Locus 13083

Sequence ID dm3.chrX
Location 4,232,685 – 4,232,836
Length 151
Max. P 0.940355
window17982 window17983 window17984

overview

Window 2

Location 4,232,685 – 4,232,799
Length 114
Sequences 6
Columns 114
Reading direction reverse
Mean pairwise identity 70.69
Shannon entropy 0.54136
G+C content 0.41602
Mean single sequence MFE -26.50
Consensus MFE -17.71
Energy contribution -19.02
Covariance contribution 1.31
Combinations/Pair 1.32
Mean z-score -1.19
Structure conservation index 0.67
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.46
SVM RNA-class probability 0.940355
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 4232685 114 - 22422827
GGUCGAGAGGUCAGAGGGCAUCUGCAUUUGCUCUUCUGAUUUUAGCCACUCCUUUAUCGUUGAUUUUGUGUGCUUCUCAUAUUAGCACUAUUAUCUAAGGCGAAACUAAUCUCC
(((...((((((((((((((........))).))))))))))).))).........((((((((..((.(((((.........)))))))..)))...)))))........... ( -30.30, z-score =  -1.71, R)
>droEre2.scaffold_4690 1602799 114 - 18748788
GGCUGAGAGGUCAGAGGGCAUCUGCAUUUGCUCUUCAGAUUUCAGCCACUCCCUAAUCGUUGAUUUUGUGUGCUUUUCAUAUUAGCACUAUUAUCUAAGGCGGCACUAAUCUCU
((((((((.....(((((((........)))))))....))))))))..............((((..(((((((((..(((.((....)).)))..))))).)))).))))... ( -32.90, z-score =  -1.69, R)
>droYak2.chrX 17562576 114 + 21770863
GGCUAAGAGGUCAGAGGGCACCUGCAUUUGCUCUUCUGAUUUUAGACACUUCUUUAUCGUUGAUUUUGUGUAUUUUUCAUAUAAACACUAUUAUCUAAGGCGGAACUAAUCUCU
.....(((((((((((((((........))).)))))))).((((...((.(((((....((((..(((.(((.......))).)))..))))..))))).))..)))).)))) ( -22.10, z-score =  -0.30, R)
>droSec1.super_4 3684156 100 + 6179234
GGUCGAGAGGUCAGAGGGCAUCUGCAUUUGCUCUUCUGAUUUCAGC--------------UGAUUCUGUGUGCCUUUCAUAUUGGCACUAUUAUCUAAGGCAAAACUAAUCUCC
.(((..((((((((((((((........))).)))))))))))...--------------.(((.....(((((.........)))))....)))...)))............. ( -31.10, z-score =  -2.28, R)
>droSim1.chrX 3215922 100 - 17042790
GGUCGAGAGGUCAGAGGGCAUCUGCAUUUGCUCUUCUGAUUUCAGC--------------UGAUUUUGUGUGCCUUUCAUAUUGGCACUAUUAUCUAAGGCAAAACUAAUCUCC
.(((..((((((((((((((........))).)))))))))))...--------------.(((..((.(((((.........)))))))..)))...)))............. ( -31.80, z-score =  -2.66, R)
>droWil1.scaffold_181150 2816363 103 + 4952429
-GACACACGGCGAAUUUCCAUCUGCGAUUGGUUUUAAGUUUUUACC-------AUAUGCCUUAUACCACCCAACU-UCAGUUUAACAU--ACAUUAAAUGUGACGCGAACUUGC
-........(((...........(((..((((...........)))-------)..)))................-(((((((((...--...)))))).))))))........ ( -10.80, z-score =   1.49, R)
>consensus
GGUCGAGAGGUCAGAGGGCAUCUGCAUUUGCUCUUCUGAUUUCAGC_______UUAUCGUUGAUUUUGUGUGCCUUUCAUAUUAGCACUAUUAUCUAAGGCGAAACUAAUCUCC
.(((..((((((((((((((........))).)))))))))))..................(((.....(((((.........)))))....)))...)))............. (-17.71 = -19.02 +   1.31)

