Locus 6426

Sequence ID dm3.chr3L
Location 6,641,079 – 6,641,204
Length 125
Max. P 0.874325
window8847 window8848 window8849

overview

Window 7

Location 6,641,079 – 6,641,129
Length 50
Sequences 4
Columns 50
Reading direction forward
Mean pairwise identity 86.67
Shannon entropy 0.20980
G+C content 0.39500
Mean single sequence MFE -10.98
Consensus MFE -7.84
Energy contribution -8.65
Covariance contribution 0.81
Combinations/Pair 1.14
Mean z-score -2.39
Structure conservation index 0.71
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.02
SVM RNA-class probability 0.874325
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 6641079 50 + 24543557
ACGUUUCAAUUAAAAUGAAGACAAAGGUGGUCUGGAAAACAGGACGGCAA
..((((((.......)).))))....((.((((........)))).)).. (  -8.30, z-score =  -0.89, R)
>droSim1.chr3L 6113257 50 + 22553184
AGGUUUCAAUUAAAAUUGAAACAAAGGUGCUCUGGAAAACAGGACGGCAA
..((((((((....))))))))...(.((..(((.....)))..)).).. ( -13.70, z-score =  -3.48, R)
>droSec1.super_2 6577907 50 + 7591821
AGGUUUCAAUUAAAAUUGAAACAAAGGUGCUCUGGAAAACAGGACGGCAA
..((((((((....))))))))...(.((..(((.....)))..)).).. ( -13.70, z-score =  -3.48, R)
>droYak2.chr3L 7214930 50 + 24197627
ACGUUUCAAUUAAAAUGGAGACAAAGCUAGUCGGGAACACAGGAGAGCAU
..(((((..........)))))...(((..((.(.....).))..))).. (  -8.20, z-score =  -1.71, R)
>consensus
ACGUUUCAAUUAAAAUGGAAACAAAGGUGCUCUGGAAAACAGGACGGCAA
..((((((((....))))))))...(.((..(((.....)))..)).).. ( -7.84 =  -8.65 +   0.81)

