Locus 9437

Sequence ID dm3.chr3R
Location 6,678,100 – 6,678,205
Length 105
Max. P 0.994385
window12942 window12943

overview

Window 2

Location 6,678,100 – 6,678,205
Length 105
Sequences 7
Columns 118
Reading direction forward
Mean pairwise identity 68.68
Shannon entropy 0.59510
G+C content 0.53357
Mean single sequence MFE -38.06
Consensus MFE -21.05
Energy contribution -21.04
Covariance contribution -0.01
Combinations/Pair 1.43
Mean z-score -2.00
Structure conservation index 0.55
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.70
SVM RNA-class probability 0.994385
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 6678100 105 + 27905053
CAGCCCCUUCAUCGCUCCGAAAUGG--AAACCCAACUGGCUGGGG---------GAGGAGUGGG--AAAUCCACCACGGUGGAGCGGUGACAACUCACCAUGCAGGGGAAAUCUGAAA
((((((((.(((.((((((...(((--...((((......)))).---------..(((.....--...))).)))...))))))(((((....)))))))).)))))....)))... ( -41.10, z-score =  -1.70, R)
>droSim1.chr3R 12829042 104 - 27517382
CAGCCCCUUCAUCGCUCCGAAAUGG--AAACCCAACACGAUGGG----------GAGGAGUGGG--AAAUCCACCACGGUGGAGCGGUGGCAACUCACCAUGCAGGGGAAAUCUGAAA
((((((((.((((((((((...(((--...((((......))))----------..(((.....--...))).)))...))))))))))(((........))))))))....)))... ( -40.90, z-score =  -2.19, R)
>droSec1.super_0 5847825 105 - 21120651
CAGCCCCUUCAUCGCUCCGAAAUGG--AAACCCAACACGCUGGGC---------GAGGAGUGGG--AAAUCCACCACGGUGGAGCGGUGGCAACUCACCAUGCAGGGGAAAUCUGAAA
((((((((.((((((((((...(((--...((((......)))).---------..(((.....--...))).)))...))))))))))(((........))))))))....)))... ( -40.20, z-score =  -1.69, R)
>droYak2.chr3R 10712423 102 + 28832112
CAGCCCCUUCAUCGCUCCGAAAUGG--AAACCCACCACGGUGG------------AGGAGUGGG--AAGUCCACCAUGGUGGAGCGGUGGCAACUCAACAUGCAGGGGAAAUCUGAAA
((((((((.((((((((((..((((--....((((....))))------------.(((.(...--.).))).))))..))))))))))(((........))))))))....)))... ( -45.40, z-score =  -3.26, R)
>droEre2.scaffold_4770 2813741 102 - 17746568
CAGCCCCUUCAUCGCUCCGAAAUGG--UAACCCACCACGAUGG------------AGGAGUGGG--AAAUCCACCAUGGUGGAGCGGUGGGCACUCAACAUGCAGGGGAAAUCUCAAA
...((((((((((((((((..((((--(..(((((..(.....------------.)..)))))--......)))))..)))))))))))(((.......)))))))).......... ( -43.60, z-score =  -3.03, R)
>droAna3.scaffold_13340 6995729 110 + 23697760
CAGCCCCUUCAUCGCUCCGAAAUGGGGAAACUCAACACGCCGGCGCUGGGCAUUGGGGAGUGGGGGAAAUUAAAAACGGUGGAGCAGUGGAAAUUCAACAUGCAGGGGAA--------
...(((((((.(((((((....((((....))))....(((.......))).....)))))))..)))...............(((.(((....)))...))).))))..-------- ( -35.10, z-score =  -0.60, R)
>droVir3.scaffold_12855 130165 99 + 10161210
CGAAUACUU-ACAAAUUUUUAACGC--AAACUAAAUGUUUGAUCACUUAAUCUUGGGCACUUAG--CCAUAGGUGACAAUUAAUUAGCUUGAGUU-AAUGUGCAG-------------
........(-(((.....(((((.(--((.((((.((.(((.(((((((......(((.....)--)).)))))))))).)).)))).))).)))-))))))...------------- ( -20.10, z-score =  -1.52, R)
>consensus
CAGCCCCUUCAUCGCUCCGAAAUGG__AAACCCAACACGCUGGG__________GAGGAGUGGG__AAAUCCACCACGGUGGAGCGGUGGCAACUCAACAUGCAGGGGAAAUCUGAAA
...((((((((((((((((...(((.....((((..........................))))......)))......))))))))))).............))))).......... (-21.05 = -21.04 +  -0.01)

