Locus 1939

Sequence ID dm3.chr2L
Location 14,911,430 – 14,911,550
Length 120
Max. P 0.910802
window2675 window2676

overview

Window 5

Location 14,911,430 – 14,911,550
Length 120
Sequences 7
Columns 132
Reading direction forward
Mean pairwise identity 73.97
Shannon entropy 0.50004
G+C content 0.50945
Mean single sequence MFE -32.82
Consensus MFE -17.35
Energy contribution -17.99
Covariance contribution 0.63
Combinations/Pair 1.44
Mean z-score -1.45
Structure conservation index 0.53
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.65
SVM RNA-class probability 0.775096
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 14911430 120 + 23011544
CACCGCCCAGAUUGCCAGGACAAUGG--------GACAUCGGGACCACGAAGUCUGGGCAAUAGAAGCCCAGUUAAUACGAACCGCAACUGACAACUGACAGACGUUAAA----CGCUCCAACUGGGCUGGC
..(((((((((((.(((......)))--------....(((......))))))))))))......(((((((((....((....((..(((........)))..))....----))....))))))))))). ( -40.70, z-score =  -2.95, R)
>droSim1.chr2L_random 571474 115 + 909653
CAC-GCCCAGAU-GC--AGACAAAGG--------GACAUCGGGACCACGAAGUCUGGGCAAUAGAAGCCCAGUUAAUACGAACCGCAACUGACAACUGACAGACGU-AAA----CGCUCCAACUGGGCUGGC
...-((((((((-..--.......((--------..(....)..)).....))))))))......(((((((((....((....((..(((........)))..))-...----))....)))))))))... ( -34.74, z-score =  -2.05, R)
>droSec1.super_3 1181420 120 + 7220098
CACCGCCCAGAUUGCCAGGAUAAAGG--------GACAUCGGGACCACGAAGUCUGGGCAAUAGAAGCCCAGUUAAUACGAACCGCAACUGACAACUGACAGACGUUAAA----CGCUCCAACUGGGCUGGC
..(((((((((((.((........))--------....(((......))))))))))))......(((((((((....((....((..(((........)))..))....----))....))))))))))). ( -38.80, z-score =  -2.53, R)
>droYak2.chr2L 15023447 127 + 22324452
CACCGCCCAGAUUGCCAGGACAAAGGA-CAUCGGGACAUCGGGACCACGAAGUCUGGGUAAUAGAAGCCCAGUUAAUACGAACCGCAACUGACAACUGACAGACGUUAAA----CGCUCCAACUGGGCUGGC
..(((((((((((.((........)).-....((..(....)..))....)))))))))......(((((((((....((....((..(((........)))..))....----))....))))))))))). ( -37.50, z-score =  -1.34, R)
>droEre2.scaffold_4929 6656875 128 + 26641161
CAUCGCCCAGAUUGCCAGGACAAAGGGACAAAGGGACAACGGGACCACGAAGUCUGGGCAAUAGAAGCCCAGUUAAUACGAACCGCAACUGACAACUGACAGACGUUAAA----CGGUCCAACUGGGCUGGC
....(((((((((.((........))......((..(....)..))....)))))))))......(((((((((....((....((..(((........)))..))....----))....)))))))))... ( -39.80, z-score =  -2.06, R)
>droAna3.scaffold_12916 15242576 109 - 16180835
CACAGACCAGAUUGCAAAGACAAAGG---------ACAGCGGGCCCACAAAGUCUGG----------CCCUGCAAAUGCGCACCGCAACUGACAACUGACAGACGUUAAA----CUGUUCUCCUGAACUAGU
..(((..(((.((((...........---------.....(((((..........))----------)))(((......)))..)))))))....)))...........(----((((((....)))).))) ( -24.30, z-score =   0.26, R)
>droGri2.scaffold_15252 705520 118 + 17193109
AACCGGUCCAAAAACAAAAAUAUAAAA-------AAGAAUGAAAACAUGAAAAUUGU-------CAACGUGGCUAAUAAUAACCGAAAUUGACAAGUAGCAGAUAUCGUUUCCUCGUUUCCAAUCAAAUGGC
...........................-------..((((((.....((....((((-------(((..(((.((....)).)))...)))))))....))....))))))..((((((......)))))). ( -13.90, z-score =   0.57, R)
>consensus
CACCGCCCAGAUUGCCAGGACAAAGG________GACAUCGGGACCACGAAGUCUGGGCAAUAGAAGCCCAGUUAAUACGAACCGCAACUGACAACUGACAGACGUUAAA____CGCUCCAACUGGGCUGGC
....((((((.............................(((...........((((((.......))))))..........)))...(((........)))....................)))))).... (-17.35 = -17.99 +   0.63)

