Locus 10365

Sequence ID dm3.chr3R
Location 13,346,245 – 13,346,363
Length 118
Max. P 0.981397
window14254 window14255

overview

Window 4

Location 13,346,245 – 13,346,337
Length 92
Sequences 4
Columns 99
Reading direction reverse
Mean pairwise identity 68.54
Shannon entropy 0.49312
G+C content 0.39330
Mean single sequence MFE -15.95
Consensus MFE -9.80
Energy contribution -10.18
Covariance contribution 0.37
Combinations/Pair 1.59
Mean z-score -1.95
Structure conservation index 0.61
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.07
SVM RNA-class probability 0.981397
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 13346245 92 - 27905053
-------CCCCGUUUUUUUUUUUUGUAUGUACAUAUAAAAAAGUAUAUAUACAUCUAUCUGCGGCUGUAGUCCUCCGCCGUGUAUCAUUUGGAAAUUCA
-------..(((...........(((((((((..........))))))))).........(((((.(.......).)))))........)))....... ( -14.90, z-score =  -1.20, R)
>droAna3.scaffold_13340 5889309 96 + 23697760
CCCACAUCCCUGUAUUGUCCAGCUGUCUGCCUGUCUGUCCUUCUGUCCACCCAUCUGGCCACGGCUCC---CUUCUUUCGUGUAUCAUUUCGAAAUUCA
....................((((((..(((((..((..(....)..))..))...))).))))))..---....(((((..........))))).... ( -13.90, z-score =  -0.83, R)
>droEre2.scaffold_4770 9466837 88 + 17746568
--------CCCG---UUUUUACGUGUGUAUAUAUAAAAAAAUGUAUAUAUACAUCUGUCUGCGGCUCUAGUCCUCCGCCGUGUAUCAUUUUGAAAUUCA
--------....---....((((((((((((((((......)))))))))))))......(((((...........))))))))............... ( -19.10, z-score =  -3.50, R)
>droYak2.chr3R 1896420 88 - 28832112
--------CCCG---UUUUUAUGUAUGUAUAUAUAUAAAAAUGUAUAUAUAAAUCUGUCUGCGGCUCUAGUCCUCCGCCGUCUAUCAUUUGGAAAUUCA
--------((((---(((((((((((....))))))))))))).................(((((...........))))).........))....... ( -15.90, z-score =  -2.29, R)
>consensus
________CCCG___UUUUUAUGUGUGUAUAUAUAUAAAAAUGUAUAUAUACAUCUGUCUGCGGCUCUAGUCCUCCGCCGUGUAUCAUUUGGAAAUUCA
.......................(((((((((((......)))))))))))........((((((...........))))))................. ( -9.80 = -10.18 +   0.37)

alignment

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secondary structure

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dotplot

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Window 5

Location 13,346,271 – 13,346,363
Length 92
Sequences 5
Columns 94
Reading direction reverse
Mean pairwise identity 57.08
Shannon entropy 0.69817
G+C content 0.46728
Mean single sequence MFE -17.77
Consensus MFE -3.52
Energy contribution -5.16
Covariance contribution 1.64
Combinations/Pair 1.56
Mean z-score -2.28
Structure conservation index 0.20
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.31
SVM RNA-class probability 0.640521
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 13346271 92 - 27905053
--UCCUUUGCCGGCUUAGUGUGUCCGCCCCCCGUUUUUUUUUUUUGUAUGUACAUAUAAAAAAGUAUAUAUACAUCUAUCUGCGGCUGUAGUCC
--..((..((((.(.((((((((.((.....)).....(((((((((((....))))))))))).....))))).)))...)))))...))... ( -16.00, z-score =  -1.28, R)
>droEre2.scaffold_4770 9466863 87 + 17746568
--UCCUUUGGCUGCUUAGU-UGUCCGCCCCC----GUUUUUACGUGUGUAUAUAUAAAAAAAUGUAUAUAUACAUCUGUCUGCGGCUCUAGUCC
--..((..((((((.(((.-..........(----((....)))((((((((((((......)))))))))))).)))...))))))..))... ( -22.10, z-score =  -3.93, R)
>droYak2.chr3R 1896446 86 - 28832112
UAGCUUUUGGCUGCUUAGA----CCGCCCCC----GUUUUUAUGUAUGUAUAUAUAUAAAAAUGUAUAUAUAAAUCUGUCUGCGGCUCUAGUCC
..(((...((((((.((((----.......(----((((((((((((....)))))))))))))..........))))...))))))..))).. ( -20.33, z-score =  -2.39, R)
>dp4.chr2 21716251 78 + 30794189
--UCCUUUUGCGACUUUAGUUGUCCGCCCCC---GCCGUCCAACUGCCUGUCUGUAUAUCUGUCUG-GCACUCCCCCGCACACU----------
--......((((.....(((((..(((....---).))..)))))(((.(.(.........).).)-)).......))))....---------- ( -15.20, z-score =  -1.95, R)
>droPer1.super_0 8931943 77 + 11822988
--UCCUUUUGCGACUUUAGUUGUCCGCCCCC---GCCGUCCAACUGCCUGUCUGUAUAUCUGUCUG-GCACU-CCCCGCACACU----------
--......((((.....(((((..(((....---).))..)))))(((.(.(.........).).)-))...-...))))....---------- ( -15.20, z-score =  -1.86, R)
>consensus
__UCCUUUGGCGGCUUAGG_UGUCCGCCCCC____CUUUUUAACUGUCUGUAUAUAUAAAAAUGUAUAUAUACAUCUGUCUGCGGCU_UAGUCC
........((((((.......))).....................((((((((((((....))))))))))))....))).............. ( -3.52 =  -5.16 +   1.64)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 00:22:36 2011