alignment

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secondary structure

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dotplot

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Window 3

Location 6,678,100 – 6,678,205
Length 105
Sequences 7
Columns 118
Reading direction reverse
Mean pairwise identity 68.68
Shannon entropy 0.59510
G+C content 0.53357
Mean single sequence MFE -35.71
Consensus MFE -18.89
Energy contribution -20.19
Covariance contribution 1.29
Combinations/Pair 1.40
Mean z-score -2.04
Structure conservation index 0.53
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.63
SVM RNA-class probability 0.993677
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 6678100 105 - 27905053
UUUCAGAUUUCCCCUGCAUGGUGAGUUGUCACCGCUCCACCGUGGUGGAUUU--CCCACUCCUC---------CCCCAGCCAGUUGGGUUU--CCAUUUCGGAGCGAUGAAGGGGCUG
...(((....(((((.((((((((....)))))(((((...(..((((....--.))))..)..---------.(((((....)))))...--.......))))).))).)))))))) ( -40.40, z-score =  -2.25, R)
>droSim1.chr3R 12829042 104 + 27517382
UUUCAGAUUUCCCCUGCAUGGUGAGUUGCCACCGCUCCACCGUGGUGGAUUU--CCCACUCCUC----------CCCAUCGUGUUGGGUUU--CCAUUUCGGAGCGAUGAAGGGGCUG
...(((....(((((.(((((((......))))(((((...(..((((....--.))))..)..----------((((......))))...--.......))))).))).)))))))) ( -38.70, z-score =  -1.92, R)
>droSec1.super_0 5847825 105 + 21120651
UUUCAGAUUUCCCCUGCAUGGUGAGUUGCCACCGCUCCACCGUGGUGGAUUU--CCCACUCCUC---------GCCCAGCGUGUUGGGUUU--CCAUUUCGGAGCGAUGAAGGGGCUG
...(((....(((((.(((((((......))))(((((...(..((((....--.))))..)..---------((((((....))))))..--.......))))).))).)))))))) ( -41.00, z-score =  -2.03, R)
>droYak2.chr3R 10712423 102 - 28832112
UUUCAGAUUUCCCCUGCAUGUUGAGUUGCCACCGCUCCACCAUGGUGGACUU--CCCACUCCU------------CCACCGUGGUGGGUUU--CCAUUUCGGAGCGAUGAAGGGGCUG
...(((....((((((((........)))((.(((((((((((((((((...--........)------------))))))))))((....--)).....)))))).)).)))))))) ( -42.20, z-score =  -3.04, R)
>droEre2.scaffold_4770 2813741 102 + 17746568
UUUGAGAUUUCCCCUGCAUGUUGAGUGCCCACCGCUCCACCAUGGUGGAUUU--CCCACUCCU------------CCAUCGUGGUGGGUUA--CCAUUUCGGAGCGAUGAAGGGGCUG
..........(((((((((.....)))).((.(((((((((((((((((...--........)------------))))))))))((....--)).....)))))).)).)))))... ( -41.80, z-score =  -2.91, R)
>droAna3.scaffold_13340 6995729 110 - 23697760
--------UUCCCCUGCAUGUUGAAUUUCCACUGCUCCACCGUUUUUAAUUUCCCCCACUCCCCAAUGCCCAGCGCCGGCGUGUUGAGUUUCCCCAUUUCGGAGCGAUGAAGGGGCUG
--------..((((((((.((.(.....).)))))..((.(((((..((........((((....(((((.......)))))...))))........))..))))).)).)))))... ( -25.59, z-score =  -0.19, R)
>droVir3.scaffold_12855 130165 99 - 10161210
-------------CUGCACAUU-AACUCAAGCUAAUUAAUUGUCACCUAUGG--CUAAGUGCCCAAGAUUAAGUGAUCAAACAUUUAGUUU--GCGUUAAAAAUUUGU-AAGUAUUCG
-------------.((((..((-(((.((((((((....(((((((.((.((--(.....)))......)).)))).)))....)))))))--).))))).....)))-)........ ( -20.30, z-score =  -1.96, R)
>consensus
UUUCAGAUUUCCCCUGCAUGUUGAGUUGCCACCGCUCCACCGUGGUGGAUUU__CCCACUCCUC__________CCCAGCGUGUUGGGUUU__CCAUUUCGGAGCGAUGAAGGGGCUG
..........(((((.(((..((......)).((((((.....(((((.......)))))...............((((....)))).............))))))))).)))))... (-18.89 = -20.19 +   1.29)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 00:04:25 2011