Locus 4598

Sequence ID dm3.chr2R
Location 14,449,144 – 14,449,259
Length 115
Max. P 0.996150
window6301 window6302

overview

Window 1

Location 14,449,144 – 14,449,236
Length 92
Sequences 5
Columns 95
Reading direction forward
Mean pairwise identity 66.96
Shannon entropy 0.57829
G+C content 0.54759
Mean single sequence MFE -30.62
Consensus MFE -13.17
Energy contribution -15.24
Covariance contribution 2.07
Combinations/Pair 1.26
Mean z-score -1.76
Structure conservation index 0.43
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.12
SVM RNA-class probability 0.894490
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 14449144 92 + 21146708
AACGAGACCCAGUCAGAACGUGGCCAUCAGUCAGAGUGUGUGCAUUCUGGCUCCG--UCCGAAACGAAGUUGGAGCUAAAGCUUCG-CCUCGGAG
...((...(((((....)).)))...))((((((((((....))))))))))...--(((((..(((((((........)))))))-..))))). ( -32.60, z-score =  -1.97, R)
>droSim1.chr2R 13164463 94 + 19596830
AACGAGCCCCAGUCAGAACGUGGCCAUCAGUCAGAGUGUGUGCAUUCUGGCUCCGCGUCCGAAUCGAAGUUGGAGCUGAAGCUUCG-CCUCGGAG
..................(((((.....((((((((((....)))))))))))))))(((((..(((((((........)))))))-..))))). ( -35.50, z-score =  -1.97, R)
>droYak2.chr2R 6397977 89 - 21139217
AACGAGCUGCAGUCAGAACGUGGCCAUCAGUCAGUGUGUGUGCAUUCUGGCUCCG------AGUCCAAGUUGGAGCUGAAGCCUUGUGCUCGGAG
...(.((..(.((....)))..)))....(((((.(((....))).)))))((((------((..((((.....((....))))))..)))))). ( -28.80, z-score =  -0.12, R)
>droEre2.scaffold_4845 8651697 88 + 22589142
AACGAGCCGCAGUCAGAACGUGGCCAUCAGUCAGAGUGUGUGCAUUCUGGCUCCG------AGUCGAAGCUGGAGCUGAAGCUUUG-GCUCGGAG
...(.(((((.((....))))))))....(((((((((....)))))))))((((------((((((((((........)))))))-))))))). ( -44.20, z-score =  -4.29, R)
>droGri2.scaffold_15245 10492409 70 + 18325388
-----AACAAGAAUAAAACGUGGCCAUCAGUCAAGGCACAAAAGGCAAGCCUUCA------ACUUCGGCAUCGACUUCAGA--------------
-----.............((..(((...(((.(((((...........)))))..------)))..)))..))........-------------- ( -12.00, z-score =  -0.42, R)
>consensus
AACGAGCCCCAGUCAGAACGUGGCCAUCAGUCAGAGUGUGUGCAUUCUGGCUCCG______AAUCGAAGUUGGAGCUGAAGCUUCG_CCUCGGAG
..((((...............((.....((((((((((....))))))))))))..........(((((((........)))))))..))))... (-13.17 = -15.24 +   2.07)

alignment

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secondary structure

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dotplot

Postscript

Window 2

Location 14,449,163 – 14,449,259
Length 96
Sequences 4
Columns 98
Reading direction forward
Mean pairwise identity 65.02
Shannon entropy 0.58296
G+C content 0.55008
Mean single sequence MFE -36.70
Consensus MFE -20.12
Energy contribution -21.00
Covariance contribution 0.87
Combinations/Pair 1.36
Mean z-score -2.18
Structure conservation index 0.55
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.89
SVM RNA-class probability 0.996150
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 14449163 96 + 21146708
GUGGCCAUCAGUCAGAGUGUGUGCAUUCUGGCUCCG--UCCGAAACGAAGUUGGAGCUAAAGCUUCGCCUCGGAGCUGGACCUGGAACUGUAGCUGGA
..(((((.(((((((((((....))))))))))...--(((((..(((((((........)))))))..)))))).))).))................ ( -35.00, z-score =  -1.07, R)
>droSim1.chr2R 13164482 98 + 19596830
GUGGCCAUCAGUCAGAGUGUGUGCAUUCUGGCUCCGCGUCCGAAUCGAAGUUGGAGCUGAAGCUUCGCCUCGGAGCUGGAGCUGGAACUGUUGCUGGA
..(((...(((((((((((....)))))))(((((((.(((((..(((((((........)))))))..))))))).)))))....))))..)))... ( -42.80, z-score =  -2.35, R)
>droEre2.scaffold_4845 8651716 87 + 22589142
GUGGCCAUCAGUCAGAGUGUGUGCAUUCUGGCUCCG------AGUCGAAGCUGGAGCUGAAGCUUUGGCUCGGAGCU-----UGGAACUGGUGCUGGA
..(((.(((((((((((((....)))))))((((((------((((((((((........)))))))))))))))).-----....)))))))))... ( -47.80, z-score =  -5.31, R)
>droMoj3.scaffold_6496 23412238 81 - 26866924
GCGGCCAUCAGUCAAGGCA-ACAAGUCAAGACAUCGACUUCUACUUCUGCUUGGAGUUCGAGUUUGAGCUCG-AGUUUGAGUU---------------
(..(((.........))).-.)(((((........)))))........(((..((.(((((((....)))))-))))..))).--------------- ( -21.20, z-score =  -0.01, R)
>consensus
GUGGCCAUCAGUCAGAGUGUGUGCAUUCUGGCUCCG__UCCGAAUCGAAGUUGGAGCUGAAGCUUCGCCUCGGAGCUGGAGCUGGAACUGUUGCUGGA
..(((.....(((((((((....)))))))))......(((((.((((((((........)))))))).))))))))..................... (-20.12 = -21.00 +   0.87)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:32:14 2011