Locus 6809

Sequence ID dm3.chr3L
Location 9,987,422 – 9,987,616
Length 194
Max. P 0.944041
window9362 window9363 window9364 window9365

overview

Window 2

Location 9,987,422 – 9,987,540
Length 118
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 88.94
Shannon entropy 0.19465
G+C content 0.35686
Mean single sequence MFE -24.30
Consensus MFE -19.56
Energy contribution -20.20
Covariance contribution 0.64
Combinations/Pair 1.12
Mean z-score -1.68
Structure conservation index 0.80
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.30
SVM RNA-class probability 0.636371
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 9987422 118 - 24543557
GAUGCAGCU--AGUGCAUCAUUAUCAUCUGAAAUACAGCACCUUUUCAACGCACAACAAAGUGGAAAAUGGUAAAUUAGAUAAAUUUCGGAUAACUCGCAAUUAUCGGAUAGCCAAAAUC
((((((...--..)))))).(((((..(((.....))).((((((((..(((........)))))))).)))......)))))...((.(((((.......))))).))........... ( -21.60, z-score =  -0.99, R)
>droEre2.scaffold_4784 9970795 118 - 25762168
GAUGCAUCU--AGUGCAUCAUUAUACCAUGAAAUACAGCACCUUUUUGGCGCACAUAAAAGUGAAAAAUGGUAAAUUAGAUUAAUUUCGCAUUACUCGCAAUUAUCUGAAAGCCAAAAUC
(((((((..--.)))))))........................(((((((.((.((((..((((..(((((.((((((...))))))).))))..))))..)))).))...))))))).. ( -25.80, z-score =  -2.30, R)
>droYak2.chr3L 9963576 118 - 24197627
GAUGCAUCU--ACUGCAUCAUUAUUACAUGACAUACAGCACCUUUUUGGCGCACAUCAAAGUGGAAAAUGGUAAAUUAGAUUAAUUUCGAAUUACCAGCAAUUAUCUGAACGCCAAAAUC
((((((...--..))))))........................(((((((((((......))).....((((((....((......))...)))))).............)))))))).. ( -26.10, z-score =  -2.57, R)
>droSec1.super_0 2210695 120 - 21120651
GAUGCAUCUCCAGUGCAUCAUUAUCAUCUGAAAUUCAGCACCUUUUCAACGCACAACAAAGUGGAAAAUGGUAAAUUGGAUUAAAUUCGGAUUACUCGCAAUUAUCUGAUAGCCAAAAUC
(((((((.....)))))))......(((((((((((((.((((((((..(((........)))))))).)))...))))))....))))))).....((.(((....))).))....... ( -23.50, z-score =  -1.10, R)
>droSim1.chr3L 9373223 120 - 22553184
GAUGCAUCUCUAGUGCAUCAUUAUCAUCUGAAAUGCAGCACCUUUUCAACGCACAACAAAGUGGAAAAUGGUAAAUUAGAUUAAUUUCGGAUUACUCGCAAUUAUCUGAUAGCCAAAAUC
(((((((.....)))))))..................((((((((((..(((........)))))))).)))..(((((((.((((.(((.....))).))))))))))).))....... ( -24.50, z-score =  -1.43, R)
>consensus
GAUGCAUCU__AGUGCAUCAUUAUCAUCUGAAAUACAGCACCUUUUCAACGCACAACAAAGUGGAAAAUGGUAAAUUAGAUUAAUUUCGGAUUACUCGCAAUUAUCUGAUAGCCAAAAUC
(((((((.....)))))))..................((((((((((.((..........)).))))).)))...((((((.((((.(((.....))).))))))))))..))....... (-19.56 = -20.20 +   0.64)

