Locus 8647

Sequence ID	dm3.chr3R
Location	298,224 – 298,315
Length	91
Max. P	0.765655

overview

Window 4

Location	298,224 – 298,315
Length	91
Sequences	8
Columns	106
Reading direction	forward
Mean pairwise identity	66.36
Shannon entropy	0.64224
G+C content	0.55056
Mean single sequence MFE	-31.98
Consensus MFE	-13.75
Energy contribution	-13.48
Covariance contribution	-0.27
Combinations/Pair	1.61
Mean z-score	-1.23
Structure conservation index	0.43
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	0.62
SVM RNA-class probability	0.765655
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 298224 91 + 27905053
------------CAUUUCCAUCCAUGGCUACGAUU-UGGCUAGGUG-GCUAGCUGGCCAGUUGGCUGUGGGCCACUAGAGC-GUCGUCGAAACCACUUUCGCUUUC
------------.............(((.(((((.-..(((.((((-(((.((.((((....)))))).)))))))..)))-))))).((((....)))))))... ( -28.50, z-score =  -0.33, R)
>droSim1.chr3R 358623 91 + 27517382
------------CAUUUCCAUCCAUGGCUGCGAUU-UGGCUAGCUG-GCUAGCUGGCCAGUUGGCUGUGGGCCACUAGAGC-GCCGUCGAAACCACUUUCGCUUUC
------------........((.(((((..(((((-.((((((((.-...)))))))))))))(((.(((....))).)))-))))).))................ ( -32.30, z-score =  -0.81, R)
>droSec1.super_6 404111 91 + 4358794
------------CAUUUCCAUCCAUGGCUGCGAUU-UGGCUAGCUA-GCUAGCUGGCCAGUUGGCUGUGGGCCACUAGAGC-GCCGUCGAAACCACUUUCGCUUUC
------------........((.(((((..(((((-.((((((((.-...)))))))))))))(((.(((....))).)))-))))).))................ ( -32.60, z-score =  -1.26, R)
>droYak2.chr3R 677779 83 + 28832112
------------CAUUUUCAUUCAUGGCUGCGAUU-UG---------GCUAGCUGGCCAGUUGGCUGUGGGCCACUAGGGU-ACCGUCGAAAUCACUUUCGCUUUC
------------........(((((((.(((..(.-((---------(((.((.((((....)))))).)))))..)..))-))))).)))............... ( -21.20, z-score =   0.33, R)
>droEre2.scaffold_4770 645761 87 + 17746568
------------CAUUUCCAUUCAUGGCUGCGAUU-UGGCUA-----GCUGGCUGGCCAGUUGGCUGUGGGCCACUAGAGC-GCCGUCGAAACCACUUUCGCUUUC
------------........((((((((..(((((-.(((((-----(....)))))))))))(((.(((....))).)))-))))).)))............... ( -29.30, z-score =  -0.62, R)
>droAna3.scaffold_13340 8021509 79 - 23697760
------------------------UGGACACAUUU--GACCAGAGGCUCUGAACCGUCAGAGCCAGAGCCAGAGCCAGAGC-GGUGCUGAAACCACUUUCGCUUUC
------------------------(((.((....)--).)))..((((((((....))))))))......(((((.((((.-(((......))).)))).))))). ( -28.10, z-score =  -2.43, R)
>dp4.chr2 6321916 106 - 30794189
UAUGCAUUCGUUUGGUUUGGCCAACGGCUCUGGCUGUGGCCUGCUCUGCUGGCUAGAUGGCUGGCUGUCGGCUAUUAGAGCUGCUGCCAAAACCACUUUCGCUUUC
............(((((((((...((((((((...((((((.((...((..(((....)))..)).)).))))))))))))))..))).))))))........... ( -41.90, z-score =  -2.30, R)
>droPer1.super_3 122760 106 - 7375914
UAUGCAUUCGUUUGGUUUGGCCAACGGCUCUGGCUGUGGCCUGCUCUGCUGGCUAGAUAGCUGGCUGUCGGCUAUUAGAGCUGCUGCCAAAACCACUUUCGCUUUC
............(((((((((...((((((((...((((((.((...((..(((....)))..)).)).))))))))))))))..))).))))))........... ( -41.90, z-score =  -2.45, R)
>consensus
____________CAUUUCCAUCCAUGGCUGCGAUU_UGGCUAGCUG_GCUAGCUGGCCAGUUGGCUGUGGGCCACUAGAGC_GCCGUCGAAACCACUUUCGCUUUC
.........................((...((((..(((((......(((((((....)))))))....)))))...........))))...))............ (-13.75 = -13.48 +  -0.27)

