Locus 13773

Sequence ID	dm3.chrX
Location	9,105,125 – 9,105,232
Length	107
Max. P	0.775702

overview

Window 9

Location	9,105,125 – 9,105,232
Length	107
Sequences	7
Columns	114
Reading direction	forward
Mean pairwise identity	72.40
Shannon entropy	0.49344
G+C content	0.51690
Mean single sequence MFE	-33.29
Consensus MFE	-20.13
Energy contribution	-19.86
Covariance contribution	-0.27
Combinations/Pair	1.43
Mean z-score	-1.07
Structure conservation index	0.60
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	0.36
SVM RNA-class probability	0.658850
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chrX 9105125 107 + 22422827
AGUUGAAUGUACGAAUGAAAUGGAUGGAUGGAUGCUUGUCGGGCGGCGGAUGUACA----GAUAUCCGCACAUCCGAAACGAGUGUUCAAA-AUUGUCGGCACACAC--GGAUC
...........((..((...(.((..(.((((((((((((((..(((((((((...----.)))))))).)..))))..))))))))))..-.)..)).)..))..)--).... ( -31.40, z-score =  -0.86, R)
>dp4.chrXL_group1a 2170380 98 - 9151740
------ACGAGCGGACGGGCCGGACGGACGA---CUUGUCGGCUGGCGGAUGUACAUGCAGGCAUCUGUACAUUCUAGAUGUAUCCACGUAUGUUGUUCAUACAAAU-------
------....(.(((...(((((.(.(((..---...))).))))))(((((((((((....))..)))))))))........))).)(((((.....)))))....------- ( -31.70, z-score =  -0.98, R)
>droPer1.super_25 307585 98 + 1448063
------ACGAGCGGACGGGCCGGACGGACGA---CUUGUCGGCUGGCGGAUGUACAUGCAGGCAUCUGUACAUUCUAGAUGUAUCCACGUAUGUUGUUCAUACAAAU-------
------....(.(((...(((((.(.(((..---...))).))))))(((((((((((....))..)))))))))........))).)(((((.....)))))....------- ( -31.70, z-score =  -0.98, R)
>droSim1.chrX 7262399 108 + 17042790
AGUUGAAUGUACGGACGAA-UGGAUGGAUGGAUGCUUGUCGGGCGGCGGAUGUACA----GAUAUCCGCACAUCCGAAACGAGUGUUCAAA-AUUGUCGGCACACACACGGAUC
.((.(..(((.(.(((((.-........((((((((((((((..(((((((((...----.)))))))).)..))))..))))))))))..-.))))).).)))..)))..... ( -33.50, z-score =  -0.97, R)
>droSec1.super_345 6814 108 + 13804
AGUUGAAUGUACGGACGAA-UGGAUGGAUGGAUGCUUGUCGGGCGGCGGAUGUACA----GAUAUCCGCACAUCCGAAACGAGUGUUCAAA-AUUGUCGGCACACACACGGAUC
.((.(..(((.(.(((((.-........((((((((((((((..(((((((((...----.)))))))).)..))))..))))))))))..-.))))).).)))..)))..... ( -33.50, z-score =  -0.97, R)
>droYak2.chrX 17702181 102 + 21770863
AGUUGAAUGUACGGAC-----GGAUGGAUGGCUGCUUGUCGGGCGGCGGAUGUACA----GAUAUCCGCACAUCCGAAACAAGUGUUCAAA-AUUGUCGGCACACAC--GGAUC
..(((..(((.(.(((-----((.(((((....(((((((((..(((((((((...----.)))))))).)..))))..))))))))))..-.))))).).)))..)--))... ( -31.70, z-score =  -0.88, R)
>droEre2.scaffold_4690 12737576 103 - 18748788
AGUUGAAUGCACGAGC-----GGAUGGAUGGCUGCUUGUCGGACGGCGGAUGUACA----GAUAUCCGCACAUCCGAAACGAGUGUUCGAGUGUUGUCGGCACACAC--GGAUC
..((((((((.(((((-----((........)))))))(((((.(((((((((...----.)))))))).).))))).....))))))))((((((....)).))))--..... ( -39.50, z-score =  -1.88, R)
>consensus
AGUUGAAUGUACGGACGAA_UGGAUGGAUGGAUGCUUGUCGGGCGGCGGAUGUACA____GAUAUCCGCACAUCCGAAACGAGUGUUCAAA_AUUGUCGGCACACAC__GGAUC
......................(((((.(((.(((((((((((.(((((((((........)))))))).).))))..))))))).)))....)))))................ (-20.13 = -19.86 +  -0.27)

