Locus 5382

Sequence ID dm3.chr2R
Location 19,932,480 – 19,932,578
Length 98
Max. P 0.804013
window7381 window7382

overview

Window 1

Location 19,932,480 – 19,932,578
Length 98
Sequences 10
Columns 100
Reading direction forward
Mean pairwise identity 71.27
Shannon entropy 0.62686
G+C content 0.49416
Mean single sequence MFE -28.40
Consensus MFE -10.98
Energy contribution -11.11
Covariance contribution 0.13
Combinations/Pair 1.40
Mean z-score -1.57
Structure conservation index 0.39
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.74
SVM RNA-class probability 0.804013
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 19932480 98 + 21146708
AUGGGUCUGGGUGUCUCUA-ACCGGCGG-AACUUACCGGCACUCUCCAGGUCCGCAUUUCUGGAUAUCUUCUAGAAACUGGUCGUACUCGGCGUUGCGAU
..((..((((((.......-)))(.(((-......))).)......)))..))(((((((((((.....))))))))...((((....))))..)))... ( -33.30, z-score =  -1.57, R)
>droSim1.chr2R 18468772 98 + 19596830
AGUGCUCUGGGUGUCUCUA-GCCAGCGG-UACUUACCGGCACUCUCCAGGUCCGCAUUUCUGGAUAUCUUCUAGAAACUGGUCGUACUCGGCGUUGCGAU
(((((.((((.((....))-.))))(((-(....))))))))).........((((((((((((.....))))))))...((((....))))..)))).. ( -31.60, z-score =  -1.04, R)
>droSec1.super_5 185894 98 + 5866729
AUUGCUCUGGGUGUCUCUA-GCCGGUGG-UACUUACCGGCACUCUCCAGGUCCGCAUUUCUGGAUAUCUUCUAGAAACUGGUCGUACUCGGCGUUGCGAU
...((.(((((.((.....-(((((((.-....))))))))).).)))))).((((((((((((.....))))))))...((((....))))..)))).. ( -33.40, z-score =  -1.97, R)
>droYak2.chr2R 19911239 99 + 21139217
UUUUCUUUAGGGGUCUCCAAGCUGGCGA-AACUUACCGGCACUCUCCGGGUCCGCAUUUCUGGAUAUCUUCUAGAAACUGGUCGUACUCGGCGUUGCGAU
.......((((..((.((.....)).))-..))))...(((..(.((((((.(((.((((((((.....))))))))...).)).)))))).).)))... ( -29.70, z-score =  -0.99, R)
>droEre2.scaffold_4845 21307922 99 + 22589142
UUUGCCCUGAGGGUCUCUAAGCCCGCGG-AACUUACCGGCACUCUCCAGGUCCGCAUUUCUGGAUAUCUUCUAGAAACUGGUCGUACUCGGCGUUGCGAU
.....((((.((((......))))((((-......)).))......))))..((((((((((((.....))))))))...((((....))))..)))).. ( -30.60, z-score =  -0.64, R)
>droAna3.scaffold_13266 5415727 98 - 19884421
--UGGGAUAUAUAACCAUAUAGUUAUGAUGACUUACCGGCACUCGCCGGGUCCGCACUUCUGGAUAUCUUCCAGAAACUGGUCGUAUUCGGCGUUGCGGU
--((((.((((((((......))))).))).))))(((((....)))))..(((((.(((((((.....)))))))....((((....))))..))))). ( -33.90, z-score =  -2.22, R)
>dp4.chr3 7620285 95 + 19779522
-AUGGUAUAGGG---UAUAUGGAAGUAA-AACUUACCGGCAUUCGCCAGGACCGCAUUUCUGGAUAUCUUCUAGAAACUGGUCGUAUUCGCUGUUGCGAU
-..((((.((..---(((......))).-..))))))(((....)))..(((((..((((((((.....)))))))).)))))....((((....)))). ( -28.80, z-score =  -1.92, R)
>droPer1.super_2 7815932 75 + 9036312
------------------------GUAA-AACUUACCGGCAUUCGCCAGGACCGCAUUUCUGGAUAUCUUCUAGAAACUGGUCGUAUUCGCUGUUGCGAU
------------------------....-....(((.(((....)))..(((((..((((((((.....)))))))).)))))))).((((....)))). ( -24.40, z-score =  -3.20, R)
>droMoj3.scaffold_6496 12169410 74 - 26866924
-------------------------CAG-AACUUACCGGCAUUCUCCAGGACCGCAUUUCUGGAUAUCUUCUAGAAACUGAUCGUAUUCGCUAUUCCGAU
-------------------------...-........((......)).(((..((.((((((((.....))))))))..((......))))...)))... ( -13.20, z-score =  -0.14, R)
>apiMel3.Group2 2839598 99 + 14465785
AUUGAUGAGUGUAUUCAAA-AUCGAAAAGGCCAUAGCGACAUUCUCCGCUACCACCUUUUUGCAAAUCUUCAAGGAAGGCAUCAUAUGCUGCAUCACGAG
..((((((((((((.....-..((((((((...(((((........)))))...))))))))....(((((...)))))....))))))).))))).... ( -25.10, z-score =  -2.00, R)
>consensus
_UUGCUCUGGGUGUCUCUA_GCCGGCGA_AACUUACCGGCACUCUCCAGGUCCGCAUUUCUGGAUAUCUUCUAGAAACUGGUCGUACUCGGCGUUGCGAU
...................................((((......)).))....((((((((((.....)))))))).))((((((........)))))) (-10.98 = -11.11 +   0.13)

