Locus 3213

Sequence ID dm3.chr2R
Location 3,477,524 – 3,477,705
Length 181
Max. P 0.998833
window4417 window4418 window4419 window4420 window4421

overview

Window 7

Location 3,477,524 – 3,477,633
Length 109
Sequences 6
Columns 111
Reading direction reverse
Mean pairwise identity 66.67
Shannon entropy 0.64716
G+C content 0.43752
Mean single sequence MFE -26.00
Consensus MFE -10.66
Energy contribution -12.99
Covariance contribution 2.34
Combinations/Pair 1.28
Mean z-score -1.12
Structure conservation index 0.41
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.22
SVM RNA-class probability 0.597375
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 3477524 109 - 21146708
GGCAGGGUGGCAGCUCUGUCGCACAUCAAUGGUUAAACCGGUUCACCAAUCACACAUAUUUACCGGUUUAAUUUCGGCCGACAGCUGUUUAUUUUUCUUAAAGCGUUAU--
((((((((....))))))))((........((((((((((((...................)))))))))))).((((.....))))...............)).....-- ( -29.61, z-score =  -2.53, R)
>dp4.chr3 7514465 101 + 19779522
---------GAUAUUCCGUGGAAUAUUACUAGCUACAUAGAAUACUUAGCCAUGCCCAGACAGUUUAAUACGAUUGAUGAAUCGAUUUUCUACUUGAUUGGCUUAAUUUA-
---------(((((((....))))))).(((......))).......(((((....(((..((...(((.(((((....))))))))..))..)))..))))).......- ( -17.10, z-score =  -0.94, R)
>droSim1.chr2R 2207896 109 - 19596830
AGCAGGGUGGCAGCUCUGUCUCACAUCAAUGGUUGAACCGGUUCGGCAAUCGCACAUAUUUACCGGUUUAAUUUCGGCCGACAGCUGUUUACUUUUCUAAAAGAGUUAU--
.(((((((....)))))))(((........((((((((((((...((....))........)))))))))))).((((.....))))...............)))....-- ( -27.90, z-score =  -1.04, R)
>droSec1.super_1 1140570 109 - 14215200
CGCAGGGUGGCAGCUCUGUUUCACAUCAAUGGUUGAACCGGUUCGGCAAUCGCACAUAUUUACCGGUUUAAUUUCGGCCGACAGCUGUUUACUUUUCUUAAAGCGUUAU--
.(((((((....)))))))........(((((((((((((((...((....))........)))))))))))..((((.....))))................))))..-- ( -26.20, z-score =  -0.43, R)
>droYak2.chr2L 16155417 109 - 22324452
CGCAGGGUGGCAGCUCUGU--CACAUCGAUUAUUAAACCGGUUCGCCAAUCGCACAUAUUUACCGGAUAAAUGUAGACUGCCAGCUGUUUACGUUGUUUAAAGCGGUUUAG
(((...((((((....)))--)))........((((((((((...................)))))...(((((((((........))))))))).))))).)))...... ( -26.91, z-score =  -0.25, R)
>droEre2.scaffold_4929 7520839 106 + 26641161
CGCAGGGUGGCAGCUCUGU--CACAUCGGUUUUUAAACCGGUUCACUAAUCGCACAUAUUUUCCGGUUACAGUU-GCCCGACGGCUGUUUACGUCUCUUAAAGCCUUAU--
...((((((((((((....--...(((((((....)))))))....((((((...........)))))).))))-))).((((........)))).......)))))..-- ( -28.30, z-score =  -1.53, R)
>consensus
CGCAGGGUGGCAGCUCUGU__CACAUCAAUGGUUAAACCGGUUCGCCAAUCGCACAUAUUUACCGGUUUAAUUUCGGCCGACAGCUGUUUACUUUUCUUAAAGCGUUAU__
.(((((((....)))))))............(((((((((((...................)))))))))))....................................... (-10.66 = -12.99 +   2.34)

