Locus 5452

Sequence ID dm3.chr2R
Location 20,389,136 – 20,389,314
Length 178
Max. P 0.877145
window7483 window7484

overview

Window 3

Location 20,389,136 – 20,389,314
Length 178
Sequences 5
Columns 195
Reading direction forward
Mean pairwise identity 77.32
Shannon entropy 0.39162
G+C content 0.45050
Mean single sequence MFE -57.66
Consensus MFE -29.54
Energy contribution -30.66
Covariance contribution 1.12
Combinations/Pair 1.27
Mean z-score -1.80
Structure conservation index 0.51
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.06
SVM RNA-class probability 0.525231
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 20389136 178 + 21146708
---------GCAUGGGAAGCGGAAAGGACAUAAAAGGUAAAUCCAAAUUUGCCUAGGGGGAUGCACUGAGAGAACAGUUCUUAACUUUUUCGAAAGGGCAGGAAAAAGUAUGCAUGAGUAUUUUGUGGUUUGCAACUCAGCUCAUUCACUGCAUACUUUUCCCU--------GUGUAGGCAGUGCUCUUCCUCAC
---------((.......))..............((((((((....))))))))(((((((.((((((.(((((.(((.....))))))))....(.(((((.((((((((((((((((...((((.....))))....))))).....))))))))))).)))--------)).)...)))))))))))))... ( -56.80, z-score =  -2.04, R)
>droEre2.scaffold_4845 21756386 182 + 22589142
---GCAAUGGAAGCACAAGCAGCAAAGCUAUAAAAGCUAAUCUCAAGUC-GCCUG-GGGGCUGCACUGAGGGAAUAGUUCCCAACUUCUUUGCUGGCACAGCAAAAAGUAUGCAAGGGUAUUUUGUGGUUCGCUACCCAGCUCCUUCACUGCAUACUUUUCCCC--------GUGCAGCGAGUGCUUCUGCUCAC
---(((...(((((((..(((((..((((.....))))..(((((....-...))-)))))))).....((((.....)))).......((((((.(((.(..(((((((((((((((....(((.(((.....))))))..))))...)))))))))))..).--------))))))))))))))))))).... ( -65.60, z-score =  -2.27, R)
>droYak2.chr2R 20357634 192 + 21139217
GCAACGGAGGCAAUGGAAGC--AAAGGGCAUGAAAGCUAAAUCCAAAUCAGCCUA-GUGGCUGCACUGAGGAAAUAGUUCUGCACUUCUUUGAAAGCACAGCAAAAAGUAUGCAAGAGUGUUUUGUGGUGUGCCACCCAAGUUAUUCACUGCAUACUUUUUCCCUUUUCUCAGUGUACUUAGUACUUUUCCUCAC
......((((.((.((..((--.....))......(((((.........((((..-..))))((((((((((((..(((.(((............))).)))((((((((((((.(((((.((((.((((...)))))))).)))))..))))))))))))...))))))))))))..))))).)).)))))).. ( -59.50, z-score =  -1.98, R)
>droSec1.super_23 261845 178 + 989336
---------GCAUGGGAAGCGGAAAGGACAUAAAAGGUAACUCCAAAUUAGCCUAAGGGGCUUCACUGAGAGAACAGUUGCUAACUUUUUCGAAAGGGAAGCAAAAAGUAUGCAAGAGUAUUUUGUGGUUCGCAACUCUGCUCUCUCAUUGCAUACUUUUCCCU--------GUGUAGACAGUGCUCUUCCUCAC
---------....((((((.(.(..(.((((...((((............)))).(((((((((.((..(((((.(((.....))))))))...)).))))).(((((((((((((((((..(((((...)))))...)))))).....)))))))))))))))--------))))...)..).).))))))... ( -51.50, z-score =  -1.02, R)
>droSim1.chr2R 18848118 178 + 19596830
---------GCAUGGGAAGCGGAAAGGACAUAAAAGGUAAAUCCAAAUUAGCCCAAGGGGCUGCACUGAGAGAACAGUUCCUAACUUUUUCGAAUGAGCAGCAAAAAGUAUGCAAGAGUAUUUUGUGGUUCGCAACUCUGCUCUCUCAUUGCAUACUUUUUCCU--------GUGUAGGCAGUGCUCUUCCUCAC
---------....((((((.(((....((.......))...))).....(((((...)))))((((((.(((((.(((.....))))))))......((((.((((((((((((((((((..(((((...)))))...)))))).....)))))))))))).))--------)).....)))))).))))))... ( -54.90, z-score =  -1.67, R)
>consensus
_________GCAUGGGAAGCGGAAAGGACAUAAAAGGUAAAUCCAAAUUAGCCUA_GGGGCUGCACUGAGAGAACAGUUCCUAACUUUUUCGAAAGCGCAGCAAAAAGUAUGCAAGAGUAUUUUGUGGUUCGCAACUCAGCUCAUUCACUGCAUACUUUUCCCU________GUGUAGGCAGUGCUCUUCCUCAC
..............(((((((......((((....((.....))............((((((((.((..(((((.(((.....))))))))...)).))))).((((((((((((((((...((((.....))))....))))).....)))))))))))))).........))))......))))..))).... (-29.54 = -30.66 +   1.12)

