Locus 7032

Sequence ID dm3.chr3L
Location 11,627,357 – 11,627,506
Length 149
Max. P 0.997247
window9682 window9683 window9684 window9685

overview

Window 2

Location 11,627,357 – 11,627,474
Length 117
Sequences 5
Columns 117
Reading direction forward
Mean pairwise identity 83.58
Shannon entropy 0.28287
G+C content 0.37486
Mean single sequence MFE -31.89
Consensus MFE -20.63
Energy contribution -20.51
Covariance contribution -0.12
Combinations/Pair 1.19
Mean z-score -3.28
Structure conservation index 0.65
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.64
SVM RNA-class probability 0.993741
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 11627357 117 + 24543557
UUGACUUUUACGUUUGGCGUAUGGAUUCUGUGGGUCGUCGAUCUGGUGGCCAAUUGAAAUACUUGAACUUGAAAAAAAUCACCGCAAUUAGCAUACAAUUCAAGUUCAAGUUCAAAC
((((((..((((.....)))).)).(((....((((..(.....)..))))....)))..(((((((((((((..........((.....))......))))))))))))))))).. ( -27.59, z-score =  -1.17, R)
>droSim1.chr3L 10999868 109 + 22553184
UUGACUUUUACGAUUGGC--------UCUGCGGGUCGUCGAUCUGUUUGCCAAUUGAAAUACUUGAACUUGAAAAAGAUCACUGCAAUUAGCAUGCAAUUCAAGUUCAAGUUUAAAC
..........((((((((--------...(((((((...)))))))..))))))))....(((((((((((((......((.(((.....)))))...)))))))))))))...... ( -36.30, z-score =  -4.83, R)
>droSec1.super_0 3814606 103 + 21120651
------UUUACGAUUGGC--------UCUGCGGGUCGUCGAUCUGUUUGCCAAUUGAAAUACUUGAACUUGAAAAAGAUCACUGCAAUUAGCAUACAAUUCAAGUUCAAGUUUAAAC
------....((((((((--------...(((((((...)))))))..))))))))....(((((((((((((.........(((.....))).....)))))))))))))...... ( -35.24, z-score =  -5.53, R)
>droYak2.chr3L 11655882 116 + 24197627
CUGACUUUUACGAUUGGUAUAUGG-CUCUGUGGGUCGUCGAUCUGGUGGGUAAUUGAAAAACUUGAACUUGAAAAAGAUCGCUUGUAUUAGCAUACAAUUCAAGUUCAAGUUAAAAC
((.(((.....(((((....((((-((.....))))))))))).))).)).........((((((((((((((....((.(((......)))))....))))))))))))))..... ( -30.80, z-score =  -2.96, R)
>droEre2.scaffold_4784 11611873 115 + 25762168
UUGACUUUUACGAUUGCUAUAUGG-CUCUGUAGGUCAUCGAUCUGGUGGGUAAUUGAAAUACCUGAUCUUGAAAAAGAUCGCUGGUAUUAGCAUACAAU-CAAGUUCAAGUUUAAGC
..(((((..(((((((...(((((-(((..((((((...))))))..))))......(((((((((((((....)))))))..))))))..))))))))-)..))..)))))..... ( -29.50, z-score =  -1.89, R)
>consensus
UUGACUUUUACGAUUGGC_UAUGG__UCUGUGGGUCGUCGAUCUGGUGGCCAAUUGAAAUACUUGAACUUGAAAAAGAUCACUGCAAUUAGCAUACAAUUCAAGUUCAAGUUUAAAC
..........((((((((............((((((...))))))...))))))))....(((((((((((((.........................)))))))))))))...... (-20.63 = -20.51 +  -0.12)

