Locus 5451

Sequence ID dm3.chr2R
Location 20,386,786 – 20,386,882
Length 96
Max. P 0.983624
window7481 window7482

overview

Window 1

Location 20,386,786 – 20,386,882
Length 96
Sequences 7
Columns 112
Reading direction forward
Mean pairwise identity 60.64
Shannon entropy 0.68180
G+C content 0.50164
Mean single sequence MFE -29.60
Consensus MFE -13.87
Energy contribution -13.43
Covariance contribution -0.44
Combinations/Pair 1.31
Mean z-score -0.85
Structure conservation index 0.47
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.59
SVM RNA-class probability 0.754741
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 20386786 96 + 21146708
UAUGGCCAGCGUGGACCGAA-UGGUGUGA-------AGUGUUUAGGGCAGAGAGAGUG---CACCCAUGUGU---UAGUGGUCGCUGGCCAUAUCAACGCAUUGGGGAAA--
((((((((((...(((((.(-(((.(((.-------(.(.(((.......))).).).---)))))))....---...)))))))))))))))((..(.....)..))..-- ( -30.50, z-score =  -0.64, R)
>droEre2.scaffold_4845 21754075 90 + 22589142
UAUGGCCAGCUUUGACCAAAACAGUGUGGGCUA---AGUGUUUGGGGCAG--------------CCAUGUGU---AUGUGGUAUCUGGCCAUAUCAACGCACUGGGG--AAU
(((((((((...((.((.(((((.(........---).))))).)).))(--------------((((....---..)))))..)))))))))((..(.....)..)--).. ( -26.60, z-score =   0.56, R)
>droYak2.chr2R 20355156 111 + 21139217
UAUGGCCAGCUUUGAACAAA-CAGUGUGAACUAGUAAGUGUUUAGGGUAGAGUACCCAAGGUACCCAUAGGUGGUAUGUGGUAUCUGGCCAUAUCAACGCACUGGGGGCAAU
(((((((.((((((((((.(-((((....))).))...))))))))))(((.((((((.(.((((....)))).).)).)))))))))))))).....((.(....)))... ( -35.30, z-score =  -0.84, R)
>droSec1.super_23 259499 88 + 989336
UAUGGCCAGCUUGAACCGAA-UAGUGUGA-------AGUGUUUAGGGCAGAGAGAGCA---CACCCAUGUGU---AAGUGGUCACUGGCCAUAUCAACGCAU----------
(((((((((..(((.(((..-..(..((.-------.((((((..........)))))---)...))..)..---...))))))))))))))).........---------- ( -25.60, z-score =  -0.99, R)
>droSim1.chr2R 18845880 88 + 19596830
UAUGGCCAGCUUGAACCGAA-UAGUGUGA-------AGUGUUUAGGGCAGAGAGAGCA---CACCCAUGUGU---AAGUGGUCACUGGCCAUAUCAACGCAU----------
(((((((((..(((.(((..-..(..((.-------.((((((..........)))))---)...))..)..---...))))))))))))))).........---------- ( -25.60, z-score =  -0.99, R)
>dp4.chr3 1498404 87 - 19779522
UAUCGCCAGCGAACUCUUUUGCAGUGUGU--------CUUCAUAGUGUGAG------------UGUGUGAGUGUGGUGCUGGCGCUGGCGAUAUCCAUGCACUGAGA-----
((((((((((..((((....(((.((((.--------...)))).))))))------------)..((.(((.....))).))))))))))))..............----- ( -31.80, z-score =  -1.54, R)
>droPer1.super_34 690570 87 - 916997
UAUCGCCAGCGAACUCUUUUGCAGUGUGU--------CUUCAUAGUGUGAG------------UGUGUGAGUGUGGUGCUGGCGCUGGCGAUAUCCAUGCACUGAGA-----
((((((((((..((((....(((.((((.--------...)))).))))))------------)..((.(((.....))).))))))))))))..............----- ( -31.80, z-score =  -1.54, R)
>consensus
UAUGGCCAGCUUGGACCGAA_CAGUGUGA_______AGUGUUUAGGGCAGAG__________ACCCAUGUGU___AUGUGGUCGCUGGCCAUAUCAACGCACUGGGG_____
(((((((((.............................(((.....)))...............((((.........))))...)))))))))................... (-13.87 = -13.43 +  -0.44)

