Locus 10052

Sequence ID dm3.chr3R
Location 10,874,378 – 10,874,503
Length 125
Max. P 0.737406
window13816 window13817

overview

Window 6

Location 10,874,378 – 10,874,503
Length 125
Sequences 6
Columns 140
Reading direction forward
Mean pairwise identity 80.10
Shannon entropy 0.35973
G+C content 0.45316
Mean single sequence MFE -34.95
Consensus MFE -21.34
Energy contribution -22.35
Covariance contribution 1.01
Combinations/Pair 1.36
Mean z-score -1.69
Structure conservation index 0.61
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.31
SVM RNA-class probability 0.637994
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 10874378 125 + 27905053
------------UUUGAGCCUCGACUUGGCCAAUUUGGCACUGCAAAGACAUUUUCCCUAUUUAUGGGAUUGUGUUAGUUUCCCGACCAGUCCCAUCAUCACCAGAACGAAU---GUCGGUUGCCAACUUAAGUCUAAAA
------------..........(((((((((.....)))...((((.(((((((((.......(((((((((.((..(....)..)))))))))))........))..))))---)))..)))).....))))))..... ( -35.36, z-score =  -2.65, R)
>droAna3.scaffold_13340 5952347 137 + 23697760
UCGCCUCGCCCGGGAGAGCCUCGACUGGGCCAAUUUGGCACGCAAUAGAGAUUUUCCCGACCACUGGG--UGUGUUAGCUUCCC-AUUACCAUCACCACCGACCGGGCCAACUAAAUCUGAUGCCAAAAUAAAUUUUUAA
.......((((((..(.....)..))))))...((((((((......)((((((.((((.....((((--.((....))..)))-)......((......)).))))......))))))..)))))))............ ( -33.50, z-score =   0.36, R)
>droSim1.chr3R 16931909 125 - 27517382
------------UUUGAGCCUCGACUUGGCCAAUUUGGCACUGCAAAGACAUUUUCCCUAUUUAUGGGGCUGUGUUAGUUUCCCAGCCAGUCCCAUCAUCACCAGAAUGAAU---GUCGGUUGCCAACUUAAGUUUAAAA
------------.(((.(((.......)))))).((((((..((...(((((((...((....(((((((((.(((........)))))))))))).......))...))))---))).))))))))............. ( -35.70, z-score =  -2.00, R)
>droSec1.super_0 10054165 125 - 21120651
------------UUUGAGCCUCGACUUGGCCAAUUUGGCACUGCAAAGACAUUUUCCCUAUUUAUGGGAUUGUGUUAGUUUCCCGAACAGUCCCAUCAUCACCAGAAUGAAU---GUCGGUUGCCAACUUAAGUCUAAAA
------------..........(((((((((.....)))...((((.(((((((...((....((((((((((.............)))))))))).......))...))))---)))..)))).....))))))..... ( -34.32, z-score =  -2.28, R)
>droYak2.chr3R 13284922 125 - 28832112
------------UUUGAGUCACGGCUUGGCCAAUUUGGCACUGCAAAGACAUUUCCCCCAUUUAUGGGAUUGUGUUAGUUUCCCGACCAGCCCCAUCAUCAGCAGAAUGAAU---GUCGCUUGCCAAGUUAAGUCUAAAA
------------..........((((((((....((((((..((...(((((((.........(((((..((.((..(....)..))))..)))))..((....))..))))---))))).))))))))))))))..... ( -31.70, z-score =  -0.83, R)
>droEre2.scaffold_4770 10407868 125 + 17746568
------------UUUGAGCCUCGGCUUGGCCAAUUUGGCACUGCAAGGCCAUUUUCCCUAUUUAUGGGACUGUGUUAGUUUCCCGACCAGUCCCAUCAUCAGCAGCAUGAAU---GUCGUUUGCCAAGUUAAAUUUAAAA
------------.(..(((....)))..)..(((((((((((((.(((........)))....(((((((((.((..(....)..))))))))))).....)))).(((...---..))).))))))))).......... ( -39.10, z-score =  -2.73, R)
>consensus
____________UUUGAGCCUCGACUUGGCCAAUUUGGCACUGCAAAGACAUUUUCCCUAUUUAUGGGAUUGUGUUAGUUUCCCGACCAGUCCCAUCAUCACCAGAAUGAAU___GUCGGUUGCCAACUUAAGUCUAAAA
.............(((.(((.......)))))).(((((((((......((((((........(((((((((.(((........)))))))))))).......))))))........))).))))))............. (-21.34 = -22.35 +   1.01)