alignment

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secondary structure

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dotplot

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Window 3

Location 9,987,462 – 9,987,579
Length 117
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 87.71
Shannon entropy 0.21291
G+C content 0.34447
Mean single sequence MFE -26.74
Consensus MFE -21.50
Energy contribution -21.10
Covariance contribution -0.40
Combinations/Pair 1.15
Mean z-score -1.85
Structure conservation index 0.80
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.74
SVM RNA-class probability 0.803644
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 9987462 117 - 24543557
UAAAUAGGCACAG-GAAAUUAUUUUGCUAAUACGAUUAGUGAUGCAGCU--AGUGCAUCAUUAUCAUCUGAAAUACAGCACCUUUUCAACGCACAACAAAGUGGAAAAUGGUAAAUUAGA
.......((..((-.(((....))).)).....(((.(((((((((...--..))))))))))))............))((((((((..(((........)))))))).)))........ ( -22.50, z-score =  -0.82, R)
>droEre2.scaffold_4784 9970835 113 - 25762168
UUAAUAGGAAC-----AUUUAUUUGGCUAAUACGAUUAGUGAUGCAUCU--AGUGCAUCAUUAUACCAUGAAAUACAGCACCUUUUUGGCGCACAUAAAAGUGAAAAAUGGUAAAUUAGA
...........-----..........(((((.....(((((((((((..--.)))))))))))((((((........((.((.....)).)).(((....)))....)))))).))))). ( -26.50, z-score =  -2.44, R)
>droYak2.chr3L 9963616 118 - 24197627
UUAAUGGGAACAGCCAAUGUAUUUGGCUAAUACGAUUAGUGAUGCAUCU--ACUGCAUCAUUAUUACAUGACAUACAGCACCUUUUUGGCGCACAUCAAAGUGGAAAAUGGUAAAUUAGA
(((((......((((((.....))))))..(((.((((((((((((...--..)))))))))....(((........((.((.....)).))........)))...))).))).))))). ( -27.39, z-score =  -1.30, R)
>droSec1.super_0 2210735 119 - 21120651
UAAAUAGGCACAG-CAAAUUAUUUUGCUAAUACGAUUAGUGAUGCAUCUCCAGUGCAUCAUUAUCAUCUGAAAUUCAGCACCUUUUCAACGCACAACAAAGUGGAAAAUGGUAAAUUGGA
.......((..((-((((....)))))).....(((.((((((((((.....)))))))))))))............))((((((((..(((........)))))))).)))........ ( -28.40, z-score =  -2.32, R)
>droSim1.chr3L 9373263 119 - 22553184
UAAAUAGGCACAG-CAAAUUAUUUUGCUAAUACGAUUAGUGAUGCAUCUCUAGUGCAUCAUUAUCAUCUGAAAUGCAGCACCUUUUCAACGCACAACAAAGUGGAAAAUGGUAAAUUAGA
.......(((.((-((((....)))))).....(((.((((((((((.....)))))))))))))........)))...((((((((..(((........)))))))).)))........ ( -28.90, z-score =  -2.39, R)
>consensus
UAAAUAGGCACAG_CAAAUUAUUUUGCUAAUACGAUUAGUGAUGCAUCU__AGUGCAUCAUUAUCAUCUGAAAUACAGCACCUUUUCAACGCACAACAAAGUGGAAAAUGGUAAAUUAGA
..........................(((((.....(((((((((((.....)))))))))))................((((((((.((..........)).))))).)))..))))). (-21.50 = -21.10 +  -0.40)

alignment

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secondary structure

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dotplot

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Window 4

Location 9,987,502 – 9,987,613
Length 111
Sequences 4
Columns 116
Reading direction reverse
Mean pairwise identity 89.20
Shannon entropy 0.17436
G+C content 0.33698
Mean single sequence MFE -31.15
Consensus MFE -25.08
Energy contribution -25.45
Covariance contribution 0.37
Combinations/Pair 1.15
Mean z-score -2.45
Structure conservation index 0.80
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.50
SVM RNA-class probability 0.944041
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 9987502 111 - 24543557
GUAAGCCUUUAUGACUUGUGCAA--GUGUAUAUAUUUAAAUAGGCACAGGAAAU-UAUUUUGCUAAUACGAUUAGUGAUGCAGCU--AGUGCAUCAUUAUCAUCUGAAAUACAGCA
(((.((((....((..(((((..--..)))))..)).....)))).((((..((-((......))))..(((.(((((((((...--..)))))))))))).))))...))).... ( -25.80, z-score =  -0.71, R)
>droYak2.chr3L 9963656 114 - 24197627
GUAAGCCUUUAUGGCUUGUUCAACUGUAUAUGUAUUUUAAUGGGAACAGCCAAUGUAUUUGGCUAAUACGAUUAGUGAUGCAUCU--ACUGCAUCAUUAUUACAUGACAUACAGCA
.((((((.....)))))).....((((((.((((((.....(....)((((((.....))))))))))))..((((((((((...--..)))))))))).........)))))).. ( -35.00, z-score =  -3.45, R)
>droSec1.super_0 2210775 113 - 21120651
GUAAGCCUUUAUGAUUUGUGCAA--GUGUAUAUAUUUAAAUAGGCACAGCAAAU-UAUUUUGCUAAUACGAUUAGUGAUGCAUCUCCAGUGCAUCAUUAUCAUCUGAAAUUCAGCA
(((.((((....(((.(((((..--..))))).))).....))))..((((((.-...))))))..)))(((.((((((((((.....)))))))))))))..(((.....))).. ( -32.80, z-score =  -3.54, R)
>droSim1.chr3L 9373303 113 - 22553184
GUAAGCCUUUAUGACUUGUGCAA--GUGUAUAUAUUUAAAUAGGCACAGCAAAU-UAUUUUGCUAAUACGAUUAGUGAUGCAUCUCUAGUGCAUCAUUAUCAUCUGAAAUGCAGCA
(((.((((....((..(((((..--..)))))..)).....))))..((((((.-...))))))..)))(((.((((((((((.....)))))))))))))..(((.....))).. ( -31.00, z-score =  -2.08, R)
>consensus
GUAAGCCUUUAUGACUUGUGCAA__GUGUAUAUAUUUAAAUAGGCACAGCAAAU_UAUUUUGCUAAUACGAUUAGUGAUGCAUCU__AGUGCAUCAUUAUCAUCUGAAAUACAGCA
(((.((((....((..((((((....))))))..)).....))))..((((((.....))))))..)))(((.((((((((((.....)))))))))))))............... (-25.08 = -25.45 +   0.37)

