Locus 3236

Sequence ID	dm3.chr2R
Location	3,639,654 – 3,639,759
Length	105
Max. P	0.923176

overview

Window 1

Location	3,639,654 – 3,639,758
Length	104
Sequences	4
Columns	105
Reading direction	forward
Mean pairwise identity	90.24
Shannon entropy	0.15229
G+C content	0.50233
Mean single sequence MFE	-32.48
Consensus MFE	-27.36
Energy contribution	-26.93
Covariance contribution	-0.44
Combinations/Pair	1.12
Mean z-score	-2.11
Structure conservation index	0.84
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	1.12
SVM RNA-class probability	0.895139
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 3639654 104 + 21146708
GCAAACAUUCUGCGAAGUUGCUGCUGCGGGCAAUGCUUCGUUGCACGACAGCAACACAGCAACACCAACA-ACAGCAGCGACGACGGAUUGGUUUCAACUUUUCG
(.((((..((((((..(((((((.((..((...((((..(((((......)))))..))))...))..))-.)))))))..)).))))...)))))......... ( -36.20, z-score =  -2.94, R)
>droSec1.super_1 1295125 101 + 14215200
GCAAACAUUCUGCGAAGUUGCUGCUGCAGGCAAUGCUUCGUUGCACGACAGCAACAC--CAGCAACAACA--CAGCAGCGACGACGGAUUGGUUUCAACUUUUCG
(.((((..((((....((((((((((.......((((..(((((......)))))..--.))))......--))))))))))..))))...)))))......... ( -32.52, z-score =  -1.95, R)
>droYak2.chr2L 16311683 105 + 22324452
GCAAAUAUUCUGCGAAGUUGCGGCUGCGGGCAAUGCUUCGUUGCACGACUGCAACACAGCAACACAGCCAUACAGCAACAACGACGGAUUGGUUUCAACUUUUCA
(.((((..((((((..((((((((((.(.....((((..((((((....))))))..)))).).))))).....)))))..)).))))...)))))......... ( -31.80, z-score =  -1.82, R)
>droEre2.scaffold_4929 7672354 100 - 26641161
GCAAACAUUCUGCGAAGUUGCUGCUGCAGGCAAUGCUUCGUUGCACGACAGCAACAC---AGCAACA-CA-ACAGCAACAACGACGGAUUGGUUUCAACUUUUCA
(.((((..((((((..(((((((.((....)).((((..(((((......)))))..---))))...-..-.)))))))..)).))))...)))))......... ( -29.40, z-score =  -1.75, R)
>consensus
GCAAACAUUCUGCGAAGUUGCUGCUGCAGGCAAUGCUUCGUUGCACGACAGCAACAC__CAACAACAACA_ACAGCAACAACGACGGAUUGGUUUCAACUUUUCA
(.((((..((((((..(((((((..(((.....)))...(((((......))))).................)))))))..)).))))...)))))......... (-27.36 = -26.93 +  -0.44)

alignment

secondary structure

dotplot

Window 2

Location	3,639,654 – 3,639,758
Length	104
Sequences	4
Columns	105
Reading direction	reverse
Mean pairwise identity	90.24
Shannon entropy	0.15229
G+C content	0.50233
Mean single sequence MFE	-36.00
Consensus MFE	-30.59
Energy contribution	-31.65
Covariance contribution	1.06
Combinations/Pair	1.09
Mean z-score	-1.98
Structure conservation index	0.85
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	0.99
SVM RNA-class probability	0.869045
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 3639654 104 - 21146708
CGAAAAGUUGAAACCAAUCCGUCGUCGCUGCUGU-UGUUGGUGUUGCUGUGUUGCUGUCGUGCAACGAAGCAUUGCCCGCAGCAGCAACUUCGCAGAAUGUUUGC
(((...((((....))))...)))....((((((-(((.(((..((((.((((((......)))))).))))..))).))))))))).....(((((...))))) ( -38.00, z-score =  -2.09, R)
>droSec1.super_1 1295125 101 - 14215200
CGAAAAGUUGAAACCAAUCCGUCGUCGCUGCUG--UGUUGUUGCUG--GUGUUGCUGUCGUGCAACGAAGCAUUGCCUGCAGCAGCAACUUCGCAGAAUGUUUGC
(((...((((....))))...)))...((((..--(((((((((.(--((..((((.(((.....)))))))..))).))))))))).....))))......... ( -34.20, z-score =  -1.13, R)
>droYak2.chr2L 16311683 105 - 22324452
UGAAAAGUUGAAACCAAUCCGUCGUUGUUGCUGUAUGGCUGUGUUGCUGUGUUGCAGUCGUGCAACGAAGCAUUGCCCGCAGCCGCAACUUCGCAGAAUAUUUGC
.((...((((....))))...))(((((.(((((..(((.(((((....(((((((....))))))).))))).))).))))).)))))...(((((...))))) ( -35.20, z-score =  -1.84, R)
>droEre2.scaffold_4929 7672354 100 + 26641161
UGAAAAGUUGAAACCAAUCCGUCGUUGUUGCUGU-UG-UGUUGCU---GUGUUGCUGUCGUGCAACGAAGCAUUGCCUGCAGCAGCAACUUCGCAGAAUGUUUGC
.((...((((....))))...))(((((((((((-.(-(..((((---.((((((......)))))).))))..))..)))))))))))...(((((...))))) ( -36.60, z-score =  -2.85, R)
>consensus
CGAAAAGUUGAAACCAAUCCGUCGUCGCUGCUGU_UGUUGGUGCUG__GUGUUGCUGUCGUGCAACGAAGCAUUGCCCGCAGCAGCAACUUCGCAGAAUGUUUGC
.((...((((....))))...))(((((((((((....(((((((....((((((......)))))).)))))))...)))))))))))...(((((...))))) (-30.59 = -31.65 +   1.06)

