Locus 1118

Sequence ID dm3.chr2L
Location 8,421,236 – 8,421,386
Length 150
Max. P 0.984219
window1526 window1527 window1528

overview

Window 6

Location 8,421,236 – 8,421,337
Length 101
Sequences 3
Columns 101
Reading direction forward
Mean pairwise identity 79.93
Shannon entropy 0.28098
G+C content 0.35745
Mean single sequence MFE -26.67
Consensus MFE -11.21
Energy contribution -13.44
Covariance contribution 2.23
Combinations/Pair 1.08
Mean z-score -3.54
Structure conservation index 0.42
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.63
SVM RNA-class probability 0.956526
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 8421236 101 + 23011544
UUCGUAUGCGCCAUUUCGGGUUUUGCGCCUUGCAAAAAAGAAGUUGGCAUACGUUUCUAGCCAUCAUACAAUUCAUACAUAUAUACAUACAUAUAUGUAAA
..(((((((.(.(((((...((((((.....))))))..))))).))))))))......................(((((((((......))))))))).. ( -26.80, z-score =  -3.35, R)
>droEre2.scaffold_4929 17329950 88 + 26641161
UUCAUAUGC--CAUUUCGGGUUUUGCGCCUUGCAAAA--GUUGUUGGUAUAUGUUUCUAGCCAUCAUACA-UACAUACUUAUAU--------GUAUGUAAA
..(((((((--((...(((.((((((.....))))))--.))).))))))))).............((((-((((((....)))--------))))))).. ( -29.00, z-score =  -4.75, R)
>droYak2.chr2L 11059084 96 + 22324452
UUCUUAGGC--CAUUUCGGGUUU-GCGCAUUGCAAAAA-GAAGUUGGCAUACGCUUCUAGCCAUCAUACA-UACAAACUAACAUACAGAUUUGUAUGUAAA
.......((--((((((...(((-((.....)))))..-)))).))))....((.....)).....((((-((((((((.......)).)))))))))).. ( -24.20, z-score =  -2.52, R)
>consensus
UUCAUAUGC__CAUUUCGGGUUUUGCGCCUUGCAAAAA_GAAGUUGGCAUACGUUUCUAGCCAUCAUACA_UACAUACUUAUAUACA_A__UGUAUGUAAA
..(((((((...(((((...((((((.....))))))..)))))..)))))))..................(((((((..............))))))).. (-11.21 = -13.44 +   2.23)

alignment

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secondary structure

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dotplot

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Window 7

Location 8,421,278 – 8,421,386
Length 108
Sequences 3
Columns 108
Reading direction forward
Mean pairwise identity 84.21
Shannon entropy 0.21874
G+C content 0.38005
Mean single sequence MFE -30.52
Consensus MFE -16.13
Energy contribution -15.92
Covariance contribution -0.21
Combinations/Pair 1.24
Mean z-score -3.71
Structure conservation index 0.53
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.16
SVM RNA-class probability 0.984219
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 8421278 108 + 23011544
GUUGGCAUACGUUUCUAGCCAUCAUACAAUUCAUACAUAUAUACAUACAUAUAUGUAAAUAGUGAAGGAACGGUCGUACAAAGACAUAUCGGACGUUCUCAACGAGCU
(.((((...........)))).)......(((.(((((((((......)))))))))....((...((((((..((.............))..))))))..))))).. ( -22.22, z-score =  -1.55, R)
>droEre2.scaffold_4929 17329988 106 + 26641161
GUUGGUAUAUGUUUCUAGCCAUCAUACA-UACAUACUUAUAUGUAUGUAAAUG-GCAGAAUAUGAAGGAACGUUCGUACAAAGACAUAUCGGACGUUCUCAACGAGCU
((((...((((((.((.(((((..((((-((((((....)))))))))).)))-))))))))))..((((((((((.............))))))))))))))..... ( -36.22, z-score =  -5.19, R)
>droYak2.chr2L 11059122 107 + 22324452
GUUGGCAUACGCUUCUAGCCAUCAUACA-UACAAACUAACAUACAGAUUUGUAUGUAAAUGGUGAAGGAACGUUCGUACAAAGACAUAUCGGACGUUCUCAACGAGCU
(((((......((((..(((((..((((-((((((((.......)).)))))))))).)))))))))(((((((((.............))))))))))))))..... ( -33.12, z-score =  -4.39, R)
>consensus
GUUGGCAUACGUUUCUAGCCAUCAUACA_UACAUACUUAUAUACAUAUAUAUAUGUAAAUAGUGAAGGAACGUUCGUACAAAGACAUAUCGGACGUUCUCAACGAGCU
(.((((...........)))).)..................((((((....)))))).........((((((((((.............))))))))))......... (-16.13 = -15.92 +  -0.21)

alignment

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secondary structure

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dotplot

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Window 8

Location 8,421,278 – 8,421,386
Length 108
Sequences 3
Columns 108
Reading direction reverse
Mean pairwise identity 84.21
Shannon entropy 0.21874
G+C content 0.38005
Mean single sequence MFE -28.57
Consensus MFE -14.94
Energy contribution -15.40
Covariance contribution 0.46
Combinations/Pair 1.24
Mean z-score -2.58
Structure conservation index 0.52
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.03
SVM RNA-class probability 0.509785
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 8421278 108 - 23011544
AGCUCGUUGAGAACGUCCGAUAUGUCUUUGUACGACCGUUCCUUCACUAUUUACAUAUAUGUAUGUAUAUAUGUAUGAAUUGUAUGAUGGCUAGAAACGUAUGCCAAC
...((((((((((((..(((((......))).))..)))))..))).......((((((((((....))))))))))......))))((((...........)))).. ( -21.80, z-score =  -0.12, R)
>droEre2.scaffold_4929 17329988 106 - 26641161
AGCUCGUUGAGAACGUCCGAUAUGUCUUUGUACGAACGUUCCUUCAUAUUCUGC-CAUUUACAUACAUAUAAGUAUGUA-UGUAUGAUGGCUAGAAACAUAUACCAAC
.....((((.((((((.(((((......))).)).)))))).......((((((-((((((((((((((....))))))-)))).)))))).))))........)))) ( -33.40, z-score =  -4.78, R)
>droYak2.chr2L 11059122 107 - 22324452
AGCUCGUUGAGAACGUCCGAUAUGUCUUUGUACGAACGUUCCUUCACCAUUUACAUACAAAUCUGUAUGUUAGUUUGUA-UGUAUGAUGGCUAGAAGCGUAUGCCAAC
.((.((((..((((((.(((((......))).)).))))))((...(((((((((((((((.(((.....)))))))))-)))).)))))..)).))))...)).... ( -30.50, z-score =  -2.85, R)
>consensus
AGCUCGUUGAGAACGUCCGAUAUGUCUUUGUACGAACGUUCCUUCACAAUUUACAUAUAUAUAUGUAUAUAAGUAUGUA_UGUAUGAUGGCUAGAAACGUAUGCCAAC
.....((((.((((((.(((((......))).)).))))))((...((((((((((((((((..........))))))).)))).)))))..))..........)))) (-14.94 = -15.40 +   0.46)

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 21:25:56 2011