Locus 3590

Sequence ID dm3.chr2R
Location 6,580,670 – 6,580,767
Length 97
Max. P 0.697822
window4928 window4929

overview

Window 8

Location 6,580,670 – 6,580,767
Length 97
Sequences 5
Columns 98
Reading direction forward
Mean pairwise identity 82.13
Shannon entropy 0.32295
G+C content 0.43801
Mean single sequence MFE -29.60
Consensus MFE -12.44
Energy contribution -14.72
Covariance contribution 2.28
Combinations/Pair 1.23
Mean z-score -2.71
Structure conservation index 0.42
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.44
SVM RNA-class probability 0.697822
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 6580670 97 + 21146708
GGUGGGCCAAUGGAUAUUUGCGGAGGGAAAUGUGUUUUAUAUUCCAGCAAUUUAGCAGAAAUAUUUGC-AAGUACUUAUCCACAAGGGCCAUCAACGG
(((((.((..((((((..(((((((.((((....))))...)))).........(((((....)))))-..)))..))))))...)).)))))..... ( -30.50, z-score =  -3.01, R)
>droAna3.scaffold_13266 18068180 81 + 19884421
-----------------UGGGCUGGGAAAAUGUGUUUUAUAUUCCCGCAAUUUGGUAGAAAUACUCGCCAAGUGCUCUUCUGAAAGGGCCAUCAACUG
-----------------..(((((((((.(((.....))).)))))(((.((((((.((.....)))))))))))...........))))........ ( -22.90, z-score =  -1.62, R)
>droYak2.chr2R 18555171 96 - 21139217
AGUGGGC-AGUGGGUAUUUGCGGAGGGAAAUGUGUUUUAUAUUCCAGCAAUUUAGCAGAAAUAUUCGC-AAGUGCUCACCCAGAAGGGCCAUCAAAUG
....(((-.(((((((((((((((((((.(((.....))).)))).((......)).......)))))-))))))))))((....)))))........ ( -33.60, z-score =  -3.58, R)
>droSec1.super_1 4161010 96 + 14215200
GGUGGGC-AGUGGAUAUUUGUGGAGGGAAAUGUGUUUUAUAUUCCAGCAAUUUAGCAGAAAUAUUCGC-AAGUGCUUAUCCACAAGGGCCAUCAACUG
(((((.(-.(((((((((((((((((((.(((.....))).)))).((......)).......)))))-))))....))))))...).)))))..... ( -30.00, z-score =  -2.52, R)
>droSim1.chr2R 5186943 96 + 19596830
GGUGGGC-AGUGGAUAUUUGCGGAGGGAAAUGCGUUUUAUAUUCCAGCAAUUUAGCAGAAAUAUUCGC-AAGUGCUUAUCCACAAGGGCCAUCAACUG
(((((.(-.(((((((((((((((((((.(((.....))).)))).((......)).......)))))-))))....))))))...).)))))..... ( -31.00, z-score =  -2.80, R)
>consensus
GGUGGGC_AGUGGAUAUUUGCGGAGGGAAAUGUGUUUUAUAUUCCAGCAAUUUAGCAGAAAUAUUCGC_AAGUGCUUAUCCACAAGGGCCAUCAACUG
(((((.(...((((((...(((((((((.(((.....))).)))).((......)).......)))))........))))))....).)))))..... (-12.44 = -14.72 +   2.28)

alignment

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secondary structure

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dotplot

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Window 9

Location 6,580,670 – 6,580,767
Length 97
Sequences 5
Columns 98
Reading direction reverse
Mean pairwise identity 82.13
Shannon entropy 0.32295
G+C content 0.43801
Mean single sequence MFE -21.85
Consensus MFE -13.22
Energy contribution -14.86
Covariance contribution 1.64
Combinations/Pair 1.24
Mean z-score -1.93
Structure conservation index 0.60
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.35
SVM RNA-class probability 0.655031
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 6580670 97 - 21146708
CCGUUGAUGGCCCUUGUGGAUAAGUACUU-GCAAAUAUUUCUGCUAAAUUGCUGGAAUAUAAAACACAUUUCCCUCCGCAAAUAUCCAUUGGCCCACC
..((..((((...(((((((...((....-))..(((((((.((......)).)))))))..............)))))))....))))..))..... ( -24.40, z-score =  -2.58, R)
>droAna3.scaffold_13266 18068180 81 - 19884421
CAGUUGAUGGCCCUUUCAGAAGAGCACUUGGCGAGUAUUUCUACCAAAUUGCGGGAAUAUAAAACACAUUUUCCCAGCCCA-----------------
........(((............(((.((((..((.....)).))))..)))(((((.............))))).)))..----------------- ( -15.72, z-score =  -0.07, R)
>droYak2.chr2R 18555171 96 + 21139217
CAUUUGAUGGCCCUUCUGGGUGAGCACUU-GCGAAUAUUUCUGCUAAAUUGCUGGAAUAUAAAACACAUUUCCCUCCGCAAAUACCCACU-GCCCACU
........(((.....((((((.((....-))..(((((((.((......)).)))))))......................))))))..-))).... ( -19.80, z-score =  -1.17, R)
>droSec1.super_1 4161010 96 - 14215200
CAGUUGAUGGCCCUUGUGGAUAAGCACUU-GCGAAUAUUUCUGCUAAAUUGCUGGAAUAUAAAACACAUUUCCCUCCACAAAUAUCCACU-GCCCACC
((((.((((....(((((((...((....-))..(((((((.((......)).)))))))..............))))))).)))).)))-)...... ( -24.00, z-score =  -2.99, R)
>droSim1.chr2R 5186943 96 - 19596830
CAGUUGAUGGCCCUUGUGGAUAAGCACUU-GCGAAUAUUUCUGCUAAAUUGCUGGAAUAUAAAACGCAUUUCCCUCCGCAAAUAUCCACU-GCCCACC
((((.((((....(((((((........(-(((.(((((((.((......)).)))))))....))))......))))))).)))).)))-)...... ( -25.34, z-score =  -2.82, R)
>consensus
CAGUUGAUGGCCCUUGUGGAUAAGCACUU_GCGAAUAUUUCUGCUAAAUUGCUGGAAUAUAAAACACAUUUCCCUCCGCAAAUAUCCACU_GCCCACC
........(((....(((((((.((.....))..(((((((.((......)).)))))))......................)))))))..))).... (-13.22 = -14.86 +   1.64)

alignment

Postscript

secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:13:05 2011