Locus 11794

Sequence ID dm3.chr3R
Location 23,858,203 – 23,858,338
Length 135
Max. P 0.949326
window16212 window16213 window16214

overview

Window 2

Location 23,858,203 – 23,858,306
Length 103
Sequences 6
Columns 110
Reading direction forward
Mean pairwise identity 77.76
Shannon entropy 0.40026
G+C content 0.58686
Mean single sequence MFE -42.98
Consensus MFE -23.09
Energy contribution -24.60
Covariance contribution 1.51
Combinations/Pair 1.31
Mean z-score -2.39
Structure conservation index 0.54
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.55
SVM RNA-class probability 0.949326
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 23858203 103 + 27905053
GGAUUUCAGGAGGGGCCACC---UGCAAGGACAAGCAGAUAGUGUCUGCUGUCCGU----UCGGCUCCUGAGUUGCUGAGCUGCUCAGCUCCACAGCUCCUUCCUUGCCA
((.....((((((((((...---.((..(((((.((((((...)))))))))))))----..)))))).((((((..(((((....)))))..))))))..))))..)). ( -45.50, z-score =  -2.17, R)
>droAna3.scaffold_13340 21997807 91 + 23697760
GGAUUUCAGGUGGAGCCGAC---UGCAAGGACAAGCAGAUAGCGGAUAGUGUCUGU----UCACUUAUCCUGCUGCUGG------CUUCCCGUCGGCCCUGCUC------
........((..(.((((((---.....(((..(((((.((((((((((((.....----.))).))))).)))))).)------))))).)))))).)..)).------ ( -34.20, z-score =  -1.22, R)
>droEre2.scaffold_4820 6287331 91 - 10470090
GGAUUUCAGGUGGGGCCGCC---UGCAAGGACAAGGAG----UGUUUGCUGUCCGU----UCGGCUCCUGAGCUCCA--------CAGCUCCACGGCUCCUUCCUUUCCA
(((...((((((....))))---)).(((((..(((((----(((..(((((..((----((((...))))))...)--------))))...)).)))))))))))))). ( -37.10, z-score =  -1.52, R)
>droYak2.chr3R 6192286 102 - 28832112
GGAUUUCAGGUGGGGCCGCCGCUUGCAAGGACAAGCAGAUAGUGUCUGCUGUCCGUCCAUUCGGCUACUGAGCUUCU--------CAGCUCCACAGCUCCUUCCUUUCCA
(((....(((.(((((.((((..((...(((((.((((((...)))))))))))...))..))))....(((((...--------.)))))....)))))..))).))). ( -44.10, z-score =  -3.77, R)
>droSec1.super_22 480872 103 + 1066717
GGAUUUCAGGUGGGGCCGCC---UGCAAGGACAAGCAGAUAGUGUCUGCUGUCCGU----UCGGCUCCUGAGCUGCUGAGCUGCUCAGCUCCACAGCUCCUUCCUUGCCA
........((((((((((..---.((..(((((.((((((...)))))))))))))----.))))))).((((((..(((((....)))))..)))))).......))). ( -48.50, z-score =  -2.64, R)
>droSim1.chr3R 23559949 103 + 27517382
GGAUUUCAGGUGGGGCCGCC---UGCAAGGACAAGCAGAUAUUGUCUGCUGUCCGU----UCGGCUCCUGAGCUGCUGAGCUGCUCAGCUCCACAGCUCCUUCCUUGCCA
........((((((((((..---.((..(((((.((((((...)))))))))))))----.))))))).((((((..(((((....)))))..)))))).......))). ( -48.50, z-score =  -3.03, R)
>consensus
GGAUUUCAGGUGGGGCCGCC___UGCAAGGACAAGCAGAUAGUGUCUGCUGUCCGU____UCGGCUCCUGAGCUGCUGA______CAGCUCCACAGCUCCUUCCUUGCCA
(((........(((((((..........(((((.(((((.....)))))))))).......))))))).((((((..................))))))..)))...... (-23.09 = -24.60 +   1.51)

