Locus 5094

Sequence ID	dm3.chr2R
Location	17,733,370 – 17,733,496
Length	126
Max. P	0.656969

overview

Window 9

Location	17,733,370 – 17,733,460
Length	90
Sequences	6
Columns	95
Reading direction	forward
Mean pairwise identity	69.20
Shannon entropy	0.55745
G+C content	0.53838
Mean single sequence MFE	-22.75
Consensus MFE	-10.52
Energy contribution	-10.83
Covariance contribution	0.31
Combinations/Pair	1.59
Mean z-score	-1.20
Structure conservation index	0.46
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	0.08
SVM RNA-class probability	0.533943
Prediction	RNA
WARNING	Out of training range. z-scores are NOT reliable.

Download alignment: ClustalW | MAF

>dm3.chr2R 17733370 90 + 21146708
CCCCGUUGCAGGCACUACAGGCACU---ACUUGGCCUACAACUCCGUCUCUUUCGAAGUCUUCCGAUGGCCAUUCUAGUUGGUCA--UGACUAUG
....((((.((((....((((....---.)))))))).))))...(((....(((........)))((((((.......))))))--.))).... ( -21.90, z-score =  -0.69, R)
>droYak2.chr2R 9685158 86 - 21139217
CCCCGUUGCAGGCACUACU---------ACUUGGCCUCAAACUCCGUCUCUUUCGACGUCUUGUGUUGGCCAUUCUAGUUGGCUAGUUGGCCAUG
.....(((.((((.(....---------....))))))))....((((......))))........((((((..((((....)))).)))))).. ( -25.30, z-score =  -1.87, R)
>droEre2.scaffold_4845 11866659 95 + 22589142
CCCCGUUGCUGGCACUACUUGGCCUCAAACUCCGUCUACGUCUCCGUCUCUUUCGACGUCUUGCGAUGGCCAUUCUAGUUGGCUAGAUGGCUAUG
....(((...(((.(.....))))...)))..(((..(((((............)))))...)))((((((((.((((....)))))))))))). ( -28.20, z-score =  -2.25, R)
>droSec1.super_9 1048397 81 + 3197100
CCCCGCUGCAGGCACUACU------------UGGCCUACAACUCCGUAUCUUUCGACGUCUUCCGAUAGCCAUUUUAGUUGGCCA--UGACUAUG
..........(((((((..------------((((.(((......)))....(((........)))..))))...))))..))).--........ ( -13.90, z-score =   0.32, R)
>droSim1.chr2R 16367686 81 + 19596830
CCCCGUUGCAGGCACUACU------------UGGCCUACAACUCCGUCUCUUUCGACGUCUUCCGAUGGCCAUUCUAGUUGGCCA--UGACUAUG
....((((.((((.(....------------.))))).))))..((((......)))).......(((((((.......))))))--)....... ( -25.30, z-score =  -3.36, R)
>droWil1.scaffold_180701 3023632 78 + 3904529
CCCCGUUGGAAGCGCAA----------------ACCUGGUGCGUGUUUUGUUUGGCCUCUUUGGCUUGGUCGGUCGAAU-GGUCGGAUGGUCGAA
..(((((.((.(((((.----------------......)))))...(..(((((((.((.......))..))))))).-.))).)))))..... ( -21.90, z-score =   0.65, R)
>consensus
CCCCGUUGCAGGCACUACU____________UGGCCUACAACUCCGUCUCUUUCGACGUCUUCCGAUGGCCAUUCUAGUUGGCCA__UGACUAUG
....((((.((((....................)))).))))...............(((......((((((.......))))))...))).... (-10.52 = -10.83 +   0.31)

alignment

secondary structure

dotplot

Window 0

Location	17,733,370 – 17,733,460
Length	90
Sequences	6
Columns	95
Reading direction	reverse
Mean pairwise identity	69.20
Shannon entropy	0.55745
G+C content	0.53838
Mean single sequence MFE	-25.34
Consensus MFE	-9.84
Energy contribution	-12.82
Covariance contribution	2.97
Combinations/Pair	1.25
Mean z-score	-1.69
Structure conservation index	0.39
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	0.35
SVM RNA-class probability	0.656969
Prediction	RNA
WARNING	Out of training range. z-scores are NOT reliable.

Download alignment: ClustalW | MAF

>dm3.chr2R 17733370 90 - 21146708
CAUAGUCA--UGACCAACUAGAAUGGCCAUCGGAAGACUUCGAAAGAGACGGAGUUGUAGGCCAAGU---AGUGCCUGUAGUGCCUGCAACGGGG
........--......((((...(((((.((....))(((((.......))))).....)))))..)---))).(((((.((....)).))))). ( -24.70, z-score =  -0.48, R)
>droYak2.chr2R 9685158 86 + 21139217
CAUGGCCAACUAGCCAACUAGAAUGGCCAACACAAGACGUCGAAAGAGACGGAGUUUGAGGCCAAGU---------AGUAGUGCCUGCAACGGGG
..((((((.((((....))))..))))))...((((.((((......))))...))))...((..((---------.((((...)))).))..)) ( -25.60, z-score =  -1.59, R)
>droEre2.scaffold_4845 11866659 95 - 22589142
CAUAGCCAUCUAGCCAACUAGAAUGGCCAUCGCAAGACGUCGAAAGAGACGGAGACGUAGACGGAGUUUGAGGCCAAGUAGUGCCAGCAACGGGG
.....((.(((((....))))).(((((.((....))((((.......(((....))).))))........))))).((.((....)).)))).. ( -28.20, z-score =  -1.90, R)
>droSec1.super_9 1048397 81 - 3197100
CAUAGUCA--UGGCCAACUAAAAUGGCUAUCGGAAGACGUCGAAAGAUACGGAGUUGUAGGCCA------------AGUAGUGCCUGCAGCGGGG
....((((--((((((.......))))))).....)))(((....))).....((((((((((.------------....).))))))))).... ( -28.10, z-score =  -2.93, R)
>droSim1.chr2R 16367686 81 - 19596830
CAUAGUCA--UGGCCAACUAGAAUGGCCAUCGGAAGACGUCGAAAGAGACGGAGUUGUAGGCCA------------AGUAGUGCCUGCAACGGGG
....(((.--((((((.......))))))((....))..((....)))))...((((((((((.------------....).))))))))).... ( -32.00, z-score =  -4.08, R)
>droWil1.scaffold_180701 3023632 78 - 3904529
UUCGACCAUCCGACC-AUUCGACCGACCAAGCCAAAGAGGCCAAACAAAACACGCACCAGGU----------------UUGCGCUUCCAACGGGG
........((((...-..((....))..........((((((((((..............))----------------))).)))))...)))). ( -13.44, z-score =   0.86, R)
>consensus
CAUAGCCA__UGGCCAACUAGAAUGGCCAUCGCAAGACGUCGAAAGAGACGGAGUUGUAGGCCA____________AGUAGUGCCUGCAACGGGG
.....((....(((((.......))))).........((((......))))..(((((((((....................))))))))))).. ( -9.84 = -12.82 +   2.97)

