Locus 12045

Sequence ID dm3.chr3R
Location 25,299,365 – 25,299,474
Length 109
Max. P 0.996839
window16557 window16558 window16559 window16560

overview

Window 7

Location 25,299,365 – 25,299,458
Length 93
Sequences 6
Columns 96
Reading direction forward
Mean pairwise identity 78.67
Shannon entropy 0.39512
G+C content 0.52835
Mean single sequence MFE -27.48
Consensus MFE -21.09
Energy contribution -21.87
Covariance contribution 0.78
Combinations/Pair 1.19
Mean z-score -1.73
Structure conservation index 0.77
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.63
SVM RNA-class probability 0.956723
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 25299365 93 + 27905053
AGCCAACAUUUU-GUUGGCCUGCCAAGUGGGCAACAAUGUAGACCUCACCUACC--ACCCCCCUGCGUUAUGUCAAUCGAGUCGGCUUAUCGCGGC
.((((((.....-))))))..(((.((.(((.......((((.......)))).--...)))))(((.((.(((.........))).)).)))))) ( -24.80, z-score =  -0.27, R)
>droSim1.chr3R 24972660 95 + 27517382
AGCCAACAUUUU-GUUGGCCUGCCAAGUGGGCAACAAUGUACACCUCACCCCCCCAUUCCCCCUGCGAUAUGUCAAUCGAGUCGGCUUAUCGCGGC
.((((((.....-))))))..(((.((((((......((.......))....))))))......((((((.(((.........))).))))))))) ( -27.60, z-score =  -1.51, R)
>droSec1.super_4 4157966 94 + 6179234
AGCCAACAUUUU-GUUGGCCUGCCAAGUGGGCAACAAUGUACACCUCACCCCCC-AUCCCCCCUGCGAUAUGUCAAUCGAGUCGGCUUAUCGCGGC
.((((((.....-))))))..(((..(((..((....))..)))..........-.........((((((.(((.........))).))))))))) ( -27.50, z-score =  -1.39, R)
>droYak2.chr3R 7647078 90 - 28832112
AGCCAACAUUUUAGUUGGCCUGCCAAGUGGGCAACAUUUGUUGUUUG------UUGUUCACCCCGCGAUAUGUCAAUCGAGUCGGCUUAUCGCGGC
.((((((......)))))).......((((((((((.........))------)))))))).((((((((.(((.........))).)))))))). ( -35.80, z-score =  -4.07, R)
>droEre2.scaffold_4820 7763234 81 - 10470090
AGCCAACAUUUU-GUUGACCCGCCAAGUGGGCAGCAUUGUUG--------------UCCACCCUGCGAUAUGUCAAUCGAGUCGGCUUAUCGCGGC
...(((((...(-((((.(((((...)))))))))).)))))--------------......((((((((.(((.........))).)))))))). ( -30.00, z-score =  -2.65, R)
>droAna3.scaffold_12911 4987212 81 + 5364042
AGUAACCAUUUU-AUGGCCCUGCCAAGUUGGCAACAUUGUUG--------------UCCGUUUUGUGAUAUGUCAAUCGUGUCGGCUUAUCGCAGC
.....((((...-))))..((((.(((((((((..((((.((--------------((........))))...))))..)))))))))...)))). ( -19.20, z-score =  -0.51, R)
>consensus
AGCCAACAUUUU_GUUGGCCUGCCAAGUGGGCAACAAUGUAGACCUC______C__UCCCCCCUGCGAUAUGUCAAUCGAGUCGGCUUAUCGCGGC
.((((((......)))))).((((.....)))).............................((((((((.(((.........))).)))))))). (-21.09 = -21.87 +   0.78)

