Locus 3574

Sequence ID dm3.chr2R
Location 6,483,767 – 6,483,889
Length 122
Max. P 0.965250
window4902 window4903 window4904 window4905

overview

Window 2

Location 6,483,767 – 6,483,858
Length 91
Sequences 6
Columns 96
Reading direction forward
Mean pairwise identity 79.45
Shannon entropy 0.39072
G+C content 0.42985
Mean single sequence MFE -22.62
Consensus MFE -15.29
Energy contribution -15.02
Covariance contribution -0.27
Combinations/Pair 1.31
Mean z-score -1.56
Structure conservation index 0.68
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.83
SVM RNA-class probability 0.829814
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 6483767 91 + 21146708
--AAAUUUUCCCUUUCGCGGC---AACCUGAGACCAUUAGAUUUGGCCAACGAAGAAGAACCUGUUUAAUGGAACACGUUUUCUUAUUUGGCCCUC
--((((((....(((((.(..---..).))))).....))))))((((((..(((((((...(((((....)))))..)))))))..))))))... ( -23.80, z-score =  -2.53, R)
>droSim1.chr2R 5107812 94 + 19596830
--AAAUUUUCCCUUUCGCGGCGGCAACCUGAGACCAUUAGAUUUGGCCAACGAAGAAGAACCUGUUUAAUGGAACACGUUUUCUUAUUUGGCCCUC
--((((((......((.(((.(....)))).)).....))))))((((((..(((((((...(((((....)))))..)))))))..))))))... ( -24.50, z-score =  -1.73, R)
>droSec1.super_1 4086169 94 + 14215200
--AAAUUUUCCCUUUCGCGGCGGCAACCUGAGACCAUUAGAUUUGGCCAACGAAGAAGAACCUGUUUAAUGGAACACGUUUUCUUAUUUGGCCCUC
--((((((......((.(((.(....)))).)).....))))))((((((..(((((((...(((((....)))))..)))))))..))))))... ( -24.50, z-score =  -1.73, R)
>droYak2.chr2R 18475318 91 - 21139217
--AAAUUUUUCCUUUCGCGGC---AACAUGAGACCAAUAGAUUUGGCCAACGAAGAAGAACCUGUUUAAUGGAACACGUUUUCCUCUUUGGCCCUC
--((((((....(((((.(..---..).))))).....))))))((((((.((.(((((...(((((....)))))..))))).)).))))))... ( -23.40, z-score =  -2.17, R)
>droEre2.scaffold_4845 3315053 91 - 22589142
--AAAUUUUCCCUUUCGCGGC---AACCUGAGACCAUUAGGCUUGGCCAACGAAGAAGAACCUGUUUAAUGGAACACGUUUUCUUAUUUGGCCCUC
--..........(((((.(..---..).)))))((....))...((((((..(((((((...(((((....)))))..)))))))..))))))... ( -22.60, z-score =  -1.31, R)
>droWil1.scaffold_180569 381475 90 + 1405142
GGAAGUGUCUAAGAGCGCGACCUCCAUAUGUGUUCACUGGA--UGA--AAAGAAAAAUAACCUGUUUUCUAGAGA--GUUAGUUCAGUUACUUUUU
(((((((.((..((((..(((((((((..((....))...)--)).--..((((((........)))))).))).--))).)))))).))))))). ( -16.90, z-score =   0.09, R)
>consensus
__AAAUUUUCCCUUUCGCGGC___AACCUGAGACCAUUAGAUUUGGCCAACGAAGAAGAACCUGUUUAAUGGAACACGUUUUCUUAUUUGGCCCUC
............(((((.((......)))))))...........((((((..((((.((((.(((((....))))).))))))))..))))))... (-15.29 = -15.02 +  -0.27)