alignment

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secondary structure

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dotplot

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Window 8

Location 6,641,129 – 6,641,204
Length 75
Sequences 10
Columns 87
Reading direction forward
Mean pairwise identity 72.04
Shannon entropy 0.53540
G+C content 0.43741
Mean single sequence MFE -19.10
Consensus MFE -10.77
Energy contribution -9.02
Covariance contribution -1.75
Combinations/Pair 1.73
Mean z-score -1.00
Structure conservation index 0.56
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.34
SVM RNA-class probability 0.653330
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 6641129 75 + 24543557
CUGGAAUGGCCGUUGAAACUUUUUUCCAAGUGCCAUUUGGCAUACAAAGAG---------AGAUGAUA---AGAGUGAAACACUCAA
..((.....)).......(((((((....(((((....)))))...)))))---------))......---.(((((...))))).. ( -16.40, z-score =  -0.99, R)
>droSim1.chr3L 6113307 75 + 22553184
AUGGAAUGGCCGUUGAAACUUUUUUCCAAGUGCCAUUUGGCAUACAAAGAG---------AGAUGAUA---AGAGUGAAACACUCAA
((((.....)))).....(((((((....(((((....)))))...)))))---------))......---.(((((...))))).. ( -17.10, z-score =  -1.44, R)
>droSec1.super_2 6577957 75 + 7591821
CUGGAAUGGCCGUUGAAACUUUUUUCCAAGUGCCAUUUGGCAUACAAAGAG---------AGAUGAUA---AGAGUGAAACACUCAA
..((.....)).......(((((((....(((((....)))))...)))))---------))......---.(((((...))))).. ( -16.40, z-score =  -0.99, R)
>droYak2.chr3L 7214980 75 + 24197627
CUGGGAUGGCCGUUGAAACUUUUUUUCAAGUGCCAUUUGGCAUACAAAGAC---------AGAUGAUA---AGAGUGAAACACUCAA
((((((((((..((((((.....))))))..)))))))(.....).....)---------))......---.(((((...))))).. ( -18.10, z-score =  -1.42, R)
>droEre2.scaffold_4784 9316399 77 + 25762168
CUGGGAUGGCCAUUGAAACUUUUUUCCAAGUGCCAUUCGGCAUACAUAGAGGG-------AGAUGAUA---AGAGUGAAACACUCAA
.(((.....)))......(((((((....(((((....))))).....)))))-------))......---.(((((...))))).. ( -16.10, z-score =  -0.14, R)
>droAna3.scaffold_13337 3000042 80 - 23293914
AGGAAGUGGUUGCGGCAACUUUUUUCCAAGUACCAUUUGGCAUACAAUAAAGG-------AGGGAUUCUUAAGAGCAAACCACUUAA
...(((((((((((....).(((((((..(((((....))..)))......))-------))))).........)).)))))))).. ( -18.40, z-score =  -1.01, R)
>dp4.chrXR_group8 3911681 87 - 9212921
CGGAAGUGGUUGCGGCAACUUUUUGCCGAGUACCAUUUGGCAUAAAAAAGGCAGAAGUGUGGAUAAGAGAGAGAGCGAGCCACUCAA
..((.(((((((((((((....))))).....(((((((.(........).)))....))))............)).)))))))).. ( -22.90, z-score =  -1.06, R)
>droPer1.super_38 392030 87 + 801819
CGGAAGUGGUUGCGGCAACUUUUUGCCGAGUACCAUUUGGCAUAAAAAAGGCAGAAGUGUGGAUAAGAGAGAGAGCGAGCCACUCAA
..((.(((((((((((((....))))).....(((((((.(........).)))....))))............)).)))))))).. ( -22.90, z-score =  -1.06, R)
>droMoj3.scaffold_6680 14950763 76 - 24764193
CGGAAGUGGUUGCAGCAACUUUU-GCCGAGUGCCAUUUGGCACACAAAAGAU--------GGAUGACGU--CGACUGAGACAGACAA
(((....(((((...)))))...-.))).(((((....))))).((...(((--------(.....)))--)...)).......... ( -20.40, z-score =  -0.83, R)
>droGri2.scaffold_15110 16256803 75 - 24565398
CGGAAGUGGUUGCAGCAACUUUU-GCCGAGUGCCAUUUGGCACACAAAAGAU--------GGAUGACGC--UGAAUAAGGCAGUCA-
(((....(((((...)))))...-.))).(((((....))))).........--------...((((((--(......))).))))- ( -22.30, z-score =  -1.07, R)
>consensus
CGGAAAUGGCCGCUGAAACUUUUUUCCAAGUGCCAUUUGGCAUACAAAAAG_________AGAUGAUA___AGAGUGAAACACUCAA
...(((((((..(.((((....)))).)...)))))))..................................(((.......))).. (-10.77 =  -9.02 +  -1.75)

