Locus 1871

Sequence ID dm3.chr2L
Location 14,502,546 – 14,502,611
Length 65
Max. P 0.999674
window2578 window2579

overview

Window 8

Location 14,502,546 – 14,502,611
Length 65
Sequences 12
Columns 73
Reading direction forward
Mean pairwise identity 85.56
Shannon entropy 0.29527
G+C content 0.43049
Mean single sequence MFE -25.56
Consensus MFE -18.50
Energy contribution -18.63
Covariance contribution 0.13
Combinations/Pair 1.13
Mean z-score -5.09
Structure conservation index 0.72
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 4.17
SVM RNA-class probability 0.999674
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 14502546 65 + 23011544
CUUCCAGCUGUCAAGUUGGUCUAAGUUUUUGAGCGCAAAAUA--------AAAGCCGACUUGACAGCUGAACG
....((((((((((((((((......(((((....)))))..--------...)))))))))))))))).... ( -30.30, z-score =  -6.50, R)
>droSim1.chr2L 14249789 65 + 22036055
CUUCCAGCUGUCAAGUUGGUCUAAGUUUUUGAGCGCAAAAUA--------AAAGCCGACUUGACAGCUGAACG
....((((((((((((((((......(((((....)))))..--------...)))))))))))))))).... ( -30.30, z-score =  -6.50, R)
>droSec1.super_3 765771 65 + 7220098
CUUCCAGCUGUCAAGUUGGUCUAAGUUUUUGAGCGCAAAAUA--------AAAGCCGACUUGACAGCUGAACG
....((((((((((((((((......(((((....)))))..--------...)))))))))))))))).... ( -30.30, z-score =  -6.50, R)
>droYak2.chr2L 14611312 65 + 22324452
CUUCCAACUGUCAAGUUGGUCUAAGUUUUUGAGCGCAAAAUA--------AAGGCCGACUUGACAGCUGAACG
....((.(((((((((((((((....(((((....)))))..--------.))))))))))))))).)).... ( -27.70, z-score =  -5.65, R)
>droEre2.scaffold_4929 6257049 65 + 26641161
CUUCCAACUGUCAAGUUGGUCUAAGUUUUUGAGCGCAAAAUA--------AAGGCCGACUUGACAGCUGAACG
....((.(((((((((((((((....(((((....)))))..--------.))))))))))))))).)).... ( -27.70, z-score =  -5.65, R)
>droAna3.scaffold_12916 14864911 65 - 16180835
CUUCCAACUGUCAAGUUGGUCUAAGUUUUUGAGCGCAAAAUA--------AAAGCCGACUUGACAGCUGAACG
....((.(((((((((((((......(((((....)))))..--------...))))))))))))).)).... ( -23.70, z-score =  -4.58, R)
>dp4.chr4_group1 1910345 65 - 5278887
CUUCCAACUGUCAAGUUGGUCUAAGUUUUUGAGCGCAAAAUA--------AAAGCCAACUUGACAGCUGAACG
....((.(((((((((((((......(((((....)))))..--------...))))))))))))).)).... ( -24.00, z-score =  -4.99, R)
>droPer1.super_5 1849355 65 + 6813705
CUUCCAACUGUCAAGUUGGUCUAAGUUUUUGAGCGCAAAAUA--------AAAGCCAACUUGACAGCUGAACG
....((.(((((((((((((......(((((....)))))..--------...))))))))))))).)).... ( -24.00, z-score =  -4.99, R)
>droWil1.scaffold_180764 2818868 65 + 3949147
CGUUCAGCUGUCAAGUCGGCUUUUAUUUU-GCGCUCAAAAACU-------UAGACCAACUUGACAGUUGGAAG
..((((((((((((((.((((....((((-(....)))))...-------.)).)).)))))))))))))).. ( -25.20, z-score =  -4.89, R)
>droVir3.scaffold_12723 3124526 69 - 5802038
CUUCCAACUGUCAAGUUGGUAUAAGUUUU-GAGCGCAAAAUACAAAAUACAAAGCCGACUUGACAGCUGG---
...(((.(((((((((((((....(((((-(...........)))))).....))))))))))))).)))--- ( -25.40, z-score =  -5.44, R)
>droMoj3.scaffold_6500 16442255 69 - 32352404
CUUCCAACUGUCAAGUUGGUAUAAGUUUU-GAGCGCAAAAUACAAAAUACAAAGCCGCCUUGACAGCUGG---
...(((.((((((((.((((....(((((-(...........)))))).....)))).)))))))).)))--- ( -20.80, z-score =  -3.36, R)
>droGri2.scaffold_15126 839420 72 + 8399593
CUUCCAACUGUCAGGUUUGUCUAAGUUUU-GAGCGCAAAAUACAAAAUACAAAGCCGACUUGACAGCUGAACG
....((.((((((((((.((....(((((-(...........)))))).....)).)))))))))).)).... ( -17.30, z-score =  -1.99, R)
>consensus
CUUCCAACUGUCAAGUUGGUCUAAGUUUUUGAGCGCAAAAUA________AAAGCCGACUUGACAGCUGAACG
....((.(((((((((((((.................................))))))))))))).)).... (-18.50 = -18.63 +   0.13)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 9

