Locus 5659

Sequence ID dm3.chr3L
Location 315,212 – 315,439
Length 227
Max. P 0.941170
window7775 window7776 window7777 window7778

overview

Window 5

Location 315,212 – 315,331
Length 119
Sequences 3
Columns 119
Reading direction forward
Mean pairwise identity 96.64
Shannon entropy 0.04630
G+C content 0.50140
Mean single sequence MFE -34.49
Consensus MFE -31.89
Energy contribution -32.22
Covariance contribution 0.33
Combinations/Pair 1.00
Mean z-score -1.44
Structure conservation index 0.92
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.21
SVM RNA-class probability 0.596029
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 315212 119 + 24543557
GUUUAGUGAAACAACCCGCAAGAUGAAAGCUCACAGCGAAGCCAUGCUGUUUAACGAGUAUUGUUUAAGUAAUGUGCUCGGGCUCCCCGAGCAGUUCUCCGGCCAUUCCGUUCAGUGAC
..(((.((((.......((..((.(((.((((((((((......)))))).....))))...............((((((((...)))))))).)))))..)).......)))).))). ( -31.34, z-score =  -0.91, R)
>droSim1.chr2R 8541040 119 + 19596830
GUUUAGUGAAACAGCCCGCAAGAUGAAAGCUCACAGCGAAGCCAUGCUGUUUUACGAGUAUUGUUUAAGUAAUGUGCUCGGGCUCCCCGAGCAGUUCUCCGGCCUUUCCGUUCACUGAC
..((((((((.......((..((.(((.((((((((((......)))))).....))))...............((((((((...)))))))).)))))..)).......)))))))). ( -35.24, z-score =  -1.64, R)
>droSec1.super_2 347003 119 + 7591821
GUUUAGUGAAACAGCCCGCAAGAUGAAAGCUCACAGCGAAGCCAUGCUGUUUAGCGAGUAUUGUUUAAGUAAUGUGCUCGGGCUCCCCGAGCAGUUCUACGGCCUUUCCGUUCACUGAC
..((((((((...(((.((((.((....(((.((((((......))))))..)))..)).))))....(((...((((((((...))))))))....)))))).......)))))))). ( -36.90, z-score =  -1.77, R)
>consensus
GUUUAGUGAAACAGCCCGCAAGAUGAAAGCUCACAGCGAAGCCAUGCUGUUUAACGAGUAUUGUUUAAGUAAUGUGCUCGGGCUCCCCGAGCAGUUCUCCGGCCUUUCCGUUCACUGAC
..((((((((.....(((..(((.....((((((((((......)))))).....))))...............((((((((...))))))))..))).)))........)))))))). (-31.89 = -32.22 +   0.33)

alignment

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secondary structure

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dotplot

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Window 6

Location 315,291 – 315,403
Length 112
Sequences 4
Columns 112
Reading direction forward
Mean pairwise identity 77.38
Shannon entropy 0.36614
G+C content 0.59537
Mean single sequence MFE -37.63
Consensus MFE -24.06
Energy contribution -25.00
Covariance contribution 0.94
Combinations/Pair 1.18
Mean z-score -2.16
Structure conservation index 0.64
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.47
SVM RNA-class probability 0.941170
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 315291 112 + 24543557
GGGCUCCCCGAGCAGUUCUCCGGCCAUUCCGUUCAGUGACUCCAAUUCCGGCUGAAGCUGCAGCUGCACGCCAAACCCAAGCAACUGCAAGUCCAGCAAACCACUGAAUUCA
.((((....(((.....))).)))).....((((((((....(......)((((..(((((((.(((.............))).)))).))).))))....))))))))... ( -29.32, z-score =  -0.30, R)
>droSim1.chr2R 8541119 112 + 19596830
GGGCUCCCCGAGCAGUUCUCCGGCCUUUCCGUUCACUGACUCCGAUUCCGGCUGCAGCUGCAGCUGCACGCCAAACCCAAGCAACUGCGAGUCCAGCAAACCACUGGAUUCA
(((......(((((((....(((.....)))...)))).))).......(((((((((....)))))).)))...)))..((....))((((((((.......)))))))). ( -42.60, z-score =  -3.15, R)
>droSec1.super_2 347082 112 + 7591821
GGGCUCCCCGAGCAGUUCUACGGCCUUUCCGUUCACUGACUCCGAUUCCGGCUGCAGCUGCAGCUGCACACCAAACCCAAGCAACUGCGAGUCCAGCAAACCACUGGAUUCA
(((......(((((((...((((.....))))..)))).))).......((.((((((....))))))..))...)))..((....))((((((((.......)))))))). ( -40.50, z-score =  -3.13, R)
>droYak2.chr3L 294607 88 + 24197627
GGGCUGCCCGAGCAGCUCUCCUGCCACUCCGUUCAGUGACUCCGAUUUCGGCUGCAGUUGCAGCUGCA-GCUGCAUGCCACUGGAUUCA-----------------------
(((((((....)))))))............((((((((....((....))(((((((((((....)))-)))))).))))))))))...----------------------- ( -38.10, z-score =  -2.05, R)
>consensus
GGGCUCCCCGAGCAGUUCUCCGGCCAUUCCGUUCACUGACUCCGAUUCCGGCUGCAGCUGCAGCUGCACGCCAAACCCAAGCAACUGCAAGUCCAGCAAACCACUGGAUUCA
(((...)))..((((((((..((.......(((....))).........(((((((((....)))))).)))...))..)).))))))((((((((.......)))))))). (-24.06 = -25.00 +   0.94)

