Locus 1308

Sequence ID dm3.chr2L
Location 10,082,095 – 10,082,206
Length 111
Max. P 0.996127
window1786 window1787

overview

Window 6

Location 10,082,095 – 10,082,206
Length 111
Sequences 6
Columns 116
Reading direction forward
Mean pairwise identity 65.10
Shannon entropy 0.62417
G+C content 0.34690
Mean single sequence MFE -22.69
Consensus MFE -10.82
Energy contribution -10.72
Covariance contribution -0.10
Combinations/Pair 1.65
Mean z-score -1.62
Structure conservation index 0.48
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.73
SVM RNA-class probability 0.964288
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 10082095 111 + 23011544
GAAAGACACAGUCGUGGUCAGGAAAACAAUG-ACAAGCCAUAGCCACGACUGUAAGUGGAAAUAAUAUCUACAGUAGCUUUAGUUACUUAUUUAGUUACUCUCUACUGCUUA----
..(((.((((((((((((..((.........-.....))...))))))))))).((((((..((((......((((((....))))))......))))...)))))))))).---- ( -29.84, z-score =  -2.47, R)
>droAna3.scaffold_12916 13913125 103 + 16180835
AGGAAACAAGGACGAAGU-----GUAUCUUGCACUA--CAAAAAUAACACUUUUAAUUAAUAAGAUAAUUAGAUGAUAA------AGUUAGCUGGAUGUUUUAAAGUUCUUAAAGG
.(....)(((((((.(((-----((.....))))).--).....................(((((((.((((.((((..------.)))).)))).)))))))..))))))..... ( -17.60, z-score =  -1.24, R)
>droEre2.scaffold_4929 10697908 97 + 26641161
GAAAGACACAGUCGUGGUCAGAAAAACGAUAUACUAGCUAUCAGCACCACUGUGAAUGGAAAUAGUAUCCGCAAUGUAA-------------UACUCAG--UGCAUUGAUUA----
......((((((.(((((.......))((((.......))))..))).))))))...(((.......))).(((((((.-------------.......--)))))))....---- ( -19.30, z-score =  -0.33, R)
>droYak2.chr2L 12766175 99 + 22324452
GAAAGCCACAGUCGUGGUCAGGAAUACUAUAUACUAGCCAUAACCACGACUGUAAAUUGAAAUAAAAGCUACAAUAUAA-------------UAUUCACACUGUAUUGCUUA----
..((((.(((((((((((..((....(((.....)))))...)))))))))))...................((((((.-------------.........)))))))))).---- ( -21.80, z-score =  -2.72, R)
>droSec1.super_3 5520304 102 + 7220098
GAAAGACACAGUCGUGGUCAGAAAAACAAUGUGCUAGUUAUAACCACGACUGUAAGUGGAAAUAAUAUCUACAGUAGCU----------AUUUAGUUACUCUGUAUUGCUUA----
.......(((((((((((.(....(((.........))).).)))))))))))..(((((.......)))))(((((((----------....)))))))............---- ( -26.20, z-score =  -2.09, R)
>droSim1.chr2L 9870211 102 + 22036055
GAAAGACACAGUCGUGGUCAGAAAAACUAUGUGCUAGUUAUAACCAAGACUGUAAAUGGAAAUAAUAUCUACAGUAGCU----------AUUUAGUUACUCUGUAUUGCUUA----
..(((..((((((.((((.(....(((((.....))))).).)))).)))))).........((((((....(((((((----------....)))))))..))))))))).---- ( -21.40, z-score =  -0.85, R)
>consensus
GAAAGACACAGUCGUGGUCAGAAAAACAAUGUACUAGCCAUAACCACGACUGUAAAUGGAAAUAAUAUCUACAGUAGAA__________AUUUAGUUACUCUGUAUUGCUUA____
.......(((((((((((........................)))))))))))..................((((((.........................))))))........ (-10.82 = -10.72 +  -0.10)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 7

Location 10,082,095 – 10,082,206
Length 111
Sequences 6
Columns 116
Reading direction reverse
Mean pairwise identity 65.10
Shannon entropy 0.62417
G+C content 0.34690
Mean single sequence MFE -25.25
Consensus MFE -10.56
Energy contribution -12.23
Covariance contribution 1.67
Combinations/Pair 1.21
Mean z-score -2.57
Structure conservation index 0.42
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.89
SVM RNA-class probability 0.996127
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 10082095 111 - 23011544
----UAAGCAGUAGAGAGUAACUAAAUAAGUAACUAAAGCUACUGUAGAUAUUAUUUCCACUUACAGUCGUGGCUAUGGCUUGU-CAUUGUUUUCCUGACCACGACUGUGUCUUUC
----...(((((((..(((.(((.....))).)))....)))))))................((((((((((((...(((....-....))).....).)))))))))))...... ( -31.80, z-score =  -2.82, R)
>droAna3.scaffold_12916 13913125 103 - 16180835
CCUUUAAGAACUUUAAAACAUCCAGCUAACU------UUAUCAUCUAAUUAUCUUAUUAAUUAAAAGUGUUAUUUUUG--UAGUGCAAGAUAC-----ACUUCGUCCUUGUUUCCU
....((((.((....................------........((((((......)))))).((((((...(((((--.....))))).))-----)))).)).))))...... ( -12.10, z-score =  -0.93, R)
>droEre2.scaffold_4929 10697908 97 - 26641161
----UAAUCAAUGCA--CUGAGUA-------------UUACAUUGCGGAUACUAUUUCCAUUCACAGUGGUGCUGAUAGCUAGUAUAUCGUUUUUCUGACCACGACUGUGUCUUUC
----........(((--.((....-------------...)).)))(((.......)))...((((((.(((..((((.......))))(((.....)))))).))))))...... ( -20.00, z-score =  -0.31, R)
>droYak2.chr2L 12766175 99 - 22324452
----UAAGCAAUACAGUGUGAAUA-------------UUAUAUUGUAGCUUUUAUUUCAAUUUACAGUCGUGGUUAUGGCUAGUAUAUAGUAUUCCUGACCACGACUGUGGCUUUC
----.((((..((((((((((...-------------))))))))))...............((((((((((((((..((((.....)))).....)))))))))))))))))).. ( -34.40, z-score =  -5.17, R)
>droSec1.super_3 5520304 102 - 7220098
----UAAGCAAUACAGAGUAACUAAAU----------AGCUACUGUAGAUAUUAUUUCCACUUACAGUCGUGGUUAUAACUAGCACAUUGUUUUUCUGACCACGACUGUGUCUUUC
----(((....((((((((........----------.))).)))))....)))........((((((((((((((.((..(((.....))).)).))))))))))))))...... ( -28.30, z-score =  -3.50, R)
>droSim1.chr2L 9870211 102 - 22036055
----UAAGCAAUACAGAGUAACUAAAU----------AGCUACUGUAGAUAUUAUUUCCAUUUACAGUCUUGGUUAUAACUAGCACAUAGUUUUUCUGACCACGACUGUGUCUUUC
----(((....((((((((........----------.))).)))))....)))........(((((((.((((((.(((((.....)))))....)))))).)))))))...... ( -24.90, z-score =  -2.70, R)
>consensus
____UAAGCAAUACAGAGUAACUAAAU__________AGAUACUGUAGAUAUUAUUUCCAUUUACAGUCGUGGUUAUAGCUAGUACAUAGUUUUUCUGACCACGACUGUGUCUUUC
..............................................................((((((((((((((....................))))))))))))))...... (-10.56 = -12.23 +   1.67)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 21:29:30 2011