Locus 3307

Sequence ID dm3.chr2R
Location 4,249,865 – 4,250,017
Length 152
Max. P 0.999910
window4555 window4556 window4557

overview

Window 5

Location 4,249,865 – 4,249,980
Length 115
Sequences 6
Columns 116
Reading direction reverse
Mean pairwise identity 77.24
Shannon entropy 0.43810
G+C content 0.43276
Mean single sequence MFE -31.53
Consensus MFE -18.24
Energy contribution -19.13
Covariance contribution 0.90
Combinations/Pair 1.37
Mean z-score -1.78
Structure conservation index 0.58
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.06
SVM RNA-class probability 0.882721
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 4249865 115 - 21146708
CUCAUACGCAGACCAAUUACUCCACGCUCAUUUUAGCGUAGUGAUUGGGUUGCACUUGCGAUUGGCAUCAGGGGUCCAAG-AUUCUCCACAAUUAGCCGUAUUAAAGAUGUAAUGU
....(((((((.(((((((((..(((((......)))))))))))))).)))).(((.....((((....((((......-...)))).......)))).....)))..))).... ( -31.60, z-score =  -1.60, R)
>droSim1.chr2R_random 1390107 115 - 2996586
CUCAUACGCAGAGCAAUUACUGCACGCGCAUUUUAGCGUAGUGAUUGGGUUGCACUUGAGAUUGGCAACAAGGGUCCAAG-AUUCUCCACAAUUCGACGUAUUAAAGAUGUAAUGU
...(((((..((((((((....(((((((......)))).)))....)))))).((((.(((((....))...)))))))-............))..))))).............. ( -28.50, z-score =  -0.48, R)
>droSec1.super_1 1895875 115 - 14215200
CUCAUACGCAGACCAAUUACUGCACGCGCAUUUUAGCGUAGUGAUUGGGUUGCACUUGAGAUUGGCAACAAGGGUCCAAG-AUUCUCCACAAUUCGACGUAUUAAAGAUGUAAUGU
...((((((((.(((((((((..((((........))))))))))))).)))).((((.(((((....))...)))))))-.................)))).............. ( -30.90, z-score =  -1.45, R)
>droYak2.chr2L 16905840 108 - 22324452
CUCAUAUGCACCUCAAUAACU------UCACUUUAGCGUUGUGAUUGGGUUGUACUUGCGAUUGGCAACAUGGGUUCAAG-ACUCUCCACAAUUCGACGUAUUAAAGAUGU-AUGU
...(((((((...........------...(((((((((((.(((((((..((.((((....((....))......))))-))...)).)))))))))))..))))).)))-)))) ( -22.26, z-score =   0.27, R)
>droEre2.scaffold_4929 8257772 113 + 26641161
CUCAUACGCAGCUCAAUUACUUGACGUGCAUUUUAGCGUUGUGAUUGGGUUGCACUUGCGAUUGGCACCAGGAGUCCGAG-AUUCUCCACAAUUCGACGUAUUAAAGAUGUAAU--
....((((((((((((((((..(((((........))))))))))))))))))...((((.((((.....((((......-...)))).....))))))))........)))..-- ( -32.80, z-score =  -1.83, R)
>droAna3.scaffold_13266 18139357 113 + 19884421
CUCAGAUGCAGCUCAGCCACAA-ACGCGAAAACGUGUUUUGUGACUGAGUUGCAGAUGAGAAGGGCAACAGAUAUCCGGGAACGGACCAAUUAUAAUUGUAUUAAAUGUUUCGU--
((((..((((((((((.(((((-(((((....)))).)))))).))))))))))..))))...((.((((....((((....)))).((((....)))).......))))))..-- ( -43.10, z-score =  -5.58, R)
>consensus
CUCAUACGCAGAUCAAUUACUGCACGCGCAUUUUAGCGUAGUGAUUGGGUUGCACUUGAGAUUGGCAACAGGGGUCCAAG_AUUCUCCACAAUUCGACGUAUUAAAGAUGUAAUGU
...((((((((.(((((((((..((((........))))))))))))).)))).((((.(((((....))...)))))))..................)))).............. (-18.24 = -19.13 +   0.90)

