Locus 9506

Sequence ID dm3.chr3R
Location 7,098,240 – 7,098,349
Length 109
Max. P 0.939628
window13038 window13039

overview

Window 8

Location 7,098,240 – 7,098,343
Length 103
Sequences 5
Columns 118
Reading direction forward
Mean pairwise identity 69.38
Shannon entropy 0.53646
G+C content 0.50139
Mean single sequence MFE -35.82
Consensus MFE -22.46
Energy contribution -23.10
Covariance contribution 0.64
Combinations/Pair 1.45
Mean z-score -1.31
Structure conservation index 0.63
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.43
SVM RNA-class probability 0.939628
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 7098240 103 + 27905053
UGAGGCUAUUUGCAUAAUGGUUUAUAGAAAAGACAAAGCC-GGGGCUUCGGAUCUGGGUCCUUGGUUU-GGGUUCCCGGGUUCUCGGGUUCCUGGGUUCUCGGUU-------------
..((((((((.....)))))))).............((((-.(((((..((((....))))..)))))-.)))).(((((..(((((....)))))..)))))..------------- ( -34.50, z-score =  -0.71, R)
>droSim1.chr3R 13252340 111 - 27517382
UGAGGCUAUUUGCAUAAUGGUUUAUAGAAAAGACAAAGCC-GGGGCUUCGGAUCUGGGGCUCUGGUUU-GGGUUCCCGGGUUCUCCGGUUCUCGGGUUCCUGGGUUCUCGGUU-----
..((((((((.....))))))))........(((.(((((-(((((((((....))))))))))))))-(((..((((((..(.(((.....))))..))))))..))).)))----- ( -44.70, z-score =  -2.56, R)
>droSec1.super_0 6264235 103 - 21120651
UGAGGCUAUUUGCAUAAUGGUUUAUAGAAAAGACAAAGCC-GGGGCUUCGGAUCUGGGGCUCUGUUUU-GGGUUCCCGGGUUCUCGGGUUCCUGGGUUCUCGGUU-------------
..((((((((.....))))))))...(((....((((((.-(((((((((....))))))))))))))-)..)))(((((..(((((....)))))..)))))..------------- ( -37.10, z-score =  -1.69, R)
>droYak2.chr3R 11133124 89 + 28832112
UGAGGCUAUUUGCAUAAUGGUUUAUAGAAAAGACAAAGCC-GGGGCUUGGGAUCUGGGGCCCAGGUUUUGGGUUGCCUAGUCCUCGGGUU----------------------------
.(((((((((.....)))))....(((..((..(((((((-.((((((.(....).)))))).)))))))..))..)))..)))).....---------------------------- ( -29.60, z-score =  -0.67, R)
>droWil1.scaffold_181089 7982202 118 - 12369635
CCAACCUAUUUACAUAAUGGUUUAUAGAAAAGACAAAGCCCAGAGUGUGGUCACAGUGUCCCUUGGUCCGGGUACAAAAGGACAAUGGCUUCCUGCUUGGGCUACUUUCUUUUUUGUG
..((((.(((.....)))))))(((((((((((...((((((.((((.(((((...(((((.(((.........)))..))))).)))))...))))))))))....))))))))))) ( -33.20, z-score =  -0.90, R)
>consensus
UGAGGCUAUUUGCAUAAUGGUUUAUAGAAAAGACAAAGCC_GGGGCUUCGGAUCUGGGGCCCUGGUUU_GGGUUCCCGGGUUCUCGGGUUCCCGGGUUCUCGGUU_____________
..((((((((.....))))))))...............((.((((((..(((((((((((((.......))).))))))))))...)))))).))....................... (-22.46 = -23.10 +   0.64)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 9

Location 7,098,251 – 7,098,349
Length 98
Sequences 5
Columns 113
Reading direction forward
Mean pairwise identity 67.95
Shannon entropy 0.55903
G+C content 0.52190
Mean single sequence MFE -35.12
Consensus MFE -17.54
Energy contribution -17.10
Covariance contribution -0.44
Combinations/Pair 1.40
Mean z-score -1.18
Structure conservation index 0.50
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.44
SVM RNA-class probability 0.696043
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 7098251 98 + 27905053
GCAUAAUGGUUUAUAGAAAAGACAAAGCC-GGGGCUUCGGAUCUGGGUCCUUGGUUU-GGGUUCCCGGGUUCU--------CGGGUUCCUGGGUUCUCGGUUGCUAGA-----
........((((.......)))).(((((-((((.((((....)))).)))))))))-.(((..(((((..((--------(((....)))))..)))))..)))...----- ( -32.70, z-score =  -0.40, R)
>droSim1.chr3R 13252351 106 - 27517382
GCAUAAUGGUUUAUAGAAAAGACAAAGCC-GGGGCUUCGGAUCUGGGGCUCUGGUUU-GGGUUCCCGGGUUCUCCGGUUCUCGGGUUCCUGGGUUCUCGGUUGCUGGA-----
.............(((....(((.(((((-(((((((((....))))))))))))))-(((..((((((..(.(((.....))))..))))))..))).))).)))..----- ( -42.30, z-score =  -1.91, R)
>droSec1.super_0 6264246 98 - 21120651
GCAUAAUGGUUUAUAGAAAAGACAAAGCC-GGGGCUUCGGAUCUGGGGCUCUGUUUU-GGGUUCCCGGGUUCU--------CGGGUUCCUGGGUUCUCGGUUGCUGGA-----
......................((((((.-(((((((((....))))))))))))))-)(((..(((((..((--------(((....)))))..)))))..)))...----- ( -35.90, z-score =  -1.37, R)
>droYak2.chr3R 11133135 83 + 28832112
GCAUAAUGGUUUAUAGAAAAGACAAAGCC-GGGGCUUGGGAUCUGGGGCCCAGGUUUUGGGUUGCCUAGUCCU--------CGGGUUCUGGA---------------------
........((((.......))))....((-(((((((((((.(((((((((((...))))))..)))))))).--------)))))))))).--------------------- ( -31.40, z-score =  -1.52, R)
>droWil1.scaffold_181089 7982213 113 - 12369635
ACAUAAUGGUUUAUAGAAAAGACAAAGCCCAGAGUGUGGUCACAGUGUCCCUUGGUCCGGGUACAAAAGGACAAUGGCUUCCUGCUUGGGCUACUUUCUUUUUUGUGGCUCUU
.......(..((((((((((((...((((((.((((.(((((...(((((.(((.........)))..))))).)))))...))))))))))....))))))))))))..).. ( -33.30, z-score =  -0.70, R)
>consensus
GCAUAAUGGUUUAUAGAAAAGACAAAGCC_GGGGCUUCGGAUCUGGGGCCCUGGUUU_GGGUUCCCGGGUUCU________CGGGUUCCUGGGUUCUCGGUUGCUGGA_____
((.....(((((............)))))....))...(((((((((((((.......))).))))))))))......................................... (-17.54 = -17.10 +  -0.44)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 00:05:44 2011