alignment

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secondary structure

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dotplot

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Window 8

Location 25,299,365 – 25,299,458
Length 93
Sequences 6
Columns 96
Reading direction reverse
Mean pairwise identity 78.67
Shannon entropy 0.39512
G+C content 0.52835
Mean single sequence MFE -29.35
Consensus MFE -18.28
Energy contribution -19.03
Covariance contribution 0.75
Combinations/Pair 1.20
Mean z-score -1.51
Structure conservation index 0.62
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.38
SVM RNA-class probability 0.666715
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 25299365 93 - 27905053
GCCGCGAUAAGCCGACUCGAUUGACAUAACGCAGGGGGGU--GGUAGGUGAGGUCUACAUUGUUGCCCACUUGGCAGGCCAAC-AAAAUGUUGGCU
((((((.((.(.(((.....))).).)).)))(((.((((--..((((((.....))).)))..)))).)))))).(((((((-.....))))))) ( -30.30, z-score =  -0.35, R)
>droSim1.chr3R 24972660 95 - 27517382
GCCGCGAUAAGCCGACUCGAUUGACAUAUCGCAGGGGGAAUGGGGGGGUGAGGUGUACAUUGUUGCCCACUUGGCAGGCCAAC-AAAAUGUUGGCU
(((((((((.(.(((.....))).).))))))..(((.((..(....(((.....))).)..)).)))....))).(((((((-.....))))))) ( -32.60, z-score =  -0.77, R)
>droSec1.super_4 4157966 94 - 6179234
GCCGCGAUAAGCCGACUCGAUUGACAUAUCGCAGGGGGGAU-GGGGGGUGAGGUGUACAUUGUUGCCCACUUGGCAGGCCAAC-AAAAUGUUGGCU
(((((((((.(.(((.....))).).))))))..(((.((.-.(...(((.....))).)..)).)))....))).(((((((-.....))))))) ( -33.60, z-score =  -1.07, R)
>droYak2.chr3R 7647078 90 + 28832112
GCCGCGAUAAGCCGACUCGAUUGACAUAUCGCGGGGUGAACAA------CAAACAACAAAUGUUGCCCACUUGGCAGGCCAACUAAAAUGUUGGCU
(((((((((.(.(((.....))).).)))))).(((((..(((------((.........)))))..)))))))).(((((((......))))))) ( -32.00, z-score =  -3.48, R)
>droEre2.scaffold_4820 7763234 81 + 10470090
GCCGCGAUAAGCCGACUCGAUUGACAUAUCGCAGGGUGGA--------------CAACAAUGCUGCCCACUUGGCGGGUCAAC-AAAAUGUUGGCU
(((((((((.(.(((.....))).).)))))).(((..(.--------------((....)))..)))....))).(((((((-.....))))))) ( -30.50, z-score =  -2.60, R)
>droAna3.scaffold_12911 4987212 81 - 5364042
GCUGCGAUAAGCCGACACGAUUGACAUAUCACAAAACGGA--------------CAACAAUGUUGCCAACUUGGCAGGGCCAU-AAAAUGGUUACU
.((((((((.(.(((.....))).).)))).(((...((.--------------((((...))))))...)))))))((((((-...))))))... ( -17.10, z-score =  -0.77, R)
>consensus
GCCGCGAUAAGCCGACUCGAUUGACAUAUCGCAGGGGGGA__G______GAGGUCAACAAUGUUGCCCACUUGGCAGGCCAAC_AAAAUGUUGGCU
(((((((((.(.(((.....))).).)))))).(((.((.......................)).)))....))).(((((((......))))))) (-18.28 = -19.03 +   0.75)

