Locus 2400

Sequence ID dm3.chr2L
Location 18,741,610 – 18,741,700
Length 90
Max. P 0.998632
window3301 window3302

overview

Window 1

Location 18,741,610 – 18,741,700
Length 90
Sequences 7
Columns 105
Reading direction forward
Mean pairwise identity 83.15
Shannon entropy 0.31184
G+C content 0.50719
Mean single sequence MFE -32.63
Consensus MFE -21.13
Energy contribution -21.99
Covariance contribution 0.86
Combinations/Pair 1.14
Mean z-score -2.34
Structure conservation index 0.65
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.37
SVM RNA-class probability 0.932905
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 18741610 90 + 23011544
AUGUUGCAUAAUAUUUUAUGCAUGCAGAGCUG--GCAGAUUGCAACAUGUUGCCAUGUUGCAGCUCC----AACUUCGAC--GCCGGCCC-CGGCCGAU------
.((((((((((....))))))).)))(((.((--(.((.((((((((((....))))))))))))))----).)))....--..((((..-..))))..------ ( -35.20, z-score =  -2.97, R)
>droSim1.chr2L 18429080 90 + 22036055
AUGUUGCAUAAUAUUUUAUGCAUGCAGAGCUG--GCAGAUUGCAACAUGUUGCCAUGUUGCAGCUCC----AACUUCGAC--GCCGGCCC-CGGCCGAC------
.((((((((((....))))))).)))(((.((--(.((.((((((((((....))))))))))))))----).)))....--..((((..-..))))..------ ( -35.20, z-score =  -3.17, R)
>droSec1.super_7 2362840 89 + 3727775
AUGUUGCAUAAUAUUUUAUGCAUGCAGAGCUG--GCAGAUUGCAACAUGUUGCCAUGUUGCAGCUCC----AACUUCGAC--GCCGGCCC--GGCCGAU------
.((((((((((....))))))).)))(((.((--(.((.((((((((((....))))))))))))))----).)))....--..((((..--.))))..------ ( -32.20, z-score =  -1.98, R)
>droYak2.chr2R 5255205 88 + 21139217
AUGUUGCAUAAUAUUUUAUGCAUGCAGAGCUG--GCAGAUUGCAACAUGUUGCCAUGUUGCAGCUCC----AGCUUCGAC--GCCAGCCC-CGGCCG--------
.((((((((((....))))))).)))((((((--(.((.((((((((((....))))))))))))))----)))))....--(((.....-.)))..-------- ( -37.90, z-score =  -4.15, R)
>droEre2.scaffold_4845 17054120 87 - 22589142
AUGUUGCAUAAUAUUUUAUGCAUGCAGAGCUG--GCAGAUUGCAACAUGUUGCCAUGUUGCAGCUCC----AACUUCGAC--GCCAGCCC--GGCCG--------
....(((((((....))))))).((.(.((((--((.((((((((((((....)))))))))).))(----......)..--)))))).)--.))..-------- ( -32.40, z-score =  -2.71, R)
>droAna3.scaffold_12916 8214244 97 + 16180835
AUGUUGCAUAAUAUUUUAUACAUGCAGAGCUG--GCAGAUUGCAACAUGUUGCCAUGUUGCAGCUCC----GACUGCGAA--GCCGGCCUGCUGCUGCCGCCGCU
..((.((((((....)))).((.((((.((((--((....(((((((((....)))))))))((...----....))...--)))))))))))).....)).)). ( -35.30, z-score =  -1.24, R)
>droWil1.scaffold_180708 1415789 105 - 12563649
AUGUUGCAUAAUAUUUUAUACAUGCAGAGCUCUCGCAUAUUGCAACAUGUUGCCAUGAGACGACGACUAUAGACCAGGGACAACAGACACACGGACGACGACGUC
.((((((((((....))))..((((((....)).))))...))))))(((((((.((.................)).)).)))))........((((....)))) ( -20.23, z-score =  -0.12, R)
>consensus
AUGUUGCAUAAUAUUUUAUGCAUGCAGAGCUG__GCAGAUUGCAACAUGUUGCCAUGUUGCAGCUCC____AACUUCGAC__GCCGGCCC_CGGCCGAC______
.((((((((((....))))))).)))..((....)).((((((((((((....)))))))))).))..................((((.....))))........ (-21.13 = -21.99 +   0.86)