alignment

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secondary structure

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dotplot

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Window 8

Location 3,477,553 – 3,477,668
Length 115
Sequences 6
Columns 115
Reading direction forward
Mean pairwise identity 70.03
Shannon entropy 0.58070
G+C content 0.47807
Mean single sequence MFE -31.10
Consensus MFE -12.58
Energy contribution -13.67
Covariance contribution 1.09
Combinations/Pair 1.24
Mean z-score -1.55
Structure conservation index 0.40
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.40
SVM RNA-class probability 0.677981
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 3477553 115 + 21146708
CGGCCGAAAUUAAACCGGUAAAUAUGUGUGAUUGGUGAACCGGUUUAACCAUUGAUGUGCGACAGAGCUGCCACCCUGCCAAAUACGACAAAGUGGCAGCCCUUGGCAACUCACC
..(((((..((((((((((..((...........))..))))))))))................(.((((((((..((.(......).))..)))))))).))))))........ ( -34.00, z-score =  -1.52, R)
>dp4.chr3 7514499 105 - 19779522
CAAUCGUA-UUAAACUGUC---UGGGCAUGGCUAAGUAUUCUAUGUAGCUAGUAAUAUUCCACGGAAUAUCAAAAACGAUGAAUAUG-UAAACUAGAACUUG-----AAUUCGUC
....((.(-((......((---(((((.((((((.(((...))).)))))))).((((((....)))))).................-....))))).....-----))).)).. ( -16.60, z-score =   0.12, R)
>droSim1.chr2R 2207925 115 + 19596830
CGGCCGAAAUUAAACCGGUAAAUAUGUGCGAUUGCCGAACCGGUUCAACCAUUGAUGUGAGACAGAGCUGCCACCCUGCUAAAUACGACAGUGUGGCACCCACUGGCAACUCACC
..((((.........))))......(((.(.((((((....(((((..((((....))).)...)))))(((((.((((.......).))).)))))......))))))).))). ( -29.80, z-score =  -0.64, R)
>droSec1.super_1 1140599 115 + 14215200
CGGCCGAAAUUAAACCGGUAAAUAUGUGCGAUUGCCGAACCGGUUCAACCAUUGAUGUGAAACAGAGCUGCCACCCUGCGAAAUCCGACAGUGUGGCAGCCACUGGCAACUCACC
..((((.........))))......(((.(.((((((....((.....))..............(.((((((((.(((((.....)).))).)))))))))..))))))).))). ( -37.50, z-score =  -2.54, R)
>droYak2.chr2L 16155448 113 + 22324452
CAGUCUACAUUUAUCCGGUAAAUAUGUGCGAUUGGCGAACCGGUUUAAUAAUCGAUGUG--ACAGAGCUGCCACCCUGCGAAAUCCGAUAUGGUGGCAGCUAAUGGAAACUCACC
((((((((((.............))))).)))))......(((((....)))))..(((--(...((((((((((.((((.....)).)).))))))))))...(....))))). ( -34.82, z-score =  -2.37, R)
>droEre2.scaffold_4929 7520868 112 - 26641161
CGGGCAAC-UGUAACCGGAAAAUAUGUGCGAUUAGUGAACCGGUUUAAAAACCGAUGUG--ACAGAGCUGCCACCCUGCGAAAUACGAUAGUGUGGCAGCCACUGCAAACUCACC
(((....)-)).......................((((..(((((....)))))...((--.(((.((((((((.(((((.....)).))).))))))))..)))))...)))). ( -33.90, z-score =  -2.36, R)
>consensus
CGGCCGAAAUUAAACCGGUAAAUAUGUGCGAUUGGCGAACCGGUUUAACCAUUGAUGUG__ACAGAGCUGCCACCCUGCGAAAUACGACAGUGUGGCAGCCACUGGCAACUCACC
............(((((((...((........))....))))))).....................((((((((..................))))))))............... (-12.58 = -13.67 +   1.09)

