Locus 8173

Sequence ID dm3.chr3L
Location 20,743,577 – 20,743,671
Length 94
Max. P 0.989767
window11241 window11242

overview

Window 1

Location 20,743,577 – 20,743,671
Length 94
Sequences 7
Columns 127
Reading direction forward
Mean pairwise identity 62.97
Shannon entropy 0.62756
G+C content 0.56140
Mean single sequence MFE -38.93
Consensus MFE -15.57
Energy contribution -17.11
Covariance contribution 1.54
Combinations/Pair 1.56
Mean z-score -2.37
Structure conservation index 0.40
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.38
SVM RNA-class probability 0.989767
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 20743577 94 + 24543557
CAUCCUCAUCUCC-AUCGCC--ACGGCCAUAGCUUUGGCUAUAGCCAUGGCUAGAUAGCUAUAGCCGUGUCU---AUCUGGCAGAUCGGAACGGGGCGAA---------------------------
..(((((...(((-((((((--(.(((((......)))))((((.((((((((........)))))))).))---)).)))).))).)))...))).)).--------------------------- ( -36.40, z-score =  -2.30, R)
>droSim1.chr3L 20100096 94 + 22553184
CAUCCUCAUCUCC-AUCGCC--ACGGCCAUAGCUUUGGCUAUAGCCAUGGCUAGAUAGCUAUAGCCGUGGCU---AUCUGGCGGAUCGGAACGGGGCGAA---------------------------
..(((((...(((-.(((((--(.(((((......)))))(((((((((((((........)))))))))))---)).))))))...)))...))).)).--------------------------- ( -43.60, z-score =  -3.68, R)
>droSec1.super_11 632835 94 + 2888827
CAUCCUCAUCUCC-AUCGCC--ACGUCCUUAGCUUUGGCUAUAGCCAUGGCUAGAUAGCUAUAGCCGUGGCU---AUCUGGCGGAUCGGAACGGGGCGAA---------------------------
.............-.(((((--.(((((.......((((....))))..(((((((((((((....))))))---))))))).....)).))).))))).--------------------------- ( -40.10, z-score =  -3.06, R)
>droEre2.scaffold_4784 20436209 92 + 25762168
CAUCCUCAUCUCC-AUCGCC--CCGGCUAUAGCUUUGGCCAUAGCCAUAGCAAUA--GCUAUAGCCGUGGCU---AUCUGGCGGAUCGGACCGGGGCGAA---------------------------
.............-.(((((--((((((((.(((.((((((..((.(((((....--))))).))..)))))---)...)))..)).)).))))))))).--------------------------- ( -44.50, z-score =  -4.01, R)
>droYak2.chr3L 4394041 91 - 24197627
CAUCCUCAUCUCC-AUCGCC--CUGGCUGUAGCUUUGGCUAUAGCUAUAGCCAU---GCUAUAGCCGUGGCU---AUCUGGCGGAUCGGACAGGGGCGAA---------------------------
.............-.(((((--(.(((((((((..(((((((....))))))).---)))))))))....((---.(((((....))))).)))))))).--------------------------- ( -41.70, z-score =  -3.13, R)
>droAna3.scaffold_13337 11099341 121 + 23293914
CAUCGACAUCGCC-AUCGUC-AUAGCC-AACGCUAUGGCCAUUGCCAUC-CUCAUUCUCAU--GGUGGGGGCUAUAUCCAUCGCUUUGGAAGAUCGGGUGGAUUGGUGGGAGGUGAUGGUGGGCGAU
.((((...(((((-((((.(-(((((.-...))))))((((...(((((-(...(((.((.--((((((((.....))).))))).)))))....))))))..))))......))))))))).)))) ( -47.50, z-score =  -1.37, R)
>dp4.chrXR_group8 8173019 85 + 9212921
CAUCGCCAUUGCCCAUCGCCCAUCGCCCAAUGCCAUUGCCAUUGCCAUGGCUCCAGCAGAUCAGGAGAGGACAGAACACAGCGCA------------------------------------------
...(((..(((.((.((.((.(((((.....(((((.((....)).)))))....)).)))..)).)))).)))......)))..------------------------------------------ ( -18.70, z-score =   0.93, R)
>consensus
CAUCCUCAUCUCC_AUCGCC__ACGGCCAUAGCUUUGGCUAUAGCCAUGGCUAGAUAGCUAUAGCCGUGGCU___AUCUGGCGGAUCGGAACGGGGCGAA___________________________
...((((..........(((..(((((..((((..(((((((....)))))))....))))..)))))))).....((((......))))..))))............................... (-15.57 = -17.11 +   1.54)

