Locus 15696

Sequence ID dm3.chrX
Location 20,442,771 – 20,442,897
Length 126
Max. P 0.989495
window21632 window21633

overview

Window 2

Location 20,442,771 – 20,442,897
Length 126
Sequences 11
Columns 144
Reading direction forward
Mean pairwise identity 78.07
Shannon entropy 0.43728
G+C content 0.48663
Mean single sequence MFE -41.41
Consensus MFE -23.89
Energy contribution -23.72
Covariance contribution -0.17
Combinations/Pair 1.14
Mean z-score -2.36
Structure conservation index 0.58
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.10
SVM RNA-class probability 0.982399
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 20442771 126 + 22422827
----------GAAAACGGGGCGAAAGGCAGGUCAUGAGUGACGGCGCCGCUGCGUCAGCGGCAUGUAAUUUUCACGGUUUUUCGCAAAUACGAAAAACGAAAUA-CGC-UAGACGAAAAUUCCCUCGCUCCAAAAACU------
----------......(((((((...((..((((....)))).))(((((((...)))))))....(((((((...((((((((......))))))))......-(..-..)..)))))))...))))))).......------ ( -42.00, z-score =  -2.42, R)
>droPer1.super_22 549006 142 - 1688296
GAGAGCGGGAGAGAGGACAUGGGAAGGCAGGUCAUGAGUGACGGCGCCGCUGCGUCAGCGGCAUGUAAUUUUCACGGUUUUUCGCAAAUACGAAAAACGAAAUA-CGU-UAGACGAAAAUUCCCUCGUGCUCGUGCCACAUUCU
.((((.(((...(((.((..(((((.((..((((....)))).))(((((((...)))))))(((((..((((...((((((((......))))))))))))))-)))-..........)))))..)).)))...)).).)))) ( -48.00, z-score =  -1.66, R)
>dp4.chrXL_group1e 9069155 142 + 12523060
GAGAGUGGGGGAGAGGACAUGGGAAGGCAGGUCAUGAGUGACGGCGCCGCUGCGUCAGCGGCAUGUAAUUUUCACGGUUUUUCGCAAAUACGAAAAACGAAAUA-CGU-UAGACGAAAAUUCCCUCGUGCUCGUGCCACAUUCU
.((((((((.(.(((.((..(((((.((..((((....)))).))(((((((...)))))))(((((..((((...((((((((......))))))))))))))-)))-..........)))))..)).))).).)).)))))) ( -52.30, z-score =  -2.83, R)
>droAna3.scaffold_12903 520364 123 - 802071
------------GAAAUGGGAGAAAGGCAGGUCAUGAGUGACGGCGCCGCUGCGUCAGCGGCAUGUAAUUUUCACGGUUUUUCGCAAAUACGAAAAACGAAAUUUCGC-UAGACGAAAAUUUUAUCGCUC-CAAGCU-------
------------(((((..(((((..(((.((((....))))...(((((((...))))))).)))..)))))...((((((((......))))))))...)))))((-(.(((((........))).))-..))).------- ( -37.50, z-score =  -1.54, R)
>droEre2.scaffold_4690 17043273 126 + 18748788
----------GAAAACGGGGCGAAAGGCAGGUCAUGAGUGACGGCGCCGCUGCGUCAGCGGCAUGUAAUUUUCACGGUUUUUCGCAAAUACGAAAAACGAAAUA-CGC-UAGACGAAAAUUCCCUCGCUCCAAAAACU------
----------......(((((((...((..((((....)))).))(((((((...)))))))....(((((((...((((((((......))))))))......-(..-..)..)))))))...))))))).......------ ( -42.00, z-score =  -2.42, R)
>droYak2.chrX 19670324 126 + 21770863
----------GAAAACGGGGCGAAAGGCAGGUCAUGAGUGACGGCGCCGCUGCGUCAGCGGCAUGUAAUUUUCCCGGUUUUUCGCAAAUACGAAAAACGAAAUA-CGC-UAGACGAAAAUUCCCUCGCUCCAAAAACU------
----------......(((((((..((...((((....))))((((((((((...)))))))..(((..((((...((((((((......))))))))))))))-)))-)............))))))))).......------ ( -41.70, z-score =  -2.03, R)
>droSec1.super_8 2673594 126 + 3762037
----------GAAAACGGGGCGAAAGGCAGGUCAUGAGUGACGGCGCCGCUGCGUCAGCGGCAUGUAAUUUUCACGGUUUUUCGCAAAUACGAAAAACGAAAUA-CGC-UAGACGAAAAUUCCCUCGCUCCAAAAACU------
----------......(((((((...((..((((....)))).))(((((((...)))))))....(((((((...((((((((......))))))))......-(..-..)..)))))))...))))))).......------ ( -42.00, z-score =  -2.42, R)
>droSim1.chrX 15671353 126 + 17042790
----------GAAAACGGGGCGAAAGGCAGGUCAUGAGUGACGGCGCCGCUGCGUCAGCGGCAUGUAAUUUUCACGGUUUUUCGCAAAUACGAAAAACGAAAUA-CGC-UAGACGAAAAUUCCCUCGCUCCAAAAACU------
----------......(((((((...((..((((....)))).))(((((((...)))))))....(((((((...((((((((......))))))))......-(..-..)..)))))))...))))))).......------ ( -42.00, z-score =  -2.42, R)
>droVir3.scaffold_12970 4729855 119 + 11907090
-------------AAAAACCGAGCAGCCUCAUCAUGAGUGACGGCGCCGCUGCGUCAGCGGCAUGUAAUUUUCACGGUUUUUCGCAAAUACGAAAAACG--AAAAUACGUAAACGAAAACUGGAUGCCAAAACU----------
-------------.......(.((((((((((.....)))).)))(((((((...)))))))(((((.(((((...((((((((......)))))))))--)))))))))..............))))......---------- ( -35.30, z-score =  -2.33, R)
>droMoj3.scaffold_6473 4163737 118 + 16943266
----------------AACCGAGCAGCCUCAUCAUGAGUGACGGCGCCGCUGCGUCAGCGGCAUGUAAUUUUCACGGUUUUUCGCAAAUACGAAAAACGAGAAAAUACGUAAACGAAAACUCGAUGCCAAAAAC----------
----------------...((((..(((((((.....)))).)))(((((((...)))))))(((((.(((((.((.(((((((......))))))))).)))))))))).........))))...........---------- ( -38.30, z-score =  -3.30, R)
>droGri2.scaffold_15081 3688391 112 - 4274704
-------------AAUAACCGAGCAGCCCCAUCAUGAGUGACGGCGCCGCUGCGUCAGCGGCAUGUAAUUUUCACGAUUUUUCGCAAAUACGGAAAACGAGAAAAUACGUAAACGAAAACUCGCU-------------------
-------------......((((..(((...(((....))).)))(((((((...)))))))(((((.(((((.((.(((((((......))))))))).)))))))))).........))))..------------------- ( -34.40, z-score =  -2.54, R)
>consensus
__________GAAAACAGGGCGAAAGGCAGGUCAUGAGUGACGGCGCCGCUGCGUCAGCGGCAUGUAAUUUUCACGGUUUUUCGCAAAUACGAAAAACGAAAUA_CGC_UAGACGAAAAUUCCCUCGCUCCAAAAACU______
...................................((((..((..(((((((...)))))))..............((((((((......))))))))...............))...))))...................... (-23.89 = -23.72 +  -0.17)