alignment

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secondary structure

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dotplot

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Window 3

Location 6,483,767 – 6,483,858
Length 91
Sequences 6
Columns 96
Reading direction reverse
Mean pairwise identity 79.45
Shannon entropy 0.39072
G+C content 0.42985
Mean single sequence MFE -24.85
Consensus MFE -16.14
Energy contribution -17.20
Covariance contribution 1.06
Combinations/Pair 1.30
Mean z-score -1.61
Structure conservation index 0.65
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.74
SVM RNA-class probability 0.802487
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 6483767 91 - 21146708
GAGGGCCAAAUAAGAAAACGUGUUCCAUUAAACAGGUUCUUCUUCGUUGGCCAAAUCUAAUGGUCUCAGGUU---GCCGCGAAAGGGAAAAUUU--
(((((((((..((((((((.((((......)))).))).)))))..))))))..(((....)))))).....---.((.(....))).......-- ( -25.90, z-score =  -2.10, R)
>droSim1.chr2R 5107812 94 - 19596830
GAGGGCCAAAUAAGAAAACGUGUUCCAUUAAACAGGUUCUUCUUCGUUGGCCAAAUCUAAUGGUCUCAGGUUGCCGCCGCGAAAGGGAAAAUUU--
((.((((((..((((((((.((((......)))).))).)))))..))))))...)).(((..((((...((((....))))..))))..))).-- ( -27.50, z-score =  -1.85, R)
>droSec1.super_1 4086169 94 - 14215200
GAGGGCCAAAUAAGAAAACGUGUUCCAUUAAACAGGUUCUUCUUCGUUGGCCAAAUCUAAUGGUCUCAGGUUGCCGCCGCGAAAGGGAAAAUUU--
((.((((((..((((((((.((((......)))).))).)))))..))))))...)).(((..((((...((((....))))..))))..))).-- ( -27.50, z-score =  -1.85, R)
>droYak2.chr2R 18475318 91 + 21139217
GAGGGCCAAAGAGGAAAACGUGUUCCAUUAAACAGGUUCUUCUUCGUUGGCCAAAUCUAUUGGUCUCAUGUU---GCCGCGAAAGGAAAAAUUU--
((.((((((.(((((((((.((((......)))).))).)))))).))))))...))....(((........---))).(....).........-- ( -26.90, z-score =  -2.21, R)
>droEre2.scaffold_4845 3315053 91 + 22589142
GAGGGCCAAAUAAGAAAACGUGUUCCAUUAAACAGGUUCUUCUUCGUUGGCCAAGCCUAAUGGUCUCAGGUU---GCCGCGAAAGGGAAAAUUU--
(((((((((..((((((((.((((......)))).))).)))))..))))))..(((....)))))).....---.((.(....))).......-- ( -28.80, z-score =  -2.35, R)
>droWil1.scaffold_180569 381475 90 - 1405142
AAAAAGUAACUGAACUAAC--UCUCUAGAAAACAGGUUAUUUUUCUUU--UCA--UCCAGUGAACACAUAUGGAGGUCGCGCUCUUAGACACUUCC
.((((((((((...(((..--....)))......))))))))))...(--(((--(...))))).......(((((((.........))).)))). ( -12.50, z-score =   0.73, R)
>consensus
GAGGGCCAAAUAAGAAAACGUGUUCCAUUAAACAGGUUCUUCUUCGUUGGCCAAAUCUAAUGGUCUCAGGUU___GCCGCGAAAGGGAAAAUUU__
(((((((((..((((((((.((((......)))).))).)))))..))))))..(((....)))))).........((.(....)))......... (-16.14 = -17.20 +   1.06)

alignment

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secondary structure

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dotplot

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Window 4

Location 6,483,795 – 6,483,889
Length 94
Sequences 6
Columns 94
Reading direction forward
Mean pairwise identity 82.41
Shannon entropy 0.34473
G+C content 0.36863
Mean single sequence MFE -19.20
Consensus MFE -14.21
Energy contribution -14.77
Covariance contribution 0.56
Combinations/Pair 1.26
Mean z-score -1.72
Structure conservation index 0.74
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.08
SVM RNA-class probability 0.888022
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 6483795 94 + 21146708
CCAUUAGAUUUGGCCAACGAAGAAGAACCUGUUUAAUGGAACACGUUUUCUUAUUUGGCCCUCUGCUCCUUGUUAUUAUUAUUAUCUCUUUUGG
(((..(((...((((((..(((((((...(((((....)))))..)))))))..))))))....((.....)).............)))..))) ( -21.90, z-score =  -2.69, R)
>droSim1.chr2R 5107843 94 + 19596830
CCAUUAGAUUUGGCCAACGAAGAAGAACCUGUUUAAUGGAACACGUUUUCUUAUUUGGCCCUCUGCUCCUUGUUAUUAUUAUUAUCUCUUUUGG
(((..(((...((((((..(((((((...(((((....)))))..)))))))..))))))....((.....)).............)))..))) ( -21.90, z-score =  -2.69, R)
>droSec1.super_1 4086200 94 + 14215200
CCAUUAGAUUUGGCCAACGAAGAAGAACCUGUUUAAUGGAACACGUUUUCUUAUUUGGCCCUCUGCUCCUUGUUAUUAUUAUUAUCUCUUUUGG
(((..(((...((((((..(((((((...(((((....)))))..)))))))..))))))....((.....)).............)))..))) ( -21.90, z-score =  -2.69, R)
>droYak2.chr2R 18475346 94 - 21139217
CCAAUAGAUUUGGCCAACGAAGAAGAACCUGUUUAAUGGAACACGUUUUCCUCUUUGGCCCUCUGCUCCUUGUUGUUAUUAUUAUUUCUUUUGA
.(((.(((...((((((.((.(((((...(((((....)))))..))))).)).))))))....((.....)).............))).))). ( -19.90, z-score =  -1.87, R)
>droEre2.scaffold_4845 3315081 94 - 22589142
CCAUUAGGCUUGGCCAACGAAGAAGAACCUGUUUAAUGGAACACGUUUUCUUAUUUGGCCCUCUGCUCCUUGUUAUUAUUAUUAUCUCUUUUGG
.((...(((..((((((..(((((((...(((((....)))))..)))))))..))))))....)))...))...................... ( -21.20, z-score =  -1.79, R)
>droWil1.scaffold_180569 381508 88 + 1405142
UCACUGGAUGA----AAAGAAAAAUAACCUGUUUUCUAGAGA--GUUAGUUCAGUUACUUUUUUCCCUUUUGUUAAUGUUGUUCCCCCUUUUUU
..((..((..(----((.((((((....(((....((((...--.))))..))).....))))))..)))..))...))............... (  -8.40, z-score =   1.39, R)
>consensus
CCAUUAGAUUUGGCCAACGAAGAAGAACCUGUUUAAUGGAACACGUUUUCUUAUUUGGCCCUCUGCUCCUUGUUAUUAUUAUUAUCUCUUUUGG
....((((...((((((..((((.((((.(((((....))))).))))))))..)))))).))))............................. (-14.21 = -14.77 +   0.56)