alignment

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secondary structure

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dotplot

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Window 3

Location 23,858,203 – 23,858,306
Length 103
Sequences 6
Columns 110
Reading direction reverse
Mean pairwise identity 77.76
Shannon entropy 0.40026
G+C content 0.58686
Mean single sequence MFE -40.22
Consensus MFE -22.12
Energy contribution -24.07
Covariance contribution 1.95
Combinations/Pair 1.19
Mean z-score -1.99
Structure conservation index 0.55
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.86
SVM RNA-class probability 0.838771
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 23858203 103 - 27905053
UGGCAAGGAAGGAGCUGUGGAGCUGAGCAGCUCAGCAACUCAGGAGCCGA----ACGGACAGCAGACACUAUCUGCUUGUCCUUGCA---GGUGGCCCCUCCUGAAAUCC
.....((((..(((.(((.(((((....))))).))).))).((.((((.----..((((((((((.....))))).))))).....---..)))).))))))....... ( -39.50, z-score =  -0.85, R)
>droAna3.scaffold_13340 21997807 91 - 23697760
------GAGCAGGGCCGACGGGAAG------CCAGCAGCAGGAUAAGUGA----ACAGACACUAUCCGCUAUCUGCUUGUCCUUGCA---GUCGGCUCCACCUGAAAUCC
------((.((((((((((((....------))....(((((((((((..----(.((.(.......))).)..)))))))).))).---))))))....))))...)). ( -33.60, z-score =  -2.02, R)
>droEre2.scaffold_4820 6287331 91 + 10470090
UGGAAAGGAAGGAGCCGUGGAGCUG--------UGGAGCUCAGGAGCCGA----ACGGACAGCAAACA----CUCCUUGUCCUUGCA---GGCGGCCCCACCUGAAAUCC
.(((.(((..((.(((...(((((.--------...)))))....(((..----..((((((......----....)))))).....---))))))))..)))....))) ( -31.00, z-score =  -0.15, R)
>droYak2.chr3R 6192286 102 + 28832112
UGGAAAGGAAGGAGCUGUGGAGCUG--------AGAAGCUCAGUAGCCGAAUGGACGGACAGCAGACACUAUCUGCUUGUCCUUGCAAGCGGCGGCCCCACCUGAAAUCC
.(((.(((..((.(((...(((((.--------...)))))....((((..((.(.((((((((((.....))))).))))).).))..)))))))))..)))....))) ( -43.00, z-score =  -3.33, R)
>droSec1.super_22 480872 103 - 1066717
UGGCAAGGAAGGAGCUGUGGAGCUGAGCAGCUCAGCAGCUCAGGAGCCGA----ACGGACAGCAGACACUAUCUGCUUGUCCUUGCA---GGCGGCCCCACCUGAAAUCC
.....(((...(((((((.(((((....))))).))))))).((.((((.----..((((((((((.....))))).))))).....---..)))).)).)))....... ( -47.10, z-score =  -2.63, R)
>droSim1.chr3R 23559949 103 - 27517382
UGGCAAGGAAGGAGCUGUGGAGCUGAGCAGCUCAGCAGCUCAGGAGCCGA----ACGGACAGCAGACAAUAUCUGCUUGUCCUUGCA---GGCGGCCCCACCUGAAAUCC
.....(((...(((((((.(((((....))))).))))))).((.((((.----..((((((((((.....))))).))))).....---..)))).)).)))....... ( -47.10, z-score =  -2.98, R)
>consensus
UGGCAAGGAAGGAGCUGUGGAGCUG______UCAGCAGCUCAGGAGCCGA____ACGGACAGCAGACACUAUCUGCUUGUCCUUGCA___GGCGGCCCCACCUGAAAUCC
.....(((..((.(((((.((((((..........))))))...............((((((((((.....))))).))))).........)))))))..)))....... (-22.12 = -24.07 +   1.95)

