Locus 14989

Sequence ID	dm3.chrX
Location	16,836,551 – 16,836,622
Length	71
Max. P	0.990939

overview

Window 5

Location	16,836,551 – 16,836,622
Length	71
Sequences	11
Columns	72
Reading direction	forward
Mean pairwise identity	87.28
Shannon entropy	0.27168
G+C content	0.52196
Mean single sequence MFE	-27.87
Consensus MFE	-24.18
Energy contribution	-23.54
Covariance contribution	-0.64
Combinations/Pair	1.22
Mean z-score	-2.49
Structure conservation index	0.87
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	2.45
SVM RNA-class probability	0.990939
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chrX 16836551 71 + 22422827
UGAUGGCCUCCAGUUUGG-CGUAGUAGUGCCGCUCAUUGGAGCUCGAGAUCUCGCUGGUGGCCAUUGUAGAU
.(((((((.(((((..((-((......))))((((....))))..........))))).)))))))...... ( -30.50, z-score =  -2.88, R)
>droSim1.chrX_random 4373015 72 + 5698898
UGAUGGCCUCCAGUUUGGGCGUAGUAGUGCCGCUCAUUGGAGCUCGAGAUCUCGCUGGUGGCCAUUGUAGAU
.(((((((.(((((..(((((......))))((((....)))).......)..))))).)))))))...... ( -30.80, z-score =  -2.62, R)
>droSec1.super_17 670243 71 + 1527944
UGAUGGCUUCCAGUUUGG-CGUAGUAGUGCCGCUCAUUGGAGCUCGAGAUCUCGCUGGUGGCCAUUAUAGAU
((((((((.(((((..((-((......))))((((....))))..........))))).))))))))..... ( -28.60, z-score =  -2.59, R)
>droYak2.chrX 15446848 71 + 21770863
UGAUGGCCUCCAGUUUGG-CGUAGUAGUGGCGCUCAUUGGAGCUCGAGAUCUCGCUGGUGGCCAUUGUAGAU
.(((((((.(((.....(-((..((..(((.((((....)))))))..))..)))))).)))))))...... ( -27.00, z-score =  -1.56, R)
>droEre2.scaffold_4690 7190400 71 + 18748788
UGAUGGCCUCCAGUUUGG-CAUAGUAGUGACGCUCAUUGGAGCUCGAUAUCUCGCUGGUGGCCAUUGUAGAU
.(((((((.(((((..((-.(((....(((.((((....))))))).))))).))))).)))))))...... ( -27.90, z-score =  -2.53, R)
>droAna3.scaffold_13334 976533 67 - 1562580
UGAUGGCUUCCAGCUUGG-CGUAGUAGUGGCGCUCGUUGGAGCUGGAAAUCUCGCUGGUGGCCAUUUU----
.(((((((.(((((..((-(((.......))))).....(((.(....).)))))))).)))))))..---- ( -27.10, z-score =  -2.16, R)
>dp4.chrXL_group3b 152235 71 - 386183
UGAUGGCCUCUAGCUUGG-CAUAGUAGUGUCGCUCGUUGGAGCUGGAUAUCUCGCUGGUGGCCAUUUUGUGU
.(((((((.(((((..((-(((....)))))((((....))))..........))))).)))))))...... ( -29.60, z-score =  -3.13, R)
>droPer1.super_56 171143 71 - 431378
UGAUGGCUUCUAGCUUGG-CAUAGUAGUGUCGCUCGUUGGAGCUGGAUAUCUCGCUGGUGGCCAUUUUGUGU
.(((((((.(((((..((-(((....)))))((((....))))..........))))).)))))))...... ( -27.00, z-score =  -2.59, R)
>droWil1.scaffold_181150 328952 71 - 4952429
UAAUGGCUUCUAGCUUGG-CAUAGUAGUGGCGCUCAUUGGAGCUGGAUAUCUCGCUGGUGGCCAUUUUUACC
.(((((((.(((((..(.-(((....))).)((((....))))..........))))).)))))))...... ( -24.50, z-score =  -1.68, R)
>droVir3.scaffold_12970 5413775 71 - 11907090
UAAUUGCCUCCAGCUUGG-CGUAAUAGUGCCGCUCGUUGGAGCUAGAAAUCUCGCUGGUGGCCAUUUUGAAU
.....(((.(((((..((-((......))))((((....))))..........))))).))).......... ( -25.80, z-score =  -2.57, R)
>droGri2.scaffold_14853 5998449 71 + 10151454
UGAUUGCCUCCAGCUUGG-CAUAAUAAUGCCGCUCGUUGGAGCUGGAAAUCUCGCUGGUGGCCAUUUUGUAU
.(((.(((.(((((..((-(((....)))))((((....))))..........))))).))).)))...... ( -27.80, z-score =  -3.08, R)
>consensus
UGAUGGCCUCCAGCUUGG_CGUAGUAGUGCCGCUCAUUGGAGCUCGAGAUCUCGCUGGUGGCCAUUUUAGAU
.(((((((.(((((.................((((....))))..((....))))))).)))))))...... (-24.18 = -23.54 +  -0.64)

