Locus 3891

Sequence ID	dm3.chr2R
Location	8,707,420 – 8,707,522
Length	102
Max. P	0.900005

overview

Window 4

Location	8,707,420 – 8,707,522
Length	102
Sequences	4
Columns	103
Reading direction	forward
Mean pairwise identity	63.81
Shannon entropy	0.55814
G+C content	0.47943
Mean single sequence MFE	-26.25
Consensus MFE	-14.04
Energy contribution	-14.35
Covariance contribution	0.31
Combinations/Pair	1.28
Mean z-score	-1.41
Structure conservation index	0.53
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	1.15
SVM RNA-class probability	0.900005
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 8707420 102 + 21146708
GAGCCAGGAGAAUUACGCUCC-CAACUCCGCGCCAGCUGUGCAGUUGUUUCCCCUAACCUGGAAGGUAUGCCAACUCAAUCUACGGUCUCCAGCUUAAUGGUG
..((((((((.......))))-(((((..((((.....))))))))).......(((.(((((.((....))........(....)..))))).))).)))). ( -24.00, z-score =   0.47, R)
>droYak2.chrU 8888297 92 - 28119190
ACUCCAGCAGAGAUACGAGCUAUGAUUGCCUCAAGGCAAUACGAUUCUCUUGGCCUUUCGGCAAUGCAAAUCUUGGUAAAACCAGCUCUGCU-----------
.....(((((((..........((((((((..(((((...............)))))..)))))).))....((((.....)))))))))))----------- ( -27.26, z-score =  -1.92, R)
>droSec1.super_1989 542 90 - 3922
ACUCCAGCAGAGAUACGAGCCAUGAUUGCCUCAAGGCAAUACGAUUCUUUUGGCCUUUCA-CAAGG-AAGUCUUGGUAAAACCAGCUCUGCU-----------
.....(((((((......((((..((((((....))))))..((((..((((........-)))).-.)))).))))........)))))))----------- ( -27.04, z-score =  -2.05, R)
>droSim1.chr2L 20995066 90 + 22036055
ACUCCAGCAGAGAUACGAGCUAUGAUUGCCUCAAGGCAAUAAGAUUCUUUUGGCCUUUCA-CAAAG-AAGUCUUGGUAACACCAGCUCUGCU-----------
.....(((((((............((((((....))))))((((((..((((........-)))).-.))))))((.....))..)))))))----------- ( -26.70, z-score =  -2.12, R)
>consensus
ACUCCAGCAGAGAUACGAGCCAUGAUUGCCUCAAGGCAAUACGAUUCUUUUGGCCUUUCA_CAAGG_AAGUCUUGGUAAAACCAGCUCUGCU___________
......((((((............((((((....))))))..((((......((......))......)))).............))))))............ (-14.04 = -14.35 +   0.31)

alignment

secondary structure

dotplot

Window 5

Location	8,707,420 – 8,707,522
Length	102
Sequences	4
Columns	103
Reading direction	reverse
Mean pairwise identity	63.81
Shannon entropy	0.55814
G+C content	0.47943
Mean single sequence MFE	-29.70
Consensus MFE	-16.30
Energy contribution	-14.86
Covariance contribution	-1.44
Combinations/Pair	1.47
Mean z-score	-1.31
Structure conservation index	0.55
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	1.11
SVM RNA-class probability	0.893000
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 8707420 102 - 21146708
CACCAUUAAGCUGGAGACCGUAGAUUGAGUUGGCAUACCUUCCAGGUUAGGGGAAACAACUGCACAGCUGGCGCGGAGUUG-GGAGCGUAAUUCUCCUGGCUC
..(((......)))...((((....(.((((((((..(((........)))(....)...))).))))).).))))(((..-((((.......))))..))). ( -29.70, z-score =   0.37, R)
>droYak2.chrU 8888297 92 + 28119190
-----------AGCAGAGCUGGUUUUACCAAGAUUUGCAUUGCCGAAAGGCCAAGAGAAUCGUAUUGCCUUGAGGCAAUCAUAGCUCGUAUCUCUGCUGGAGU
-----------(((((((.(((.....))).....(((...(((....)))...(((....(.((((((....)))))))....)))))).)))))))..... ( -31.40, z-score =  -2.15, R)
>droSec1.super_1989 542 90 + 3922
-----------AGCAGAGCUGGUUUUACCAAGACUU-CCUUG-UGAAAGGCCAAAAGAAUCGUAUUGCCUUGAGGCAAUCAUGGCUCGUAUCUCUGCUGGAGU
-----------(((((((.(((((((.(((((....-.))))-.).)))))))...((..(((((((((....)))))).)))..))....)))))))..... ( -32.30, z-score =  -2.75, R)
>droSim1.chr2L 20995066 90 - 22036055
-----------AGCAGAGCUGGUGUUACCAAGACUU-CUUUG-UGAAAGGCCAAAAGAAUCUUAUUGCCUUGAGGCAAUCAUAGCUCGUAUCUCUGCUGGAGU
-----------(((((((.(((.((((..((((.((-((((.-((......))))))))))))((((((....))))))..)))).).)).)))))))..... ( -25.40, z-score =  -0.71, R)
>consensus
___________AGCAGAGCUGGUUUUACCAAGACUU_CCUUG_UGAAAGGCCAAAAGAAUCGUAUUGCCUUGAGGCAAUCAUAGCUCGUAUCUCUGCUGGAGU
............((((((.(((.....))).........(((((..(((((...............)))))..))))).............))))))...... (-16.30 = -14.86 +  -1.44)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:18:47 2011