alignment

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secondary structure

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dotplot

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Window 2

Location 19,932,480 – 19,932,578
Length 98
Sequences 10
Columns 100
Reading direction reverse
Mean pairwise identity 71.27
Shannon entropy 0.62686
G+C content 0.49416
Mean single sequence MFE -23.94
Consensus MFE -10.89
Energy contribution -10.29
Covariance contribution -0.60
Combinations/Pair 1.50
Mean z-score -1.00
Structure conservation index 0.45
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.22
SVM RNA-class probability 0.601221
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 19932480 98 - 21146708
AUCGCAACGCCGAGUACGACCAGUUUCUAGAAGAUAUCCAGAAAUGCGGACCUGGAGAGUGCCGGUAAGUU-CCGCCGGU-UAGAGACACCCAGACCCAU
...((.((.....)).......((((((.((.....)).))))))))((..((((.(.((((((((.....-..))))))-.....)).)))))..)).. ( -22.60, z-score =  -0.33, R)
>droSim1.chr2R 18468772 98 - 19596830
AUCGCAACGCCGAGUACGACCAGUUUCUAGAAGAUAUCCAGAAAUGCGGACCUGGAGAGUGCCGGUAAGUA-CCGCUGGC-UAGAGACACCCAGAGCACU
...((.((.....)).......((((((((.......((((...(((..(((.((......)))))..)))-...)))))-))))))).......))... ( -24.01, z-score =  -0.12, R)
>droSec1.super_5 185894 98 - 5866729
AUCGCAACGCCGAGUACGACCAGUUUCUAGAAGAUAUCCAGAAAUGCGGACCUGGAGAGUGCCGGUAAGUA-CCACCGGC-UAGAGACACCCAGAGCAAU
...((.((.....)).......(((((((.......(((((..........)))))....((((((.....-..))))))-))))))).......))... ( -25.30, z-score =  -1.53, R)
>droYak2.chr2R 19911239 99 - 21139217
AUCGCAACGCCGAGUACGACCAGUUUCUAGAAGAUAUCCAGAAAUGCGGACCCGGAGAGUGCCGGUAAGUU-UCGCCAGCUUGGAGACCCCUAAAGAAAA
.......(.((((((.(((((.((((((.((.....)).))))))..))..((((......))))......-)))...)))))).).............. ( -22.30, z-score =  -0.06, R)
>droEre2.scaffold_4845 21307922 99 - 22589142
AUCGCAACGCCGAGUACGACCAGUUUCUAGAAGAUAUCCAGAAAUGCGGACCUGGAGAGUGCCGGUAAGUU-CCGCGGGCUUAGAGACCCUCAGGGCAAA
.(((((((((((.((((..(((((((((.((.....)).))))).......))))...))))))))..)))-..))))(((..(((...)))..)))... ( -27.11, z-score =   0.26, R)
>droAna3.scaffold_13266 5415727 98 + 19884421
ACCGCAACGCCGAAUACGACCAGUUUCUGGAAGAUAUCCAGAAGUGCGGACCCGGCGAGUGCCGGUAAGUCAUCAUAACUAUAUGGUUAUAUAUCCCA--
.(((((....((....)).....((((((((.....)))))))))))))..(((((....))))).........((((((....))))))........-- ( -28.60, z-score =  -1.76, R)
>dp4.chr3 7620285 95 - 19779522
AUCGCAACAGCGAAUACGACCAGUUUCUAGAAGAUAUCCAGAAAUGCGGUCCUGGCGAAUGCCGGUAAGUU-UUACUUCCAUAUA---CCCUAUACCAU-
.((((....))))....((((.((((((.((.....)).))))))..))))..(((....)))((.(((..-...))))).....---...........- ( -23.10, z-score =  -2.14, R)
>droPer1.super_2 7815932 75 - 9036312
AUCGCAACAGCGAAUACGACCAGUUUCUAGAAGAUAUCCAGAAAUGCGGUCCUGGCGAAUGCCGGUAAGUU-UUAC------------------------
.((((....))))....((((.((((((.((.....)).))))))..))))(((((....)))))......-....------------------------ ( -22.60, z-score =  -2.71, R)
>droMoj3.scaffold_6496 12169410 74 + 26866924
AUCGGAAUAGCGAAUACGAUCAGUUUCUAGAAGAUAUCCAGAAAUGCGGUCCUGGAGAAUGCCGGUAAGUU-CUG-------------------------
..((((((.........((((.((((((.((.....)).))))))..))))((((......))))...)))-)))------------------------- ( -16.50, z-score =  -0.30, R)
>apiMel3.Group2 2839598 99 - 14465785
CUCGUGAUGCAGCAUAUGAUGCCUUCCUUGAAGAUUUGCAAAAAGGUGGUAGCGGAGAAUGUCGCUAUGGCCUUUUCGAU-UUUGAAUACACUCAUCAAU
...(((.((((((((...))))((((...))))...))))(((((((.(((((((......))))))).)))))))....-........)))........ ( -27.30, z-score =  -1.35, R)
>consensus
AUCGCAACGCCGAAUACGACCAGUUUCUAGAAGAUAUCCAGAAAUGCGGACCUGGAGAGUGCCGGUAAGUU_CCGCCGGC_UAGAGACACCCAGAGCAA_
.((((.....((....))....((((((.((.....)).))))))))))..((((......))))................................... (-10.89 = -10.29 +  -0.60)

alignment

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secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:47:14 2011