alignment

secondary structure

dotplot

Window 6

Location	16,836,551 – 16,836,622
Length	71
Sequences	11
Columns	72
Reading direction	reverse
Mean pairwise identity	87.28
Shannon entropy	0.27168
G+C content	0.52196
Mean single sequence MFE	-22.45
Consensus MFE	-9.08
Energy contribution	-9.26
Covariance contribution	0.18
Combinations/Pair	1.00
Mean z-score	-3.11
Structure conservation index	0.40
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	0.60
SVM RNA-class probability	0.756518
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chrX 16836551 71 - 22422827
AUCUACAAUGGCCACCAGCGAGAUCUCGAGCUCCAAUGAGCGGCACUACUACG-CCAAACUGGAGGCCAUCA
.......((((((.(((((((....))).((((....))))(((........)-))...)))).)))))).. ( -27.40, z-score =  -4.09, R)
>droSim1.chrX_random 4373015 72 - 5698898
AUCUACAAUGGCCACCAGCGAGAUCUCGAGCUCCAAUGAGCGGCACUACUACGCCCAAACUGGAGGCCAUCA
.......((((((.(((((((....))).((((....))))(((........)))....)))).)))))).. ( -26.50, z-score =  -3.67, R)
>droSec1.super_17 670243 71 - 1527944
AUCUAUAAUGGCCACCAGCGAGAUCUCGAGCUCCAAUGAGCGGCACUACUACG-CCAAACUGGAAGCCAUCA
.......(((((..(((((((....))).((((....))))(((........)-))...))))..))))).. ( -23.20, z-score =  -3.10, R)
>droYak2.chrX 15446848 71 - 21770863
AUCUACAAUGGCCACCAGCGAGAUCUCGAGCUCCAAUGAGCGCCACUACUACG-CCAAACUGGAGGCCAUCA
.......((((((.(((((((....))).((((....))))............-.....)))).)))))).. ( -23.20, z-score =  -3.07, R)
>droEre2.scaffold_4690 7190400 71 - 18748788
AUCUACAAUGGCCACCAGCGAGAUAUCGAGCUCCAAUGAGCGUCACUACUAUG-CCAAACUGGAGGCCAUCA
.......((((((.(((((((....))).((((....))))............-.....)))).)))))).. ( -23.10, z-score =  -2.94, R)
>droAna3.scaffold_13334 976533 67 + 1562580
----AAAAUGGCCACCAGCGAGAUUUCCAGCUCCAACGAGCGCCACUACUACG-CCAAGCUGGAAGCCAUCA
----...(((((..(((((..........((((....))))((.........)-)...)))))..))))).. ( -20.80, z-score =  -3.10, R)
>dp4.chrXL_group3b 152235 71 + 386183
ACACAAAAUGGCCACCAGCGAGAUAUCCAGCUCCAACGAGCGACACUACUAUG-CCAAGCUAGAGGCCAUCA
.......((((((.(.(((((....))..((((....))))............-....))).).)))))).. ( -18.50, z-score =  -2.78, R)
>droPer1.super_56 171143 71 + 431378
ACACAAAAUGGCCACCAGCGAGAUAUCCAGCUCCAACGAGCGACACUACUAUG-CCAAGCUAGAAGCCAUCA
.......(((((..(.(((((....))..((((....))))............-....))).)..))))).. ( -14.30, z-score =  -1.92, R)
>droWil1.scaffold_181150 328952 71 + 4952429
GGUAAAAAUGGCCACCAGCGAGAUAUCCAGCUCCAAUGAGCGCCACUACUAUG-CCAAGCUAGAAGCCAUUA
......((((((..(.(((((....))..((((....))))............-....))).)..)))))). ( -15.70, z-score =  -0.84, R)
>droVir3.scaffold_12970 5413775 71 + 11907090
AUUCAAAAUGGCCACCAGCGAGAUUUCUAGCUCCAACGAGCGGCACUAUUACG-CCAAGCUGGAGGCAAUUA
..........(((.(((((..........((((....))))(((........)-))..))))).)))..... ( -25.90, z-score =  -3.89, R)
>droGri2.scaffold_14853 5998449 71 - 10151454
AUACAAAAUGGCCACCAGCGAGAUUUCCAGCUCCAACGAGCGGCAUUAUUAUG-CCAAGCUGGAGGCAAUCA
..........(((.(((((..........((((....))))(((((....)))-))..))))).)))..... ( -28.40, z-score =  -4.79, R)
>consensus
AUCUAAAAUGGCCACCAGCGAGAUAUCCAGCUCCAAUGAGCGGCACUACUACG_CCAAGCUGGAGGCCAUCA
.......(((((.......((....))..((((....))))........................))))).. ( -9.08 =  -9.26 +   0.18)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 01:50:55 2011