Locus 151

Sequence ID dm3.chr2L
Location 1,046,062 – 1,046,251
Length 189
Max. P 0.913296
window212 window213 window214 window215

overview

Window 2

Location 1,046,062 – 1,046,155
Length 93
Sequences 3
Columns 93
Reading direction forward
Mean pairwise identity 95.70
Shannon entropy 0.05924
G+C content 0.45161
Mean single sequence MFE -27.77
Consensus MFE -23.03
Energy contribution -23.70
Covariance contribution 0.67
Combinations/Pair 1.00
Mean z-score -2.26
Structure conservation index 0.83
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.71
SVM RNA-class probability 0.794678
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 1046062 93 + 23011544
UCCGUGAAUGGGUCACCAUAUCGCCCUGACAUUAUUAUGCCAGCUUUCCGCUGGUCUAUUUGUGGGUGUGACAUGACCAUUCAAGCUUUUUGU
....(((((((.(((......(((((..(((....((.((((((.....)))))).))..)))))))).....)))))))))).......... ( -29.50, z-score =  -2.41, R)
>droSim1.chr2L 1016665 93 + 22036055
UCCGCGAAUGGGUCACCAUAUCCCCCUGACAUUAUUAUGCCAGCUUUCUGCUGGUCUAUUUGUGGGUGCGACAUGACCAUUAAAUCUUUUUGU
(((((((((((((((...........))))........((((((.....)))))))))))))))))........................... ( -25.00, z-score =  -1.64, R)
>droSec1.super_14 999478 93 + 2068291
UCCGUGAAUGGGUCACCAUAUCCCCCUGACAUUAUUAUGCCAGCUUUCUGCUGGUCUAUUUGUGGGUGUGACAUGACCAUUCAAUCUUUUUGU
....(((((((.(((.(((((((.....(((....((.((((((.....)))))).))..))))))))))...)))))))))).......... ( -28.80, z-score =  -2.73, R)
>consensus
UCCGUGAAUGGGUCACCAUAUCCCCCUGACAUUAUUAUGCCAGCUUUCUGCUGGUCUAUUUGUGGGUGUGACAUGACCAUUCAAUCUUUUUGU
....(((((((.....(((.((.((((.(((....((.((((((.....)))))).))..)))))).).)).))).))))))).......... (-23.03 = -23.70 +   0.67)

alignment

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secondary structure

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dotplot

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Window 3

Location 1,046,062 – 1,046,155
Length 93
Sequences 3
Columns 93
Reading direction reverse
Mean pairwise identity 95.70
Shannon entropy 0.05924
G+C content 0.45161
Mean single sequence MFE -25.50
Consensus MFE -25.22
Energy contribution -25.33
Covariance contribution 0.11
Combinations/Pair 1.04
Mean z-score -1.53
Structure conservation index 0.99
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.23
SVM RNA-class probability 0.913296
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 1046062 93 - 23011544
ACAAAAAGCUUGAAUGGUCAUGUCACACCCACAAAUAGACCAGCGGAAAGCUGGCAUAAUAAUGUCAGGGCGAUAUGGUGACCCAUUCACGGA
........(.((((((((((((((...((((((..((..(((((.....)))))..))....)))..))).)))))))....))))))).).. ( -26.40, z-score =  -1.71, R)
>droSim1.chr2L 1016665 93 - 22036055
ACAAAAAGAUUUAAUGGUCAUGUCGCACCCACAAAUAGACCAGCAGAAAGCUGGCAUAAUAAUGUCAGGGGGAUAUGGUGACCCAUUCGCGGA
.......((((....))))...((((.((((((..((..(((((.....)))))..))....)))..)))((((..(....)..)))))))). ( -22.40, z-score =  -0.49, R)
>droSec1.super_14 999478 93 - 2068291
ACAAAAAGAUUGAAUGGUCAUGUCACACCCACAAAUAGACCAGCAGAAAGCUGGCAUAAUAAUGUCAGGGGGAUAUGGUGACCCAUUCACGGA
..........((((((((((((((...((((((..((..(((((.....)))))..))....)))..))).)))))))....))))))).... ( -27.70, z-score =  -2.38, R)
>consensus
ACAAAAAGAUUGAAUGGUCAUGUCACACCCACAAAUAGACCAGCAGAAAGCUGGCAUAAUAAUGUCAGGGGGAUAUGGUGACCCAUUCACGGA
..........((((((((((((((...((((((..((..(((((.....)))))..))....)))..))).)))))))....))))))).... (-25.22 = -25.33 +   0.11)