alignment

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secondary structure

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dotplot

Postscript

Window 3

Location 20,442,771 – 20,442,897
Length 126
Sequences 11
Columns 144
Reading direction reverse
Mean pairwise identity 78.07
Shannon entropy 0.43728
G+C content 0.48663
Mean single sequence MFE -40.51
Consensus MFE -26.45
Energy contribution -25.86
Covariance contribution -0.59
Combinations/Pair 1.14
Mean z-score -2.30
Structure conservation index 0.65
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.37
SVM RNA-class probability 0.989495
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 20442771 126 - 22422827
------AGUUUUUGGAGCGAGGGAAUUUUCGUCUA-GCG-UAUUUCGUUUUUCGUAUUUGCGAAAAACCGUGAAAAUUACAUGCCGCUGACGCAGCGGCGCCGUCACUCAUGACCUGCCUUUCGCCCCGUUUUC----------
------.......((.(((((((((((((((....-.).-......(((((((((....)))))))))...)))))))....(((((((...)))))))((.((((....))))..))))))))).))......---------- ( -41.20, z-score =  -2.26, R)
>droPer1.super_22 549006 142 + 1688296
AGAAUGUGGCACGAGCACGAGGGAAUUUUCGUCUA-ACG-UAUUUCGUUUUUCGUAUUUGCGAAAAACCGUGAAAAUUACAUGCCGCUGACGCAGCGGCGCCGUCACUCAUGACCUGCCUUCCCAUGUCCUCUCUCCCGCUCUC
.((..((((...(((.(((.(((((.....(((..-...-......(((((((((....))))))))).((((........((((((((...))))))))...))))....))).....))))).))).)))....))))..)) ( -44.20, z-score =  -2.46, R)
>dp4.chrXL_group1e 9069155 142 - 12523060
AGAAUGUGGCACGAGCACGAGGGAAUUUUCGUCUA-ACG-UAUUUCGUUUUUCGUAUUUGCGAAAAACCGUGAAAAUUACAUGCCGCUGACGCAGCGGCGCCGUCACUCAUGACCUGCCUUCCCAUGUCCUCUCCCCCACUCUC
.((..((((...(((.(((.(((((.....(((..-...-......(((((((((....))))))))).((((........((((((((...))))))))...))))....))).....))))).))).)))....))))..)) ( -44.60, z-score =  -3.04, R)
>droAna3.scaffold_12903 520364 123 + 802071
-------AGCUUG-GAGCGAUAAAAUUUUCGUCUA-GCGAAAUUUCGUUUUUCGUAUUUGCGAAAAACCGUGAAAAUUACAUGCCGCUGACGCAGCGGCGCCGUCACUCAUGACCUGCCUUUCUCCCAUUUC------------
-------.(((.(-((.(((........)))))))-))(((((...(((((((((....))))))))).(.((((.......(((((((...)))))))((.((((....))))..)).)))).)..)))))------------ ( -35.40, z-score =  -2.29, R)
>droEre2.scaffold_4690 17043273 126 - 18748788
------AGUUUUUGGAGCGAGGGAAUUUUCGUCUA-GCG-UAUUUCGUUUUUCGUAUUUGCGAAAAACCGUGAAAAUUACAUGCCGCUGACGCAGCGGCGCCGUCACUCAUGACCUGCCUUUCGCCCCGUUUUC----------
------.......((.(((((((((((((((....-.).-......(((((((((....)))))))))...)))))))....(((((((...)))))))((.((((....))))..))))))))).))......---------- ( -41.20, z-score =  -2.26, R)
>droYak2.chrX 19670324 126 - 21770863