alignment

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secondary structure

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dotplot

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Window 5

Location 9,987,505 – 9,987,616
Length 111
Sequences 4
Columns 116
Reading direction reverse
Mean pairwise identity 89.20
Shannon entropy 0.17436
G+C content 0.32811
Mean single sequence MFE -30.10
Consensus MFE -25.08
Energy contribution -25.45
Covariance contribution 0.37
Combinations/Pair 1.15
Mean z-score -2.16
Structure conservation index 0.83
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.25
SVM RNA-class probability 0.916807
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 9987505 111 - 24543557
AUGGUAAGCCUUUAUGACUUGUGCAA--GUGUAUAUAUUUAAAUAGGCACAGGAAAU-UAUUUUGCUAAUACGAUUAGUGAUGCAGCU--AGUGCAUCAUUAUCAUCUGAAAUACA
.(((((((.....((..(((((((..--...((......)).....)))))))..))-...)))))))....(((.(((((((((...--..))))))))))))............ ( -26.00, z-score =  -0.90, R)
>droYak2.chr3L 9963659 114 - 24197627
AUGGUAAGCCUUUAUGGCUUGUUCAACUGUAUAUGUAUUUUAAUGGGAACAGCCAAUGUAUUUGGCUAAUACGAUUAGUGAUGCAUCU--ACUGCAUCAUUAUUACAUGACAUACA
....((((((.....))))))......(((.((((((...((((.(....((((((.....))))))....).))))((((((((...--..))))))))...))))))))).... ( -32.20, z-score =  -2.58, R)
>droSec1.super_0 2210778 113 - 21120651
AUGGUAAGCCUUUAUGAUUUGUGCAA--GUGUAUAUAUUUAAAUAGGCACAGCAAAU-UAUUUUGCUAAUACGAUUAGUGAUGCAUCUCCAGUGCAUCAUUAUCAUCUGAAAUUCA
...(((.((((....(((.(((((..--..))))).))).....))))..((((((.-...))))))..)))(((.((((((((((.....)))))))))))))............ ( -31.60, z-score =  -3.07, R)
>droSim1.chr3L 9373306 113 - 22553184
AUGGUAAGCCUUUAUGACUUGUGCAA--GUGUAUAUAUUUAAAUAGGCACAGCAAAU-UAUUUUGCUAAUACGAUUAGUGAUGCAUCUCUAGUGCAUCAUUAUCAUCUGAAAUGCA
...(((.((((....((..(((((..--..)))))..)).....))))..((((((.-...))))))..)))(((.((((((((((.....)))))))))))))............ ( -30.60, z-score =  -2.07, R)
>consensus
AUGGUAAGCCUUUAUGACUUGUGCAA__GUGUAUAUAUUUAAAUAGGCACAGCAAAU_UAUUUUGCUAAUACGAUUAGUGAUGCAUCU__AGUGCAUCAUUAUCAUCUGAAAUACA
...(((.((((....((..((((((....))))))..)).....))))..((((((.....))))))..)))(((.((((((((((.....)))))))))))))............ (-25.08 = -25.45 +   0.37)

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 23:14:48 2011