alignment

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secondary structure

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dotplot

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Window 4

Location 1,046,155 – 1,046,250
Length 95
Sequences 5
Columns 113
Reading direction forward
Mean pairwise identity 75.05
Shannon entropy 0.40047
G+C content 0.43602
Mean single sequence MFE -24.16
Consensus MFE -16.38
Energy contribution -17.34
Covariance contribution 0.96
Combinations/Pair 1.23
Mean z-score -1.35
Structure conservation index 0.68
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.52
SVM RNA-class probability 0.727765
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 1046155 95 + 23011544
CUCAGGUCAACGAGGUGCCUCGAAUUGUUAUUCAGUUGACC---------------AGACCU---UAACUGCAGGCAAAUAAAUCAUGUUUGCAAAUGCCCAUUUAUGGGAAG
....((((((((((....)))((((....)))).)))))))---------------......---....((((((((.........))))))))....((((....))))... ( -30.00, z-score =  -3.10, R)
>droSim1.chr2L 1016758 91 + 22036055
CUCAGGCCAGCGAGGUGCCUCGAAUUGGGACUCAGUUGACC---------------AGACCU---UAUCUGCAGUCAAAUAAAUCAUGAUUGCAAUUGCCCAUUUCUGU----
....(((((((..(((.((.......)).)))..))))...---------------......---....((((((((.........))))))))...))).........---- ( -23.00, z-score =  -0.37, R)
>droSec1.super_14 999571 91 + 2068291
CUCAGGUCAACGAGGUGCCUCGAAUUGGAACUCAGUUGACC---------------AGACCU---UAUCUGCAGUCAAAUAAAUCAUGAUUGCAAUUGCCCAUUUCUGU----
....((((((((((...((.......))..))).)))))))---------------......---....((((((((.........))))))))...............---- ( -25.80, z-score =  -2.21, R)
>droEre2.scaffold_4929 1087964 89 + 26641161
CCCAGGUAAACGAGGUGCCUCGAAUUAUAAUUCAGUUGGC---------------AAGAUAUGUGUAUCUGCGGUCAAAUAUCUCAUGCUCGCAAUUGCCCAAU---------
....(((((.((((....))))............((.(((---------------(((((((.((.((.....)))).))))))..)))).))..)))))....--------- ( -21.50, z-score =  -1.01, R)
>droYak2.chr2L 1021877 113 + 22324452
CUCAGCUUAACGAGGUGCCUCGAAUUAUAAUUCAGUUGGCCAGACCAUAAUAGCCAAGAUAUGUUUACCUGCAGUCAAAUAUAUCAUGUUCGCAAUUGCCCAAUUACGUGAAA
..........((((....)))).............(((((.(........).)))))(((((((((..(....)..)))))))))...(((((((((....))))..))))). ( -20.50, z-score =  -0.06, R)
>consensus
CUCAGGUCAACGAGGUGCCUCGAAUUGUAAUUCAGUUGACC_______________AGACCU___UAUCUGCAGUCAAAUAAAUCAUGAUUGCAAUUGCCCAUUUAUGU____
....((((((((((....)))((((....)))).)))))))............................((((((((.........))))))))................... (-16.38 = -17.34 +   0.96)

alignment

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secondary structure

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dotplot

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Window 5

Location 1,046,156 – 1,046,251
Length 95
Sequences 5
Columns 113
Reading direction forward
Mean pairwise identity 74.39
Shannon entropy 0.40906
G+C content 0.43233
Mean single sequence MFE -24.72
Consensus MFE -16.38
Energy contribution -17.34
Covariance contribution 0.96
Combinations/Pair 1.23
Mean z-score -1.57
Structure conservation index 0.66
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.90
SVM RNA-class probability 0.847341
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 1046156 95 + 23011544
UCAGGUCAACGAGGUGCCUCGAAUUGUUAUUCAGUUGACC---------------AGACCU---UAACUGCAGGCAAAUAAAUCAUGUUUGCAAAUGCCCAUUUAUGGGAAGG
...((((((((((....)))((((....)))).)))))))---------------...(((---(...((((((((.........))))))))....((((....)))))))) ( -32.80, z-score =  -3.73, R)
>droSim1.chr2L 1016759 90 + 22036055
UCAGGCCAGCGAGGUGCCUCGAAUUGGGACUCAGUUGACC---------------AGACCU---UAUCUGCAGUCAAAUAAAUCAUGAUUGCAAUUGCCCAUUUCUGU-----
...(((((((..(((.((.......)).)))..))))...---------------......---....((((((((.........))))))))...))).........----- ( -23.00, z-score =  -0.48, R)
>droSec1.super_14 999572 90 + 2068291
UCAGGUCAACGAGGUGCCUCGAAUUGGAACUCAGUUGACC---------------AGACCU---UAUCUGCAGUCAAAUAAAUCAUGAUUGCAAUUGCCCAUUUCUGU-----
...((((((((((...((.......))..))).)))))))---------------......---....((((((((.........))))))))...............----- ( -25.80, z-score =  -2.30, R)
>droEre2.scaffold_4929 1087965 88 + 26641161
CCAGGUAAACGAGGUGCCUCGAAUUAUAAUUCAGUUGGC---------------AAGAUAUGUGUAUCUGCGGUCAAAUAUCUCAUGCUCGCAAUUGCCCAAU----------
...(((((.((((....))))............((.(((---------------(((((((.((.((.....)))).))))))..)))).))..)))))....---------- ( -21.50, z-score =  -1.07, R)
>droYak2.chr2L 1021878 113 + 22324452
UCAGCUUAACGAGGUGCCUCGAAUUAUAAUUCAGUUGGCCAGACCAUAAUAGCCAAGAUAUGUUUACCUGCAGUCAAAUAUAUCAUGUUCGCAAUUGCCCAAUUACGUGAAAG
.........((((....)))).............(((((.(........).)))))(((((((((..(....)..)))))))))...(((((((((....))))..))))).. ( -20.50, z-score =  -0.27, R)
>consensus
UCAGGUCAACGAGGUGCCUCGAAUUGUAAUUCAGUUGACC_______________AGACCU___UAUCUGCAGUCAAAUAAAUCAUGAUUGCAAUUGCCCAUUUAUGU_____
...((((((((((....)))((((....)))).)))))))............................((((((((.........)))))))).................... (-16.38 = -17.34 +   0.96)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 21:07:38 2011