Locus 12928

Sequence ID	dm3.chrX
Location	3,343,454 – 3,343,546
Length	92
Max. P	0.997282

overview

Window 6

Location	3,343,454 – 3,343,546
Length	92
Sequences	4
Columns	115
Reading direction	forward
Mean pairwise identity	65.55
Shannon entropy	0.56027
G+C content	0.44821
Mean single sequence MFE	-34.80
Consensus MFE	-21.27
Energy contribution	-21.15
Covariance contribution	-0.12
Combinations/Pair	1.43
Mean z-score	-2.22
Structure conservation index	0.61
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	3.07
SVM RNA-class probability	0.997282
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chrX 3343454 92 + 22422827
UUUGGCUCGACUGCUGGUGGGCCAAGGGCACAAUUGUCGAGUGUGCAAAUGAUGUACGUAUGUAUGUACA---AUGUACA--------------------ACGAACGACGACUAA
(((((((((.(....).))))))))).......((((((.(((((((.....(((((((....)))))))---.))))).--------------------))...)))))).... ( -27.70, z-score =  -1.27, R)
>droAna3.scaffold_13334 6805 105 + 1562580
UUUAGUGUUCCAAGUUGAGGGCGAAGGGCA-ACUUGGAAUGUGUGCAAAAAAAAUGAAAAAAAAAACA-----AUAUUUUUGCGUCACUUGGAAAUUU---UUUACGAUGACAG-
....(..((((((((((....(....).))-))))))))..)..(((((((.(.((..........))-----.).)))))))((((.(((.......---....)))))))..- ( -24.40, z-score =  -1.85, R)
>droSec1.super_4 2859694 115 - 6179234
UUUGGCUCGACUGGUGGAGGGCCAAGGGCACGAUUGUCGAGUGUGCAAAUGAUGUACGUAUGUGUACAUACAUAUGUACAUGCGUCACUCGCUGUUUCGAACGAACGACGACUAA
((((((((..(....)..)))))))).......((((((((((((((.....((((((((((((....)))))))))))))))).)))))...((((.....))))))))).... ( -42.30, z-score =  -2.64, R)
>droSim1.chrX_random 1456272 115 + 5698898
UUUGGCUCGACUGGUGGAGGGCCAAGGGCACGCUUGUCGAGUGUGCAAAUGAUGUACGUAUGUGUACAUACAUAUGUACAUGCGUCACUCGCUGUUUCCAACGAACGACGACUAA
((((((((..(....)..)))))))).((((((((...)))))))).....(((((((((((((....))))))))))))).((((..(((.((....)).)))..))))..... ( -44.80, z-score =  -3.11, R)
>consensus
UUUGGCUCGACUGGUGGAGGGCCAAGGGCACAAUUGUCGAGUGUGCAAAUGAUGUACGUAUGUAUACAUA___AUGUACAUGCGUCACUCGCUGUUUC__ACGAACGACGACUAA
.((((((((((.((((....((.....)).)))).))))))).........((((((((((((......))))))))))))...........................))).... (-21.27 = -21.15 +  -0.12)

alignment

secondary structure

dotplot

Window 7

Location	3,343,454 – 3,343,546
Length	92
Sequences	4
Columns	115
Reading direction	reverse
Mean pairwise identity	65.55
Shannon entropy	0.56027
G+C content	0.44821
Mean single sequence MFE	-27.64
Consensus MFE	-10.40
Energy contribution	-9.09
Covariance contribution	-1.31
Combinations/Pair	1.60
Mean z-score	-2.18
Structure conservation index	0.38
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	1.25
SVM RNA-class probability	0.916241
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chrX 3343454 92 - 22422827
UUAGUCGUCGUUCGU--------------------UGUACAU---UGUACAUACAUACGUACAUCAUUUGCACACUCGACAAUUGUGCCCUUGGCCCACCAGCAGUCGAGCCAAA
......(((((..((--------------------(((((..---.))))).))..))).))............((((((..(((.(((...)))....)))..))))))..... ( -18.30, z-score =  -0.27, R)
>droAna3.scaffold_13334 6805 105 - 1562580
-CUGUCAUCGUAAA---AAAUUUCCAAGUGACGCAAAAAUAU-----UGUUUUUUUUUUCAUUUUUUUUGCACACAUUCCAAGU-UGCCCUUCGCCCUCAACUUGGAACACUAAA
-.............---.........((((..(((((((...-----((..........))...))))))).....((((((((-((...........))))))))))))))... ( -21.20, z-score =  -3.25, R)
>droSec1.super_4 2859694 115 + 6179234
UUAGUCGUCGUUCGUUCGAAACAGCGAGUGACGCAUGUACAUAUGUAUGUACACAUACGUACAUCAUUUGCACACUCGACAAUCGUGCCCUUGGCCCUCCACCAGUCGAGCCAAA
...(.(((((((((((......)))))))))))).(((.((.(((.((((((......))))))))).)).)))((((((......(((...))).........))))))..... ( -31.66, z-score =  -1.82, R)
>droSim1.chrX_random 1456272 115 - 5698898
UUAGUCGUCGUUCGUUGGAAACAGCGAGUGACGCAUGUACAUAUGUAUGUACACAUACGUACAUCAUUUGCACACUCGACAAGCGUGCCCUUGGCCCUCCACCAGUCGAGCCAAA
...(.((((((((((((....)))))))))))))((((((.(((((......))))).)))))).....((((.((.....)).))))..(((((.(..(....)..).))))). ( -39.40, z-score =  -3.37, R)
>consensus
UUAGUCGUCGUUCGU__GAAACAGCGAGUGACGCAUGUACAU___UAUGUACACAUACGUACAUCAUUUGCACACUCGACAAGCGUGCCCUUGGCCCUCCACCAGUCGAGCCAAA
...................................(((((((....))))))).....................((((((......((.....)).........))))))..... (-10.40 =  -9.09 +  -1.31)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 01:11:29 2011