alignment

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secondary structure

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dotplot

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Window 9

Location 3,477,553 – 3,477,668
Length 115
Sequences 6
Columns 115
Reading direction reverse
Mean pairwise identity 70.03
Shannon entropy 0.58070
G+C content 0.47807
Mean single sequence MFE -36.67
Consensus MFE -20.14
Energy contribution -20.24
Covariance contribution 0.09
Combinations/Pair 1.50
Mean z-score -2.60
Structure conservation index 0.55
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 3.51
SVM RNA-class probability 0.998833
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 3477553 115 - 21146708
GGUGAGUUGCCAAGGGCUGCCACUUUGUCGUAUUUGGCAGGGUGGCAGCUCUGUCGCACAUCAAUGGUUAAACCGGUUCACCAAUCACACAUAUUUACCGGUUUAAUUUCGGCCG
(((((..(((..((((((((((((((((((....))))))))))))))))))...)))..))...((((((((((((...................))))))))))))...))). ( -52.21, z-score =  -6.29, R)
>dp4.chr3 7514499 105 + 19779522
GACGAAUU-----CAAGUUCUAGUUUA-CAUAUUCAUCGUUUUUGAUAUUCCGUGGAAUAUUACUAGCUACAUAGAAUACUUAGCCAUGCCCA---GACAGUUUAA-UACGAUUG
........-----...(((((((....-).........(((..((((((((....))))))))..)))....))))))...............---..(((((...-...))))) ( -12.80, z-score =   0.67, R)
>droSim1.chr2R 2207925 115 - 19596830
GGUGAGUUGCCAGUGGGUGCCACACUGUCGUAUUUAGCAGGGUGGCAGCUCUGUCUCACAUCAAUGGUUGAACCGGUUCGGCAAUCGCACAUAUUUACCGGUUUAAUUUCGGCCG
.(((((....(((.((.((((((.((((........)))).)))))).))))).)))))......((((((((((((...((....))........))))))......)))))). ( -42.00, z-score =  -2.56, R)
>droSec1.super_1 1140599 115 - 14215200
GGUGAGUUGCCAGUGGCUGCCACACUGUCGGAUUUCGCAGGGUGGCAGCUCUGUUUCACAUCAAUGGUUGAACCGGUUCGGCAAUCGCACAUAUUUACCGGUUUAAUUUCGGCCG
.(((((....(((.(((((((((.(((.((.....))))).)))))))))))).)))))......((((((((((((...((....))........))))))......)))))). ( -44.80, z-score =  -3.14, R)
>droYak2.chr2L 16155448 113 - 22324452
GGUGAGUUUCCAUUAGCUGCCACCAUAUCGGAUUUCGCAGGGUGGCAGCUCUGU--CACAUCGAUUAUUAAACCGGUUCGCCAAUCGCACAUAUUUACCGGAUAAAUGUAGACUG
....(((((.((((((((((((((....((.....))...))))))))))....--................(((((...................)))))...)))).))))). ( -32.31, z-score =  -1.81, R)
>droEre2.scaffold_4929 7520868 112 + 26641161
GGUGAGUUUGCAGUGGCUGCCACACUAUCGUAUUUCGCAGGGUGGCAGCUCUGU--CACAUCGGUUUUUAAACCGGUUCACUAAUCGCACAUAUUUUCCGGUUACA-GUUGCCCG
(((((((..((((.(((((((((.((..((.....))..)))))))))))))))--.))(((((((....)))))))))))).................(((....-...))).. ( -35.90, z-score =  -2.51, R)
>consensus
GGUGAGUUGCCAGUGGCUGCCACACUAUCGUAUUUCGCAGGGUGGCAGCUCUGU__CACAUCAAUGGUUAAACCGGUUCGCCAAUCGCACAUAUUUACCGGUUUAAUUUCGGCCG
(((((((.......(((((((((..................))))))))).......)).))...((((((((((((...................))))))))))))...))). (-20.14 = -20.24 +   0.09)