alignment

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secondary structure

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dotplot

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Window 7

Location 315,331 – 315,439
Length 108
Sequences 4
Columns 108
Reading direction forward
Mean pairwise identity 80.09
Shannon entropy 0.32423
G+C content 0.55155
Mean single sequence MFE -38.06
Consensus MFE -22.74
Energy contribution -25.48
Covariance contribution 2.75
Combinations/Pair 1.10
Mean z-score -2.40
Structure conservation index 0.60
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.27
SVM RNA-class probability 0.919185
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 315331 108 + 24543557
UCCAAUUCCGGCUGAAGCUGCAGCUGCACGCCAAACCCAAGCAACUGCAAGUCCAGCAAACCACUGAAUUCAGUUUCUUUCGAACAGCUGGGCUGCUCCAGCGGUUUG
..(((..(((.(((.((((((((.(((.............))).)))))((((((((.....((((....))))(((....)))..))))))))))).)))))).))) ( -37.92, z-score =  -2.54, R)
>droSim1.chr2R 8541159 108 + 19596830
UCCGAUUCCGGCUGCAGCUGCAGCUGCACGCCAAACCCAAGCAACUGCGAGUCCAGCAAACCACUGGAUUCAGUUUCUUGCGAACAGCUGUGCUGCUCCAGCGAUUUG
..(((.(((((..(((((.(((((((..(((.((((....((....))((((((((.......)))))))).))))...)))..)))))))))))).)).).)).))) ( -41.60, z-score =  -2.92, R)
>droSec1.super_2 347122 108 + 7591821
UCCGAUUCCGGCUGCAGCUGCAGCUGCACACCAAACCCAAGCAACUGCGAGUCCAGCAAACCACUGGAUUCAGUUUCUUGCACACAGCUGUGCUGCUCCAGCGAUUUG
..(((.(((((..(((((.(((((((..((..((((....((....))((((((((.......)))))))).))))..))....)))))))))))).)).).)).))) ( -37.00, z-score =  -2.09, R)
>droYak2.chr3L 294647 82 + 24197627
UCCGAUUUCGGCUGCAGUUGCAGCUGCA---------------GCUGCAUG---------CCACUGGAUUCAGUUUCUU--GAACAGCUGUGCGGCUGCAGUGGUUUG
........((((((((((....))))))---------------))))((.(---------((((((..(((((....))--)))(((((....)))))))))))).)) ( -35.70, z-score =  -2.07, R)
>consensus
UCCGAUUCCGGCUGCAGCUGCAGCUGCACGCCAAACCCAAGCAACUGCAAGUCCAGCAAACCACUGGAUUCAGUUUCUUGCGAACAGCUGUGCUGCUCCAGCGAUUUG
..........((((.(((.(((((((...........((((.(((((..(((((((.......)))))))))))).))))....)))))))...))).))))...... (-22.74 = -25.48 +   2.75)

alignment

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secondary structure

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dotplot

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Window 8

Location 315,331 – 315,439
Length 108
Sequences 4
Columns 108
Reading direction reverse
Mean pairwise identity 80.09
Shannon entropy 0.32423
G+C content 0.55155
Mean single sequence MFE -41.85
Consensus MFE -29.52
Energy contribution -30.90
Covariance contribution 1.37
Combinations/Pair 1.20
Mean z-score -1.82
Structure conservation index 0.71
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.91
SVM RNA-class probability 0.851129
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 315331 108 - 24543557
CAAACCGCUGGAGCAGCCCAGCUGUUCGAAAGAAACUGAAUUCAGUGGUUUGCUGGACUUGCAGUUGCUUGGGUUUGGCGUGCAGCUGCAGCUUCAGCCGGAAUUGGA
....((((((((((((.(((((..(((....)))((((....)))).....))))).))(((((((((.((.......)).)))))))))))))))).)))....... ( -47.20, z-score =  -2.69, R)
>droSim1.chr2R 8541159 108 - 19596830
CAAAUCGCUGGAGCAGCACAGCUGUUCGCAAGAAACUGAAUCCAGUGGUUUGCUGGACUCGCAGUUGCUUGGGUUUGGCGUGCAGCUGCAGCUGCAGCCGGAAUCGGA
.((((((((((((((((...)))))((....)).......)))))))))))((..(((((((....))..)))))..)).((((((....)))))).(((....))). ( -46.60, z-score =  -1.82, R)
>droSec1.super_2 347122 108 - 7591821
CAAAUCGCUGGAGCAGCACAGCUGUGUGCAAGAAACUGAAUCCAGUGGUUUGCUGGACUCGCAGUUGCUUGGGUUUGGUGUGCAGCUGCAGCUGCAGCCGGAAUCGGA
.......((((.(((((.((((((((..(...(((((((.((((((.....)))))).))((....))...))))).)..))))))))..)))))..))))....... ( -43.20, z-score =  -0.88, R)
>droYak2.chr3L 294647 82 - 24197627
CAAACCACUGCAGCCGCACAGCUGUUC--AAGAAACUGAAUCCAGUGG---------CAUGCAGC---------------UGCAGCUGCAACUGCAGCCGAAAUCGGA
.......((((((..((...(((((((--(......))))..)))).)---------).((((((---------------....)))))).))))))(((....))). ( -30.40, z-score =  -1.90, R)
>consensus
CAAACCGCUGGAGCAGCACAGCUGUUCGCAAGAAACUGAAUCCAGUGGUUUGCUGGACUCGCAGUUGCUUGGGUUUGGCGUGCAGCUGCAGCUGCAGCCGGAAUCGGA
(((((((((((((((((...)))))((....)).......))))))))))))........((((((((.............))))))))........(((....))). (-29.52 = -30.90 +   1.37)

alignment

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secondary structure

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dotplot

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Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:52:42 2011