------AGUUUUUGGAGCGAGGGAAUUUUCGUCUA-GCG-UAUUUCGUUUUUCGUAUUUGCGAAAAACCGGGAAAAUUACAUGCCGCUGACGCAGCGGCGCCGUCACUCAUGACCUGCCUUUCGCCCCGUUUUC----------
------.......((.(((((((((((((((....-.).-......(((((((((....)))))))))...)))))))....(((((((...)))))))((.((((....))))..))))))))).))......---------- ( -41.20, z-score =  -1.69, R)
>droSec1.super_8 2673594 126 - 3762037
------AGUUUUUGGAGCGAGGGAAUUUUCGUCUA-GCG-UAUUUCGUUUUUCGUAUUUGCGAAAAACCGUGAAAAUUACAUGCCGCUGACGCAGCGGCGCCGUCACUCAUGACCUGCCUUUCGCCCCGUUUUC----------
------.......((.(((((((((((((((....-.).-......(((((((((....)))))))))...)))))))....(((((((...)))))))((.((((....))))..))))))))).))......---------- ( -41.20, z-score =  -2.26, R)
>droSim1.chrX 15671353 126 - 17042790
------AGUUUUUGGAGCGAGGGAAUUUUCGUCUA-GCG-UAUUUCGUUUUUCGUAUUUGCGAAAAACCGUGAAAAUUACAUGCCGCUGACGCAGCGGCGCCGUCACUCAUGACCUGCCUUUCGCCCCGUUUUC----------
------.......((.(((((((((((((((....-.).-......(((((((((....)))))))))...)))))))....(((((((...)))))))((.((((....))))..))))))))).))......---------- ( -41.20, z-score =  -2.26, R)
>droVir3.scaffold_12970 4729855 119 - 11907090
----------AGUUUUGGCAUCCAGUUUUCGUUUACGUAUUUU--CGUUUUUCGUAUUUGCGAAAAACCGUGAAAAUUACAUGCCGCUGACGCAGCGGCGCCGUCACUCAUGAUGAGGCUGCUCGGUUUUU-------------
----------......(((((..((((((((....).......--.(((((((((....)))))))))...)))))))..)))))(((((.((((((((...))).(((.....)))))))))))))....------------- ( -37.90, z-score =  -2.15, R)
>droMoj3.scaffold_6473 4163737 118 - 16943266
----------GUUUUUGGCAUCGAGUUUUCGUUUACGUAUUUUCUCGUUUUUCGUAUUUGCGAAAAACCGUGAAAAUUACAUGCCGCUGACGCAGCGGCGCCGUCACUCAUGAUGAGGCUGCUCGGUU----------------
----------.........(((((((..........((((((((.((((((((((....)))))))).)).))))).)))..(((((((...)))))))(((.((((....).)))))).))))))).---------------- ( -40.30, z-score =  -2.66, R)
>droGri2.scaffold_15081 3688391 112 + 4274704
-------------------AGCGAGUUUUCGUUUACGUAUUUUCUCGUUUUCCGUAUUUGCGAAAAAUCGUGAAAAUUACAUGCCGCUGACGCAGCGGCGCCGUCACUCAUGAUGGGGCUGCUCGGUUAUU-------------
-------------------..(((((..((......((((((((.((((((.(((....))).)))).)).))))).)))..(((((((...))))))).((((((....))))))))..)))))......------------- ( -37.20, z-score =  -1.98, R)
>consensus
______AGUUUUUGGAGCGAGGGAAUUUUCGUCUA_GCG_UAUUUCGUUUUUCGUAUUUGCGAAAAACCGUGAAAAUUACAUGCCGCUGACGCAGCGGCGCCGUCACUCAUGACCUGCCUUUCCCCCCGUUUUC__________
.......................((((((((......)........(((((((((....)))))))))...)))))))....(((((((...)))))))...((((....)))).............................. (-26.45 = -25.86 +  -0.59)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 02:04:12 2011