alignment

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secondary structure

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dotplot

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Window 3

Location 11,627,357 – 11,627,474
Length 117
Sequences 5
Columns 117
Reading direction reverse
Mean pairwise identity 83.58
Shannon entropy 0.28287
G+C content 0.37486
Mean single sequence MFE -23.87
Consensus MFE -17.02
Energy contribution -17.82
Covariance contribution 0.80
Combinations/Pair 1.16
Mean z-score -1.96
Structure conservation index 0.71
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.82
SVM RNA-class probability 0.827762
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 11627357 117 - 24543557
GUUUGAACUUGAACUUGAAUUGUAUGCUAAUUGCGGUGAUUUUUUUCAAGUUCAAGUAUUUCAAUUGGCCACCAGAUCGACGACCCACAGAAUCCAUACGCCAAACGUAAAAGUCAA
..(((((((((((((((((..((.(((.....)))...))....)))))))))))))...))))(((((.....((((...........).))).....)))))............. ( -25.90, z-score =  -1.55, R)
>droSim1.chr3L 10999868 109 - 22553184
GUUUAAACUUGAACUUGAAUUGCAUGCUAAUUGCAGUGAUCUUUUUCAAGUUCAAGUAUUUCAAUUGGCAAACAGAUCGACGACCCGCAGA--------GCCAAUCGUAAAAGUCAA
......((((((((((((((..(.(((.....))))..)).....))))))))))))......((((((.......((..((...))..))--------))))))............ ( -26.11, z-score =  -1.88, R)
>droSec1.super_0 3814606 103 - 21120651
GUUUAAACUUGAACUUGAAUUGUAUGCUAAUUGCAGUGAUCUUUUUCAAGUUCAAGUAUUUCAAUUGGCAAACAGAUCGACGACCCGCAGA--------GCCAAUCGUAAA------
......(((((((((((((..(..(((.....))).....)...)))))))))))))......((((((.......((..((...))..))--------))))))......------ ( -24.51, z-score =  -1.98, R)
>droYak2.chr3L 11655882 116 - 24197627
GUUUUAACUUGAACUUGAAUUGUAUGCUAAUACAAGCGAUCUUUUUCAAGUUCAAGUUUUUCAAUUACCCACCAGAUCGACGACCCACAGAG-CCAUAUACCAAUCGUAAAAGUCAG
.....((((((((((((((..(..((((......))))..)...))))))))))))))................(((..((((.........-...........))))....))).. ( -22.45, z-score =  -3.20, R)
>droEre2.scaffold_4784 11611873 115 - 25762168
GCUUAAACUUGAACUUG-AUUGUAUGCUAAUACCAGCGAUCUUUUUCAAGAUCAGGUAUUUCAAUUACCCACCAGAUCGAUGACCUACAGAG-CCAUAUAGCAAUCGUAAAAGUCAA
......((((.....((-(((((..(((......)))((((((....))))))((((...((.(((........))).))..))))......-.......)))))))...))))... ( -20.40, z-score =  -1.18, R)
>consensus
GUUUAAACUUGAACUUGAAUUGUAUGCUAAUUGCAGUGAUCUUUUUCAAGUUCAAGUAUUUCAAUUGGCCACCAGAUCGACGACCCACAGA__CCAUA_GCCAAUCGUAAAAGUCAA
......(((((((((((((.....((((......))))......)))))))))))))......((((((.......((...........))........))))))............ (-17.02 = -17.82 +   0.80)

alignment

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secondary structure

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dotplot

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Window 4

Location 11,627,397 – 11,627,506
Length 109
Sequences 5
Columns 117
Reading direction forward
Mean pairwise identity 77.51
Shannon entropy 0.39469
G+C content 0.31068
Mean single sequence MFE -24.51
Consensus MFE -14.11
Energy contribution -15.51
Covariance contribution 1.40
Combinations/Pair 1.12
Mean z-score -2.40
Structure conservation index 0.58
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.79
SVM RNA-class probability 0.967661
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 11627397 109 + 24543557
AUCUGGUGGCCAAUUGAAAUACUUGAACUUGAAAAAAAUCACCGCAAUUAGCAUACAAUUCAAGUUCAAGUUCAAACUCUAUUAGAAGAGCUAACUGGUAAAAAAUUAA--------
.((((((((....((((...(((((((((((((..........((.....))......)))))))))))))))))...)))))))).......................-------- ( -23.69, z-score =  -2.85, R)
>droSim1.chr3L 10999900 114 + 22553184
AUCUGUUUGCCAAUUGAAAUACUUGAACUUGAAAAAGAUCACUGCAAUUAGCAUGCAAUUCAAGUUCAAGUUUAAACUUUACCAGAAGAGCUAACUGGUACUGCAACAAUAUAU---
...((((.((..........(((((((((((((......((.(((.....)))))...)))))))))))))........((((((.........))))))..))))))......--- ( -26.60, z-score =  -2.58, R)
>droSec1.super_0 3814632 114 + 21120651
AUCUGUUUGCCAAUUGAAAUACUUGAACUUGAAAAAGAUCACUGCAAUUAGCAUACAAUUCAAGUUCAAGUUUAAACUCUAUUUGAAGAGCUAACUGGUACUGCAACAAUAUAU---
...(((.(((((.(((....(((((((((((((.........(((.....))).....))))))))))))).....((((......)))).))).)))))..))).........--- ( -25.84, z-score =  -2.75, R)
>droYak2.chr3L 11655921 95 + 24197627
AUCUGGUGGGUAAUUGAAAAACUUGAACUUGAAAAAGAUCGCUUGUAUUAGCAUACAAUUCAAGUUCAAGUUAAAACUUUCUUAGAAUAUUAUAU----------------------
.(((((..(((..((....((((((((((((((....((.(((......)))))....)))))))))))))).)))))..).)))).........---------------------- ( -21.90, z-score =  -3.22, R)
>droEre2.scaffold_4784 11611912 116 + 25762168
AUCUGGUGGGUAAUUGAAAUACCUGAUCUUGAAAAAGAUCGCUGGUAUUAGCAUACAAU-CAAGUUCAAGUUUAAGCUUUAUCAGAAGAGCUAAUUGGUACUGCAUGAAUAUUCUAU
.......(((((.....(((((((((((((....)))))))..)))))).((((((...-..(((((((((....))))........))))).....))).))).....)))))... ( -24.50, z-score =  -0.62, R)
>consensus
AUCUGGUGGCCAAUUGAAAUACUUGAACUUGAAAAAGAUCACUGCAAUUAGCAUACAAUUCAAGUUCAAGUUUAAACUUUAUUAGAAGAGCUAACUGGUACUGCAACAAUAU_____
.((((((((....((((...(((((((((((((.........................)))))))))))))))))...))))))))............................... (-14.11 = -15.51 +   1.40)

