Locus 8890

Sequence ID	dm3.chr3R
Location	2,437,710 – 2,437,859
Length	149
Max. P	0.921091

overview

Window 8

Location	2,437,710 – 2,437,824
Length	114
Sequences	7
Columns	115
Reading direction	reverse
Mean pairwise identity	76.42
Shannon entropy	0.47244
G+C content	0.53832
Mean single sequence MFE	-39.64
Consensus MFE	-19.35
Energy contribution	-22.13
Covariance contribution	2.78
Combinations/Pair	1.17
Mean z-score	-1.56
Structure conservation index	0.49
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	0.24
SVM RNA-class probability	0.608790
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 2437710 114 - 27905053
GCGUUCGAGAACGGAUGCGGAUGCUGAUUCGGAUCCGUGUUCGU-GGUCCGGGGCCCGUUACGGAUAUUACGUAAUGAAAGUUAACAAUUACGCCCCCGUGCGUGGGCUUCAAUU
......((..((((((((((((.(......).))))))))))))-..)).(((((((((((((.......))))))..............((((......))))))))))).... ( -41.90, z-score =  -1.31, R)
>droSim1.chr3R 2467834 114 - 27517382
GCGUUCGAGAACGGAUGCGGAUGCGGAUUCGGAUCCGUGUUCGU-GGUCCGGGGCCCGUUACGGAUAUUACGUAAUGAAAGUUAACAAUUACGCCCCCGUGCGUGGGCUUCAAUU
..(((((...((((((((((((((((((....))))))))))))-.))))(((((.(((((((.......)))))))...((........))))))).))...)))))....... ( -43.90, z-score =  -1.45, R)
>droSec1.super_6 2531614 113 - 4358794
GCGUUCGAGAACGGAUGCGGAUGCGGAUUCGGAUCCGUGUUCGU-GGUCCGGGGCCCGUUACGGAUAUUACGUAAUGAAAGUUAACAAUUACG-CCCCGUGCGUGGGCUUCAAUU
..(((((...((((((((((((.((....)).))))))))))))-.(..((((((.(((((((.......)))))))...((........)))-)))))..).)))))....... ( -45.60, z-score =  -2.15, R)
>droYak2.chr3R 18354665 105 - 28832112
---------ACUGGCUCCGGAUUCGGAUUCGGAUCCGUGUUCGU-GGUCCGUGCCCCGUUACGGAUAUUACGUAAUGAAAGUUAACAAUUACGCCCCCGUGCGUGGGCUUCAAUU
---------((.(((..(((((.(((((....))))).))))).-.))).))(((((((.((((......((((((...........))))))...))))))).))))....... ( -36.70, z-score =  -1.60, R)
>droAna3.scaffold_13340 13664340 100 - 23697760
-----------GGGACACGGUCCCGG--CUGAAUGCUUCUGC-C-GAUCCGGGGCCCGUUACGGAUAUUACGUAAUGAAAGUUAACAAUUACGCCCCCGUGCGUGGGCUUCAAUA
-----------(((((...)))))..--.((((.(((..(((-(-(....(((((.(((((((.......)))))))...((........))))))))).)))..)))))))... ( -35.80, z-score =  -1.16, R)
>droEre2.scaffold_4770 2681361 114 - 17746568
GCAUUCGAGUCCGGCUCCGGAUCCGGACUCGGAUCCGCGUUCGU-GGUCCGGGGCCCGUUACGGAUAUUACGUAAUGAAAGUUAACAAUUACGCCCCCGUGCGUGGGCUUCAAUU
..(((.((((((((((((((((((((((.((....)).))))).-)))))))))))(((((((.......))))))).............((((......)))))))))).))). ( -51.20, z-score =  -3.34, R)
>droWil1.scaffold_181089 670541 91 - 12369635
------------------------AGAGUCAAAUGGGGAGCGGCGGGGACAAGGCCAUGAAACGAUUUCACGUAAUGAAACUUAACAAUUACGCCCUCGGCCGGAGGCUUCAAUU
------------------------............(((((..((....)..((((.((((.....))))((((((...........)))))).....)))).)..))))).... ( -22.40, z-score =   0.05, R)
>consensus
GC_UUCGAGAACGGAUGCGGAUGCGGAUUCGGAUCCGUGUUCGU_GGUCCGGGGCCCGUUACGGAUAUUACGUAAUGAAAGUUAACAAUUACGCCCCCGUGCGUGGGCUUCAAUU
..................((((.(((((.((....)).)))))...))))((((((((..((((......((((((...........))))))...))))...)))))))).... (-19.35 = -22.13 +   2.78)

