Locus 5135

Sequence ID dm3.chr2R
Location 17,967,901 – 17,967,998
Length 97
Max. P 0.994229
window7045 window7046

overview

Window 5

Location 17,967,901 – 17,967,998
Length 97
Sequences 3
Columns 108
Reading direction forward
Mean pairwise identity 77.64
Shannon entropy 0.30144
G+C content 0.58400
Mean single sequence MFE -41.34
Consensus MFE -29.06
Energy contribution -30.40
Covariance contribution 1.34
Combinations/Pair 1.10
Mean z-score -2.15
Structure conservation index 0.70
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.26
SVM RNA-class probability 0.917379
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 17967901 97 + 21146708
------AAACACACGCACGC-GCCAGCAGUGAGUGGGAGAGAGCGAGAGAGAGCACAGCUGCCGCCGGUGCAUGUCAUUGCUGUGUGUGCGUGUGUGGGUGAAC----
------..((((((((((((-((.((((((((((((.((...((........))....)).)))).........))))))))))))))))))))))........---- ( -45.00, z-score =  -3.09, R)
>droEre2.scaffold_4845 12106328 95 + 22589142
------ACACACACACACGC-AUAAGCGGAGAGUGGGAGAGAGCGAGAGAGAGCACAGCUGUCGCCGGUGCAUGUGAGUGCUACGUGUGUGUGUGCGUGAAC------
------.(((.(((((((((-((............((.((.(((.............))).)).)).((((((....)))).))))))))))))).)))...------ ( -35.62, z-score =  -1.63, R)
>droYak2.chr2R 9928514 108 - 21139217
ACACAAACACACACACACACGACAAGCAGAGAGUGUGAGAGAGCGAGAGAGAGCACAGCUGUCGCCGGUGCAUGUGAGUGCUGCCUGUGCGUGUGUGUGUGCGUGAAC
......((.(((((((((((((((.((((...(..((...(.((((.((.........)).)))))....))..).....)))).))).)))))))))))).)).... ( -43.40, z-score =  -1.73, R)
>consensus
______ACACACACACACGC_ACAAGCAGAGAGUGGGAGAGAGCGAGAGAGAGCACAGCUGUCGCCGGUGCAUGUGAGUGCUGCGUGUGCGUGUGUGUGUGC______
......((((((((((((((....((((....(((.(...(.((((.((.........)).)))))..).))).....))))..)))))))))))))).......... (-29.06 = -30.40 +   1.34)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 6

Location 17,967,901 – 17,967,998
Length 97
Sequences 3
Columns 108
Reading direction reverse
Mean pairwise identity 77.64
Shannon entropy 0.30144
G+C content 0.58400
Mean single sequence MFE -37.85
Consensus MFE -30.14
Energy contribution -29.92
Covariance contribution -0.22
Combinations/Pair 1.17
Mean z-score -2.78
Structure conservation index 0.80
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.68
SVM RNA-class probability 0.994229
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 17967901 97 - 21146708
----GUUCACCCACACACGCACACACAGCAAUGACAUGCACCGGCGGCAGCUGUGCUCUCUCUCGCUCUCUCCCACUCACUGCUGGC-GCGUGCGUGUGUUU------
----........((((((((((.....(((......)))....(((.((((.(((......................))).)))).)-))))))))))))..------ ( -34.75, z-score =  -2.18, R)
>droEre2.scaffold_4845 12106328 95 - 22589142
------GUUCACGCACACACACACGUAGCACUCACAUGCACCGGCGACAGCUGUGCUCUCUCUCGCUCUCUCCCACUCUCCGCUUAU-GCGUGUGUGUGUGU------
------......(((((((((((((.(((........((((.(((....)))))))........)))).............((....-))))))))))))))------ ( -33.69, z-score =  -3.04, R)
>droYak2.chr2R 9928514 108 + 21139217
GUUCACGCACACACACACGCACAGGCAGCACUCACAUGCACCGGCGACAGCUGUGCUCUCUCUCGCUCUCUCACACUCUCUGCUUGUCGUGUGUGUGUGUGUUUGUGU
....(((((((((((((((.((((((((.........((((.(((....)))))))........(........).....)))))))))))))))))))))))...... ( -45.10, z-score =  -3.12, R)
>consensus
______GCACACACACACGCACACGCAGCACUCACAUGCACCGGCGACAGCUGUGCUCUCUCUCGCUCUCUCCCACUCUCUGCUUGU_GCGUGUGUGUGUGU______
..........((((((((((((....(((........((((.(((....)))))))........)))..............((.....))))))))))))))...... (-30.14 = -29.92 +  -0.22)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:42:29 2011