alignment

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secondary structure

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dotplot

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Window 0

Location 3,477,593 – 3,477,705
Length 112
Sequences 6
Columns 112
Reading direction forward
Mean pairwise identity 70.50
Shannon entropy 0.57142
G+C content 0.47680
Mean single sequence MFE -29.83
Consensus MFE -13.18
Energy contribution -12.77
Covariance contribution -0.41
Combinations/Pair 1.52
Mean z-score -1.52
Structure conservation index 0.44
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.67
SVM RNA-class probability 0.782596
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 3477593 112 + 21146708
CGGUUUAACCAUUGAUGUGCGACAGAGCUGCCACCCUGCCAAAUACGACAAAGUGGCAGCCCUUGGCAACUCACCACUGGCAUUUUCUCCCCAAUUUCGGUAUUUCGUCGUG
.((.....))........(((((.(((.(((((..((((((............))))))....))))).)))...(((((.(((........))).))))).....))))). ( -30.50, z-score =  -1.19, R)
>dp4.chr3 7514535 104 - 19779522
CUAUGUAGCUAGUAAUAUUCCACGGAAUAUCAAAAACGAUGAAUAUG-UAAACUAGAACUUG-----AAUUCGUCA--GUCUAUUUUUCAAAUGAGACCGCAUAUUAUAGUA
(((((((((.....((((((....)))))).......(((((((..(-(........))...-----.))))))).--(((((((.....))).)))).)).)).))))).. ( -14.80, z-score =   0.27, R)
>droSim1.chr2R 2207965 112 + 19596830
CGGUUCAACCAUUGAUGUGAGACAGAGCUGCCACCCUGCUAAAUACGACAGUGUGGCACCCACUGGCAACUCACCACUGGCAUUUUCUCCCCAAUUUCGGUUUUUCGCCGUG
((((..((((......(((((.(((.(.((((((.((((.......).))).)))))).)..)))....)))))...(((..........))).....))))....)))).. ( -28.50, z-score =  -0.44, R)
>droSec1.super_1 1140639 112 + 14215200
CGGUUCAACCAUUGAUGUGAAACAGAGCUGCCACCCUGCGAAAUCCGACAGUGUGGCAGCCACUGGCAACUCACCACUGGCAUUUUCUCCCCAAUUUCGGUUUUUCGCCGUG
((((..((((((((..(.((((......((((((.(((((.....)).))).))))))((((.(((.......))).))))..)))).)..))))...))))....)))).. ( -34.90, z-score =  -1.89, R)
>droYak2.chr2L 16155488 110 + 22324452
CGGUUUAAUAAUCGAUGUG--ACAGAGCUGCCACCCUGCGAAAUCCGAUAUGGUGGCAGCUAAUGGAAACUCACCACGAGCUUGUUCUACCUAAAUUCGGUAUUUCACCGUG
.(((..((((((((..(((--(...((((((((((.((((.....)).)).))))))))))...(....)))))..)))..)))))..)))......((((.....)))).. ( -36.60, z-score =  -3.74, R)
>droEre2.scaffold_4929 7520907 110 - 26641161
CGGUUUAAAAACCGAUGUG--ACAGAGCUGCCACCCUGCGAAAUACGAUAGUGUGGCAGCCACUGCAAACUCACCACAGGCGUGUUCUCCACAAAUUCGGUAUUUCAUCGUG
((((..(((.(((((((((--.(((.((((((((.(((((.....)).))).))))))))..)))..(((.(.((...)).).)))...))))...))))).))).)))).. ( -33.70, z-score =  -2.16, R)
>consensus
CGGUUUAACCAUUGAUGUG__ACAGAGCUGCCACCCUGCGAAAUACGACAGUGUGGCAGCCACUGGCAACUCACCACUGGCAUUUUCUCCCCAAAUUCGGUAUUUCACCGUG
((((......(((((..((....(((((((((((..................))))))))....(....)...............)))...))...))))).....)))).. (-13.18 = -12.77 +  -0.41)

