Locus 15580

Sequence ID	dm3.chrX
Location	19,736,709 – 19,736,808
Length	99
Max. P	0.956110

overview

Window 5

Location	19,736,709 – 19,736,808
Length	99
Sequences	4
Columns	103
Reading direction	forward
Mean pairwise identity	82.19
Shannon entropy	0.26423
G+C content	0.39599
Mean single sequence MFE	-19.27
Consensus MFE	-15.10
Energy contribution	-15.35
Covariance contribution	0.25
Combinations/Pair	1.00
Mean z-score	-2.25
Structure conservation index	0.78
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	1.63
SVM RNA-class probability	0.956110
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chrX 19736709 99 + 22422827
GCAGGCCAAAAAAAAAGAAAAAAAAAAUGCCGAUGACGU----UCGUCCGCUUAUUUAAGCAUGUUUUUUCUUUUUGUUUUGUUCUCAUCUUGCCUGUUUCUU
(((((((((((((((((((((((...((((.(((((((.----.....)).)))))...)))).)))))))))))).)))))..........))))))..... ( -25.00, z-score =  -3.38, R)
>droSim1.chrX 15211293 87 + 17042790
GCAGGCCCAAAAAAAAAAA--------UGCCGAUGACGU----UCGUCCGCUUAUUUAAGCAUGUUUUUUUU----GUUUUGUUCCCGUCUUGCCUGUUUCUU
((((((.(((((.((((((--------.((.((((....----.)))).((((....))))..)).))))))----.)))))..........))))))..... ( -18.10, z-score =  -1.91, R)
>droSec1.super_8 2000731 83 + 3762037
GCAGGCCCAAAAAAAAA-----------GCCGAUGACGU----UCGUCCGCUUAUUUAAGCAUGUUUUUUU-----GUUUUGUUCCCAUCUUGCCUGUUUCUU
((((((.....(((.((-----------((.((((....----.)))).)))).)))(((((........)-----))))............))))))..... ( -18.90, z-score =  -2.58, R)
>droYak2.chrX 10140397 84 - 21770863
GCAGGCCCAAAAAAAAA----------UGCUGAUGACGUCCGUUCGUCCGCUUAUUUAAGCAUGUUUUU-------GUUUC--UACCAUCUUGCCCGUUUCUU
..(((..((((((...(----------(((((((((((..(....)..)).)))))..))))).)))))-------)..))--)................... ( -15.10, z-score =  -1.13, R)
>consensus
GCAGGCCCAAAAAAAAA__________UGCCGAUGACGU____UCGUCCGCUUAUUUAAGCAUGUUUUUUU_____GUUUUGUUCCCAUCUUGCCUGUUUCUU
((((((............................((((......)))).((((....))))...............................))))))..... (-15.10 = -15.35 +   0.25)

alignment

secondary structure

dotplot

Window 6

Location	19,736,709 – 19,736,808
Length	99
Sequences	4
Columns	103
Reading direction	reverse
Mean pairwise identity	82.19
Shannon entropy	0.26423
G+C content	0.39599
Mean single sequence MFE	-20.55
Consensus MFE	-16.75
Energy contribution	-16.88
Covariance contribution	0.12
Combinations/Pair	1.10
Mean z-score	-1.97
Structure conservation index	0.81
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	1.35
SVM RNA-class probability	0.930269
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chrX 19736709 99 - 22422827
AAGAAACAGGCAAGAUGAGAACAAAACAAAAAGAAAAAACAUGCUUAAAUAAGCGGACGA----ACGUCAUCGGCAUUUUUUUUUUCUUUUUUUUUGGCCUGC
......(((((..........(((((.((((((((((((..(((((....)))))(((..----..)))...........)))))))))))))))))))))). ( -23.00, z-score =  -2.05, R)
>droSim1.chrX 15211293 87 - 17042790
AAGAAACAGGCAAGACGGGAACAAAAC----AAAAAAAACAUGCUUAAAUAAGCGGACGA----ACGUCAUCGGCA--------UUUUUUUUUUUGGGCCUGC
......(((((.....(....)....(----((((((((..(((((....)))))(((..----..))).......--------...))))))))).))))). ( -21.00, z-score =  -2.48, R)
>droSec1.super_8 2000731 83 - 3762037
AAGAAACAGGCAAGAUGGGAACAAAAC-----AAAAAAACAUGCUUAAAUAAGCGGACGA----ACGUCAUCGGC-----------UUUUUUUUUGGGCCUGC
......(((((....((....))...(-----(((((((..(((((....)))))(((..----..)))......-----------..)))))))).))))). ( -20.80, z-score =  -2.51, R)
>droYak2.chrX 10140397 84 + 21770863
AAGAAACGGGCAAGAUGGUA--GAAAC-------AAAAACAUGCUUAAAUAAGCGGACGAACGGACGUCAUCAGCA----------UUUUUUUUUGGGCCUGC
......(((((((((((.(.--((...-------.......(((((....)))))((((......)))).))).))----------)))).......))))). ( -17.41, z-score =  -0.86, R)
>consensus
AAGAAACAGGCAAGAUGGGAACAAAAC_____AAAAAAACAUGCUUAAAUAAGCGGACGA____ACGUCAUCGGCA__________UUUUUUUUUGGGCCUGC
......(((((..((..((((....................(((((....)))))((((......))))..................))))..))..))))). (-16.75 = -16.88 +   0.12)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 02:02:10 2011