Locus 2502

Sequence ID dm3.chr2L
Location 19,558,457 – 19,558,601
Length 144
Max. P 0.978132
window3443 window3444

overview

Window 3

Location 19,558,457 – 19,558,601
Length 144
Sequences 5
Columns 151
Reading direction forward
Mean pairwise identity 84.19
Shannon entropy 0.27842
G+C content 0.46015
Mean single sequence MFE -49.38
Consensus MFE -39.32
Energy contribution -40.40
Covariance contribution 1.08
Combinations/Pair 1.15
Mean z-score -2.36
Structure conservation index 0.80
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.99
SVM RNA-class probability 0.978132
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 19558457 144 + 23011544
UGGAAGAACAGGAAUGACUGGUGACUUUGGGUUAGGAUGGGAGGUGCAAUCCUAAGACGAUGGGUCCAUUGACCAGUCCAGUUAACCAAUCAGGGUUCUGCUGUGAGUGCAGCA-------CAUUUAGUUCUGUUUUAUCCUUCGAAGAAU
.((((((((((((.(((.((..((((((((((((((((.(((((......)))....(((((....))))).)).))))...)))))...))))))).((((((....))))))-------)).))).))))))))).))).......... ( -44.20, z-score =  -0.79, R)
>droSim1.chr2L 19246035 149 + 22036055
--GAAGAACAGGAAUGACUGGUGACUUUGAGUUAGGAUGGAAGGUGCAGACCCAAGACGAUGGGUCCAUUGACCAUUCCAGUUAACCAGUCAAGGUUCUGCUGUGAGUGCAGCAGGAGGCACAUUUAGUUCUGUUUAAUCCUUCGAAGAAU
--(((((((((((.(((((((((((.....))).((((((..((((..((((((......))))))))))..))))))......))))))))...(((((((((....)))))))))...........))))))).....))))....... ( -52.80, z-score =  -3.12, R)
>droYak2.chr2R 6054647 140 + 21139217
--GAAGAACAGGAAUGACUGGUGACUU------AGGAUGG-AGUUGCAGUCCUAAGACGAUAAGUCCAAUGUCCAUUCGAGU-AACCAGUCAAGGUUCGGCUGUGAGUGCAGCAGGAGGCAAAUUCAUAUCUGUCUUUUCCCU-GAAGAAU
--......((((..((((((((.((((------.((((((-(((((..(((....)))((....)))))).)))))))))))-.)))))))).......(((((....)))))((((((((.((....)).)))))))).)))-)...... ( -45.40, z-score =  -2.23, R)
>droSec1.super_7 3172515 151 + 3727775
UAGAAGAACAGGAAUGACUGGUGACUUUGAGUCAGGAUGGAAGGUGCAGACCCAAGACGAUGGGUCCAUUGAUCAUUCCAGUUAACCAGUCAAGGUUCUGCUGUGAGUGCAGCAGGAGGUACAUUUAGUUCUGUUUUAUCCUUCGAAGAAU
..(((((((((((.(((((((((((.....))).((((((..((((..((((((......))))))))))..))))))......))))))))...(((((((((....)))))))))...........))))))).....))))....... ( -53.00, z-score =  -3.05, R)
>droEre2.scaffold_4845 17856907 142 - 22589142
UAGAAGAACAGGAAUGACUGGUGACUU------AGAAUGGGAGGUGCAGUCCUUAGCCGGUGGGUUCACUGUCCAUUUCAGUUAACCAGUCAAGGUUCUGCUGUGAGUGCAGCAGGAGG--CACAUAGUUCUGUUUUAUCCCU-GAAGAAU
....(((((((((.((((((((((((.------.((((((..((((.(..((.........))..)))))..)))))).)))).))))))))...(((((((((....)))))))))..--.......)))))))))......-....... ( -51.50, z-score =  -2.61, R)
>consensus
U_GAAGAACAGGAAUGACUGGUGACUUUG_GU_AGGAUGGAAGGUGCAGUCCUAAGACGAUGGGUCCAUUGACCAUUCCAGUUAACCAGUCAAGGUUCUGCUGUGAGUGCAGCAGGAGG_ACAUUUAGUUCUGUUUUAUCCUUCGAAGAAU
..(((((((((((.((((((((((((........((((((..((((....((((......))))..))))..)))))).)))).))))))))...(((((((((....)))))))))...........))))))))).))........... (-39.32 = -40.40 +   1.08)

