Locus 9688

Sequence ID	dm3.chr3R
Location	8,269,508 – 8,269,641
Length	133
Max. P	0.997126

overview

Window 0

Location	8,269,508 – 8,269,641
Length	133
Sequences	6
Columns	136
Reading direction	forward
Mean pairwise identity	79.50
Shannon entropy	0.38826
G+C content	0.44632
Mean single sequence MFE	-28.72
Consensus MFE	-16.83
Energy contribution	-17.61
Covariance contribution	0.78
Combinations/Pair	1.14
Mean z-score	-2.10
Structure conservation index	0.59
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	1.25
SVM RNA-class probability	0.915718
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 8269508 133 + 27905053
CUUAUUAGAUAUGGCCAAAGUCCCCCCGUAUAGAGUCUAG-ACAU--AUCAAAUCUAACCCUGACCUCAGCAAUGGGCAAAUAAAACCGCCCAUUUGGCCAACAUCUACCACAUCUAAUCUGCUAAUGAGAAUACA
((((((((...((((((((.............(((..(((-....--.............)))..))).....(((((..........)))))))))))))..........((.......))))))))))...... ( -28.33, z-score =  -2.36, R)
>droSim1.chr3R 14397406 133 - 27517382
CCGAUUAGAUACGGCCAAAGUCCCCCCGUCUAGAGUCUAG-ACAU--AUCAAAUCUAACCCUGACCUCAGCAAUGGGCAAAUAAAACCGCCCAUUUGGCCAACAUCUACCACAUCUAAUCUGCUAAUGAGAAUACG
..((((((((..(((((((........((((((...))))-))..--.............(((....)))...(((((..........))))))))))))............))))))))................ ( -31.04, z-score =  -3.40, R)
>droSec1.super_0 7442769 133 - 21120651
UCGAUUACAUGCGGCCAAAGUCCCCCCGUCUAGAGUCUAG-ACAU--AUGAAAUCUAACCCUGACCUCAGCAAUGGGCAAAUAAAACCGCCCAUUUGGCCAACAUCUACCACAUCUAAUCUGCUAAUGAGAAUACG
..(((((.(((.(((((((........((((((...))))-))..--.............(((....)))...(((((..........))))))))))))...........))).)))))................ ( -27.80, z-score =  -1.86, R)
>droYak2.chr3R 12592908 132 + 28832112
CCGAUUAGAUAGGGCUAAAGUCUCUUCGUCUAUAGUCUAG-ACAU--AUCAAAUCUAACCCUGACCUCAGCAAUGGGCAAAUAAAAUCGCCCAACUGGCCAACAUCUACCACAUCUAAUCUGCUAAUGAGAGGCC-
..((((.((((((((....))))....(((((.....)))-)).)--))).)))).........((((((((.(((((..........)))))..(((..........))).........)))).....))))..- ( -27.80, z-score =  -0.78, R)
>droEre2.scaffold_4770 4395124 119 - 17746568
CUGAUUAGAUAGGGCCAAAGUCUCCC-GUCUAGAGUCUAG-ACGU--AUAAAAUCUAACCCUGACC-CAGCAAUGGGCAAAUAAAAUCGCCCAACUGGCUAACAUCUACCACCUCUAAUCUGCC------------
..((((((((((((...........(-((((((...))))-))).--...........)))))..(-(((...(((((..........))))).))))...............)))))))....------------ ( -32.10, z-score =  -3.41, R)
>droAna3.scaffold_13340 7651433 121 + 23697760
GCGAUAAGAU-UGGACAAUGUCUUCUUGUCUAGACCGCAGCACAACAGCCAAUAUUAACCCUGACCUUAGCAAUAGGCAAAU-----CGCCAAACUGGCAAAC-UGGCCAACAUCUAAUCUGCAAAUA--------
..(((((((.-.((((...)))))))))))......((((.......((((..........((.(((.......)))))...-----.(((.....)))....-))))...........)))).....-------- ( -25.27, z-score =  -0.80, R)
>consensus
CCGAUUAGAUACGGCCAAAGUCCCCCCGUCUAGAGUCUAG_ACAU__AUCAAAUCUAACCCUGACCUCAGCAAUGGGCAAAUAAAACCGCCCAACUGGCCAACAUCUACCACAUCUAAUCUGCUAAUGAGAAUAC_
..((((((((..(((((...........................................(((....)))...(((((..........)))))..)))))............))))))))................ (-16.83 = -17.61 +   0.78)