alignment

secondary structure

dotplot

Window 9

Location	2,437,747 – 2,437,859
Length	112
Sequences	7
Columns	113
Reading direction	reverse
Mean pairwise identity	73.39
Shannon entropy	0.52534
G+C content	0.57131
Mean single sequence MFE	-41.93
Consensus MFE	-18.77
Energy contribution	-22.54
Covariance contribution	3.77
Combinations/Pair	1.28
Mean z-score	-2.00
Structure conservation index	0.45
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	1.28
SVM RNA-class probability	0.921091
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 2437747 112 - 27905053
CCAUAAUCC-CCCAAGAGGCCAAGGCCACUGGAACCGCGUUCGAGAACGGAUGCGGAUGCUGAUUCGGAUCCGUGUUCGUGGUCCGGGGCCCGUUACGGAUAUUACGUAAUGA
........(-(((.((.(((....))).))(((.(((((.......((((((.(((((....))))).))))))...))))))))))))..(((((((.......))))))). ( -47.50, z-score =  -2.64, R)
>droSim1.chr3R 2467871 112 - 27517382
CCAUAAUCC-CCCAAGAGGCCAAGGCCACUGGAACCGCGUUCGAGAACGGAUGCGGAUGCGGAUUCGGAUCCGUGUUCGUGGUCCGGGGCCCGUUACGGAUAUUACGUAAUGA
........(-(((.((.(((....))).))(((.(((((((....)))((((((((((.((....)).)))))))))))))))))))))..(((((((.......))))))). ( -49.40, z-score =  -2.70, R)
>droSec1.super_6 2531650 112 - 4358794
CCAUAAUCC-CCCAAGAGGCCAAGGCCACUGGAACCGCGUUCGAGAACGGAUGCGGAUGCGGAUUCGGAUCCGUGUUCGUGGUCCGGGGCCCGUUACGGAUAUUACGUAAUGA
........(-(((.((.(((....))).))(((.(((((((....)))((((((((((.((....)).)))))))))))))))))))))..(((((((.......))))))). ( -49.40, z-score =  -2.70, R)
>droYak2.chr3R 18354702 101 - 28832112
CCAUAAUCC-CCCAAGAGGCCAAGGCCACU--------GGCCA---CUGGCUCCGGAUUCGGAUUCGGAUCCGUGUUCGUGGUCCGUGCCCCGUUACGGAUAUUACGUAAUGA
.........-.......(((....)))((.--------(((((---(..((..((((((((....)))))))).))..)))))).))....(((((((.......))))))). ( -37.80, z-score =  -1.62, R)
>droAna3.scaffold_13340 13664377 97 - 23697760
CCAUAAUCCGGCAAAGAGGCCAAGGCUACU--------GUCCG-----GGACACGGUCCCGG--CUGAAUGCUUCUGC-CGAUCCGGGGCCCGUUACGGAUAUUACGUAAUGA
......(((((...((.(((....))).))--------..)))-----))....((((((((--......((....))-....))))))))(((((((.......))))))). ( -37.50, z-score =  -1.49, R)
>droEre2.scaffold_4770 2681398 112 - 17746568
CCAUAAUCC-CCAAAGAGGCCAAGGCCACUCGAACCGCAUUCGAGUCCGGCUCCGGAUCCGGACUCGGAUCCGCGUUCGUGGUCCGGGGCCCGUUACGGAUAUUACGUAAUGA
.........-.......(((....)))(((((((.....)))))))..((((((((((((((((.((....)).))))).)))))))))))(((((((.......))))))). ( -52.50, z-score =  -3.77, R)
>droWil1.scaffold_181089 670578 87 - 12369635
CCAUAAUCC-CCCAAUGGAUGAGAA--ACU------------------GGAGCCAGAGUCAAAUGGGGAGCGGCG-----GGGACAAGGCCAUGAAACGAUUUCACGUAAUGA
.(((....(-((((...(((.....--.((------------------(....))).)))...)))))...((((-----....)...))))))..(((......)))..... ( -19.40, z-score =   0.93, R)
>consensus
CCAUAAUCC_CCCAAGAGGCCAAGGCCACU_GAACCGCGUUCGAG_ACGGAUCCGGAUGCGGAUUCGGAUCCGUGUUCGUGGUCCGGGGCCCGUUACGGAUAUUACGUAAUGA
.................((((..((((((.........(((((....))))).(((((.((....)).))))).....))))))...))))(((((((.......))))))). (-18.77 = -22.54 +   3.77)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 23:54:03 2011