alignment

secondary structure

dotplot

Window 5

Location	298,224 – 298,315
Length	91
Sequences	8
Columns	106
Reading direction	reverse
Mean pairwise identity	66.36
Shannon entropy	0.64224
G+C content	0.55056
Mean single sequence MFE	-27.87
Consensus MFE	-13.92
Energy contribution	-13.27
Covariance contribution	-0.65
Combinations/Pair	1.60
Mean z-score	-0.79
Structure conservation index	0.50
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	0.43
SVM RNA-class probability	0.690295
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 298224 91 - 27905053
GAAAGCGAAAGUGGUUUCGACGAC-GCUCUAGUGGCCCACAGCCAACUGGCCAGCUAGC-CACCUAGCCA-AAUCGUAGCCAUGGAUGGAAAUG------------
....((....))((((.(((....-(((...(((((.....(((....)))......))-)))..)))..-..))).)))).............------------ ( -24.70, z-score =  -0.22, R)
>droSim1.chr3R 358623 91 - 27517382
GAAAGCGAAAGUGGUUUCGACGGC-GCUCUAGUGGCCCACAGCCAACUGGCCAGCUAGC-CAGCUAGCCA-AAUCGCAGCCAUGGAUGGAAAUG------------
....((((...(((((.....(((-(((((((((((.....))).)))))..)))..))-)....)))))-..))))..(((....))).....------------ ( -28.40, z-score =  -0.04, R)
>droSec1.super_6 404111 91 - 4358794
GAAAGCGAAAGUGGUUUCGACGGC-GCUCUAGUGGCCCACAGCCAACUGGCCAGCUAGC-UAGCUAGCCA-AAUCGCAGCCAUGGAUGGAAAUG------------
....((....))((((.(((.(((-((((((((((((...........))))).)))).-.)))..))).-..))).)))).............------------ ( -27.30, z-score =   0.28, R)
>droYak2.chr3R 677779 83 - 28832112
GAAAGCGAAAGUGAUUUCGACGGU-ACCCUAGUGGCCCACAGCCAACUGGCCAGCUAGC---------CA-AAUCGCAGCCAUGAAUGAAAAUG------------
....((....(((((((.(..(((-...((((((((.....))).)))))...)))..)---------.)-)))))).))..............------------ ( -19.30, z-score =  -0.68, R)
>droEre2.scaffold_4770 645761 87 - 17746568
GAAAGCGAAAGUGGUUUCGACGGC-GCUCUAGUGGCCCACAGCCAACUGGCCAGCCAGC-----UAGCCA-AAUCGCAGCCAUGAAUGGAAAUG------------
....((((...(((((.....(((-...((((((((.....))).)))))...)))...-----.)))))-..))))..(((....))).....------------ ( -28.10, z-score =  -0.97, R)
>droAna3.scaffold_13340 8021509 79 + 23697760
GAAAGCGAAAGUGGUUUCAGCACC-GCUCUGGCUCUGGCUCUGGCUCUGACGGUUCAGAGCCUCUGGUC--AAAUGUGUCCA------------------------
...(((.(.((((((......)))-))).).))).(((((..((((((((....))))))))...))))--)..........------------------------ ( -29.60, z-score =  -1.79, R)
>dp4.chr2 6321916 106 + 30794189
GAAAGCGAAAGUGGUUUUGGCAGCAGCUCUAAUAGCCGACAGCCAGCCAUCUAGCCAGCAGAGCAGGCCACAGCCAGAGCCGUUGGCCAAACCAAACGAAUGCAUA
....(((....((((((.((((((.(((((....(((....((..((......))..)).).)).(((....)))))))).))).)))))))))......)))... ( -32.10, z-score =  -1.30, R)
>droPer1.super_3 122760 106 + 7375914
GAAAGCGAAAGUGGUUUUGGCAGCAGCUCUAAUAGCCGACAGCCAGCUAUCUAGCCAGCAGAGCAGGCCACAGCCAGAGCCGUUGGCCAAACCAAACGAAUGCAUA
....(((....((((((.((((((.(((((....(((....((..(((....)))..)).).)).(((....)))))))).))).)))))))))......)))... ( -33.50, z-score =  -1.57, R)
>consensus
GAAAGCGAAAGUGGUUUCGACGGC_GCUCUAGUGGCCCACAGCCAACUGGCCAGCCAGC_CAGCUAGCCA_AAUCGCAGCCAUGGAUGGAAAUG____________
....((....))((((.(((.....(((((((((((.............)))).)))).......))).....))).))))......................... (-13.92 = -13.27 +  -0.65)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 23:49:32 2011