Locus 7160

Sequence ID dm3.chr3L
Location 12,613,097 – 12,613,208
Length 111
Max. P 0.706129
window9855 window9856

overview

Window 5

Location 12,613,097 – 12,613,208
Length 111
Sequences 10
Columns 114
Reading direction forward
Mean pairwise identity 70.13
Shannon entropy 0.62980
G+C content 0.61946
Mean single sequence MFE -31.97
Consensus MFE -16.30
Energy contribution -16.03
Covariance contribution -0.27
Combinations/Pair 1.47
Mean z-score -0.65
Structure conservation index 0.51
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.12
SVM RNA-class probability 0.551777
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 12613097 111 + 24543557
CCAAGAUCUGGAGCGUGGCCGACACAGCCGCCUGCAAGACACCACCGCCCACCGCGGCGUACCUCGGCCAGAACUUCUAUCCACCCUCAUCGGCGGACCAGCAGUUGCCUC---
(((.....))).((.(((((((....(((((..((...........)).....))))).....))))))).((((.((.(((.((......)).)))..)).))))))...--- ( -33.40, z-score =  -0.14, R)
>droSim1.chr3L 11998757 111 + 22553184
CCAAGAUCUGGAGCGUGGCCGACACAGCCGCCUGCAAGACACCACCGCCCACCGCGGCGUACCUCGGCCAGAACUUCUAUCCGCCCUCAUCGGCGGACCAGCAGUUGCCCC---
.........((.((.(((((((....(((((..((...........)).....))))).....))))))).((((.((.((((((......))))))..)).)))))))).--- ( -40.00, z-score =  -1.82, R)
>droSec1.super_0 4799331 110 + 21120651
CCAAGAUCUGGAGCGUGGCCGACACAGCCGCCUGCA-GACACCACCGCCCACCGCGGCGUACCUCGGCCAGAACUUCUAUCCGCCCGCAUCGGCGGACCAGCAGUUGCCCC---
.........((.((.(((((((....(((((..((.-(......).)).....))))).....))))))).((((.((.((((((......))))))..)).)))))))).--- ( -40.40, z-score =  -1.56, R)
>droYak2.chr3L 12678001 111 + 24197627
CCAAGAUCUGGAGCGUGGCCGACACAGCCGCCUGCAAGACACCACCGCCCACCGCGGCGUACCUCGGCCAGAACUUCUACCCGCCCUCAUCGGCGGACCAGCCGUUGCCCC---
.(((...((((....(((((((....(((((..((...........)).....))))).....)))))))..........(((((......))))).))))...)))....--- ( -36.80, z-score =  -0.80, R)
>droEre2.scaffold_4784 12617453 111 + 25762168
CCAAGAUCUGGAGCGUGGCCGACACAGCCGCCUGCAAGACACCACCGCCCACCGCGGCGUACCUCGGCCAGAACUUCUACCCGCCCUCGUCGGCGGAGCAGCAGUUGCCCC---
.........((.((.(((((((....(((((..((...........)).....))))).....))))))).((((.((.((((((......))))).).)).)))))))).--- ( -39.20, z-score =  -0.64, R)
>dp4.chrXR_group6 3396889 108 + 13314419
CGAAAAUCUGGAGUGUGGCCGACACAGCCGCCUGCAAGACGCCACCGCCUAC---GGCAUACCUCGGCCAGAAUUUCUAUCCCC---AAGCGCCAGCCUCAGAGCAACAGCAGC
......(((((..(.(((((((....((((...((...........))...)---))).....))))))).)............---..((....)).)))))((....))... ( -26.30, z-score =   0.89, R)
>droWil1.scaffold_181136 2285941 92 - 2313701
CCAAAAUCUGGAGUGUGGCCGACACAGUCGCCUGCAAAACUCCACCUCCUAC---GGUAUACCUUGGCCAAAAUUUCUAUCCUC---CAGCUCAAGUG----------------
.......((((((..(((((((..(((....))).........(((......---))).....)))))))...........)))---)))........---------------- ( -19.92, z-score =  -1.17, R)
>droVir3.scaffold_13049 6018363 99 - 25233164
CCAAAAUCUGGAGUGUGGCCGACACAGUCGCCUGCAAGACACCACCGCCUAC---GGCAUAUCUCGGCCAGAAUUUCUAUCCACA-UCAGCAGCAGCAGCAGG-----------
((.....(((..(((.((((((....(((........)))......(((...---))).....))))))((.....))...))).-.)))..((....)).))----------- ( -24.80, z-score =  -0.08, R)
>droGri2.scaffold_15110 7665387 99 - 24565398
CCAAAAUCUGGAGUGUGGCCGACACAGUCGCCUGCAAGACACCACCGCCUAC---GGUAUAUCUCGGCCAGAAUUUCUAUCCACA-GCAGCAGCAAACACAAC-----------
(((.....))).((((((((((....(((........)))...((((....)---))).....))))))................-((....))..))))...----------- ( -25.90, z-score =  -1.67, R)
>anoGam1.chr2L 7502200 100 + 48795086
CCAAGGUAUGGGGGGGAGUAUGGGCAAUGGUAUGAUGAGCAGUUUCGGGAGU-ACCCCCUAUUCCCGCUAUGGGGGGUUUCUAGCCGGAGCUCAACACUAC-------------
..........((.(((((((.(((....(((((..((((....))))...))-))))))))))))).)).((..(((((((.....)))))))..))....------------- ( -33.00, z-score =   0.48, R)
>consensus
CCAAGAUCUGGAGCGUGGCCGACACAGCCGCCUGCAAGACACCACCGCCCAC_GCGGCGUACCUCGGCCAGAACUUCUAUCCACCCUCAGCGGCAGACCAGCAGUUGCC_C___
.........((((..(((((((..(((....)))............(((......))).....)))))))...))))..................................... (-16.30 = -16.03 +  -0.27)

