Locus 2478

Sequence ID	dm3.chr2L
Location	19,322,550 – 19,322,688
Length	138
Max. P	0.916453

overview

Window 4

Location	19,322,550 – 19,322,652
Length	102
Sequences	3
Columns	102
Reading direction	reverse
Mean pairwise identity	92.16
Shannon entropy	0.10803
G+C content	0.45045
Mean single sequence MFE	-25.33
Consensus MFE	-25.33
Energy contribution	-25.33
Covariance contribution	-0.00
Combinations/Pair	1.00
Mean z-score	-1.12
Structure conservation index	1.00
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	0.87
SVM RNA-class probability	0.841409
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 19322550 102 - 23011544
GAAAUCUUAAUUGCCGCUUAACGAGCAAUUGAGGACUCUAUUCAAGGGAGUGGCGGAUACAGCUAAAGACAUACUUAUAAGGCGGUAGAAGUGCUGCAUACG
....((((((((((((.....)).))))))))))(((((.......)))))(((.......))).................((((((....))))))..... ( -25.30, z-score =  -1.10, R)
>droSim1.chr2L 19015571 102 - 22036055
GAAAUCUUAAUUGCCGCUUAACGAGCAAUUGAGGACUCUAUUCGAGGGAGUGGCGGAUACAGCUAAAGACAUACUUAUAAGGCGGUAGAAGUGCUGCAAACG
....((((((((((((.....)).))))))))))(((((.......)))))(((.......))).................((((((....))))))..... ( -25.30, z-score =  -0.98, R)
>droYak2.chr2R 5830175 98 - 21139217
GAAAUCUUAAUUGCCGCUUAACGAGCAAUUGAGGACUCUAUUAGAGGGAGUGGCGGAUAUAGCUGAAGACA----UAUACGGCGGUAAGAGUGCUGCAUACG
....((((((((((((.....)).))))))))))(((((.......)))))(((.......))).......----......((((((....))))))..... ( -25.40, z-score =  -1.28, R)
>consensus
GAAAUCUUAAUUGCCGCUUAACGAGCAAUUGAGGACUCUAUUCGAGGGAGUGGCGGAUACAGCUAAAGACAUACUUAUAAGGCGGUAGAAGUGCUGCAUACG
....((((((((((((.....)).))))))))))(((((.......)))))(((.......))).................((((((....))))))..... (-25.33 = -25.33 +  -0.00)

alignment

secondary structure

dotplot

Window 5

Location	19,322,572 – 19,322,688
Length	116
Sequences	6
Columns	116
Reading direction	reverse
Mean pairwise identity	74.80
Shannon entropy	0.47333
G+C content	0.46648
Mean single sequence MFE	-30.94
Consensus MFE	-19.54
Energy contribution	-20.35
Covariance contribution	0.81
Combinations/Pair	1.23
Mean z-score	-1.53
Structure conservation index	0.63
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	1.25
SVM RNA-class probability	0.916453
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 19322572 116 - 23011544
AGGGCCUCGAAAGGGGCGUGACCCGUGAUCACAAAGGAAAUCUUAAUUGCCGCUUAACGAGCAAUUGAGGACUCUAUUCAAGGGAGUGGCGGAUACAGCUAAAGACAUACUUAUAA
((((((((....)))))(((.(((.(((.......(((..((((((((((((.....)).))))))))))..)))..))).)))..((((.......))))....))).))).... ( -35.60, z-score =  -2.36, R)
>droSim1.chr2L 19015593 116 - 22036055
AAGGCCUCAAAAGGGGCGUGACCCGUGAUCACAAAGGAAAUCUUAAUUGCCGCUUAACGAGCAAUUGAGGACUCUAUUCGAGGGAGUGGCGGAUACAGCUAAAGACAUACUUAUAA
((((((((....)))))(((..((((.((..(........((((((((((((.....)).)))))))))).(((.....))))..)).)))).))).............))).... ( -32.30, z-score =  -1.59, R)
>droSec1.super_7 2950833 116 - 3727775
AAGGCCUCAAAAGGGGCGUGACCCGUGAUCACAAAGGAAAUCUUAAUUGCCGCUUAACGAGCAAUUGAGGACUCUAUUCGAGGGAGUGGCGGAUAGAGCUAAAGACAUACUUAUAA
...(((((....)))))((((.......)))).(((....((((((((((((.....)).)))))))))).(((((((((.........)))))))))...........))).... ( -33.80, z-score =  -1.90, R)
>droYak2.chr2R 5830197 111 - 21139217
AGGGCUUC-AAAGGGGCGUGGCCCGUGAUCACAAAGGAAAUCUUAAUUGCCGCUUAACGAGCAAUUGAGGACUCUAUUAGAGGGAGUGGCGGAUAUAGCUGAAGACAUAUAC----
.(..((((-(...((((...))))((.(((..........((((((((((((.....)).))))))))))(((((.......)))))....)))...))))))).)......---- ( -29.90, z-score =  -0.98, R)
>droEre2.scaffold_4845 17627257 94 + 22589142
AGGGCCUC--AAGGGGCGUGGCCGCUGAUCACAAAGGAGAUCUUAAUUGCCGCUUAACGAGCGAUUGAGCGCUCUGUUCAAGGGAGUGGCGCAUAU--------------------
...((((.--...))))(((((((((.........((((..(((((((((((.....)).)))))))))..)))).........)))))).)))..-------------------- ( -34.97, z-score =  -1.35, R)
>droAna3.scaffold_12916 11088406 90 + 16180835
-----GAUAAAGGAGGCAUGACCUAUGAUCACAAAGGAGAUCUUAAUUGUCGAUUAA-GAGCAAUUGAAGCCUC---GUAGAGGAGUAGAAAUCUGAAA-----------------
-----.......(((((.........((((........))))(((((((((......-)).))))))).)))))---.((((..........))))...----------------- ( -19.10, z-score =  -1.02, R)
>consensus
AGGGCCUCAAAAGGGGCGUGACCCGUGAUCACAAAGGAAAUCUUAAUUGCCGCUUAACGAGCAAUUGAGGACUCUAUUCAAGGGAGUGGCGGAUACAGCUAAAGACAUACUU____
...(((((....)))))((((.......))))........((((((((((((.....)).))))))))))(((((.......)))))............................. (-19.54 = -20.35 +   0.81)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 21:51:55 2011