alignment

secondary structure

dotplot

Window 1

Location	17,733,405 – 17,733,496
Length	91
Sequences	7
Columns	114
Reading direction	forward
Mean pairwise identity	65.07
Shannon entropy	0.63443
G+C content	0.51366
Mean single sequence MFE	-28.95
Consensus MFE	-11.29
Energy contribution	-12.34
Covariance contribution	1.05
Combinations/Pair	1.45
Mean z-score	-1.25
Structure conservation index	0.39
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	0.15
SVM RNA-class probability	0.564911
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 17733405 91 + 21146708
------------CAACUCCGUCUCUUUCGAAGUCU---UCCGAUGGCCAUUCUAGUUGGUCA--UGACUAUGUG-GCG---UAUGUGCGUGUUUCUGG--CGGUCACAUGCAAU
------------.......(((.....((.((((.---....(((((((.......))))))--))))).)).)-))(---((((((..(((.....)--))..)))))))... ( -23.20, z-score =  -0.22, R)
>droAna3.scaffold_13266 11115445 102 + 19884421
------------GAACCCUGUCUUCGGCUGCUCCUCCAUUCGAUAGCCACACACUAUAUGCACCAACAUGUGUGUAUAUAUGGAGUGUGCGUGCUGGGGACCGUCGCAUGCAAU
------------.......((((((((((((.(((((((...(((..((((((...............))))))..))))))))).).))).)))))))))............. ( -31.66, z-score =  -0.62, R)
>droYak2.chr2R 9685187 96 - 21139217
------------AAACUCCGUCUCUUUCGACGUCU---UGUGUUGGCCAUUCUAGUUGGCUAGUUGGCCAUGUG-GCGGCGUAUGUGCGUGUUUCUGG--CGGUCACAUGCAAU
------------..((.(((((.(....((((...---..))))(((((..((((....)))).)))))..).)-)))).))...(((((((..(...--..)..))))))).. ( -31.60, z-score =  -1.48, R)
>droEre2.scaffold_4845 11866685 105 + 22589142
AAACUCCGUCUACGUCUCCGUCUCUUUCGACGUCU---UGCGAUGGCCAUUCUAGUUGGCUAGAUGGCUAUGUG-GCG---UAUGUGCGUGUUUCUGG--CGGUCACAUGCAAU
..........((((((..((((......))))...---.((.((((((((.((((....)))))))))))))))-)))---))..(((((((..(...--..)..))))))).. ( -34.80, z-score =  -2.03, R)
>droSec1.super_9 1048423 91 + 3197100
------------CAACUCCGUAUCUUUCGACGUCU---UCCGAUAGCCAUUUUAGUUGGCCA--UGACUAUGUG-GCG---UAUGUGCGUGUUCCUGG--CGGUCACAUGCAAU
------------......(((((...(((......---..)))..(((((..(((((.....--.))))).)))-)))---))))(((((((.((...--.))..))))))).. ( -24.00, z-score =  -0.40, R)
>droSim1.chr2R 16367712 91 + 19596830
------------CAACUCCGUCUCUUUCGACGUCU---UCCGAUGGCCAUUCUAGUUGGCCA--UGACUAUGUG-GCG---UAUGUGCGUGUUCCUGG--CGGUCACAUGCAAU
------------..((.(((((......)))(((.---....(((((((.......))))))--)))).....)-).)---)...(((((((.((...--.))..))))))).. ( -27.50, z-score =  -1.06, R)
>droWil1.scaffold_180701 3023654 82 + 3904529
-------------GUGCGUGUUUUGUUUGGCCUCU---U----UGGC----UUGGUCGGUCGAAUGGUCGGAUG-GUC------GAAUGGUUAGCUGGU-CGGUCACAUGCAAU
-------------.(((((((...((((((((..(---(----((((----(.....))))))).))))))))(-..(------((..((....))..)-))..)))))))).. ( -29.90, z-score =  -2.98, R)
>consensus
____________CAACUCCGUCUCUUUCGACGUCU___UCCGAUGGCCAUUCUAGUUGGCCA__UGACUAUGUG_GCG___UAUGUGCGUGUUCCUGG__CGGUCACAUGCAAU
..................((((......))))...........((((((.......)))))).......................(((((((..(((...)))..))))))).. (-11.29 = -12.34 +   1.05)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:41:43 2011