alignment

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secondary structure

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dotplot

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Window 6

Location 4,249,900 – 4,250,017
Length 117
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 74.47
Shannon entropy 0.49568
G+C content 0.46439
Mean single sequence MFE -39.08
Consensus MFE -21.86
Energy contribution -22.83
Covariance contribution 0.98
Combinations/Pair 1.25
Mean z-score -3.55
Structure conservation index 0.56
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 4.10
SVM RNA-class probability 0.999630
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 4249900 117 + 21146708
CUUGGACCCCUGAUGCCAAUCGCAAGUGCAACCCAAUCACUACGCUAAAAUGAGCGUGGAGUAAUUGGUCUGCGUAUGAGUUUGGCAUCAGGAUCGAAAACUUUC--AUUUUUUUCUGG-
.(..((..(((((((((((.(.((..((((..((((((.(((((((......))))))).)..)))))..))))..)).).)))))))))))...(((....)))--.......))..)- ( -43.50, z-score =  -4.68, R)
>droSim1.chr2R_random 1390142 120 + 2996586
CUUGGACCCUUGUUGCCAAUCUCAAGUGCAACCCAAUCACUACGCUAAAAUGCGCGUGCAGUAAUUGCUCUGCGUAUGAGUUUGGCAUCAGGAUCGAUAACUAUCCAAUUUUUUUUUUGG
....((.(((.(.((((((.((((..((((...((((.(((((((........))))..))).))))...))))..)))).)))))).)))).)).........((((........)))) ( -34.60, z-score =  -2.73, R)
>droSec1.super_1 1895910 119 + 14215200
CUUGGACCCUUGUUGCCAAUCUCAAGUGCAACCCAAUCACUACGCUAAAAUGCGCGUGCAGUAAUUGGUCUGCGUAUGAGUUUGGCAUCAGGAUCGAGAACUAUCCAAUUUUUUUUUUG-
(((((...((((.((((((.((((..((((..(((((.(((((((........))))..))).)))))..))))..)))).)))))).)))).))))).....................- ( -40.10, z-score =  -4.25, R)
>droYak2.chr2L 16905874 111 + 22324452
CUUGAACCCAUGUUGCCAAUCGCAAGUACAACCCAAUCACAACGCUAAA------GUGAAGUUAUUGAGGUGCAUAUGAGUUUGGCAUCAGGAUCGAAGACUGUCC-ACUUUGUUCGG--
..(((((...((.((((((.(.((.((...(((((((.((..(((....------)))..)).)))).)))..)).)).).)))))).))((((........))))-.....))))).-- ( -27.90, z-score =  -0.81, R)
>droEre2.scaffold_4929 8257805 114 - 26641161
CUCGGACUCCUGGUGCCAAUCGCAAGUGCAACCCAAUCACAACGCUAAAAUGCACGUCAAGUAAUUGAGCUGCGUAUGAGUUUGGCAUCAGGAUCGAAGACUAUCCAUGUUCGG------
..(((((((((((((((((..((....))..............(((...(((((..((((....))))..)))))...)))))))))))))))..((......))...))))).------ ( -36.40, z-score =  -2.42, R)
>droAna3.scaffold_13266 18139391 117 - 19884421
CCCGGAUAUCUGUUGCCCUUCUCAUCUGCAACUCAGUCACAAAACACGUUUUCGCGUUU-GUGGCUGAGCUGCAUCUGAGCCUGGCAACAGCACCAAGGAUGAUCCACUAGUGUCCAG--
...((((((((((((((...((((..((((.((((((((((((.(.((....)).))))-))))))))).))))..))))...))))))))......((.....))....))))))..-- ( -52.00, z-score =  -6.44, R)
>consensus
CUUGGACCCCUGUUGCCAAUCGCAAGUGCAACCCAAUCACAACGCUAAAAUGCGCGUGAAGUAAUUGAGCUGCGUAUGAGUUUGGCAUCAGGAUCGAAAACUAUCCAAUUUUGUUCUG__
.((((...((((.((((((.(.((..((((...((((.(((((((........)))))..)).))))...))))..)).).)))))).)))).))))....................... (-21.86 = -22.83 +   0.98)

