Locus 4857

Sequence ID dm3.chr2R
Location 16,041,203 – 16,041,326
Length 123
Max. P 0.700021
window6673 window6674

overview

Window 3

Location 16,041,203 – 16,041,296
Length 93
Sequences 9
Columns 99
Reading direction forward
Mean pairwise identity 74.45
Shannon entropy 0.48872
G+C content 0.49987
Mean single sequence MFE -23.31
Consensus MFE -15.47
Energy contribution -15.69
Covariance contribution 0.22
Combinations/Pair 1.00
Mean z-score -0.94
Structure conservation index 0.66
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.45
SVM RNA-class probability 0.700021
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 16041203 93 + 21146708
CAUUCGAUCCAGCGACAAGACGACAAAGGCGAUCCCAGGCGCACUUGUAAAUGGCAUGUUGCAACAAGCCUAAAUAUGCGCCACACACAAGCA------
...........((..............((.....)).((((((..(((....(((.(((....))).)))...)))))))))........)).------ ( -19.90, z-score =   0.15, R)
>droSim1.chr2R 14694099 93 + 19596830
CAUUCGAUCCAGCGACAAGACGACAAAGGCGAUCCCAGGCGCACUUGUAAAUGGCAUGUUGCAACAAGCCUAAAUAUGCGCCACACACAAGCA------
...........((..............((.....)).((((((..(((....(((.(((....))).)))...)))))))))........)).------ ( -19.90, z-score =   0.15, R)
>droSec1.super_1 13602728 93 + 14215200
CAUUCGAUCCAGCGACAAGACGACAAAGGCGAUCCCAGGCGCACUUGUAAAUGGCAUGUUGCAACAAGCCUAAAUAUGCGCCACACACAAGCA------
...........((..............((.....)).((((((..(((....(((.(((....))).)))...)))))))))........)).------ ( -19.90, z-score =   0.15, R)
>droYak2.chr2R 7974344 99 - 21139217
CAUUCGAUCCAGCGACAAGACGACAAAGGCGAUCCCAGGCGCACUUGUAAAUGGCAUGUUGCAACAAGCCUAAAUAUGCGCCACACACAAGCAGGGGCA
...........((((((.(...((((..(((........)))..))))......).)))))).....((((.....(((...........))).)))). ( -23.20, z-score =   0.40, R)
>droEre2.scaffold_4845 10191042 93 + 22589142
CAUUCGAUCCAGCGACAAGACGACAAAGGCGAUCCCAGGCGCACUUGUAAAUGGCAUGUUGCAACAAGCCUAAAUAUGCGCCACACACAAGCA------
...........((..............((.....)).((((((..(((....(((.(((....))).)))...)))))))))........)).------ ( -19.90, z-score =   0.15, R)
>dp4.chr3 13178287 75 + 19779522
------------CAGCCAGUCGCCCGAA------CGUGGCGCACUUGUAAAUGGCAUGUUGCAACAUGCCUAAAUAUGCGCCAUGCUCUUACA------
------------.............((.------(((((((((..(((....(((((((....)))))))...)))))))))))).)).....------ ( -27.10, z-score =  -2.40, R)
>droPer1.super_2 590568 75 - 9036312
------------CAGCCAGUCGCCCGAA------CGUGGCGCACUUGUAAAUGGCAUGUUGCAACAUGCCUAAAUAUGCGCCAUGCUCUUACA------
------------.............((.------(((((((((..(((....(((((((....)))))))...)))))))))))).)).....------ ( -27.10, z-score =  -2.40, R)
>droVir3.scaffold_12875 17144645 78 - 20611582
--------------ACUUGAUAUUGCAA-CGCUGUGGCGCGCACUUGUAAAUGGCAUGUUGCAACAUGCCUAAAUAUGCGCCACACACACUAA------
--------------..............-.(.((((((((((....))....(((((((....))))))).......))))))))).......------ ( -25.70, z-score =  -2.13, R)
>droGri2.scaffold_15112 2680743 91 + 5172618
--UAGUCUCCAAAAACUCGAUAUUGCAAACGCUGUGGCGCGCACUUGUAAAUGGCAUGUUGCAACAUGCCUAAAUAUGCGCCACACACACUAA------
--((((..................((....))((((((((((....))....(((((((....))))))).......))))))))...)))).------ ( -27.10, z-score =  -2.52, R)
>consensus
CAUUCGAUCCAGCGACAAGACGACAAAGGCGAUCCCAGGCGCACUUGUAAAUGGCAUGUUGCAACAAGCCUAAAUAUGCGCCACACACAAGCA______
.....................................((((((..(((....(((.(((....))).)))...)))))))))................. (-15.47 = -15.69 +   0.22)