Location 14,502,546 – 14,502,611
Length 65
Sequences 12
Columns 73
Reading direction reverse
Mean pairwise identity 85.56
Shannon entropy 0.29527
G+C content 0.43049
Mean single sequence MFE -25.67
Consensus MFE -19.09
Energy contribution -19.38
Covariance contribution 0.29
Combinations/Pair 1.12
Mean z-score -4.92
Structure conservation index 0.74
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 4.11
SVM RNA-class probability 0.999637
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 14502546 65 - 23011544
CGUUCAGCUGUCAAGUCGGCUUU--------UAUUUUGCGCUCAAAAACUUAGACCAACUUGACAGCUGGAAG
..((((((((((((((.((((..--------..(((((....)))))....)).)).)))))))))))))).. ( -27.60, z-score =  -5.56, R)
>droSim1.chr2L 14249789 65 - 22036055
CGUUCAGCUGUCAAGUCGGCUUU--------UAUUUUGCGCUCAAAAACUUAGACCAACUUGACAGCUGGAAG
..((((((((((((((.((((..--------..(((((....)))))....)).)).)))))))))))))).. ( -27.60, z-score =  -5.56, R)
>droSec1.super_3 765771 65 - 7220098
CGUUCAGCUGUCAAGUCGGCUUU--------UAUUUUGCGCUCAAAAACUUAGACCAACUUGACAGCUGGAAG
..((((((((((((((.((((..--------..(((((....)))))....)).)).)))))))))))))).. ( -27.60, z-score =  -5.56, R)
>droYak2.chr2L 14611312 65 - 22324452
CGUUCAGCUGUCAAGUCGGCCUU--------UAUUUUGCGCUCAAAAACUUAGACCAACUUGACAGUUGGAAG
..((((((((((((((.((.((.--------..(((((....)))))....)).)).)))))))))))))).. ( -24.80, z-score =  -4.72, R)
>droEre2.scaffold_4929 6257049 65 - 26641161
CGUUCAGCUGUCAAGUCGGCCUU--------UAUUUUGCGCUCAAAAACUUAGACCAACUUGACAGUUGGAAG
..((((((((((((((.((.((.--------..(((((....)))))....)).)).)))))))))))))).. ( -24.80, z-score =  -4.72, R)
>droAna3.scaffold_12916 14864911 65 + 16180835
CGUUCAGCUGUCAAGUCGGCUUU--------UAUUUUGCGCUCAAAAACUUAGACCAACUUGACAGUUGGAAG
..((((((((((((((.((((..--------..(((((....)))))....)).)).)))))))))))))).. ( -25.20, z-score =  -4.89, R)
>dp4.chr4_group1 1910345 65 + 5278887
CGUUCAGCUGUCAAGUUGGCUUU--------UAUUUUGCGCUCAAAAACUUAGACCAACUUGACAGUUGGAAG
..(((((((((((((((((((..--------..(((((....)))))....)).))))))))))))))))).. ( -29.30, z-score =  -6.35, R)
>droPer1.super_5 1849355 65 - 6813705
CGUUCAGCUGUCAAGUUGGCUUU--------UAUUUUGCGCUCAAAAACUUAGACCAACUUGACAGUUGGAAG
..(((((((((((((((((((..--------..(((((....)))))....)).))))))))))))))))).. ( -29.30, z-score =  -6.35, R)
>droWil1.scaffold_180764 2818868 65 - 3949147
CUUCCAACUGUCAAGUUGGUCUA-------AGUUUUUGAGCGC-AAAAUAAAAGCCGACUUGACAGCUGAACG
....((.(((((((((((((...-------...(((((....)-)))).....))))))))))))).)).... ( -23.70, z-score =  -4.58, R)
>droVir3.scaffold_12723 3124526 69 + 5802038
---CCAGCUGUCAAGUCGGCUUUGUAUUUUGUAUUUUGCGCUC-AAAACUUAUACCAACUUGACAGUUGGAAG
---(((((((((((((.((...((..(((((...........)-))))..))..)).)))))))))))))... ( -24.90, z-score =  -4.94, R)
>droMoj3.scaffold_6500 16442255 69 + 32352404
---CCAGCUGUCAAGGCGGCUUUGUAUUUUGUAUUUUGCGCUC-AAAACUUAUACCAACUUGACAGUUGGAAG
---((((((((((((..((...((..(((((...........)-))))..))..))..))))))))))))... ( -23.70, z-score =  -3.87, R)
>droGri2.scaffold_15126 839420 72 - 8399593
CGUUCAGCUGUCAAGUCGGCUUUGUAUUUUGUAUUUUGCGCUC-AAAACUUAGACAAACCUGACAGUUGGAAG
..(((((((((((.((..(.((((..(((((...........)-))))..)))))..)).))))))))))).. ( -19.50, z-score =  -1.95, R)
>consensus
CGUUCAGCUGUCAAGUCGGCUUU________UAUUUUGCGCUCAAAAACUUAGACCAACUUGACAGUUGGAAG
..((((((((((((((.((...................................)).)))))))))))))).. (-19.09 = -19.38 +   0.29)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 21:40:28 2011