alignment

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secondary structure

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dotplot

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Window 5

Location 11,627,397 – 11,627,506
Length 109
Sequences 5
Columns 117
Reading direction reverse
Mean pairwise identity 77.51
Shannon entropy 0.39469
G+C content 0.31068
Mean single sequence MFE -26.80
Consensus MFE -16.88
Energy contribution -16.72
Covariance contribution -0.16
Combinations/Pair 1.18
Mean z-score -3.06
Structure conservation index 0.63
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 3.07
SVM RNA-class probability 0.997247
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 11627397 109 - 24543557
--------UUAAUUUUUUACCAGUUAGCUCUUCUAAUAGAGUUUGAACUUGAACUUGAAUUGUAUGCUAAUUGCGGUGAUUUUUUUCAAGUUCAAGUAUUUCAAUUGGCCACCAGAU
--------...........((((((((((((......))))))...(((((((((((((..((.(((.....)))...))....))))))))))))).....))))))......... ( -29.40, z-score =  -3.71, R)
>droSim1.chr3L 10999900 114 - 22553184
---AUAUAUUGUUGCAGUACCAGUUAGCUCUUCUGGUAAAGUUUAAACUUGAACUUGAAUUGCAUGCUAAUUGCAGUGAUCUUUUUCAAGUUCAAGUAUUUCAAUUGGCAAACAGAU
---.....(((((((..((((((.........))))))........((((((((((((((..(.(((.....))))..)).....))))))))))))..........)).))))).. ( -32.80, z-score =  -3.37, R)
>droSec1.super_0 3814632 114 - 21120651
---AUAUAUUGUUGCAGUACCAGUUAGCUCUUCAAAUAGAGUUUAAACUUGAACUUGAAUUGUAUGCUAAUUGCAGUGAUCUUUUUCAAGUUCAAGUAUUUCAAUUGGCAAACAGAU
---.....(((((......((((((((((((......))))))...(((((((((((((..(..(((.....))).....)...))))))))))))).....))))))..))))).. ( -31.00, z-score =  -3.28, R)
>droYak2.chr3L 11655921 95 - 24197627
----------------------AUAUAAUAUUCUAAGAAAGUUUUAACUUGAACUUGAAUUGUAUGCUAAUACAAGCGAUCUUUUUCAAGUUCAAGUUUUUCAAUUACCCACCAGAU
----------------------..............((((.....((((((((((((((..(..((((......))))..)...))))))))))))))))))............... ( -21.50, z-score =  -4.25, R)
>droEre2.scaffold_4784 11611912 116 - 25762168
AUAGAAUAUUCAUGCAGUACCAAUUAGCUCUUCUGAUAAAGCUUAAACUUGAACUUG-AUUGUAUGCUAAUACCAGCGAUCUUUUUCAAGAUCAGGUAUUUCAAUUACCCACCAGAU
............((.((((((....((((..........))))....((((((...(-(((((............))))))...))))))....)))))).)).............. ( -19.30, z-score =  -0.70, R)
>consensus
_____AUAUUGAUGCAGUACCAGUUAGCUCUUCUAAUAAAGUUUAAACUUGAACUUGAAUUGUAUGCUAAUUGCAGUGAUCUUUUUCAAGUUCAAGUAUUUCAAUUGGCCACCAGAU
..............................................(((((((((((((.....((((......))))......))))))))))))).................... (-16.88 = -16.72 +  -0.16)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 23:19:12 2011