alignment

secondary structure

dotplot

Window 0

Location	9,105,125 – 9,105,232
Length	107
Sequences	7
Columns	114
Reading direction	reverse
Mean pairwise identity	72.40
Shannon entropy	0.49344
G+C content	0.51690
Mean single sequence MFE	-29.29
Consensus MFE	-14.14
Energy contribution	-14.31
Covariance contribution	0.17
Combinations/Pair	1.40
Mean z-score	-1.70
Structure conservation index	0.48
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	0.65
SVM RNA-class probability	0.775702
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chrX 9105125 107 - 22422827
GAUCC--GUGUGUGCCGACAAU-UUUGAACACUCGUUUCGGAUGUGCGGAUAUC----UGUACAUCCGCCGCCCGACAAGCAUCCAUCCAUCCAUUUCAUUCGUACAUUCAACU
((..(--(.((((..(((....-.))).)))).))..))((((((((((....)----)))))))))...((.......))................................. ( -26.50, z-score =  -1.45, R)
>dp4.chrXL_group1a 2170380 98 + 9151740
-------AUUUGUAUGAACAACAUACGUGGAUACAUCUAGAAUGUACAGAUGCCUGCAUGUACAUCCGCCAGCCGACAAG---UCGUCCGUCCGGCCCGUCCGCUCGU------
-------....(((((.....)))))((((((.......(.(((((((..((....))))))))).)(((.((.(((...---..))).))..)))..))))))....------ ( -27.10, z-score =  -1.18, R)
>droPer1.super_25 307585 98 - 1448063
-------AUUUGUAUGAACAACAUACGUGGAUACAUCUAGAAUGUACAGAUGCCUGCAUGUACAUCCGCCAGCCGACAAG---UCGUCCGUCCGGCCCGUCCGCUCGU------
-------....(((((.....)))))((((((.......(.(((((((..((....))))))))).)(((.((.(((...---..))).))..)))..))))))....------ ( -27.10, z-score =  -1.18, R)
>droSim1.chrX 7262399 108 - 17042790
GAUCCGUGUGUGUGCCGACAAU-UUUGAACACUCGUUUCGGAUGUGCGGAUAUC----UGUACAUCCGCCGCCCGACAAGCAUCCAUCCAUCCA-UUCGUCCGUACAUUCAACU
.....((..((((((.(((...-...............(((((((((((....)----))))))))))..((.......)).............-...))).))))))...)). ( -30.60, z-score =  -1.91, R)
>droSec1.super_345 6814 108 - 13804
GAUCCGUGUGUGUGCCGACAAU-UUUGAACACUCGUUUCGGAUGUGCGGAUAUC----UGUACAUCCGCCGCCCGACAAGCAUCCAUCCAUCCA-UUCGUCCGUACAUUCAACU
.....((..((((((.(((...-...............(((((((((((....)----))))))))))..((.......)).............-...))).))))))...)). ( -30.60, z-score =  -1.91, R)
>droYak2.chrX 17702181 102 - 21770863
GAUCC--GUGUGUGCCGACAAU-UUUGAACACUUGUUUCGGAUGUGCGGAUAUC----UGUACAUCCGCCGCCCGACAAGCAGCCAUCCAUCC-----GUCCGUACAUUCAACU
.....--(.((((((.(((...-...((((....)))).((((((((((....)----)))))))))((.((.......)).)).........-----))).)))))).).... ( -30.90, z-score =  -2.48, R)
>droEre2.scaffold_4690 12737576 103 + 18748788
GAUCC--GUGUGUGCCGACAACACUCGAACACUCGUUUCGGAUGUGCGGAUAUC----UGUACAUCCGCCGUCCGACAAGCAGCCAUCCAUCC-----GCUCGUGCAUUCAACU
((..(--(.((((..(((......))).)))).))..))((((((((((....)----)))))))))((((..((.................)-----)..)).))........ ( -32.23, z-score =  -1.79, R)
>consensus
GAUCC__GUGUGUGCCGACAAU_UUUGAACACUCGUUUCGGAUGUGCGGAUAUC____UGUACAUCCGCCGCCCGACAAGCAUCCAUCCAUCCA_UUCGUCCGUACAUUCAACU
.........((((((.(((.......((....)).....(((((((((..........)))))))))...............................))).))))))...... (-14.14 = -14.31 +   0.17)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 01:27:32 2011