alignment

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secondary structure

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dotplot

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Window 2

Location 20,386,786 – 20,386,882
Length 96
Sequences 7
Columns 112
Reading direction reverse
Mean pairwise identity 60.64
Shannon entropy 0.68180
G+C content 0.50164
Mean single sequence MFE -23.79
Consensus MFE -14.41
Energy contribution -14.19
Covariance contribution -0.22
Combinations/Pair 1.38
Mean z-score -1.09
Structure conservation index 0.61
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.14
SVM RNA-class probability 0.983624
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 20386786 96 - 21146708
--UUUCCCCAAUGCGUUGAUAUGGCCAGCGACCACUA---ACACAUGGGUG---CACUCUCUCUGCCCUAAACACU-------UCACACCA-UUCGGUCCACGCUGGCCAUA
--.................(((((((((((.......---.....((((.(---((.......)))))))......-------....(((.-...)))...))))))))))) ( -28.90, z-score =  -3.22, R)
>droEre2.scaffold_4845 21754075 90 - 22589142
AUU--CCCCAGUGCGUUGAUAUGGCCAGAUACCACAU---ACACAUGG--------------CUGCCCCAAACACU---UAGCCCACACUGUUUUGGUCAAAGCUGGCCAUA
...--..............(((((((((..((((...---(((...((--------------(((...........---))))).....)))..)))).....))))))))) ( -23.50, z-score =  -0.83, R)
>droYak2.chr2R 20355156 111 - 21139217
AUUGCCCCCAGUGCGUUGAUAUGGCCAGAUACCACAUACCACCUAUGGGUACCUUGGGUACUCUACCCUAAACACUUACUAGUUCACACUG-UUUGUUCAAAGCUGGCCAUA
...................(((((((((.((((.((((.....))))))))....(((((...))))).....((..((.(((....))))-)..))......))))))))) ( -26.70, z-score =  -0.05, R)
>droSec1.super_23 259499 88 - 989336
----------AUGCGUUGAUAUGGCCAGUGACCACUU---ACACAUGGGUG---UGCUCUCUCUGCCCUAAACACU-------UCACACUA-UUCGGUUCAAGCUGGCCAUA
----------.........((((((((((((((....---((((....)))---)((.......))..........-------........-...))))...)))))))))) ( -24.00, z-score =  -1.16, R)
>droSim1.chr2R 18845880 88 - 19596830
----------AUGCGUUGAUAUGGCCAGUGACCACUU---ACACAUGGGUG---UGCUCUCUCUGCCCUAAACACU-------UCACACUA-UUCGGUUCAAGCUGGCCAUA
----------.........((((((((((((((....---((((....)))---)((.......))..........-------........-...))))...)))))))))) ( -24.00, z-score =  -1.16, R)
>dp4.chr3 1498404 87 + 19779522
-----UCUCAGUGCAUGGAUAUCGCCAGCGCCAGCACCACACUCACACA------------CUCACACUAUGAAG--------ACACACUGCAAAAGAGUUCGCUGGCGAUA
-----..............(((((((((((..(((..............------------.(((.....)))..--------.....((.....)).)))))))))))))) ( -19.70, z-score =  -0.61, R)
>droPer1.super_34 690570 87 + 916997
-----UCUCAGUGCAUGGAUAUCGCCAGCGCCAGCACCACACUCACACA------------CUCACACUAUGAAG--------ACACACUGCAAAAGAGUUCGCUGGCGAUA
-----..............(((((((((((..(((..............------------.(((.....)))..--------.....((.....)).)))))))))))))) ( -19.70, z-score =  -0.61, R)
>consensus
_____CCCCAGUGCGUUGAUAUGGCCAGCGACCACAU___ACACAUGGGU__________CUCUGCCCUAAACACU_______UCACACUG_UUCGGUCCAAGCUGGCCAUA
...................(((((((((((.(((...........)))........................................((.....))....))))))))))) (-14.41 = -14.19 +  -0.22)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:48:36 2011