alignment

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secondary structure

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dotplot

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Window 2

Location 18,741,610 – 18,741,700
Length 90
Sequences 7
Columns 105
Reading direction reverse
Mean pairwise identity 83.15
Shannon entropy 0.31184
G+C content 0.50719
Mean single sequence MFE -39.16
Consensus MFE -27.33
Energy contribution -27.64
Covariance contribution 0.31
Combinations/Pair 1.22
Mean z-score -3.65
Structure conservation index 0.70
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 3.43
SVM RNA-class probability 0.998632
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 18741610 90 - 23011544
------AUCGGCCG-GGGCCGGC--GUCGAAGUU----GGAGCUGCAACAUGGCAACAUGUUGCAAUCUGC--CAGCUCUGCAUGCAUAAAAUAUUAUGCAACAU
------.(((((..-..))))).--((.((.(((----((((.(((((((((....)))))))))..)).)--)))))).)).(((((((....))))))).... ( -40.00, z-score =  -3.86, R)
>droSim1.chr2L 18429080 90 - 22036055
------GUCGGCCG-GGGCCGGC--GUCGAAGUU----GGAGCUGCAACAUGGCAACAUGUUGCAAUCUGC--CAGCUCUGCAUGCAUAAAAUAUUAUGCAACAU
------((((((..-..))))))--((.((.(((----((((.(((((((((....)))))))))..)).)--)))))).)).(((((((....))))))).... ( -43.90, z-score =  -4.99, R)
>droSec1.super_7 2362840 89 - 3727775
------AUCGGCC--GGGCCGGC--GUCGAAGUU----GGAGCUGCAACAUGGCAACAUGUUGCAAUCUGC--CAGCUCUGCAUGCAUAAAAUAUUAUGCAACAU
------.(((((.--..))))).--((.((.(((----((((.(((((((((....)))))))))..)).)--)))))).)).(((((((....))))))).... ( -37.00, z-score =  -3.15, R)
>droYak2.chr2R 5255205 88 - 21139217
--------CGGCCG-GGGCUGGC--GUCGAAGCU----GGAGCUGCAACAUGGCAACAUGUUGCAAUCUGC--CAGCUCUGCAUGCAUAAAAUAUUAUGCAACAU
--------..((.(-((((((((--.....(((.----...)))((((((((....)))))))).....))--))))))))).(((((((....))))))).... ( -43.00, z-score =  -4.94, R)
>droEre2.scaffold_4845 17054120 87 + 22589142
--------CGGCC--GGGCUGGC--GUCGAAGUU----GGAGCUGCAACAUGGCAACAUGUUGCAAUCUGC--CAGCUCUGCAUGCAUAAAAUAUUAUGCAACAU
--------..((.--((((((((--.........----(((..(((((((((....))))))))).)))))--)))))).)).(((((((....))))))).... ( -41.20, z-score =  -4.75, R)
>droAna3.scaffold_12916 8214244 97 - 16180835
AGCGGCGGCAGCAGCAGGCCGGC--UUCGCAGUC----GGAGCUGCAACAUGGCAACAUGUUGCAAUCUGC--CAGCUCUGCAUGUAUAAAAUAUUAUGCAACAU
....((((.(((.((((((((((--(....))))----))...(((((((((....))))))))).)))))--..))))))).(((((((....))))))).... ( -42.90, z-score =  -3.38, R)
>droWil1.scaffold_180708 1415789 105 + 12563649
GACGUCGUCGUCCGUGUGUCUGUUGUCCCUGGUCUAUAGUCGUCGUCUCAUGGCAACAUGUUGCAAUAUGCGAGAGCUCUGCAUGUAUAAAAUAUUAUGCAACAU
((((.((.(..(((.(.(.(....).)).)))......).)).)))).((((....)))).((((....((....))..))))(((((((....))))))).... ( -26.10, z-score =  -0.51, R)
>consensus
______GUCGGCCG_GGGCCGGC__GUCGAAGUU____GGAGCUGCAACAUGGCAACAUGUUGCAAUCUGC__CAGCUCUGCAUGCAUAAAAUAUUAUGCAACAU
........((((.....)))).........((((....(((..(((((((((....))))))))).))).....)))).....(((((((....))))))).... (-27.33 = -27.64 +   0.31)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 21:50:30 2011