alignment

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secondary structure

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dotplot

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Window 9

Location 6,641,129 – 6,641,204
Length 75
Sequences 10
Columns 87
Reading direction reverse
Mean pairwise identity 72.04
Shannon entropy 0.53540
G+C content 0.43741
Mean single sequence MFE -16.29
Consensus MFE -7.65
Energy contribution -7.21
Covariance contribution -0.44
Combinations/Pair 1.44
Mean z-score -1.33
Structure conservation index 0.47
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.23
SVM RNA-class probability 0.602983
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 6641129 75 - 24543557
UUGAGUGUUUCACUCU---UAUCAUCU---------CUCUUUGUAUGCCAAAUGGCACUUGGAAAAAAGUUUCAACGGCCAUUCCAG
..(((((...))))).---........---------..............((((((..((((((.....))))))..)))))).... ( -14.70, z-score =  -1.18, R)
>droSim1.chr3L 6113307 75 - 22553184
UUGAGUGUUUCACUCU---UAUCAUCU---------CUCUUUGUAUGCCAAAUGGCACUUGGAAAAAAGUUUCAACGGCCAUUCCAU
..(((((...))))).---........---------..............((((((..((((((.....))))))..)))))).... ( -14.70, z-score =  -1.26, R)
>droSec1.super_2 6577957 75 - 7591821
UUGAGUGUUUCACUCU---UAUCAUCU---------CUCUUUGUAUGCCAAAUGGCACUUGGAAAAAAGUUUCAACGGCCAUUCCAG
..(((((...))))).---........---------..............((((((..((((((.....))))))..)))))).... ( -14.70, z-score =  -1.18, R)
>droYak2.chr3L 7214980 75 - 24197627
UUGAGUGUUUCACUCU---UAUCAUCU---------GUCUUUGUAUGCCAAAUGGCACUUGAAAAAAAGUUUCAACGGCCAUCCCAG
..(((((...))))).---........---------...............(((((..((((((.....))))))..)))))..... ( -14.30, z-score =  -1.17, R)
>droEre2.scaffold_4784 9316399 77 - 25762168
UUGAGUGUUUCACUCU---UAUCAUCU-------CCCUCUAUGUAUGCCGAAUGGCACUUGGAAAAAAGUUUCAAUGGCCAUCCCAG
..(((((...))))).---........-------...............(.(((((..((((((.....))))))..))))).)... ( -13.90, z-score =  -0.43, R)
>droAna3.scaffold_13337 3000042 80 + 23293914
UUAAGUGGUUUGCUCUUAAGAAUCCCU-------CCUUUAUUGUAUGCCAAAUGGUACUUGGAAAAAAGUUGCCGCAACCACUUCCU
..((((((((.((..............-------......(((.....)))..(((((((......))).))))))))))))))... ( -17.00, z-score =  -1.55, R)
>dp4.chrXR_group8 3911681 87 + 9212921
UUGAGUGGCUCGCUCUCUCUCUUAUCCACACUUCUGCCUUUUUUAUGCCAAAUGGUACUCGGCAAAAAGUUGCCGCAACCACUUCCG
..((((((...((................................((((....))))...(((((....)))))))..))))))... ( -18.50, z-score =  -1.92, R)
>droPer1.super_38 392030 87 - 801819
UUGAGUGGCUCGCUCUCUCUCUUAUCCACACUUCUGCCUUUUUUAUGCCAAAUGGUACUCGGCAAAAAGUUGCCGCAACCACUUCCG
..((((((...((................................((((....))))...(((((....)))))))..))))))... ( -18.50, z-score =  -1.92, R)
>droMoj3.scaffold_6680 14950763 76 + 24764193
UUGUCUGUCUCAGUCG--ACGUCAUCC--------AUCUUUUGUGUGCCAAAUGGCACUCGGC-AAAAGUUGCUGCAACCACUUCCG
((((..(((......)--))......(--------(.((((((((((((....)))))...))-))))).))..))))......... ( -17.70, z-score =  -1.17, R)
>droGri2.scaffold_15110 16256803 75 + 24565398
-UGACUGCCUUAUUCA--GCGUCAUCC--------AUCUUUUGUGUGCCAAAUGGCACUCGGC-AAAAGUUGCUGCAACCACUUCCG
-((((.((........--))))))..(--------(.((((((((((((....)))))...))-))))).))............... ( -18.90, z-score =  -1.55, R)
>consensus
UUGAGUGUUUCACUCU___UAUCAUCU_________CUCUUUGUAUGCCAAAUGGCACUUGGAAAAAAGUUGCAACAACCACUCCAG
..(((((...)))))..............................((((....)))).............................. ( -7.65 =  -7.21 +  -0.44)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 23:07:34 2011