Locus 2371

Sequence ID dm3.chr2L
Location 18,401,804 – 18,401,898
Length 94
Max. P 0.829687
window3268 window3269

overview

Window 8

Location 18,401,804 – 18,401,898
Length 94
Sequences 7
Columns 116
Reading direction forward
Mean pairwise identity 66.90
Shannon entropy 0.58373
G+C content 0.37641
Mean single sequence MFE -21.16
Consensus MFE -9.23
Energy contribution -9.70
Covariance contribution 0.48
Combinations/Pair 1.56
Mean z-score -1.54
Structure conservation index 0.44
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.83
SVM RNA-class probability 0.829687
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 18401804 94 + 23011544
-----------------UUUUCCGGAUGGAGACAGCCAAACUACGAAUUGUAUUUGCUCUGGUCAUUUCAAUUGGUUGCGAACUUUAAUUGCACCAAGGCAAAUAAAAAAC-----
-----------------......((.((....)).)).............(((((((..((((.....(((((((.........))))))).))))..)))))))......----- ( -21.20, z-score =  -1.36, R)
>droAna3.scaffold_12916 2313166 87 + 16180835
-----------------CCCAAUGGAGGGAAACGGC---ACUACGAACCGUGUUUGCCCUGGUCAGUUCUAC-----GAAAACAUUA---GCACUGAAG-AAAUAUUAAACAAAGC
-----------------(((......)))....(((---(.((((...))))..))))....(((((.(((.-----........))---).)))))..-................ ( -15.30, z-score =   0.42, R)
>droEre2.scaffold_4845 16721637 94 - 22589142
-----------------UUUUCCGGGUGGAGACGGCCAAACUACGAAUUGCAUUUGCUCUGGUCAUUUAAAUUGGUUGCAAUCUUUUAUUGCACCAAAACAAAUGAAAAAC-----
-----------------....((((.((....)).))............((....))...))((((((...(((((.(((((.....))))))))))...)))))).....----- ( -22.60, z-score =  -1.63, R)
>droYak2.chr2R 4919296 94 + 21139217
-----------------UUUUCCGGUUGGAGACAGCCAAACUACGAAUUGUAUUUGCUCUGGUCAUUUCAAUUGGUUGGAAUCUUUAAUUGCACCAAAGCAAAUACAAAUC-----
-----------------......(((((....))))).......((.(((((((((((.((((((((((((....))))))........)).)))).))))))))))).))----- ( -30.90, z-score =  -4.75, R)
>droSec1.super_7 2029654 94 + 3727775
-----------------UUUUCCGGAUGGAGACAGCCAAACUACGAAUUGUAUUUGCUCUGGUCAUUUCAAUUGGUUGCAAACUUUAAUUGCACCAAAGCAAAUAAAAAAC-----
-----------------......((.((....)).)).............((((((((.(((.....))).(((((.((((.......)))))))))))))))))......----- ( -21.40, z-score =  -1.89, R)
>droSim1.chr2L 18093783 94 + 22036055
-----------------UUUUCCGGAUGGAGACAGCCAAACUACGAAUUGUAUUUGCUCUGGUCAUUUCGAUUGGUUGCAAACUUUAAUUGCACCAAAGCAAAUAAAAAAC-----
-----------------......((.((....)).)).............((((((((.((((((.......))...((((.......)))))))).))))))))......----- ( -20.80, z-score =  -1.54, R)
>droWil1.scaffold_180708 11523116 105 + 12563649
AAUGGCACAGAAGACAACCGAAUAUUUCGGAAAAGACACUUCAUGAAUUUCGAAUGCUCU--UCAUGACAAAUUGGCGAGAAGAAAAAAUUUUCUAAAAUUUUUAAA---------
.......(((((((((..((((...(((((((.......))).)))).))))..)).)))--)).))..(((((....((((((.....))))))..))))).....--------- ( -15.90, z-score =  -0.06, R)
>consensus
_________________UUUUCCGGAUGGAGACAGCCAAACUACGAAUUGUAUUUGCUCUGGUCAUUUCAAUUGGUUGCAAACUUUAAUUGCACCAAAGCAAAUAAAAAAC_____
.......................((.((....)).)).............((((((((.((((((........................)).)))).))))))))........... ( -9.23 =  -9.70 +   0.48)