alignment

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secondary structure

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dotplot

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Window 4

Location 20,389,136 – 20,389,314
Length 178
Sequences 5
Columns 195
Reading direction reverse
Mean pairwise identity 77.32
Shannon entropy 0.39162
G+C content 0.45050
Mean single sequence MFE -56.20
Consensus MFE -31.64
Energy contribution -31.60
Covariance contribution -0.04
Combinations/Pair 1.25
Mean z-score -2.08
Structure conservation index 0.56
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.03
SVM RNA-class probability 0.877145
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 20389136 178 - 21146708
GUGAGGAAGAGCACUGCCUACAC--------AGGGAAAAGUAUGCAGUGAAUGAGCUGAGUUGCAAACCACAAAAUACUCAUGCAUACUUUUUCCUGCCCUUUCGAAAAAGUUAAGAACUGUUCUCUCAGUGCAUCCCCCUAGGCAAAUUUGGAUUUACCUUUUAUGUCCUUUCCGCUUCCCAUGC---------
(((.(((((.....((((((..(--------(((((((((((((((((......))(((((...............)))))))))))))))))))))..................(.((((......)))).).......)))))).....((((...........))))......))))))))..--------- ( -48.86, z-score =  -2.26, R)
>droEre2.scaffold_4845 21756386 182 - 22589142
GUGAGCAGAAGCACUCGCUGCAC--------GGGGAAAAGUAUGCAGUGAAGGAGCUGGGUAGCGAACCACAAAAUACCCUUGCAUACUUUUUGCUGUGCCAGCAAAGAAGUUGGGAACUAUUCCCUCAGUGCAGCCCC-CAGGC-GACUUGAGAUUAGCUUUUAUAGCUUUGCUGCUUGUGCUUCCAUUGC---
(..((((.(((((((((((((((--------((.((((((((((((((......)))(((((.............)))))..))))))))))).))))).))))....(((((((((.....))))........(((..-..)))-))))))))...((((.....))))....))))).))))..).....--- ( -69.72, z-score =  -2.79, R)
>droYak2.chr2R 20357634 192 - 21139217
GUGAGGAAAAGUACUAAGUACACUGAGAAAAGGGAAAAAGUAUGCAGUGAAUAACUUGGGUGGCACACCACAAAACACUCUUGCAUACUUUUUGCUGUGCUUUCAAAGAAGUGCAGAACUAUUUCCUCAGUGCAGCCAC-UAGGCUGAUUUGGAUUUAGCUUUCAUGCCCUUU--GCUUCCAUUGCCUCCGUUGC
(.((((..(((((((((((.(((((((.(((.(((((((((((((((.((.....(((((((...)))).))).....))))))))))))))).(((..((((....))))..)))..)).))).)))))))(((((..-..))))))))))).....((......))....)--))))......)))))..... ( -61.50, z-score =  -2.39, R)
>droSec1.super_23 261845 178 - 989336
GUGAGGAAGAGCACUGUCUACAC--------AGGGAAAAGUAUGCAAUGAGAGAGCAGAGUUGCGAACCACAAAAUACUCUUGCAUACUUUUUGCUUCCCUUUCGAAAAAGUUAGCAACUGUUCUCUCAGUGAAGCCCCUUAGGCUAAUUUGGAGUUACCUUUUAUGUCCUUUCCGCUUCCCAUGC---------
(((.(((((....((((....))--------))(((((.(((((((.(((((((((((((((((((..............))))).)))..(((((...((((....))))..)))))))))))))))).)).((((.....)))).................)))).).))))).))))))))..--------- ( -49.14, z-score =  -1.34, R)
>droSim1.chr2R 18848118 178 - 19596830
GUGAGGAAGAGCACUGCCUACAC--------AGGAAAAAGUAUGCAAUGAGAGAGCAGAGUUGCGAACCACAAAAUACUCUUGCAUACUUUUUGCUGCUCAUUCGAAAAAGUUAGGAACUGUUCUCUCAGUGCAGCCCCUUGGGCUAAUUUGGAUUUACCUUUUAUGUCCUUUCCGCUUCCCAUGC---------
(((.(((((.((((((......(--------((.(((((((((((((.(((...((......))(.....)......)))))))))))))))).))).......(((..(((.....))).)))...))))))(((((...))))).....((((...........))))......))))))))..--------- ( -51.80, z-score =  -1.59, R)
>consensus
GUGAGGAAGAGCACUGCCUACAC________AGGGAAAAGUAUGCAGUGAAAGAGCUGAGUUGCGAACCACAAAAUACUCUUGCAUACUUUUUGCUGCCCUUUCGAAAAAGUUAGGAACUGUUCUCUCAGUGCAGCCCC_UAGGCUAAUUUGGAUUUACCUUUUAUGUCCUUUCCGCUUCCCAUGC_________
(((.(((((.((((((...............((.(((((((((((((..........((((...............))))))))))))))))).)).............(((.....))).......))))))((((.....)))).......................)))))))).................. (-31.64 = -31.60 +  -0.04)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:48:38 2011