Locus 3224

Sequence ID dm3.chr2R
Location 3,576,892 – 3,577,055
Length 163
Max. P 0.894352
window4435 window4436

overview

Window 5

Location 3,576,892 – 3,577,055
Length 163
Sequences 4
Columns 165
Reading direction forward
Mean pairwise identity 71.61
Shannon entropy 0.43521
G+C content 0.39588
Mean single sequence MFE -42.14
Consensus MFE -20.27
Energy contribution -21.53
Covariance contribution 1.25
Combinations/Pair 1.19
Mean z-score -2.23
Structure conservation index 0.48
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.12
SVM RNA-class probability 0.894352
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 3576892 163 + 21146708
CUAAUGCUUAUACCCUAGUAGAGGGUAUGUUACCCAAGGGCAACAUUGUUCUUUUCUGCUGA-GGUAAU-GAUAUCAAUGUGAUGGCUCUUGCUUCAAGGUUUGUAUUGUAGUUAGUUUACCACAAAGUGGCUACAAGUAUCCAUUACUGAUACAAGCGGGAUAA
....(((((.((((.((((((((((((...)))))(((((((....))))))).))))))).-))))..-..(((((..(((((((.(((((...)))))......(((((((((.(((.....))).)))))))))....)))))))))))).)))))...... ( -49.60, z-score =  -2.15, R)
>droEre2.scaffold_4929 7610164 133 - 26641161
CUAAUGCUCAUACCCUAGGAGAGGGUAUUUUGCCCAUGGGUAA----GUUCUUAUCUGCUGA-GGUAAUGCAGAUCAAUGUGGUGUCUAUUUCCUAGGGGUCU-----GUAGUUAAUUUACAGCAAAGUGACAAGAAUCGUUG----------------------
....((.((((.((((((((((((((.....)))).(((..(.----......((((((...-......))))))........)..)))))))))))))(.((-----((((.....)))))))...))))))..........---------------------- ( -40.06, z-score =  -1.79, R)
>droSec1.super_1 1232430 132 + 14215200
CUAAUGCCUAUACCCUAGCAGAGGGUAUGUCACCCAAGGGCAACAUUGUUCUUUUCUG-UGAAGGUAAU-UAUAUCAAUGUGGUGUCU--------------------GUAGUUAGUUUACCACAAAGUGGCUACAAGUAUCUAUUAUUGAUAC-----------
....((((((((((((.....))))))).((((..(((((((....)))))))....)-))))))))..-..((((((((.((((..(--------------------(((((((.(((.....))).))))))))..))))...)))))))).----------- ( -42.40, z-score =  -3.29, R)
>droSim1.chr2R 2290195 133 + 19596830
CUAAUGCUUAAACCCUAGCAGAGGGUAUGUCACACAAGGGCAACAUUGUCCUUUUCUGCUGAAGGUAAU-UAUAUCAAUGUGGUGUCU--------------------GUAGUUAUUUUACCACAAAGUGGCUACAAGUAUCUAUUACUGAUAC-----------
...........(((.(((((((((...((.....))((((((....)))))))))))))))..)))...-..(((((.((.((((..(--------------------(((((((((((.....))))))))))))..))))...)).))))).----------- ( -36.50, z-score =  -1.69, R)
>consensus
CUAAUGCUUAUACCCUAGCAGAGGGUAUGUCACCCAAGGGCAACAUUGUUCUUUUCUGCUGA_GGUAAU_UAUAUCAAUGUGGUGUCU____________________GUAGUUAGUUUACCACAAAGUGGCUACAAGUAUCUAUUACUGAUAC___________
...((((((.((((..((((((((((.....))))((((((......)))))).))))))...)))).........................................(((((((.(((.....))).)))))))))))))........................ (-20.27 = -21.53 +   1.25)

alignment

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secondary structure

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dotplot

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Window 6

Location 3,576,892 – 3,577,055
Length 163
Sequences 4
Columns 165
Reading direction reverse
Mean pairwise identity 71.61
Shannon entropy 0.43521
G+C content 0.39588
Mean single sequence MFE -34.34
Consensus MFE -15.65
Energy contribution -16.52
Covariance contribution 0.88
Combinations/Pair 1.14
Mean z-score -1.83
Structure conservation index 0.46
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.13
SVM RNA-class probability 0.558280
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 3576892 163 - 21146708
UUAUCCCGCUUGUAUCAGUAAUGGAUACUUGUAGCCACUUUGUGGUAAACUAACUACAAUACAAACCUUGAAGCAAGAGCCAUCACAUUGAUAUC-AUUACC-UCAGCAGAAAAGAACAAUGUUGCCCUUGGGUAACAUACCCUCUACUAGGGUAUAAGCAUUAG
.......((((((((((((.((((...(((((.......(((((((......)))))))..((.....))..)))))..))))...)))))))..-..((((-..((.(((........((((((((....))))))))....))).))..)))))))))..... ( -41.00, z-score =  -2.11, R)
>droEre2.scaffold_4929 7610164 133 + 26641161
----------------------CAACGAUUCUUGUCACUUUGCUGUAAAUUAACUAC-----AGACCCCUAGGAAAUAGACACCACAUUGAUCUGCAUUACC-UCAGCAGAUAAGAAC----UUACCCAUGGGCAAAAUACCCUCUCCUAGGGUAUGAGCAUUAG
----------------------....(((.((..(.......(((((.......)))-----))..((((((((................((((((......-...))))))......----........(((.......)))..)))))))).)..)).))).. ( -29.50, z-score =  -1.63, R)
>droSec1.super_1 1232430 132 - 14215200
-----------GUAUCAAUAAUAGAUACUUGUAGCCACUUUGUGGUAAACUAACUAC--------------------AGACACCACAUUGAUAUA-AUUACCUUCA-CAGAAAAGAACAAUGUUGCCCUUGGGUGACAUACCCUCUGCUAGGGUAUAGGCAUUAG
-----------(((((.......))))).....(((.(..((((((...((......--------------------))..))))))..).....-..((((((..-((((........((((..((....))..))))....))))..))))))..)))..... ( -35.70, z-score =  -2.55, R)
>droSim1.chr2R 2290195 133 - 19596830
-----------GUAUCAGUAAUAGAUACUUGUAGCCACUUUGUGGUAAAAUAACUAC--------------------AGACACCACAUUGAUAUA-AUUACCUUCAGCAGAAAAGGACAAUGUUGCCCUUGUGUGACAUACCCUCUGCUAGGGUUUAAGCAUUAG
-----------(((((.......))))).....((..(..((((((...........--------------------....))))))..).....-...(((((.((((((...((...((((..(......)..))))..)))))))))))))....))..... ( -31.16, z-score =  -1.03, R)
>consensus
___________GUAUCAGUAAUAGAUACUUGUAGCCACUUUGUGGUAAACUAACUAC____________________AGACACCACAUUGAUAUA_AUUACC_UCAGCAGAAAAGAACAAUGUUGCCCUUGGGUAACAUACCCUCUGCUAGGGUAUAAGCAUUAG
.................................((..(..((((((...................................))))))..)...............................((((((....))))))(((((((.....)))))))..))..... (-15.65 = -16.52 +   0.88)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:06:11 2011