alignment

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secondary structure

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dotplot

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Window 2

Location 20,743,577 – 20,743,671
Length 94
Sequences 7
Columns 127
Reading direction reverse
Mean pairwise identity 62.97
Shannon entropy 0.62756
G+C content 0.56140
Mean single sequence MFE -38.04
Consensus MFE -12.56
Energy contribution -13.27
Covariance contribution 0.71
Combinations/Pair 1.35
Mean z-score -2.59
Structure conservation index 0.33
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.03
SVM RNA-class probability 0.979694
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 20743577 94 - 24543557
---------------------------UUCGCCCCGUUCCGAUCUGCCAGAU---AGACACGGCUAUAGCUAUCUAGCCAUGGCUAUAGCCAAAGCUAUGGCCGU--GGCGAU-GGAGAUGAGGAUG
---------------------------.......(((((..((((.(((..(---(((...(((....))).))))((((((((((((((....)))))))))))--)))..)-))))))..))))) ( -40.70, z-score =  -3.75, R)
>droSim1.chr3L 20100096 94 - 22553184
---------------------------UUCGCCCCGUUCCGAUCCGCCAGAU---AGCCACGGCUAUAGCUAUCUAGCCAUGGCUAUAGCCAAAGCUAUGGCCGU--GGCGAU-GGAGAUGAGGAUG
---------------------------....((.(((..(.(((.((...((---(((....))))).))......((((((((((((((....)))))))))))--))))))-.)..))).))... ( -43.50, z-score =  -4.31, R)
>droSec1.super_11 632835 94 - 2888827
---------------------------UUCGCCCCGUUCCGAUCCGCCAGAU---AGCCACGGCUAUAGCUAUCUAGCCAUGGCUAUAGCCAAAGCUAAGGACGU--GGCGAU-GGAGAUGAGGAUG
---------------------------....((.(((..(.(((.(((((.(---(((...((((((((((((......))))))))))))...))))....).)--))))))-.)..))).))... ( -36.00, z-score =  -2.49, R)
>droEre2.scaffold_4784 20436209 92 - 25762168
---------------------------UUCGCCCCGGUCCGAUCCGCCAGAU---AGCCACGGCUAUAGC--UAUUGCUAUGGCUAUGGCCAAAGCUAUAGCCGG--GGCGAU-GGAGAUGAGGAUG
---------------------------.((((((((((..(......)..((---(((...(((((((((--(((....))))))))))))...))))).)))))--))))).-............. ( -43.60, z-score =  -3.47, R)
>droYak2.chr3L 4394041 91 + 24197627
---------------------------UUCGCCCCUGUCCGAUCCGCCAGAU---AGCCACGGCUAUAGC---AUGGCUAUAGCUAUAGCCAAAGCUACAGCCAG--GGCGAU-GGAGAUGAGGAUG
---------------------------.........((((.(((..(((...---.(((..((((.((((---.(((((((....)))))))..)))).))))..--)))..)-)).)))..)))). ( -36.70, z-score =  -2.76, R)
>droAna3.scaffold_13337 11099341 121 - 23293914
AUCGCCCACCAUCACCUCCCACCAAUCCACCCGAUCUUCCAAAGCGAUGGAUAUAGCCCCCACC--AUGAGAAUGAG-GAUGGCAAUGGCCAUAGCGUU-GGCUAU-GACGAU-GGCGAUGUCGAUG
(((((.(.(((((........((((((((..((...........)).)))))...(((..(..(--((....)))..-)..)))..))).((((((...-.)))))-)..)))-)).)..).)))). ( -31.40, z-score =  -0.01, R)
>dp4.chrXR_group8 8173019 85 - 9212921
------------------------------------------UGCGCUGUGUUCUGUCCUCUCCUGAUCUGCUGGAGCCAUGGCAAUGGCAAUGGCAUUGGGCGAUGGGCGAUGGGCAAUGGCGAUG
------------------------------------------..(((((((((((((((((.((..(..(((((..(((((....)))))..))))))..)).)).)))))..)))).))))))... ( -34.40, z-score =  -1.33, R)
>consensus
___________________________UUCGCCCCGUUCCGAUCCGCCAGAU___AGCCACGGCUAUAGCUAUCUAGCCAUGGCUAUAGCCAAAGCUAUGGCCGU__GGCGAU_GGAGAUGAGGAUG
.....................................(((.((.((((.(........).(((((.((((..........((((....))))..)))).)))))...)))))).))).......... (-12.56 = -13.27 +   0.71)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 23:40:45 2011