alignment

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secondary structure

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dotplot

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Window 6

Location 12,613,097 – 12,613,208
Length 111
Sequences 10
Columns 114
Reading direction reverse
Mean pairwise identity 70.13
Shannon entropy 0.62980
G+C content 0.61946
Mean single sequence MFE -42.50
Consensus MFE -22.99
Energy contribution -22.61
Covariance contribution -0.38
Combinations/Pair 1.58
Mean z-score -0.69
Structure conservation index 0.54
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.46
SVM RNA-class probability 0.706129
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 12613097 111 - 24543557
---GAGGCAACUGCUGGUCCGCCGAUGAGGGUGGAUAGAAGUUCUGGCCGAGGUACGCCGCGGUGGGCGGUGGUGUCUUGCAGGCGGCUGUGUCGGCCACGCUCCAGAUCUUGG
---(..((((((.(((.((((((......))))))))).)))).(((((((..((.(((((.(..((((....)).))..)..)))))))..))))))).))..)......... ( -46.90, z-score =  -0.16, R)
>droSim1.chr3L 11998757 111 - 22553184
---GGGGCAACUGCUGGUCCGCCGAUGAGGGCGGAUAGAAGUUCUGGCCGAGGUACGCCGCGGUGGGCGGUGGUGUCUUGCAGGCGGCUGUGUCGGCCACGCUCCAGAUCUUGG
---(((((((((.(((.((((((......))))))))).)))).(((((((..((.(((((.(..((((....)).))..)..)))))))..))))))).)))))......... ( -54.10, z-score =  -1.58, R)
>droSec1.super_0 4799331 110 - 21120651
---GGGGCAACUGCUGGUCCGCCGAUGCGGGCGGAUAGAAGUUCUGGCCGAGGUACGCCGCGGUGGGCGGUGGUGUC-UGCAGGCGGCUGUGUCGGCCACGCUCCAGAUCUUGG
---(((((((((.(((.((((((......))))))))).)))).(((((((..((.(((((.(..((((....))))-..)..)))))))..))))))).)))))......... ( -56.90, z-score =  -2.02, R)
>droYak2.chr3L 12678001 111 - 24197627
---GGGGCAACGGCUGGUCCGCCGAUGAGGGCGGGUAGAAGUUCUGGCCGAGGUACGCCGCGGUGGGCGGUGGUGUCUUGCAGGCGGCUGUGUCGGCCACGCUCCAGAUCUUGG
---(((((...((((.(((((((......)))))))...)))).(((((((..((.(((((.(..((((....)).))..)..)))))))..))))))).)))))......... ( -50.30, z-score =  -0.18, R)
>droEre2.scaffold_4784 12617453 111 - 25762168
---GGGGCAACUGCUGCUCCGCCGACGAGGGCGGGUAGAAGUUCUGGCCGAGGUACGCCGCGGUGGGCGGUGGUGUCUUGCAGGCGGCUGUGUCGGCCACGCUCCAGAUCUUGG
