Locus 12533

Sequence ID	dm3.chrX
Location	778,673 – 778,803
Length	130
Max. P	0.994719

overview

Window 3

Location	778,673 – 778,774
Length	101
Sequences	4
Columns	103
Reading direction	forward
Mean pairwise identity	75.25
Shannon entropy	0.38642
G+C content	0.51918
Mean single sequence MFE	-30.70
Consensus MFE	-24.14
Energy contribution	-24.32
Covariance contribution	0.19
Combinations/Pair	1.10
Mean z-score	-1.08
Structure conservation index	0.79
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	0.54
SVM RNA-class probability	0.733830
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chrX 778673 101 + 22422827
CUUUCGCCAAUUUCCCGAGUGGGAAAUUCGGUUCGAAGGACCAAGGUCCUUCAGGUGGGACUUUUUCGAACGACGAACGUG--UUUUUUGGCGAGCAUUCGAG
..((((((((((((((....))))))....(((((((((((....)))))))..((.(..(......)..).))))))...--....))))))))........ ( -36.30, z-score =  -1.80, R)
>droSim1.chrX 625208 103 + 17042790
CUUUCGCCAAUUUCCCGAGUGGGAAAAUCGGUUCGAAGGACCAAGGUCCUUCUGGUGGGACUUUUUCAAACGAUGAGCGUGCGUUCUUGGGCAAACAUUCGAG
.(..(((((.((((((....))))))........(((((((....))))))))))))..)..........(((......(((.(....).))).....))).. ( -33.10, z-score =  -0.90, R)
>droYak2.chrX 697492 80 + 21770863
CUUUCGGCAAUUUCCCGAGUGGGAAAAUCGCUUCGCAGGACCAAGGUCCUUCAGGUGGGACUUUUUCGAACGACGACGAG-----------------------
..(((((.((..((((((((((.....)))))).(.(((((....))))).)....))))..)).)))))..........----------------------- ( -23.50, z-score =   0.01, R)
>droEre2.scaffold_4644 741442 85 + 2521924
CUUUCAGCAAUUUCCCGAGUGGGAAAAUCGCUGCGAAGGACCAAGGUCCUUCAGGUGGGACUUUUUCGAACGGCGAGCAAUCGAG------------------
......((..((((((....)))))).((((((.(((((((....)))))))...((..(...)..))..)))))))).......------------------ ( -29.90, z-score =  -1.64, R)
>consensus
CUUUCGCCAAUUUCCCGAGUGGGAAAAUCGCUUCGAAGGACCAAGGUCCUUCAGGUGGGACUUUUUCGAACGACGAGCAUG__UU__________________
.(..((((..((((((....))))))........(((((((....))))))).))))..).....(((.....)))........................... (-24.14 = -24.32 +   0.19)

