Locus 2338

Sequence ID dm3.chr2L
Location 18,148,016 – 18,148,265
Length 249
Max. P 0.969323
window3223 window3224

overview

Window 3

Location 18,148,016 – 18,148,114
Length 98
Sequences 3
Columns 99
Reading direction reverse
Mean pairwise identity 93.49
Shannon entropy 0.09022
G+C content 0.46497
Mean single sequence MFE -32.67
Consensus MFE -26.27
Energy contribution -26.93
Covariance contribution 0.67
Combinations/Pair 1.00
Mean z-score -3.01
Structure conservation index 0.80
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.81
SVM RNA-class probability 0.969323
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 18148016 98 - 23011544
GACUCAAAUGUAUCUGGGGAAACCAUCUUUUUUGGCCAUUUUGGCCAAAGGCGAAAAAGGGGAA-AGAACUAGAUACAUUCGGGCCUAACCCGGACCUG
........((((((((((....)).((.(((((((((.....))))))))).))..........-.....))))))))((((((.....)))))).... ( -33.90, z-score =  -2.91, R)
>droSec1.super_7 1773770 94 - 3727775
GACUCGAAUGUAUCUGGGGAAACCAUCUUUUU-----AUUUUGGCCAAAGGCGAAAAAGGGGAAAAGAGCUAGAUACAUUCGGGCCUAACCCGGACCUG
..((((((((((((((((....)).(((((((-----.((((.(((...))).))))....)))))))..))))))))))))))((......))..... ( -34.90, z-score =  -3.80, R)
>droSim1.chr2L 17824177 94 - 22036055
GACUCGAAUGUAUCUGGGGAAACCAUCUUUUU-----AUUUUGGCCAAAGGAGAAAAAGGGGAACAGAACUAGAUACAUUCGGGCCUAACCCGGACCUG
..((((((((((((((((....)).(((((((-----.((((......)))).)))))))..........))))))))))))))((......))..... ( -29.20, z-score =  -2.30, R)
>consensus
GACUCGAAUGUAUCUGGGGAAACCAUCUUUUU_____AUUUUGGCCAAAGGCGAAAAAGGGGAA_AGAACUAGAUACAUUCGGGCCUAACCCGGACCUG
..((((((((((((((((....)).(((.(((......((((.(((...))).))))....))).)))..))))))))))))))((......))..... (-26.27 = -26.93 +   0.67)

alignment

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secondary structure

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dotplot

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Window 4

Location 18,148,114 – 18,148,265
Length 151
Sequences 6
Columns 157
Reading direction reverse
Mean pairwise identity 71.37
Shannon entropy 0.52467
G+C content 0.44030
Mean single sequence MFE -36.51
Consensus MFE -19.66
Energy contribution -19.55
Covariance contribution -0.11
Combinations/Pair 1.40
Mean z-score -1.77
Structure conservation index 0.54
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.59
SVM RNA-class probability 0.953446
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 18148114 151 - 23011544
UGCCUCCACA---ACAAACUUAUCAAAAAAAAAA--AAAAGAACACAAUAUU-UAUUCAGGUAGUUGGUGUUCCGUUACCGUUUCCGUAACAAAAGUUCCGUGAGCCCAUGGUCAUAACUUGGGCUCAAUCAAAACAGAAAAAAAGGAGAGCCCGUC
.((((((...---...(((((.............--....((((((..((((-(....)))))....)))))).(((((.......)))))..)))))...((((((((.(((....))))))))))).................)))).))..... ( -37.00, z-score =  -3.35, R)
>droSim1.chr2L 17824271 150 - 22036055
UGCCUCCACA---ACCAACUCCUCAAAAAAAAAA--AAAAAAACACAAUAUG-UAUUCAGGUAGUUGGUGUUCCGUUACCGUUUCCGUAACAAAAGUUCCGUGAGCCCGUGGUCAUAACUUGGGCUCAGCCAAAACAG-ACAAAAGGAGAGCCCGUC
.((((((...---((((((((((...........--................-.....))).)))))))(((..(((((.......)))))..........((((((((.(((....))))))))))).........)-))....)))).))..... ( -36.65, z-score =  -2.35, R)
>droSec1.super_7 1773864 145 - 3727775
UGCCUCCACA---ACCAACUCCUCAAAAAAAAAA-------AACACAAUAUG-UAUUCAGUUAGUUGGUGUUCCGUUACCGUUUCCGUAACAAAAGUUCCGUGAGCCCGUGGUCAUAACUUGGGCUCAGCCGAAACAG-ACAAAAGGAGAGCCCGUC
.((((((...---(((((((..............-------...........-.........)))))))(((..(((((.......)))))....(((.((((((((((.(((....)))))))))))..)).))).)-))....)))).))..... ( -34.98, z-score =  -1.80, R)
>droYak2.chr2R 4652860 132 - 21139217
----UCCUCG-------AAUACUCGUAUGUAUGU--A----AAUACAAUAUG-UAUUCAGGUAGCUGGUGUUCCGUUACUGUUUCCGUAACCAAAGUUCAG-GAGUCCAUGGUCGUAACUUCGGCUCAACGCAG-----ACAAAAGGAGAACCUGC-
----.(((.(-------(((((..((.(((((..--.----.)))))))..)-))))))))..((.(((.((((.....(((((.(((..((........)-)......((((((......)))).))))).))-----)))...)))).))).))- ( -33.60, z-score =  -1.16, R)
>droEre2.scaffold_4845 16467408 136 + 22589142
UGCCAGCACA-------ACUCCUCAAAUAUGUAA--A----UGCAAUACGAA-UAUUCAGGUAGUUGGUGUUCCGUUACUGCUUCCGUAACAAAAGUUCUG-GAGCUGAUGGUCGUAACUUCGGCUCAGCCCAG-----ACAAAAGGAGAGCCCGC-
.((..((.((-------((((((..((((((((.--.----.....)))..)-)))).))).)))))...(((((((((.......)))))....((.(((-(.(((((..((((......)))))))))))))-----))....)))).))..))- ( -38.20, z-score =  -1.48, R)
>droAna3.scaffold_12916 13410196 148 + 16180835
UAUCUCUACGGGAGUGACCUUAUCAUUCAGAAGAUGAUACGAUUAUGAUAUGAGAGUCAGGU--CUGGUGUGCCGUUAGGAGCUCCACAACAAAAGUUCUGGGAGCUUAUGGCCAUAAUUUCAGCUUAACCCAA-----ACAAAAGGAGCCCACG--
.........((((((((((.(((((((.....)))))))......((((......)))))))--)..(((.(((((...(((((((..(((....)))...))))))))))))))).......)))....((..-----......))..)))...-- ( -38.60, z-score =  -0.49, R)
>consensus
UGCCUCCACA___AC_AACUCCUCAAAAAAAAAA__A____AACACAAUAUG_UAUUCAGGUAGUUGGUGUUCCGUUACCGUUUCCGUAACAAAAGUUCCGUGAGCCCAUGGUCAUAACUUCGGCUCAACCCAA_____ACAAAAGGAGAGCCCGU_
..................................................................(((.(((((((((.......)))))...........(((((((.(.......).)))))))..................)))).))).... (-19.66 = -19.55 +  -0.11)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 21:49:25 2011