Locus 15417

Sequence ID	dm3.chrX
Location	18,937,340 – 18,937,545
Length	205
Max. P	0.614979

overview

Window 6

Location	18,937,340 – 18,937,437
Length	97
Sequences	3
Columns	118
Reading direction	forward
Mean pairwise identity	70.78
Shannon entropy	0.38623
G+C content	0.43712
Mean single sequence MFE	-19.67
Consensus MFE	-16.51
Energy contribution	-16.07
Covariance contribution	-0.44
Combinations/Pair	1.12
Mean z-score	-0.65
Structure conservation index	0.84
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	0.03
SVM RNA-class probability	0.507377
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chrX 18937340 97 + 22422827
--------GUAGCAAAGAUA------UAGAAGGCAA-CCCAUCAACUCUGAAACUGAACGUGCGGAAAGUGAAACGAGAUGGGAUUGUCCAUCCCAUCCACAAAAAAAAAAA------
--------........(((.------..((.(((((-((((((...((.......)).(((((.....))...))).)))))).))).)).))..)))..............------ ( -16.60, z-score =  -0.38, R)
>droYak2.chrX 17543718 117 + 21770863
GCGGCAAAGAUACAAGGAUACUCGCUUAGAAGGCAAACCCAUCAACGC-AAAACUGAACGUGCGGAAGGCGAAAGGAGAUGGGAUUGUCCAUCGUUCACCAAAAAUACAAAAUACAAA
..((....(((....(((((...(((.....)))...((((((..(((-(..........)))).....(....)..))))))..)))))))).....)).................. ( -24.80, z-score =  -0.92, R)
>droSim1.chrX_random 4903038 88 + 5698898
--------GUAGCAAAGAUA------UAGAAGGCAG-CCCAUCAACUC--AAACUGAACGUGCGGAAAGCGAAACGAGAUGGGAUUGUCCGUCC--ACCAAAAAAAA-----------
--------............------..((.(((((-((((((...((--.....)).(((((.....))...))).)))))).))).)).)).--...........----------- ( -17.60, z-score =  -0.64, R)
>consensus
________GUAGCAAAGAUA______UAGAAGGCAA_CCCAUCAACUC__AAACUGAACGUGCGGAAAGCGAAACGAGAUGGGAUUGUCCAUCC__ACCAAAAAAAA_AAAA______
............................((.(((((.((((((.........((.....))((.....)).......)))))).))).)).))......................... (-16.51 = -16.07 +  -0.44)

alignment

secondary structure

dotplot

Window 7

Location	18,937,437 – 18,937,545
Length	108
Sequences	4
Columns	113
Reading direction	forward
Mean pairwise identity	63.36
Shannon entropy	0.58297
G+C content	0.41650
Mean single sequence MFE	-26.44
Consensus MFE	-9.05
Energy contribution	-9.43
Covariance contribution	0.37
Combinations/Pair	1.31
Mean z-score	-1.81
Structure conservation index	0.34
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	0.25
SVM RNA-class probability	0.614979
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chrX 18937437 108 + 22422827
AAACAAAAACCAUCCAAUAGUUCCGGGAAAUGCGGUGGAAAAAACUGGAACGUUUUUAAAGCACACAAAAUGUGAGCCGCGUUUUAAAGA-----GCCAUGUUUCAAUAGUUG
...(((..........((.((((...((((((((((...((((((......))))))....((((.....)))).))))))))))...))-----)).))..........))) ( -22.85, z-score =  -0.56, R)
>droEre2.scaffold_4690 9220160 96 + 18748788
AAAAAGAAACCAUCCGAUAGUUCCGGGAAAUGC--UGGGAAAAACUGGAACAUUUUCGUAGCUC-CGUUCUAGGGAU----UCCUGGGGCUCUU-GCUCAGCUU---------
..............(((.(((((((((((..((--((.(((((.........))))).))))((-(......))).)----)))))))))).))-)........--------- ( -27.40, z-score =  -0.59, R)
>droSec1.super_8 1231210 93 + 3762037
----------------AUAGUUCGGGGAAAUGUGGCGGGAAAAACUGAAACGUUUUCAAAGCUCACAAAAUGUGAGC----UUUUGAGGAUUUAGGCUGCAUUUCAAUAGUUG
----------------..........((((((..((((......)).....(((((((((((((((.....))))))----.)))))))))....))..))))))........ ( -30.30, z-score =  -4.22, R)
>droSim1.chrX_random 4903126 95 + 5698898
----GAAAACCAUCCAAUAGUUUCGGGAAAUGCGGCGGGAAAAACUGGAACGUUUUCAAAGCACACAAAAUGUGAGC----UUUUG----------CUGCAUUUCAAUAGUUG
----......................(((((((((((.(((((.(......))))))(((((.(((.....))).))----)))))----------)))))))))........ ( -25.20, z-score =  -1.87, R)
>consensus
____AAAAACCAUCCAAUAGUUCCGGGAAAUGCGGCGGGAAAAACUGGAACGUUUUCAAAGCACACAAAAUGUGAGC____UUUUGAGGA_____GCUGCAUUUCAAUAGUUG
.........................(((((((...(((......)))...)))))))...((((((.....)))))).................................... ( -9.05 =  -9.43 +   0.37)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 01:58:50 2011