alignment

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secondary structure

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dotplot

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Window 7

Location 4,249,900 – 4,250,017
Length 117
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 74.47
Shannon entropy 0.49568
G+C content 0.46439
Mean single sequence MFE -45.08
Consensus MFE -29.96
Energy contribution -29.83
Covariance contribution -0.13
Combinations/Pair 1.40
Mean z-score -4.86
Structure conservation index 0.66
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 4.84
SVM RNA-class probability 0.999910
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 4249900 117 - 21146708
-CCAGAAAAAAAU--GAAAGUUUUCGAUCCUGAUGCCAAACUCAUACGCAGACCAAUUACUCCACGCUCAUUUUAGCGUAGUGAUUGGGUUGCACUUGCGAUUGGCAUCAGGGGUCCAAG
-.......(((((--....))))).((((((((((((((.(.((...((((.(((((((((..(((((......)))))))))))))).))))...)).).))))))))).))))).... ( -45.50, z-score =  -5.62, R)
>droSim1.chr2R_random 1390142 120 - 2996586
CCAAAAAAAAAAUUGGAUAGUUAUCGAUCCUGAUGCCAAACUCAUACGCAGAGCAAUUACUGCACGCGCAUUUUAGCGUAGUGAUUGGGUUGCACUUGAGAUUGGCAACAAGGGUCCAAG
((((........)))).........((((((..((((((.((((...((((..((((((((..((((........))))))))))))..))))...)))).))))))...)))))).... ( -43.70, z-score =  -4.98, R)
>droSec1.super_1 1895910 119 - 14215200
-CAAAAAAAAAAUUGGAUAGUUCUCGAUCCUGAUGCCAAACUCAUACGCAGACCAAUUACUGCACGCGCAUUUUAGCGUAGUGAUUGGGUUGCACUUGAGAUUGGCAACAAGGGUCCAAG
-........................((((((..((((((.((((...((((.(((((((((..((((........))))))))))))).))))...)))).))))))...)))))).... ( -44.30, z-score =  -5.32, R)
>droYak2.chr2L 16905874 111 - 22324452
--CCGAACAAAGU-GGACAGUCUUCGAUCCUGAUGCCAAACUCAUAUGCACCUCAAUAACUUCAC------UUUAGCGUUGUGAUUGGGUUGUACUUGCGAUUGGCAACAUGGGUUCAAG
--..((((...((-(..(((.........))).((((((.(.((..((((.((((((.((..(.(------....).)..)).)))))).))))..)).).)))))).)))..))))... ( -28.40, z-score =  -0.69, R)
>droEre2.scaffold_4929 8257805 114 + 26641161
------CCGAACAUGGAUAGUCUUCGAUCCUGAUGCCAAACUCAUACGCAGCUCAAUUACUUGACGUGCAUUUUAGCGUUGUGAUUGGGUUGCACUUGCGAUUGGCACCAGGAGUCCGAG
------.......(((((.(....)..(((((.((((((.(.((...(((((((((((((..(((((........))))))))))))))))))...)).).)))))).)))))))))).. ( -44.10, z-score =  -4.25, R)
>droAna3.scaffold_13266 18139391 117 + 19884421
--CUGGACACUAGUGGAUCAUCCUUGGUGCUGUUGCCAGGCUCAGAUGCAGCUCAGCCAC-AAACGCGAAAACGUGUUUUGUGACUGAGUUGCAGAUGAGAAGGGCAACAGAUAUCCGGG
--(((((((((((.((.....))))))))((((((((...((((..((((((((((.(((-(((((((....)))).)))))).))))))))))..))))...))))))))...))))). ( -64.50, z-score =  -8.27, R)
>consensus
__CAGAAAAAAAUUGGAUAGUCUUCGAUCCUGAUGCCAAACUCAUACGCAGAUCAAUUACUGCACGCGCAUUUUAGCGUAGUGAUUGGGUUGCACUUGAGAUUGGCAACAGGGGUCCAAG
.....................(((.(((((((.((((((.(.((...((((.((((((((...((((........)))).)))))))).))))...)).).)))))).)).))))).))) (-29.96 = -29.83 +  -0.13)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:07:49 2011