alignment

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secondary structure

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dotplot

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Window 9

Location 25,299,365 – 25,299,474
Length 109
Sequences 7
Columns 114
Reading direction forward
Mean pairwise identity 70.79
Shannon entropy 0.55977
G+C content 0.53883
Mean single sequence MFE -34.99
Consensus MFE -18.45
Energy contribution -19.70
Covariance contribution 1.25
Combinations/Pair 1.23
Mean z-score -2.44
Structure conservation index 0.53
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.99
SVM RNA-class probability 0.996839
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 25299365 109 + 27905053
AGCCAACAUUUU-GUUGGCCUGCCAAGUGGGCAACAAU-GUAGACCUCACCUACC--ACCCCCCUGCGUUAUGUCAAUCGAGUCGGCUUAUCGCGGCCAUUU-GGCCCGUUCUG
.((((((.....-))))))..(((((((((.(......-((((.......)))).--........(((.((.(((.........))).)).)))).))))))-)))........ ( -34.30, z-score =  -1.82, R)
>droSim1.chr3R 24972660 111 + 27517382
AGCCAACAUUUU-GUUGGCCUGCCAAGUGGGCAACAAU-GUACACCUCACCCCCCCAUUCCCCCUGCGAUAUGUCAAUCGAGUCGGCUUAUCGCGGCCAUUU-GGCCCGUUCUG
.((((((.....-))))))..((((((((((((....)-))......................((((((((.(((.........))).))))))))))))))-)))........ ( -36.60, z-score =  -2.81, R)
>droSec1.super_4 4157966 110 + 6179234
AGCCAACAUUUU-GUUGGCCUGCCAAGUGGGCAACAAU-GUACACCUCACCCCCC-AUCCCCCCUGCGAUAUGUCAAUCGAGUCGGCUUAUCGCGGCCAUUU-GGCCCGUUCUG
.((((((.....-))))))..((((((((((((....)-))..............-.......((((((((.(((.........))).))))))))))))))-)))........ ( -36.60, z-score =  -2.83, R)
>droYak2.chr3R 7647078 106 - 28832112
AGCCAACAUUUUAGUUGGCCUGCCAAGUGGGCAACAUUUGUUG-------UUUGUUGUUCACCCCGCGAUAUGUCAAUCGAGUCGGCUUAUCGCGGCCGUUU-GGCCCGGUCUG
.((((((......))))))..(((((((((((((((.......-------..)))))))))).((((((((.(((.........))).))))))))....))-)))........ ( -42.20, z-score =  -3.64, R)
>droEre2.scaffold_4820 7763234 97 - 10470090
AGCCAACAUUUU-GUUGACCCGCCAAGUGGGCAGCAUU-GUUG--------------UCCACCCUGCGAUAUGUCAAUCGAGUCGGCUUAUCGCGGCCAUUU-GGCCCGGUCUG
((((...((((.-((((((.(((...(((((((((...-))))--------------)))))...)))....)))))).)))).)))).((((.((((....-))))))))... ( -38.00, z-score =  -3.02, R)
>droAna3.scaffold_12911 4987212 98 + 5364042
AGUAACCAUUUU-AUGGCCCUGCCAAGUUGGCAACAUU-GUUG--------------UCCGUUUUGUGAUAUGUCAAUCGUGUCGGCUUAUCGCAGCCAUUUUGGCCCGGCCCA
............-..((((..((((((.((((.(((..-..))--------------)......(((((((.(((.........))).))))))))))).))))))..)))).. ( -33.00, z-score =  -2.77, R)
>droPer1.super_7 2326894 82 + 4445127
--------------------UGCCACUUUUGUUGGACCUUUUC-----------UGGGGUGCCUUGUGAUGUGUCAAUCGUGCUGGCUUAUCGCGGCCAUUU-GGCUGGGAACA
--------------------.((((........(((((((...-----------.))))).))....(((......)))....))))...((.(((((....-))))).))... ( -24.20, z-score =  -0.17, R)
>consensus
AGCCAACAUUUU_GUUGGCCUGCCAAGUGGGCAACAAU_GUUG___________C__UCCCCCCUGCGAUAUGUCAAUCGAGUCGGCUUAUCGCGGCCAUUU_GGCCCGGUCUG
.............((((.(((((...)))))))))..............................((((((.(((.........))).))))))((((.....))))....... (-18.45 = -19.70 +   1.25)