alignment

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secondary structure

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dotplot

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Window 5

Location 6,483,795 – 6,483,889
Length 94
Sequences 6
Columns 94
Reading direction reverse
Mean pairwise identity 82.41
Shannon entropy 0.34473
G+C content 0.36863
Mean single sequence MFE -20.95
Consensus MFE -15.10
Energy contribution -15.77
Covariance contribution 0.67
Combinations/Pair 1.18
Mean z-score -2.17
Structure conservation index 0.72
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.75
SVM RNA-class probability 0.965250
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 6483795 94 - 21146708
CCAAAAGAGAUAAUAAUAAUAACAAGGAGCAGAGGGCCAAAUAAGAAAACGUGUUCCAUUAAACAGGUUCUUCUUCGUUGGCCAAAUCUAAUGG
..............................(((.((((((..((((((((.((((......)))).))).)))))..))))))...)))..... ( -22.10, z-score =  -2.63, R)
>droSim1.chr2R 5107843 94 - 19596830
CCAAAAGAGAUAAUAAUAAUAACAAGGAGCAGAGGGCCAAAUAAGAAAACGUGUUCCAUUAAACAGGUUCUUCUUCGUUGGCCAAAUCUAAUGG
..............................(((.((((((..((((((((.((((......)))).))).)))))..))))))...)))..... ( -22.10, z-score =  -2.63, R)
>droSec1.super_1 4086200 94 - 14215200
CCAAAAGAGAUAAUAAUAAUAACAAGGAGCAGAGGGCCAAAUAAGAAAACGUGUUCCAUUAAACAGGUUCUUCUUCGUUGGCCAAAUCUAAUGG
..............................(((.((((((..((((((((.((((......)))).))).)))))..))))))...)))..... ( -22.10, z-score =  -2.63, R)
>droYak2.chr2R 18475346 94 + 21139217
UCAAAAGAAAUAAUAAUAACAACAAGGAGCAGAGGGCCAAAGAGGAAAACGUGUUCCAUUAAACAGGUUCUUCUUCGUUGGCCAAAUCUAUUGG
..............................(((.((((((.(((((((((.((((......)))).))).)))))).))))))...)))..... ( -25.30, z-score =  -3.56, R)
>droEre2.scaffold_4845 3315081 94 + 22589142
CCAAAAGAGAUAAUAAUAAUAACAAGGAGCAGAGGGCCAAAUAAGAAAACGUGUUCCAUUAAACAGGUUCUUCUUCGUUGGCCAAGCCUAAUGG
.........................((.((....((((((..((((((((.((((......)))).))).)))))..))))))..))))..... ( -21.90, z-score =  -2.05, R)
>droWil1.scaffold_180569 381508 88 - 1405142
AAAAAAGGGGGAACAACAUUAACAAAAGGGAAAAAAGUAACUGAACUAAC--UCUCUAGAAAACAGGUUAUUUUUCUUU----UCAUCCAGUGA
...(((((..(((.(((.........(((((....(((......)))...--))))).........))).)))..))))----).......... ( -12.17, z-score =   0.51, R)
>consensus
CCAAAAGAGAUAAUAAUAAUAACAAGGAGCAGAGGGCCAAAUAAGAAAACGUGUUCCAUUAAACAGGUUCUUCUUCGUUGGCCAAAUCUAAUGG
......................((...((.....((((((..((((((((.((((......)))).))).)))))..))))))....))..)). (-15.10 = -15.77 +   0.67)

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 22:12:45 2011