alignment

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secondary structure

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dotplot

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Window 3

Location 4,232,725 – 4,232,836
Length 111
Sequences 5
Columns 112
Reading direction reverse
Mean pairwise identity 70.35
Shannon entropy 0.50693
G+C content 0.47825
Mean single sequence MFE -30.93
Consensus MFE -19.72
Energy contribution -20.12
Covariance contribution 0.40
Combinations/Pair 1.22
Mean z-score -0.99
Structure conservation index 0.64
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.60
SVM RNA-class probability 0.758177
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 4232725 111 - 22422827
GGCA-AUGGGUGCUAAAGUUCUUUUCGGUGUGGUUAGGGGUCGAGAGGUCAGAGGGCAUCUGCAUUUGCUCUUCUGAUUUUAGCCACUCCUUUAUCGUUGAUUUUGUGUGCU
....-...((..((((((((.....(((((.....((((((.(.((((((((((((((........))).)))))))))))..).)))))).)))))..))))))).)..)) ( -33.60, z-score =  -1.19, R)
>droEre2.scaffold_4690 1602839 110 - 18748788
GGCA-AUGGGUGCAAAAGUUCUUUUCGGGG-GGUCAGGGGCUGAGAGGUCAGAGGGCAUCUGCAUUUGCUCUUCAGAUUUCAGCCACUCCCUAAUCGUUGAUUUUGUGUGCU
....-..(.(..(((((.........((((-(((....((((((((.....(((((((........)))))))....))))))))))))))).........)))))..).). ( -37.47, z-score =  -1.03, R)
>droYak2.chrX 17562616 92 + 21770863
-------------------GGAAAUGGGUGCAA-AAGGGGCUAAGAGGUCAGAGGGCACCUGCAUUUGCUCUUCUGAUUUUAGACACUUCUUUAUCGUUGAUUUUGUGUAUU
-------------------.(((((.((((..(-((((((....((((((((((((((........))).))))))))))).....)))))))..)))).)))))....... ( -22.80, z-score =  -0.36, R)
>droSec1.super_4 3684196 98 + 6179234
GGCAUUUGGGUGCUAAAGUUCUUUUCGGUGUGGUUAGGGGUCGAGAGGUCAGAGGGCAUCUGCAUUUGCUCUUCUGAUUUCAGCUGAUUCUGUGUGCC--------------
(((((.((((.(((...(..(((..(......)..)))..)...((((((((((((((........))).))))))))))))))....)))).)))))-------------- ( -31.20, z-score =  -1.30, R)
>droSim1.chrX 3215962 98 - 17042790
GGCAUUUGGGUGCUAAAGUUCUUUUCGGUGUGGUUAGGGGUCGAGAGGUCAGAGGGCAUCUGCAUUUGCUCUUCUGAUUUCAGCUGAUUUUGUGUGCC--------------
(((((((((.(.((((....(........)...)))).).))))((((((((((((((........))).)))))))))))............)))))-------------- ( -29.60, z-score =  -1.07, R)
>consensus
GGCA_AUGGGUGCUAAAGUUCUUUUCGGUGUGGUUAGGGGUCGAGAGGUCAGAGGGCAUCUGCAUUUGCUCUUCUGAUUUCAGCCACUUCUUUAUCGUUGAUUUUGUGU__U
(((.....................(((((.(......).)))))((((((((((((((........))).))))))))))).)))........................... (-19.72 = -20.12 +   0.40)

alignment

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secondary structure

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dotplot

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Window 4

Location 4,232,725 – 4,232,836
Length 111
Sequences 5
Columns 112
Reading direction reverse
Mean pairwise identity 70.35
Shannon entropy 0.50693
G+C content 0.47825
Mean single sequence MFE -30.93
Consensus MFE -19.72
Energy contribution -20.12
Covariance contribution 0.40
Combinations/Pair 1.22
Mean z-score -0.99
Structure conservation index 0.64
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.60
SVM RNA-class probability 0.758177
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 4232725 111 - 22422827
GGCA-AUGGGUGCUAAAGUUCUUUUCGGUGUGGUUAGGGGUCGAGAGGUCAGAGGGCAUCUGCAUUUGCUCUUCUGAUUUUAGCCACUCCUUUAUCGUUGAUUUUGUGUGCU
....-...((..((((((((.....(((((.....((((((.(.((((((((((((((........))).)))))))))))..).)))))).)))))..))))))).)..)) ( -33.60, z-score =  -1.19, R)
>droEre2.scaffold_4690 1602839 110 - 18748788
GGCA-AUGGGUGCAAAAGUUCUUUUCGGGG-GGUCAGGGGCUGAGAGGUCAGAGGGCAUCUGCAUUUGCUCUUCAGAUUUCAGCCACUCCCUAAUCGUUGAUUUUGUGUGCU
....-..(.(..(((((.........((((-(((....((((((((.....(((((((........)))))))....))))))))))))))).........)))))..).). ( -37.47, z-score =  -1.03, R)
>droYak2.chrX 17562616 92 + 21770863
-------------------GGAAAUGGGUGCAA-AAGGGGCUAAGAGGUCAGAGGGCACCUGCAUUUGCUCUUCUGAUUUUAGACACUUCUUUAUCGUUGAUUUUGUGUAUU
-------------------.(((((.((((..(-((((((....((((((((((((((........))).))))))))))).....)))))))..)))).)))))....... ( -22.80, z-score =  -0.36, R)
>droSec1.super_4 3684196 98 + 6179234
GGCAUUUGGGUGCUAAAGUUCUUUUCGGUGUGGUUAGGGGUCGAGAGGUCAGAGGGCAUCUGCAUUUGCUCUUCUGAUUUCAGCUGAUUCUGUGUGCC--------------
(((((.((((.(((...(..(((..(......)..)))..)...((((((((((((((........))).))))))))))))))....)))).)))))-------------- ( -31.20, z-score =  -1.30, R)
>droSim1.chrX 3215962 98 - 17042790
GGCAUUUGGGUGCUAAAGUUCUUUUCGGUGUGGUUAGGGGUCGAGAGGUCAGAGGGCAUCUGCAUUUGCUCUUCUGAUUUCAGCUGAUUUUGUGUGCC--------------
(((((((((.(.((((....(........)...)))).).))))((((((((((((((........))).)))))))))))............)))))-------------- ( -29.60, z-score =  -1.07, R)
>consensus
GGCA_AUGGGUGCUAAAGUUCUUUUCGGUGUGGUUAGGGGUCGAGAGGUCAGAGGGCAUCUGCAUUUGCUCUUCUGAUUUCAGCCACUUCUUUAUCGUUGAUUUUGUGU__U
(((.....................(((((.(......).)))))((((((((((((((........))).))))))))))).)))........................... (-19.72 = -20.12 +   0.40)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 01:14:19 2011