alignment

secondary structure

dotplot

Window 3

Location	3,639,655 – 3,639,759
Length	104
Sequences	4
Columns	105
Reading direction	forward
Mean pairwise identity	90.24
Shannon entropy	0.15229
G+C content	0.49257
Mean single sequence MFE	-32.10
Consensus MFE	-26.96
Energy contribution	-26.52
Covariance contribution	-0.44
Combinations/Pair	1.12
Mean z-score	-2.22
Structure conservation index	0.84
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	1.30
SVM RNA-class probability	0.923176
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 3639655 104 + 21146708
CAAACAUUCUGCGAAGUUGCUGCUGCGGGCAAUGCUUCGUUGCACGACAGCAACACAGCAACACCAACA-ACAGCAGCGACGACGGAUUGGUUUCAACUUUUCGA
....((.((((((..(((((((.((..((...((((..(((((......)))))..))))...))..))-.)))))))..)).)))).))............... ( -35.80, z-score =  -2.92, R)
>droSec1.super_1 1295126 101 + 14215200
CAAACAUUCUGCGAAGUUGCUGCUGCAGGCAAUGCUUCGUUGCACGACAGCAACAC--CAGCAACAACA--CAGCAGCGACGACGGAUUGGUUUCAACUUUUCGA
....((.((((....((((((((((.......((((..(((((......)))))..--.))))......--))))))))))..)))).))............... ( -32.12, z-score =  -1.91, R)
>droYak2.chr2L 16311684 105 + 22324452
CAAAUAUUCUGCGAAGUUGCGGCUGCGGGCAAUGCUUCGUUGCACGACUGCAACACAGCAACACAGCCAUACAGCAACAACGACGGAUUGGUUUCAACUUUUCAA
...........((..((((..((((..(((..((((..((((((....))))))..)))).....)))...))))..))))..))((..(((....)))..)).. ( -31.50, z-score =  -2.07, R)
>droEre2.scaffold_4929 7672355 100 - 26641161
CAAACAUUCUGCGAAGUUGCUGCUGCAGGCAAUGCUUCGUUGCACGACAGCAACAC---AGCAACA-CA-ACAGCAACAACGACGGAUUGGUUUCAACUUUUCAA
....((.((((((..(((((((.((....)).((((..(((((......)))))..---))))...-..-.)))))))..)).)))).))............... ( -29.00, z-score =  -1.99, R)
>consensus
CAAACAUUCUGCGAAGUUGCUGCUGCAGGCAAUGCUUCGUUGCACGACAGCAACAC__CAACAACAACA_ACAGCAACAACGACGGAUUGGUUUCAACUUUUCAA
.((((..((((((..(((((((..(((.....)))...(((((......))))).................)))))))..)).))))...))))........... (-26.96 = -26.52 +  -0.44)

alignment

secondary structure

dotplot

Window 4

Location	3,639,655 – 3,639,759
Length	104
Sequences	4
Columns	105
Reading direction	reverse
Mean pairwise identity	90.24
Shannon entropy	0.15229
G+C content	0.49257
Mean single sequence MFE	-35.05
Consensus MFE	-29.09
Energy contribution	-30.15
Covariance contribution	1.06
Combinations/Pair	1.10
Mean z-score	-2.05
Structure conservation index	0.83
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	0.94
SVM RNA-class probability	0.857121
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 3639655 104 - 21146708
UCGAAAAGUUGAAACCAAUCCGUCGUCGCUGCUGU-UGUUGGUGUUGCUGUGUUGCUGUCGUGCAACGAAGCAUUGCCCGCAGCAGCAACUUCGCAGAAUGUUUG
.(((...((((....))))...)))..((((((((-(((.(((..((((.((((((......)))))).))))..))).))))))))).....)).......... ( -37.10, z-score =  -2.23, R)
>droSec1.super_1 1295126 101 - 14215200
UCGAAAAGUUGAAACCAAUCCGUCGUCGCUGCUG--UGUUGUUGCUG--GUGUUGCUGUCGUGCAACGAAGCAUUGCCUGCAGCAGCAACUUCGCAGAAUGUUUG
.(((...((((....))))...)))...((((..--(((((((((.(--((..((((.(((.....)))))))..))).))))))))).....))))........ ( -34.30, z-score =  -1.59, R)
>droYak2.chr2L 16311684 105 - 22324452
UUGAAAAGUUGAAACCAAUCCGUCGUUGUUGCUGUAUGGCUGUGUUGCUGUGUUGCAGUCGUGCAACGAAGCAUUGCCCGCAGCCGCAACUUCGCAGAAUAUUUG
..((...((((....))))...))(((((.(((((..(((.(((((....(((((((....))))))).))))).))).))))).)))))............... ( -33.70, z-score =  -1.68, R)
>droEre2.scaffold_4929 7672355 100 + 26641161
UUGAAAAGUUGAAACCAAUCCGUCGUUGUUGCUGU-UG-UGUUGCU---GUGUUGCUGUCGUGCAACGAAGCAUUGCCUGCAGCAGCAACUUCGCAGAAUGUUUG
..((...((((....))))...))(((((((((((-.(-(..((((---.((((((......)))))).))))..))..)))))))))))............... ( -35.10, z-score =  -2.69, R)
>consensus
UCGAAAAGUUGAAACCAAUCCGUCGUCGCUGCUGU_UGUUGGUGCUG__GUGUUGCUGUCGUGCAACGAAGCAUUGCCCGCAGCAGCAACUUCGCAGAAUGUUUG
..((...((((....))))...))(((((((((((....(((((((....((((((......)))))).)))))))...)))))))))))............... (-29.09 = -30.15 +   1.06)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:06:25 2011