Locus 698

Sequence ID dm3.chr2L
Location 4,848,243 – 4,848,369
Length 126
Max. P 0.982448
window925 window926 window927

overview

Window 5

Location 4,848,243 – 4,848,340
Length 97
Sequences 3
Columns 116
Reading direction forward
Mean pairwise identity 66.26
Shannon entropy 0.44472
G+C content 0.64169
Mean single sequence MFE -53.93
Consensus MFE -30.14
Energy contribution -30.71
Covariance contribution 0.57
Combinations/Pair 1.21
Mean z-score -2.36
Structure conservation index 0.56
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.05
SVM RNA-class probability 0.980376
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 4848243 97 + 23011544
-----------CAUG-GGGCCAAUGGGACCAGGAGGACCUCGCGGUCCCAUAAGCAAUAUGGGUCCCUGUGG-------UCCCAUGAGCAGUAUGGGCCCCGGUGGUCCAGUGGGC
-----------((((-((((((..((((((....(((((....)))))((((.....))))))))))..)))-------))))))).((....((((((.....))))))....)) ( -51.70, z-score =  -2.92, R)
>droSim1.chr2L 4718127 97 + 22036055
-----------CAUG-GGGCCAAUGGGACCAGGAGGACCUGGCGGUCCCAUGAGCAAUAUGGGCCCCGGUGG-------UCCCAUGGGCAAUAUGGGUCCCGGUGGUCCAGUGGGC
-----------((((-(((((..((((.((....)).))))..))))))))).((....((((((((((.((-------.((((((.....)))))))))))).))))))....)) ( -52.50, z-score =  -2.21, R)
>droAna3.scaffold_12943 2587797 115 + 5039921
CUUCGGAGGACCAUUUGGGCCAAUGGGACCGGGUGGUCCAAAUGGACCCUGUGGCCCAAUGGGACCCUUUGGACCAGGUCCCUUUGGACCAGGUGGACCCUG-UGGACCGAUGGGC
.((((.(((.((((((((.((((.((((((...(((((((((.((.(((...........))).)).))))))))))))))).)))).))))))))..))).-))))((....)). ( -57.60, z-score =  -1.97, R)
>consensus
___________CAUG_GGGCCAAUGGGACCAGGAGGACCUAGCGGUCCCAUAAGCAAUAUGGGACCCUGUGG_______UCCCAUGGGCAAUAUGGGCCCCGGUGGUCCAGUGGGC
..................(((.((.((((((.(.(((((....))))))...........((((((((((((.........)))))).......))))))...)))))).)).))) (-30.14 = -30.71 +   0.57)

alignment

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secondary structure

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dotplot

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Window 6

Location 4,848,243 – 4,848,340
Length 97
Sequences 3
Columns 116
Reading direction reverse
Mean pairwise identity 66.26
Shannon entropy 0.44472
G+C content 0.64169
Mean single sequence MFE -47.53
Consensus MFE -29.14
Energy contribution -26.93
Covariance contribution -2.21
Combinations/Pair 1.32
Mean z-score -2.22
Structure conservation index 0.61
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.10
SVM RNA-class probability 0.982448
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 4848243 97 - 23011544
GCCCACUGGACCACCGGGGCCCAUACUGCUCAUGGGA-------CCACAGGGACCCAUAUUGCUUAUGGGACCGCGAGGUCCUCCUGGUCCCAUUGGCCC-CAUG-----------
((((...((....)).))))..........((((((.-------(((..((((((((((.....))))(((((....)))))....))))))..))).))-))))----------- ( -46.50, z-score =  -3.07, R)
>droSim1.chr2L 4718127 97 - 22036055
GCCCACUGGACCACCGGGACCCAUAUUGCCCAUGGGA-------CCACCGGGGCCCAUAUUGCUCAUGGGACCGCCAGGUCCUCCUGGUCCCAUUGGCCC-CAUG-----------
((....(((.((.((((..(((((.......))))).-------...)))))).)))....)).((((((.((((((((....))))))......)).))-))))----------- ( -39.90, z-score =  -0.76, R)
>droAna3.scaffold_12943 2587797 115 - 5039921
GCCCAUCGGUCCA-CAGGGUCCACCUGGUCCAAAGGGACCUGGUCCAAAGGGUCCCAUUGGGCCACAGGGUCCAUUUGGACCACCCGGUCCCAUUGGCCCAAAUGGUCCUCCGAAG
.....((((....-..(((.(((..(((.((((.(((((((((((((((.((.(((..((.....))))).)).)))))))))...)))))).)))).)))..))).))))))).. ( -56.20, z-score =  -2.83, R)
>consensus
GCCCACUGGACCACCGGGGCCCAUAUUGCCCAUGGGA_______CCACAGGGACCCAUAUUGCUAAUGGGACCGCCAGGUCCUCCUGGUCCCAUUGGCCC_CAUG___________
.......((.(((..((((((.............((........))...((((....(((.....)))(((((....)))))))))))))))..)))))................. (-29.14 = -26.93 +  -2.21)

alignment

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secondary structure

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dotplot

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Window 7

Location 4,848,270 – 4,848,369
Length 99
Sequences 3
Columns 108
Reading direction reverse
Mean pairwise identity 64.13
Shannon entropy 0.48617
G+C content 0.63686
Mean single sequence MFE -43.41
Consensus MFE -22.46
Energy contribution -23.03
Covariance contribution 0.57
Combinations/Pair 1.27
Mean z-score -1.50
Structure conservation index 0.52
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.53
SVM RNA-class probability 0.730077
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 4848270 99 - 23011544
CGGGGCCCAGAACCACGUGGUCCUCCAAAGCCCACUGGACCACCGGGGCCCAUACUGCUCAUGGGACCACAGGGACCCAUAUUGCUUAUGGGACCGCGA---------
((.(((((....((..(((((((.............))))))).))(((((((.......))))).))...))).((((((.....)))))).)).)).--------- ( -40.62, z-score =  -1.24, R)
>droSim1.chr2L 4718154 99 - 22036055
CGGGGCCCAGAUCCACCUGGUCCUCCAAAGCCCACUGGACCACCGGGACCCAUAUUGCCCAUGGGACCACCGGGGCCCAUAUUGCUCAUGGGACCGCCA---------
.((((((((((....((((((..((((........))))..)))))).........((((.(((.....))))))).........)).)))).)).)).--------- ( -37.40, z-score =   0.39, R)
>droAna3.scaffold_12943 2587836 102 - 5039921
CGAGGUCCCGGACCA--UAGUUCU-CAGGGCCCAUCGGUCCA-CAGGGUCCACCUGGUCCAAAGGG--ACCUGGUCCAAAGGGUCCCAUUGGGCCACAGGGUCCAUUU
...((.((((((((.--..(....-).(((((....))))).-...)))))...((((((((.(((--((((........))))))).))))))))..))).)).... ( -52.20, z-score =  -3.63, R)
>consensus
CGGGGCCCAGAACCAC_UGGUCCUCCAAAGCCCACUGGACCACCGGGGCCCAUAUUGCCCAUGGGACCACCGGGACCCAUAUUGCUCAUGGGACCGCAA_________
.(.((.......((...(((((((....(((....(((.((.....)).)))....)))...)))))))...)).((((((.....)))))).)).)........... (-22.46 = -23.03 +   0.57)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 21:17:34 2011