alignment

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secondary structure

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dotplot

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Window 4

Location 16,041,222 – 16,041,326
Length 104
Sequences 7
Columns 112
Reading direction forward
Mean pairwise identity 66.51
Shannon entropy 0.59617
G+C content 0.53135
Mean single sequence MFE -30.66
Consensus MFE -15.03
Energy contribution -15.31
Covariance contribution 0.29
Combinations/Pair 1.00
Mean z-score -1.04
Structure conservation index 0.49
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.42
SVM RNA-class probability 0.688406
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 16041222 104 + 21146708
ACGACAAAGGCGAUCCCAGGCGCACUUGUAAAUGGCAUGUUGCAACAAGCCUAAAUAUGCGCCACACACAAGCACGG-GCUCAGGCGCACUAACGGGCCAGCAGC-------
.........((((.(((.((((((..(((....(((.(((....))).)))...))))))))).(......)...))-).)).(((.(......).))).))...------- ( -30.10, z-score =   0.28, R)
>droSim1.chr2R 14694118 104 + 19596830
ACGACAAAGGCGAUCCCAGGCGCACUUGUAAAUGGCAUGUUGCAACAAGCCUAAAUAUGCGCCACACACAAGCACGG-GCUCAGGCGCACUAACGGGCCAGCAGC-------
.........((((.(((.((((((..(((....(((.(((....))).)))...))))))))).(......)...))-).)).(((.(......).))).))...------- ( -30.10, z-score =   0.28, R)
>droSec1.super_1 13602747 104 + 14215200
ACGACAAAGGCGAUCCCAGGCGCACUUGUAAAUGGCAUGUUGCAACAAGCCUAAAUAUGCGCCACACACAAGCACGG-GCUCAGGCACACUAACGGGCCAGCAGC-------
.........((((.(((.((((((..(((....(((.(((....))).)))...))))))))).(......)...))-).)).(((...(....).))).))...------- ( -29.60, z-score =  -0.07, R)
>dp4.chr3 13178302 97 + 19779522
--------------ACGUGGCGCACUUGUAAAUGGCAUGUUGCAACAUGCCUAAAUAUGCGCCAUGCUCUUACACAGAGCG-AAAAAUGGUCGCGCUGGAUGGAUCUGCAGU
--------------.(((((((((..(((....(((((((....)))))))...)))))))))))).(((....(((.(((-(.......)))).)))...)))........ ( -35.20, z-score =  -2.01, R)
>droPer1.super_2 590583 80 - 9036312
--------------ACGUGGCGCACUUGUAAAUGGCAUGUUGCAACAUGCCUAAAUAUGCGCCAUGCUCUUACACAGAGCG-AAAAAUGGUAACG-----------------
--------------..((((((((..(((....(((((((....)))))))...)))))))))))(((((.....))))).-.............----------------- ( -29.60, z-score =  -3.51, R)
>droVir3.scaffold_12875 17144663 84 - 20611582
--------------GUGGCGCGCACUUGUAAAUGGCAUGUUGCAACAUGCCUAAAUAUGCGCCACACACACUAACGGCACAUGGGGCCA----CUGCGAAGA----------
--------------(((((((((....))....(((((((....))))))).......)))))))..........(((.......))).----.........---------- ( -29.10, z-score =  -1.21, R)
>droGri2.scaffold_15112 2680774 88 + 5172618
--------------GUGGCGCGCACUUGUAAAUGGCAUGUUGCAACAUGCCUAAAUAUGCGCCACACACACUAACGGCACAUGGGGCCAGCCACUGAGUAGA----------
--------------((((((((((..(((....(((((((....)))))))...)))))))).............(((.......))).)))))........---------- ( -30.90, z-score =  -1.01, R)
>consensus
______________CCGAGGCGCACUUGUAAAUGGCAUGUUGCAACAUGCCUAAAUAUGCGCCACACACAAGCACGG_GCUCAGGCACACUAACGGGCCAGC__________
..................((((((..(((....(((.(((....))).)))...)))))))))................................................. (-15.03 = -15.31 +   0.29)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:37:20 2011