Locus 9976

Sequence ID dm3.chr3R
Location 10,252,914 – 10,253,087
Length 173
Max. P 0.920655
window13711 window13712 window13713

overview

Window 1

Location 10,252,914 – 10,253,008
Length 94
Sequences 3
Columns 94
Reading direction forward
Mean pairwise identity 89.30
Shannon entropy 0.14386
G+C content 0.56599
Mean single sequence MFE -29.97
Consensus MFE -28.70
Energy contribution -28.70
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -0.83
Structure conservation index 0.96
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.06
SVM RNA-class probability 0.525271
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 10252914 94 + 27905053
AACGGGCGCCGCCUGGCUUAAGAAUUUCUUAUCAGCUGUCAUGGUGUGGCUGCCUGGCGAUGUUGCUCCCGUUGCCGAUGAUGUGGCCGAUGUU
((((((.((((((.(((.((((.....))))..(((..(......)..)))))).)))).....)).))))))((((......))))....... ( -32.30, z-score =  -0.60, R)
>droSim1.chr3R 16312553 82 - 27517382
AACGGGCGCCGCCUGGCUUAAGAAUUUCUUAUCAGCUGUCAUGGUGUGGCUGCCUGGCGAUGUUGCUCCCGUUGCCGAUGUU------------
...(((((((((((((((((((.....))))..)))).....)).))))).))))(((((((.......)))))))......------------ ( -28.70, z-score =  -1.01, R)
>droEre2.scaffold_4770 9785883 82 + 17746568
AACGGGCGCCGCCUGGCUUAAGAAUUUCUUAUCAGCUGUCAUGGUGUGGCUGCCUGGCGAUGUUGCACCCGUUGCCGAUG-UG-----------
((((((.((((((.(((.((((.....))))..(((..(......)..)))))).)))).....)).)))))).......-..----------- ( -28.90, z-score =  -0.88, R)
>consensus
AACGGGCGCCGCCUGGCUUAAGAAUUUCUUAUCAGCUGUCAUGGUGUGGCUGCCUGGCGAUGUUGCUCCCGUUGCCGAUG_UG___________
...(((((((((((((((((((.....))))..)))).....)).))))).))))(((((((.......))))))).................. (-28.70 = -28.70 +  -0.00)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 2

Location 10,252,914 – 10,253,008
Length 94
Sequences 3
Columns 94
Reading direction reverse
Mean pairwise identity 89.30
Shannon entropy 0.14386
G+C content 0.56599
Mean single sequence MFE -27.80
Consensus MFE -24.93
Energy contribution -24.93
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -1.92
Structure conservation index 0.90
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.28
SVM RNA-class probability 0.920655
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 10252914 94 - 27905053
AACAUCGGCCACAUCAUCGGCAACGGGAGCAACAUCGCCAGGCAGCCACACCAUGACAGCUGAUAAGAAAUUCUUAAGCCAGGCGGCGCCCGUU
.......(((........)))((((((.((.....((((.((((((............)))..((((.....)))).))).)))))).)))))) ( -29.40, z-score =  -1.86, R)
>droSim1.chr3R 16312553 82 + 27517382
------------AACAUCGGCAACGGGAGCAACAUCGCCAGGCAGCCACACCAUGACAGCUGAUAAGAAAUUCUUAAGCCAGGCGGCGCCCGUU
------------.........((((((.((.....((((.((((((............)))..((((.....)))).))).)))))).)))))) ( -25.10, z-score =  -1.51, R)
>droEre2.scaffold_4770 9785883 82 - 17746568
-----------CA-CAUCGGCAACGGGUGCAACAUCGCCAGGCAGCCACACCAUGACAGCUGAUAAGAAAUUCUUAAGCCAGGCGGCGCCCGUU
-----------..-.......(((((((((.....((((.((((((............)))..((((.....)))).))).))))))))))))) ( -28.90, z-score =  -2.38, R)
>consensus
___________CA_CAUCGGCAACGGGAGCAACAUCGCCAGGCAGCCACACCAUGACAGCUGAUAAGAAAUUCUUAAGCCAGGCGGCGCCCGUU
.....................((((((.((.....((((.((((((............)))..((((.....)))).))).)))))).)))))) (-24.93 = -24.93 +   0.00)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 3

Location 10,252,985 – 10,253,087
Length 102
Sequences 4
Columns 102
Reading direction forward
Mean pairwise identity 70.72
Shannon entropy 0.43339
G+C content 0.56160
Mean single sequence MFE -34.40
Consensus MFE -20.74
Energy contribution -23.17
Covariance contribution 2.44
Combinations/Pair 1.14
Mean z-score -1.27
Structure conservation index 0.60
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.14
SVM RNA-class probability 0.562099
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 10252985 102 + 27905053
UUGCCGAUGAUGUGGCCGAUGUUGCCGAUGUUGCCAAUGUUGCUCCUGUUGCAAGUGCAGCGGCAACAUUGCUUCCGUAUUGGCGGGUUCGCGGCAUGGUUG
....((((.((((.((.((..(((((((((..(.((((((((((...(((((....)))))))))))))))...)..)))))))))..)))).)))).)))) ( -41.90, z-score =  -1.64, R)
>droSim1.chr3R 16312624 90 - 27517382
------------UUGCCGAUGUUGCUCCUGUUGCCAAUGUUGCUCCUGUUGCAAGUGCAGCGGCAACAUUGCUUCCGUAUUGGCGGGUUCGCGGCAUGGUUG
------------..(((.(((((((.......((.(((((((((...(((((....)))))))))))))))).(((((....)))))...)))))))))).. ( -35.60, z-score =  -1.66, R)
>droEre2.scaffold_4770 9785954 81 + 17746568
---------------------UUGCCGAUGUGGCCGAUGUUGCUCCUGUUGCAAGUGCAGCGGCAACAUUGCUUCCGUAUUGGCGAGUUCGCGGCAUGGUUG
---------------------((((((((((((.((((((((((...(((((....)))))))))))))))...))))))))))))................ ( -32.90, z-score =  -1.66, R)
>droWil1.scaffold_181089 2327642 78 - 12369635
------------------------CUCCUGUUGCAGCCAUUGCCGAGGCAGCUACUACUAGUGCAGCAUUGCUUCCGUAUUGGCGUGUGCGAGGCAUGGUUG
------------------------.........(((((((.((((((((((((.(.......).)))..))))))(((((......))))).)))))))))) ( -27.20, z-score =  -0.14, R)
>consensus
_____________________UUGCCCAUGUUGCCAAUGUUGCUCCUGUUGCAAGUGCAGCGGCAACAUUGCUUCCGUAUUGGCGGGUUCGCGGCAUGGUUG
.......................(((.(((((((((((((((((.((((.......)))).))))))))))..(((((....)))))...)))))))))).. (-20.74 = -23.17 +   2.44)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 00:15:03 2011