Locus 4738

Sequence ID dm3.chr2R
Location 15,423,871 – 15,423,981
Length 110
Max. P 0.991209
window6502 window6503

overview

Window 2

Location 15,423,871 – 15,423,981
Length 110
Sequences 4
Columns 119
Reading direction forward
Mean pairwise identity 68.88
Shannon entropy 0.48025
G+C content 0.33328
Mean single sequence MFE -24.41
Consensus MFE -15.24
Energy contribution -15.24
Covariance contribution 0.00
Combinations/Pair 1.24
Mean z-score -2.22
Structure conservation index 0.62
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.46
SVM RNA-class probability 0.991209
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 15423871 110 + 21146708
AAAAAAAAAAGUGAAAAACAUACAGAGGGGAAGUGAUGCAAAUCGAUUUACAAUCAUGCACGAAUCCCUGCGAAUGUUUUUU-AUUUACUUUCAUUUGCUUUUUAUAUUUA--------
........(((((((((((((.(...(((((..((.((((....(((.....))).))))))..)))))..).)))))))))-))))........................-------- ( -22.90, z-score =  -2.02, R)
>droEre2.scaffold_4845 9623384 97 + 22589142
-------------------AAAU-GAGGGGAAGUGAUGCAAAUCGAUUUACAUUCGUGCACAAAUCCCUG-GGAUGUUUUUU-AUUCACUUCCAUUCGCUUUGUAUUUUCUGCUACUCA
-------------------...(-(((.((((((((((((...(((.......)))))))...((((...-)))).......-..))))))))....((............))..)))) ( -22.40, z-score =  -1.44, R)
>droYak2.chr2R 7388178 87 - 21139217
---------------GAAAAAAUAAAGGGGAAGUCAUGCAAAUCGAUUUACAUUCGUGCAUGAAUCCCUGAGGAUGUUUUUUUAUUCGCUUUCAUUUGUAAA-----------------
---------------((((.......(((((..(((((((...(((.......)))))))))).)))))..(((((......)))))..)))).........----------------- ( -22.20, z-score =  -2.44, R)
>droSim1.chr2R 14124962 113 + 19596830
----AAAAAAGAGAAAAACAAAUAGAGGGGAAGUGAUGCAAAUCGAUUUACAAUCGUGCACGAAUCCCUGCAAAUGUUUUUU-CUUCACUUUCAUUUGCUUUUUAUUUUUGGUU-CUCA
----......(((((..(.((((((((((((..((.((((...((((.....))))))))))..)))))(((((((......-.........)))))))..))))))).)..))-))). ( -30.16, z-score =  -3.00, R)
>consensus
_______________AAACAAAUAGAGGGGAAGUGAUGCAAAUCGAUUUACAAUCGUGCACGAAUCCCUGCGAAUGUUUUUU_AUUCACUUUCAUUUGCUUUUUAUUUUU_________
..........................(((((..((.((((...(((.......)))))))))..)))))(((((((................))))))).................... (-15.24 = -15.24 +   0.00)

alignment

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secondary structure

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dotplot

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Window 3

Location 15,423,871 – 15,423,981
Length 110
Sequences 4
Columns 119
Reading direction reverse
Mean pairwise identity 68.88
Shannon entropy 0.48025
G+C content 0.33328
Mean single sequence MFE -20.71
Consensus MFE -12.00
Energy contribution -13.94
Covariance contribution 1.94
Combinations/Pair 1.10
Mean z-score -1.76
Structure conservation index 0.58
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.43
SVM RNA-class probability 0.939428
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 15423871 110 - 21146708
--------UAAAUAUAAAAAGCAAAUGAAAGUAAAU-AAAAAACAUUCGCAGGGAUUCGUGCAUGAUUGUAAAUCGAUUUGCAUCACUUCCCCUCUGUAUGUUUUUCACUUUUUUUUUU
--------..............(((.((((((....-.((((((((.((.((((....(((((.(((((.....))))))))))......)))).)).)))))))).)))))).))).. ( -20.90, z-score =  -1.85, R)
>droEre2.scaffold_4845 9623384 97 - 22589142
UGAGUAGCAGAAAAUACAAAGCGAAUGGAAGUGAAU-AAAAAACAUCC-CAGGGAUUUGUGCACGAAUGUAAAUCGAUUUGCAUCACUUCCCCUC-AUUU-------------------
((((..((............))....((((((((..-.......((((-...))))...(((((((.......)))...)))))))))))).)))-)...------------------- ( -19.70, z-score =  -1.14, R)
>droYak2.chr2R 7388178 87 + 21139217
-----------------UUUACAAAUGAAAGCGAAUAAAAAAACAUCCUCAGGGAUUCAUGCACGAAUGUAAAUCGAUUUGCAUGACUUCCCCUUUAUUUUUUC---------------
-----------------..................................((((.((((((((((.......)))...)))))))..))))............--------------- ( -15.90, z-score =  -1.68, R)
>droSim1.chr2R 14124962 113 - 19596830
UGAG-AACCAAAAAUAAAAAGCAAAUGAAAGUGAAG-AAAAAACAUUUGCAGGGAUUCGUGCACGAUUGUAAAUCGAUUUGCAUCACUUCCCCUCUAUUUGUUUUUCUCUUUUUU----
.(((-((....(((((((..(((((((.........-......))))))).((((...(((((.(((((.....))))))))))....)))).....))))))))))))......---- ( -26.36, z-score =  -2.37, R)
>consensus
_________AAAAAUAAAAAGCAAAUGAAAGUGAAU_AAAAAACAUCCGCAGGGAUUCGUGCACGAAUGUAAAUCGAUUUGCAUCACUUCCCCUCUAUUUGUUU_______________
....................(((((((................))))))).((((...(((((.(((((.....))))))))))....))))........................... (-12.00 = -13.94 +   1.94)

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 22:35:01 2011