alignment

secondary structure

dotplot

Window 4

Location	778,673 – 778,774
Length	101
Sequences	4
Columns	103
Reading direction	reverse
Mean pairwise identity	75.25
Shannon entropy	0.38642
G+C content	0.51918
Mean single sequence MFE	-29.67
Consensus MFE	-25.17
Energy contribution	-24.55
Covariance contribution	-0.62
Combinations/Pair	1.14
Mean z-score	-2.38
Structure conservation index	0.85
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	2.73
SVM RNA-class probability	0.994719
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chrX 778673 101 - 22422827
CUCGAAUGCUCGCCAAAAAA--CACGUUCGUCGUUCGAAAAAGUCCCACCUGAAGGACCUUGGUCCUUCGAACCGAAUUUCCCACUCGGGAAAUUGGCGAAAG
.........(((((((....--...(((((..((((((.....))......(((((((....))))))))))))))))(((((....))))).)))))))... ( -34.80, z-score =  -3.51, R)
>droSim1.chrX 625208 103 - 17042790
CUCGAAUGUUUGCCCAAGAACGCACGCUCAUCGUUUGAAAAAGUCCCACCAGAAGGACCUUGGUCCUUCGAACCGAUUUUCCCACUCGGGAAAUUGGCGAAAG
..(((..((.(((........))).))...)))((((..............(((((((....)))))))...((((((((((.....)))))))))))))).. ( -29.30, z-score =  -1.45, R)
>droYak2.chrX 697492 80 - 21770863
-----------------------CUCGUCGUCGUUCGAAAAAGUCCCACCUGAAGGACCUUGGUCCUGCGAAGCGAUUUUCCCACUCGGGAAAUUGCCGAAAG
-----------------------....(((((((..((..((((((........))).)))..))..)))).((((((((((.....)))))))))))))... ( -23.80, z-score =  -1.23, R)
>droEre2.scaffold_4644 741442 85 - 2521924
------------------CUCGAUUGCUCGCCGUUCGAAAAAGUCCCACCUGAAGGACCUUGGUCCUUCGCAGCGAUUUUCCCACUCGGGAAAUUGCUGAAAG
------------------...((((..(((.....)))...))))......(((((((....))))))).((((((((((((.....)))))))))))).... ( -30.80, z-score =  -3.32, R)
>consensus
__________________AA__CACGCUCGUCGUUCGAAAAAGUCCCACCUGAAGGACCUUGGUCCUUCGAACCGAUUUUCCCACUCGGGAAAUUGCCGAAAG
.................................((((..............(((((((....)))))))...((((.((((((....)))))))))))))).. (-25.17 = -24.55 +  -0.62)

alignment

secondary structure

dotplot

Window 5

Location	778,696 – 778,803
Length	107
Sequences	4
Columns	109
Reading direction	reverse
Mean pairwise identity	70.06
Shannon entropy	0.48026
G+C content	0.48823
Mean single sequence MFE	-22.23
Consensus MFE	-13.57
Energy contribution	-13.33
Covariance contribution	-0.25
Combinations/Pair	1.17
Mean z-score	-0.95
Structure conservation index	0.61
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	0.05
SVM RNA-class probability	0.519487
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chrX 778696 107 - 22422827
UGUACAGUCCCAAUGCUAAUAUUCCUUCGCUCGAAUGCUCGCCAAAAAA--CACGUUCGUCGUUCGAAAAAGUCCCACCUGAAGGACCUUGGUCCUUCGAACCGAAUUU
.........................((((.(((((((..((........--......)).)))))))............((((((((....))))))))...))))... ( -20.44, z-score =  -0.71, R)
>droSim1.chrX 625231 109 - 17042790
UGUACAGCCCCAAUGAUACUGUUCCUUCGCUCGAAUGUUUGCCCAAGAACGCACGCUCAUCGUUUGAAAAAGUCCCACCAGAAGGACCUUGGUCCUUCGAACCGAUUUU
.(((((.......)).))).((((.((((..(((..((.(((........))).))...)))..))))............(((((((....)))))))))))....... ( -24.10, z-score =  -1.12, R)
>droYak2.chrX 697515 87 - 21770863
GAUAUAUCCAC----UAGAUC-CACU--GCUCUCUUGCUCG---------------UCGUCGUUCGAAAAAGUCCCACCUGAAGGACCUUGGUCCUGCGAAGCGAUUUU
...........----......-....--((......))(((---------------(..((((..((..((((((........))).)))..))..)))).)))).... ( -15.90, z-score =   0.48, R)
>droEre2.scaffold_4644 741465 97 - 2521924
CGCACAGCCACGAUUUAAUUCGUACU--GUUCUCUUGCUCG----------AUUGCUCGCCGUUCGAAAAAGUCCCACCUGAAGGACCUUGGUCCUUCGCAGCGAUUUU
(((((((..((((......)))).))--)).....(((..(----------(((..(((.....)))...))))......(((((((....)))))))))))))..... ( -28.50, z-score =  -2.45, R)
>consensus
UGUACAGCCACAAUGUAAAUCUUACU__GCUCGAAUGCUCG__________CACGCUCGUCGUUCGAAAAAGUCCCACCUGAAGGACCUUGGUCCUUCGAACCGAUUUU
............................((......))..................(((.....))).((((((......(((((((....))))))).....)))))) (-13.57 = -13.33 +  -0.25)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 01:04:06 2011