alignment

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secondary structure

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dotplot

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Window 4

Location 19,558,457 – 19,558,601
Length 144
Sequences 5
Columns 151
Reading direction reverse
Mean pairwise identity 84.19
Shannon entropy 0.27842
G+C content 0.46015
Mean single sequence MFE -40.18
Consensus MFE -26.92
Energy contribution -27.68
Covariance contribution 0.76
Combinations/Pair 1.16
Mean z-score -2.18
Structure conservation index 0.67
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.92
SVM RNA-class probability 0.853184
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 19558457 144 - 23011544
AUUCUUCGAAGGAUAAAACAGAACUAAAUG-------UGCUGCACUCACAGCAGAACCCUGAUUGGUUAACUGGACUGGUCAAUGGACCCAUCGUCUUAGGAUUGCACCUCCCAUCCUAACCCAAAGUCACCAGUCAUUCCUGUUCUUCCA
..........(((...(((((.......(.-------(((((......))))).)....((((((((..(((.((..((((....))))..))(..(((((((.(......).)))))))..)..))).))))))))...)))))..))). ( -38.30, z-score =  -1.96, R)
>droSim1.chr2L 19246035 149 - 22036055
AUUCUUCGAAGGAUUAAACAGAACUAAAUGUGCCUCCUGCUGCACUCACAGCAGAACCUUGACUGGUUAACUGGAAUGGUCAAUGGACCCAUCGUCUUGGGUCUGCACCUUCCAUCCUAACUCAAAGUCACCAGUCAUUCCUGUUCUUC--
.......(((((.....((((...............((((((......)))))).....((((((((....(((((.(((...((((((((......)))))))).)))))))).....((.....)).))))))))...)))))))))-- ( -43.90, z-score =  -2.94, R)
>droYak2.chr2R 6054647 140 - 21139217
AUUCUUC-AGGGAAAAGACAGAUAUGAAUUUGCCUCCUGCUGCACUCACAGCCGAACCUUGACUGGUU-ACUCGAAUGGACAUUGGACUUAUCGUCUUAGGACUGCAACU-CCAUCCU------AAGUCACCAGUCAUUCCUGUUCUUC--
......(-(((((..((.(((((....))))).)).(.((((......)))).).....((((((((.-..((.(((....))).))......(.(((((((.((.....-.))))))------))).)))))))))))))))......-- ( -35.10, z-score =  -0.97, R)
>droSec1.super_7 3172515 151 - 3727775
AUUCUUCGAAGGAUAAAACAGAACUAAAUGUACCUCCUGCUGCACUCACAGCAGAACCUUGACUGGUUAACUGGAAUGAUCAAUGGACCCAUCGUCUUGGGUCUGCACCUUCCAUCCUGACUCAAAGUCACCAGUCAUUCCUGUUCUUCUA
.......((((((((.....................((((((......)))))).....((((((((....(((((........(((((((......))))))).....)))))....(((.....)))))))))))....)))))))).. ( -45.52, z-score =  -3.60, R)
>droEre2.scaffold_4845 17856907 142 + 22589142
AUUCUUC-AGGGAUAAAACAGAACUAUGUG--CCUCCUGCUGCACUCACAGCAGAACCUUGACUGGUUAACUGAAAUGGACAGUGAACCCACCGGCUAAGGACUGCACCUCCCAUUCU------AAGUCACCAGUCAUUCCUGUUCUUCUA
......(-((((((...(((......))).--....((((((......))))))......(((((((..(((..(((((...(((......((......))....)))...)))))..------.))).))))))))))))))........ ( -38.10, z-score =  -1.44, R)
>consensus
AUUCUUCGAAGGAUAAAACAGAACUAAAUGU_CCUCCUGCUGCACUCACAGCAGAACCUUGACUGGUUAACUGGAAUGGUCAAUGGACCCAUCGUCUUAGGACUGCACCUCCCAUCCU_AC_CAAAGUCACCAGUCAUUCCUGUUCUUC_A
..........(((...(((((...............((((((......)))))).....((((((((..((((((.(((....((.(((((......))))..).))....))))))........))).))))))))...)))))..))). (-26.92 = -27.68 +   0.76)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 21:52:28 2011