---(((((((((.((((.(((((......))))))))).)))).(((((((..((.(((((.(..((((....)).))..)..)))))))..))))))).)))))......... ( -56.10, z-score =  -1.46, R)
>dp4.chrXR_group6 3396889 108 - 13314419
GCUGCUGUUGCUCUGAGGCUGGCGCUU---GGGGAUAGAAAUUCUGGCCGAGGUAUGCC---GUAGGCGGUGGCGUCUUGCAGGCGGCUGUGUCGGCCACACUCCAGAUUUUCG
((.(((...(((....))).)))))((---((((..((.....))((((((..((.(((---((..((((.......))))..)))))))..))))))...))))))....... ( -38.50, z-score =   1.01, R)
>droWil1.scaffold_181136 2285941 92 + 2313701
----------------CACUUGAGCUG---GAGGAUAGAAAUUUUGGCCAAGGUAUACC---GUAGGAGGUGGAGUUUUGCAGGCGACUGUGUCGGCCACACUCCAGAUUUUGG
----------------..((((.((..---(((........)))..)))))).......---...((((((((.....(((((....)))))....)))).))))......... ( -30.20, z-score =  -1.76, R)
>droVir3.scaffold_13049 6018363 99 + 25233164
-----------CCUGCUGCUGCUGCUGA-UGUGGAUAGAAAUUCUGGCCGAGAUAUGCC---GUAGGCGGUGGUGUCUUGCAGGCGACUGUGUCGGCCACACUCCAGAUUUUGG
-----------...((....))..(((.-.(((((.......))(((((((((((((((---(....)))).)))))..((((....)))).))))))))))..)))....... ( -33.10, z-score =  -0.17, R)
>droGri2.scaffold_15110 7665387 99 + 24565398
-----------GUUGUGUUUGCUGCUGC-UGUGGAUAGAAAUUCUGGCCGAGAUAUACC---GUAGGCGGUGGUGUCUUGCAGGCGACUGUGUCGGCCACACUCCAGAUUUUGG
-----------.((.((((..(......-.)..)))).))....(((((((((((((((---(....)))).)))))..((((....)))).)))))))............... ( -33.10, z-score =  -0.74, R)
>anoGam1.chr2L 7502200 100 - 48795086
-------------GUAGUGUUGAGCUCCGGCUAGAAACCCCCCAUAGCGGGAAUAGGGGGU-ACUCCCGAAACUGCUCAUCAUACCAUUGCCCAUACUCCCCCCCAUACCUUGG
-------------((((((.((((((((.((((...........)))).)))...((((..-..))))......)))))......))))))............(((.....))) ( -25.80, z-score =   0.16, R)
>consensus
___G_GGCAACUGCUGGUCCGCCGAUGAGGGCGGAUAGAAGUUCUGGCCGAGGUACGCCGC_GUGGGCGGUGGUGUCUUGCAGGCGGCUGUGUCGGCCACGCUCCAGAUCUUGG
..................((((........))))....(((.(((((........((((......))))(((((....(((((....)))))...)))))...))))).))).. (-22.99 = -22.61 +  -0.38)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 23:21:35 2011