alignment

secondary structure

dotplot

Window 1

Location	8,269,508 – 8,269,641
Length	133
Sequences	6
Columns	136
Reading direction	reverse
Mean pairwise identity	79.50
Shannon entropy	0.38826
G+C content	0.44632
Mean single sequence MFE	-44.78
Consensus MFE	-29.86
Energy contribution	-31.39
Covariance contribution	1.53
Combinations/Pair	1.22
Mean z-score	-2.97
Structure conservation index	0.67
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	3.04
SVM RNA-class probability	0.997126
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 8269508 133 - 27905053
UGUAUUCUCAUUAGCAGAUUAGAUGUGGUAGAUGUUGGCCAAAUGGGCGGUUUUAUUUGCCCAUUGCUGAGGUCAGGGUUAGAUUUGAU--AUGU-CUAGACUCUAUACGGGGGGACUUUGGCCAUAUCUAAUAAG
.................((((((((((((.(((.(..((..(((((((((......)))))))))))..).)))((((((((((.....--..))-)).))))))....(((....)))..))))))))))))... ( -46.80, z-score =  -3.53, R)
>droSim1.chr3R 14397406 133 + 27517382
CGUAUUCUCAUUAGCAGAUUAGAUGUGGUAGAUGUUGGCCAAAUGGGCGGUUUUAUUUGCCCAUUGCUGAGGUCAGGGUUAGAUUUGAU--AUGU-CUAGACUCUAGACGGGGGGACUUUGGCCGUAUCUAAUCGG
................(((((((((((((.(((.(..((..(((((((((......)))))))))))..).)))((((((((((.....--..))-)).))))))....(((....)))..))))))))))))).. ( -47.10, z-score =  -3.18, R)
>droSec1.super_0 7442769 133 + 21120651
CGUAUUCUCAUUAGCAGAUUAGAUGUGGUAGAUGUUGGCCAAAUGGGCGGUUUUAUUUGCCCAUUGCUGAGGUCAGGGUUAGAUUUCAU--AUGU-CUAGACUCUAGACGGGGGGACUUUGGCCGCAUGUAAUCGA
................(((((.((((....(((.(..((..(((((((((......)))))))))))..).)))..(((((((.(((..--.(((-((((...)))))))...))).))))))))))).))))).. ( -48.30, z-score =  -3.40, R)
>droYak2.chr3R 12592908 132 - 28832112
-GGCCUCUCAUUAGCAGAUUAGAUGUGGUAGAUGUUGGCCAGUUGGGCGAUUUUAUUUGCCCAUUGCUGAGGUCAGGGUUAGAUUUGAU--AUGU-CUAGACUAUAGACGAAGAGACUUUAGCCCUAUCUAAUCGG
-...............((((((((......(((.(..((....(((((((......)))))))..))..).)))(((((((((.((..(--.(((-(((.....)))))).)..)).))))))))))))))))).. ( -47.30, z-score =  -3.42, R)
>droEre2.scaffold_4770 4395124 119 + 17746568
------------GGCAGAUUAGAGGUGGUAGAUGUUAGCCAGUUGGGCGAUUUUAUUUGCCCAUUGCUG-GGUCAGGGUUAGAUUUUAU--ACGU-CUAGACUCUAGAC-GGGAGACUUUGGCCCUAUCUAAUCAG
------------....(((((((...............((((((((((((......)))))))..))))-)...(((((((((.(((..--.(((-((((...))))))-)..))).))))))))).))))))).. ( -47.60, z-score =  -4.48, R)
>droAna3.scaffold_13340 7651433 121 - 23697760
--------UAUUUGCAGAUUAGAUGUUGGCCA-GUUUGCCAGUUUGGCG-----AUUUGCCUAUUGCUAAGGUCAGGGUUAAUAUUGGCUGUUGUGCUGCGGUCUAGACAAGAAGACAUUGUCCA-AUCUUAUCGC
--------.......(((((.((((((((((.-....(((...((((((-----((......)))))))))))...))))))))))((((((......))))))..(((((.......))))).)-))))...... ( -31.60, z-score =   0.17, R)
>consensus
_GUAUUCUCAUUAGCAGAUUAGAUGUGGUAGAUGUUGGCCAAAUGGGCGGUUUUAUUUGCCCAUUGCUGAGGUCAGGGUUAGAUUUGAU__AUGU_CUAGACUCUAGACGGGGAGACUUUGGCCAUAUCUAAUCGG
................(((((((((((((.(((.(((((.((.(((((((......)))))))))))))).)))((((((...................))))))................))))))))))))).. (-29.86 = -31.39 +   1.53)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 00:09:12 2011