alignment

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secondary structure

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dotplot

Postscript

Window 6

Location 14,911,430 – 14,911,550
Length 120
Sequences 7
Columns 132
Reading direction reverse
Mean pairwise identity 73.97
Shannon entropy 0.50004
G+C content 0.50945
Mean single sequence MFE -39.21
Consensus MFE -17.60
Energy contribution -19.67
Covariance contribution 2.07
Combinations/Pair 1.36
Mean z-score -2.09
Structure conservation index 0.45
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.21
SVM RNA-class probability 0.910802
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 14911430 120 - 23011544
GCCAGCCCAGUUGGAGCG----UUUAACGUCUGUCAGUUGUCAGUUGCGGUUCGUAUUAACUGGGCUUCUAUUGCCCAGACUUCGUGGUCCCGAUGUC--------CCAUUGUCCUGGCAAUCUGGGCGGUG
((((((((((((((.(((----.....((((((.(....).)))..)))...))).)))))))))))......(((((((....((((..(....)..--------))))(((....))).)))))))))). ( -46.70, z-score =  -3.20, R)
>droSim1.chr2L_random 571474 115 - 909653
GCCAGCCCAGUUGGAGCG----UUU-ACGUCUGUCAGUUGUCAGUUGCGGUUCGUAUUAACUGGGCUUCUAUUGCCCAGACUUCGUGGUCCCGAUGUC--------CCUUUGUCU--GC-AUCUGGGC-GUG
...(((((((((((.(((----...-.((((((.(....).)))..)))...))).)))))))))))......(((((((((....))))..(((((.--------.........--))-))))))))-... ( -41.40, z-score =  -2.74, R)
>droSec1.super_3 1181420 120 - 7220098
GCCAGCCCAGUUGGAGCG----UUUAACGUCUGUCAGUUGUCAGUUGCGGUUCGUAUUAACUGGGCUUCUAUUGCCCAGACUUCGUGGUCCCGAUGUC--------CCUUUAUCCUGGCAAUCUGGGCGGUG
((((((((((((((.(((----.....((((((.(....).)))..)))...))).)))))))))))......((((((((.....)(((..((((..--------....))))..)))..)))))))))). ( -45.20, z-score =  -3.08, R)
>droYak2.chr2L 15023447 127 - 22324452
GCCAGCCCAGUUGGAGCG----UUUAACGUCUGUCAGUUGUCAGUUGCGGUUCGUAUUAACUGGGCUUCUAUUACCCAGACUUCGUGGUCCCGAUGUCCCGAUG-UCCUUUGUCCUGGCAAUCUGGGCGGUG
((((((((((((((.(((----.....((((((.(....).)))..)))...))).))))))))))).......((((((..(((.((.(.....).)))))((-.((........)))).)))))).))). ( -44.20, z-score =  -2.13, R)
>droEre2.scaffold_4929 6656875 128 - 26641161
GCCAGCCCAGUUGGACCG----UUUAACGUCUGUCAGUUGUCAGUUGCGGUUCGUAUUAACUGGGCUUCUAUUGCCCAGACUUCGUGGUCCCGUUGUCCCUUUGUCCCUUUGUCCUGGCAAUCUGGGCGAUG
...(((((((((((((((----(.......(((.(....).)))..))))))).....)))))))))..(((((((((((......((..(....)..)).........((((....))))))))))))))) ( -44.20, z-score =  -3.07, R)
>droAna3.scaffold_12916 15242576 109 + 16180835
ACUAGUUCAGGAGAACAG----UUUAACGUCUGUCAGUUGUCAGUUGCGGUGCGCAUUUGCAGGG----------CCAGACUUUGUGGGCCCGCUGU---------CCUUUGUCUUUGCAAUCUGGUCUGUG
(((((....(((((((((----........))))(((..(.(((((((((.......)))))(((----------((..........))))))))).---------)..)))))))).....)))))..... ( -27.90, z-score =   1.35, R)
>droGri2.scaffold_15252 705520 118 - 17193109
GCCAUUUGAUUGGAAACGAGGAAACGAUAUCUGCUACUUGUCAAUUUCGGUUAUUAUUAGCCACGUUG-------ACAAUUUUCAUGUUUUCAUUCUU-------UUUUAUAUUUUUGUUUUUGGACCGGUU
(((....((.((((((((.(....)............((((((((...(((((....)))))..))))-------))))......)))))))).))..-------............(((....))).))). ( -24.90, z-score =  -1.74, R)
>consensus
GCCAGCCCAGUUGGAGCG____UUUAACGUCUGUCAGUUGUCAGUUGCGGUUCGUAUUAACUGGGCUUCUAUUGCCCAGACUUCGUGGUCCCGAUGUC________CCUUUGUCCUGGCAAUCUGGGCGGUG
((((((((((((((.(((.........((((((.(....).)))..)))...))).))))))))))).......((((((.....((....))................((((....)))))))))).))). (-17.60 = -19.67 +   2.07)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 21:41:48 2011