alignment

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secondary structure

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dotplot

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Window 9

Location 18,401,804 – 18,401,898
Length 94
Sequences 7
Columns 116
Reading direction reverse
Mean pairwise identity 66.90
Shannon entropy 0.58373
G+C content 0.37641
Mean single sequence MFE -20.89
Consensus MFE -9.98
Energy contribution -10.19
Covariance contribution 0.21
Combinations/Pair 1.60
Mean z-score -1.21
Structure conservation index 0.48
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.56
SVM RNA-class probability 0.741205
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 18401804 94 - 23011544
-----GUUUUUUAUUUGCCUUGGUGCAAUUAAAGUUCGCAACCAAUUGAAAUGACCAGAGCAAAUACAAUUCGUAGUUUGGCUGUCUCCAUCCGGAAAA-----------------
-----(..((.(((((((.(((((.(((((.............))))).....))))).))))))).))..)....(((((.((....)).)))))...----------------- ( -16.02, z-score =   0.49, R)
>droAna3.scaffold_12916 2313166 87 - 16180835
GCUUUGUUUAAUAUUU-CUUCAGUGC---UAAUGUUUUC-----GUAGAACUGACCAGGGCAAACACGGUUCGUAGU---GCCGUUUCCCUCCAUUGGG-----------------
((((((..........-..(((((.(---((.((....)-----)))).))))).))))))....(((((.......---)))))..(((......)))----------------- ( -18.42, z-score =  -0.26, R)
>droEre2.scaffold_4845 16721637 94 + 22589142
-----GUUUUUCAUUUGUUUUGGUGCAAUAAAAGAUUGCAACCAAUUUAAAUGACCAGAGCAAAUGCAAUUCGUAGUUUGGCCGUCUCCACCCGGAAAA-----------------
-----.....(((((((..((((((((((.....))))).)))))..)))))))(((((.....(((.....))).)))))(((........)))....----------------- ( -23.00, z-score =  -1.77, R)
>droYak2.chr2R 4919296 94 - 21139217
-----GAUUUGUAUUUGCUUUGGUGCAAUUAAAGAUUCCAACCAAUUGAAAUGACCAGAGCAAAUACAAUUCGUAGUUUGGCUGUCUCCAACCGGAAAA-----------------
-----((.((((((((((((((((.((.((...((((......)))).)).)))))))))))))))))).))....(((((.((....)).)))))...----------------- ( -28.80, z-score =  -4.05, R)
>droSec1.super_7 2029654 94 - 3727775
-----GUUUUUUAUUUGCUUUGGUGCAAUUAAAGUUUGCAACCAAUUGAAAUGACCAGAGCAAAUACAAUUCGUAGUUUGGCUGUCUCCAUCCGGAAAA-----------------
-----(..((.(((((((((((((((((.......))))...((.......))))))))))))))).))..)....(((((.((....)).)))))...----------------- ( -22.80, z-score =  -1.74, R)
>droSim1.chr2L 18093783 94 - 22036055
-----GUUUUUUAUUUGCUUUGGUGCAAUUAAAGUUUGCAACCAAUCGAAAUGACCAGAGCAAAUACAAUUCGUAGUUUGGCUGUCUCCAUCCGGAAAA-----------------
-----(..((.(((((((((((((((((.......))))...((.......))))))))))))))).))..)....(((((.((....)).)))))...----------------- ( -22.80, z-score =  -1.83, R)
>droWil1.scaffold_180708 11523116 105 - 12563649
---------UUUAAAAAUUUUAGAAAAUUUUUUCUUCUCGCCAAUUUGUCAUGA--AGAGCAUUCGAAAUUCAUGAAGUGUCUUUUCCGAAAUAUUCGGUUGUCUUCUGUGCCAUU
---------...((((((((....))))))))..............((.(((((--(((.((..((((.(((..((((.....)))).)))...))))..))))))).))).)).. ( -14.40, z-score =   0.68, R)
>consensus
_____GUUUUUUAUUUGCUUUGGUGCAAUUAAAGUUUGCAACCAAUUGAAAUGACCAGAGCAAAUACAAUUCGUAGUUUGGCUGUCUCCAUCCGGAAAA_________________
...........(((((((((((((.............................)))))))))))))..........(((((.((....)).))))).................... ( -9.98 = -10.19 +   0.21)

alignment

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secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 21:50:02 2011