alignment

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secondary structure

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dotplot

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Window 0

Location 25,299,365 – 25,299,474
Length 109
Sequences 7
Columns 114
Reading direction reverse
Mean pairwise identity 70.79
Shannon entropy 0.55977
G+C content 0.53883
Mean single sequence MFE -33.59
Consensus MFE -17.67
Energy contribution -19.01
Covariance contribution 1.34
Combinations/Pair 1.28
Mean z-score -1.37
Structure conservation index 0.53
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.09
SVM RNA-class probability 0.888588
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 25299365 109 - 27905053
CAGAACGGGCC-AAAUGGCCGCGAUAAGCCGACUCGAUUGACAUAACGCAGGGGGGU--GGUAGGUGAGGUCUAC-AUUGUUGCCCACUUGGCAGGCCAAC-AAAAUGUUGGCU
.....((((((-....)))).))....((((((((...............)))((((--..((((((.....)))-.)))..))))..))))).(((((((-.....))))))) ( -37.16, z-score =  -0.78, R)
>droSim1.chr3R 24972660 111 - 27517382
CAGAACGGGCC-AAAUGGCCGCGAUAAGCCGACUCGAUUGACAUAUCGCAGGGGGAAUGGGGGGGUGAGGUGUAC-AUUGUUGCCCACUUGGCAGGCCAAC-AAAAUGUUGGCU
.....((((((-....)))).))....(((((((((((......)))).))(((.((..(....(((.....)))-.)..)).)))..))))).(((((((-.....))))))) ( -39.10, z-score =  -1.07, R)
>droSec1.super_4 4157966 110 - 6179234
CAGAACGGGCC-AAAUGGCCGCGAUAAGCCGACUCGAUUGACAUAUCGCAGGGGGGAU-GGGGGGUGAGGUGUAC-AUUGUUGCCCACUUGGCAGGCCAAC-AAAAUGUUGGCU
.....((((((-....)))).))....(((((((((((......)))).))(((.((.-.(...(((.....)))-.)..)).)))..))))).(((((((-.....))))))) ( -40.10, z-score =  -1.37, R)
>droYak2.chr3R 7647078 106 + 28832112
CAGACCGGGCC-AAACGGCCGCGAUAAGCCGACUCGAUUGACAUAUCGCGGGGUGAACAACAAA-------CAACAAAUGUUGCCCACUUGGCAGGCCAACUAAAAUGUUGGCU
........(((-(.....((((((((.(.(((.....))).).))))))))((((..(((((..-------.......)))))..)))))))).(((((((......))))))) ( -37.00, z-score =  -2.70, R)
>droEre2.scaffold_4820 7763234 97 + 10470090
CAGACCGGGCC-AAAUGGCCGCGAUAAGCCGACUCGAUUGACAUAUCGCAGGGUGGA--------------CAAC-AAUGCUGCCCACUUGGCGGGUCAAC-AAAAUGUUGGCU
.....((((((-....)))).))...(((((((....(((((...((((..(((((.--------------((..-.....)).)))))..))))))))).-.....))))))) ( -36.70, z-score =  -2.30, R)
>droAna3.scaffold_12911 4987212 98 - 5364042
UGGGCCGGGCCAAAAUGGCUGCGAUAAGCCGACACGAUUGACAUAUCACAAAACGGA--------------CAAC-AAUGUUGCCAACUUGGCAGGGCCAU-AAAAUGGUUACU
..((((..(((((..(((((......)))))....(((......))).......((.--------------((((-...))))))...)))))..))))..-............ ( -28.90, z-score =  -1.58, R)
>droPer1.super_7 2326894 82 - 4445127
UGUUCCCAGCC-AAAUGGCCGCGAUAAGCCAGCACGAUUGACACAUCACAAGGCACCCCA-----------GAAAAGGUCCAACAAAAGUGGCA--------------------
...((.(.(((-....))).).))...((((....(((......)))....((.(((...-----------.....)))))........)))).-------------------- ( -16.20, z-score =   0.19, R)
>consensus
CAGACCGGGCC_AAAUGGCCGCGAUAAGCCGACUCGAUUGACAUAUCGCAGGGGGGA__G___________CAAC_AAUGUUGCCCACUUGGCAGGCCAAC_AAAAUGUUGGCU
.......((((.....))))((((((.(.(((.....))).).))))))...............................(((((.....)))))((((((......)))))). (-17.67 = -19.01 +   1.34)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 00:54:39 2011