alignment

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secondary structure

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dotplot

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Window 4

Location 23,858,233 – 23,858,338
Length 105
Sequences 6
Columns 105
Reading direction reverse
Mean pairwise identity 77.45
Shannon entropy 0.43222
G+C content 0.53282
Mean single sequence MFE -32.98
Consensus MFE -14.32
Energy contribution -16.63
Covariance contribution 2.31
Combinations/Pair 1.21
Mean z-score -2.27
Structure conservation index 0.43
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.71
SVM RNA-class probability 0.795724
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 23858233 105 - 27905053
AAAUAAACGAAUCGUCGGACACGGCCAAGAAUUGGCAAGGAAGGAGCUGUGGAGCUGAGCAGCUCAGCAACUCAGGAGCCGAACGGACAGCAGACACUAUCUGCU
...........(((((((...(.((((.....)))).......(((.(((.(((((....))))).))).))).)...))).))))..((((((.....)))))) ( -34.30, z-score =  -2.03, R)
>droAna3.scaffold_13340 21997837 90 - 23697760
AAAUAAACGAAUCGCUGGACACGGCCAAGGAGCAGGGCCGACGG------GAAGCCA-GCAGCAGG--------AUAAGUGAACAGACACUAUCCGCUAUCUGCU
.............(((((.(.(((((.........)))))...)------....)))-))(((.((--------(((.(((......)))))))))))....... ( -28.60, z-score =  -2.05, R)
>droEre2.scaffold_4820 6287361 93 + 10470090
AAAUAAACGAAUCGUCGGACACGGCCAAGAAUUGGAAAGGAAGGAGCCGUGGAGCUGUGGAGCUCA--------GGAGCCGAACGGACAGCAAACACUCCU----
...........(((((((.(((((((.....((....))....).))))))(((((....))))).--------....))).))))...............---- ( -25.70, z-score =  -0.69, R)
>droYak2.chr3R 6192319 101 + 28832112
AAAUAAACGAAUCGUCGGACACGGCCAAGCAUUGGAAAGGAAGGAGCUGUGGAGCUGAGAAGCUCAGUAGC----CGAAUGGACGGACAGCAGACACUAUCUGCU
.......((.....((((.(((((((.....((....))....).))))))(((((....))))).....)----))).....))...((((((.....)))))) ( -29.80, z-score =  -1.61, R)
>droSec1.super_22 480902 105 - 1066717
AAAUAAACGAAUCGUCGGACACGACCAAGAAUUGGCAAGGAAGGAGCUGUGGAGCUGAGCAGCUCAGCAGCUCAGGAGCCGAACGGACAGCAGACACUAUCUGCU
.......((....((((....))))......(((((.......(((((((.(((((....))))).)))))))....))))).))...((((((.....)))))) ( -38.60, z-score =  -3.31, R)
>droSim1.chr3R 23559979 105 - 27517382
AAAUAAACGAAUCGUCGGACACGGCCAAGAAUUGGCAAGGAAGGAGCUGUGGAGCUGAGCAGCUCAGCAGCUCAGGAGCCGAACGGACAGCAGACAAUAUCUGCU
...........(((((((...(.((((.....)))).......(((((((.(((((....))))).))))))).)...))).))))..((((((.....)))))) ( -40.90, z-score =  -3.91, R)
>consensus
AAAUAAACGAAUCGUCGGACACGGCCAAGAAUUGGCAAGGAAGGAGCUGUGGAGCUGAGCAGCUCAGCAGC___GGAGCCGAACGGACAGCAGACACUAUCUGCU
.............(((.(.(((((((.....((....))....).))))))(((((....)))))..................).)))((((((.....)))))) (-14.32 = -16.63 +   2.31)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 00:49:50 2011