAUGA------CCAUACCAUAGAUCUGGCUUUGGCUAUGGCUAUGGCUAUGGAUCU----GGCUCUGACUCUGGCU------------
(((.(((((((((((......)))))))((------(((((((((((.((((((....)))).)))))))).))))).)).----.)))).))).......------------ ( -34.90, z-score =  -2.84, R)
>droYak2.chr2R 6771369 107 - 21139217
GUCUGGGCAUGGCUAAUGCAAUGGCUAUGA------CCAUACCAUAGCCAUGGCUAUGGCUAUGGAUCUGCCUCUCGGAGUCAGAGGCUCUGGCUCUGGCUUUUGCUUUGGCU
(((..((((.(((.........(((...((------((((((((((((....))))))).))))).)).)))...(((((((((.....))))))))))))..))))..))). ( -50.30, z-score =  -3.95, R)
>droSec1.super_1 12333534 91 + 14215200
GUCUGGGCAUGGCUAAUGCAAUGGCUAUGACCAUAGCCAUACCAUAGACCUGGCUUUGGCUAUGGCUAUGG------AUCU----GGCUCUGACUCUGGCU------------
(((.(((((((((((......)))))))((((((((((((((((.((......)).))).)))))))))))------.)).----.)))).))).......------------ ( -39.00, z-score =  -3.60, R)
>droSim1.chr2R 13526401 97 + 19596830
GUCUGGGCAUGGCUAAUGCAAUGGCUAUGACCAUAGCCAUACCAUAGACCUGGCUUUGGCUAUGGCUAUGGCUGUGGAUCU----GGCUCUGACUCUGGCU------------
(((.(((((((((((......)))))))(((((((((((((((((((.((.......)))))))).))))))))))).)).----.)))).))).......------------ ( -46.00, z-score =  -4.66, R)
>consensus
GUCUGGGCAUGGCUAAUGCAAUGGCUAUGA______CCAUACCAUAGACCUGGCUUUGGCUAUGGCUAUGGCU_UGGAUCU____GGCUCUGACUCUGGCU____________
(((.(((((((((((......)))))))..((((((((((((((.((......)).))).)))))))))))...............)))).)))................... (-27.71 = -30.53 +   2.81)

alignment

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secondary structure

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dotplot

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Window 7

Location 14,827,269 – 14,827,362
Length 93
Sequences 4
Columns 112
Reading direction forward
Mean pairwise identity 81.16
Shannon entropy 0.28368
G+C content 0.53540
Mean single sequence MFE -32.15
Consensus MFE -20.20
Energy contribution -21.45
Covariance contribution 1.25
Combinations/Pair 1.00
Mean z-score -1.92
Structure conservation index 0.63
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.17
SVM RNA-class probability 0.577536
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 14827269 93 + 21146708
---CCAUACCAUAGAUCUGGCUUUGGCUAUGGCUAUG----------------GCUAUGGAUCUGGCUCUGACUCUGGCUAACUAAGAUCCGUAACCCGCUCGCUUCGAUGC
---(((((((((((.((.......)))))))).))))----------------).(((((((((((((........)))).....)))))))))....(((((...))).)) ( -26.70, z-score =  -1.24, R)
>droYak2.chr2R 6771399 109 - 21139217
---CCAUACCAUAGCCAUGGCUAUGGCUAUGGAUCUGCCUCUCGGAGUCAGAGGCUCUGGCUCUGGCUUUUGCUUUGGCUAACUAAGAUCCGUAACCCGCUCGCUCCGAUGC
---.....(((((((....))))))).(((((((((((((((.......))))))..(((((..(((....)))..)))))....)))))))))....(((((...))).)) ( -42.30, z-score =  -2.81, R)
>droSec1.super_1 12333567 90 + 14215200
UAGCCAUACCAUAGACCUGGCUUUGGCUAUGGCUAU----------------------GGAUCUGGCUCUGACUCUGGCUAACUAAGAUCCGUAACCCGCUCGCUCCGAUGC
..(((((((((.((......)).))).))))))(((----------------------((((((((((........)))).....)))))))))....(((((...))).)) ( -26.80, z-score =  -1.45, R)
>droSim1.chr2R 13526434 96 + 19596830
UAGCCAUACCAUAGACCUGGCUUUGGCUAUGGCUAUG----------------GCUGUGGAUCUGGCUCUGACUCUGGCUAACUAAGAUCCGUAACCCGCUCGCUCCGAUGC
((((((((((((((.((.......)))))))).))))----------------)))).((((((((((........)))).....)))))).......(((((...))).)) ( -32.80, z-score =  -2.17, R)
>consensus
___CCAUACCAUAGACCUGGCUUUGGCUAUGGCUAUG________________GCU_UGGAUCUGGCUCUGACUCUGGCUAACUAAGAUCCGUAACCCGCUCGCUCCGAUGC
.((((((((((.((......)).))).)))))))........................((((((((((........)))).....)))))).......(((((...))).)) (-20.20 = -21.45 +   1.25)

alignment

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secondary structure

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dotplot

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Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:33:16 2011