alignment

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secondary structure

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dotplot

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Window 7

Location 10,874,378 – 10,874,503
Length 125
Sequences 6
Columns 140
Reading direction reverse
Mean pairwise identity 80.10
Shannon entropy 0.35973
G+C content 0.45316
Mean single sequence MFE -40.27
Consensus MFE -23.22
Energy contribution -24.42
Covariance contribution 1.20
Combinations/Pair 1.20
Mean z-score -1.92
Structure conservation index 0.58
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.54
SVM RNA-class probability 0.737406
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 10874378 125 - 27905053
UUUUAGACUUAAGUUGGCAACCGAC---AUUCGUUCUGGUGAUGAUGGGACUGGUCGGGAAACUAACACAAUCCCAUAAAUAGGGAAAAUGUCUUUGCAGUGCCAAAUUGGCCAAGUCGAGGCUCAAA------------
.....(((((......((((..(((---(((..(((((......((((((.((((..(....)..)).)).))))))...)))))..)))))).)))).(.(((.....)))))))))..........------------ ( -39.60, z-score =  -2.37, R)
>droAna3.scaffold_13340 5952347 137 - 23697760
UUAAAAAUUUAUUUUGGCAUCAGAUUUAGUUGGCCCGGUCGGUGGUGAUGGUAAU-GGGAAGCUAACACA--CCCAGUGGUCGGGAAAAUCUCUAUUGCGUGCCAAAUUGGCCCAGUCGAGGCUCUCCCGGGCGAGGCGA
............((((((((..(((..((((..((((..((.(((((.((....(-((....))).))))--.))).))..))))..)).))..)))..))))))))...(((..(((..((.....)).)))..))).. ( -42.80, z-score =   0.25, R)
>droSim1.chr3R 16931909 125 + 27517382
UUUUAAACUUAAGUUGGCAACCGAC---AUUCAUUCUGGUGAUGAUGGGACUGGCUGGGAAACUAACACAGCCCCAUAAAUAGGGAAAAUGUCUUUGCAGUGCCAAAUUGGCCAAGUCGAGGCUCAAA------------
.......((..(.(((((....(((---(((..(((((......(((((.((((.(((....))).).))).)))))...)))))..))))))....((((.....))))))))).)..)).......------------ ( -37.80, z-score =  -1.66, R)
>droSec1.super_0 10054165 125 + 21120651
UUUUAGACUUAAGUUGGCAACCGAC---AUUCAUUCUGGUGAUGAUGGGACUGUUCGGGAAACUAACACAAUCCCAUAAAUAGGGAAAAUGUCUUUGCAGUGCCAAAUUGGCCAAGUCGAGGCUCAAA------------
.....(((((......((((..(((---(((..(((((......((((((.(((..((....))...))).))))))...)))))..)))))).)))).(.(((.....)))))))))..........------------ ( -36.20, z-score =  -1.75, R)
>droYak2.chr3R 13284922 125 + 28832112
UUUUAGACUUAACUUGGCAAGCGAC---AUUCAUUCUGCUGAUGAUGGGGCUGGUCGGGAAACUAACACAAUCCCAUAAAUGGGGGAAAUGUCUUUGCAGUGCCAAAUUGGCCAAGCCGUGACUCAAA------------
.....((.(((.(((((((((.(((---(((...(((.(((...(((((..((((..(....)..)).))..)))))...))).))))))))))))))...(((.....)))))))...))).))...------------ ( -40.20, z-score =  -2.16, R)
>droEre2.scaffold_4770 10407868 125 - 17746568
UUUUAAAUUUAACUUGGCAAACGAC---AUUCAUGCUGCUGAUGAUGGGACUGGUCGGGAAACUAACACAGUCCCAUAAAUAGGGAAAAUGGCCUUGCAGUGCCAAAUUGGCCAAGCCGAGGCUCAAA------------
............((((((.......---......(((((.....(((((((((((..(....)..)).)))))))))....((((.......)))))))))(((.....)))...)))))).......------------ ( -45.00, z-score =  -3.86, R)
>consensus
UUUUAAACUUAAGUUGGCAACCGAC___AUUCAUUCUGGUGAUGAUGGGACUGGUCGGGAAACUAACACAAUCCCAUAAAUAGGGAAAAUGUCUUUGCAGUGCCAAAUUGGCCAAGUCGAGGCUCAAA____________
.............((((((..(((....(((..(((((......((((((.((((.((....)).)).)).))))))...)))))..)))....)))...)))))).((((((.......))).)))............. (-23.22 = -24.42 +   1.20)

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 00:16:28 2011