alignment

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secondary structure

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dotplot

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Window 1

Location 3,477,593 – 3,477,705
Length 112
Sequences 6
Columns 112
Reading direction reverse
Mean pairwise identity 70.50
Shannon entropy 0.57142
G+C content 0.47680
Mean single sequence MFE -36.28
Consensus MFE -14.21
Energy contribution -14.38
Covariance contribution 0.17
Combinations/Pair 1.39
Mean z-score -2.16
Structure conservation index 0.39
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.42
SVM RNA-class probability 0.938043
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 3477593 112 - 21146708
CACGACGAAAUACCGAAAUUGGGGAGAAAAUGCCAGUGGUGAGUUGCCAAGGGCUGCCACUUUGUCGUAUUUGGCAGGGUGGCAGCUCUGUCGCACAUCAAUGGUUAAACCG
............(((....)))((.......((((.(((((...(((..((((((((((((((((((....))))))))))))))))))...)))))))).))))....)). ( -45.80, z-score =  -3.74, R)
>dp4.chr3 7514535 104 + 19779522
UACUAUAAUAUGCGGUCUCAUUUGAAAAAUAGAC--UGACGAAUU-----CAAGUUCUAGUUUA-CAUAUUCAUCGUUUUUGAUAUUCCGUGGAAUAUUACUAGCUACAUAG
..((((((((((((((((...((....)).))))--))..((((.-----...)))).......-))))))....(((..((((((((....))))))))..)))...)))) ( -20.40, z-score =  -1.64, R)
>droSim1.chr2R 2207965 112 - 19596830
CACGGCGAAAAACCGAAAUUGGGGAGAAAAUGCCAGUGGUGAGUUGCCAGUGGGUGCCACACUGUCGUAUUUAGCAGGGUGGCAGCUCUGUCUCACAUCAAUGGUUGAACCG
..(((.....((((...(((((.((((.....(((.((((.....)))).))).((((((.((((........)))).))))))......))))...)))))))))...))) ( -38.00, z-score =  -1.16, R)
>droSec1.super_1 1140639 112 - 14215200
CACGGCGAAAAACCGAAAUUGGGGAGAAAAUGCCAGUGGUGAGUUGCCAGUGGCUGCCACACUGUCGGAUUUCGCAGGGUGGCAGCUCUGUUUCACAUCAAUGGUUGAACCG
..(((.....(((((..(((((.(......).))))).(((((....(((.(((((((((.(((.((.....))))).)))))))))))).))))).....)))))...))) ( -40.10, z-score =  -1.43, R)
>droYak2.chr2L 16155488 110 - 22324452
CACGGUGAAAUACCGAAUUUAGGUAGAACAAGCUCGUGGUGAGUUUCCAUUAGCUGCCACCAUAUCGGAUUUCGCAGGGUGGCAGCUCUGU--CACAUCGAUUAUUAAACCG
..(((((...((((.......))))((..((((((.....)))))).....((((((((((....((.....))...))))))))))...)--).)))))............ ( -34.00, z-score =  -2.42, R)
>droEre2.scaffold_4929 7520907 110 + 26641161
CACGAUGAAAUACCGAAUUUGUGGAGAACACGCCUGUGGUGAGUUUGCAGUGGCUGCCACACUAUCGUAUUUCGCAGGGUGGCAGCUCUGU--CACAUCGGUUUUUAAACCG
.....(((((.(((((...((((..((((.((((...)))).))))((((.(((((((((.((..((.....))..)))))))))))))))--))))))))))))))..... ( -39.40, z-score =  -2.55, R)
>consensus
CACGACGAAAUACCGAAAUUGGGGAGAAAAUGCCAGUGGUGAGUUGCCAGUGGCUGCCACACUAUCGUAUUUCGCAGGGUGGCAGCUCUGU__CACAUCAAUGGUUAAACCG
..(((((.....((........))...........(((((.((((......)))))))))..)))))......(((((((....)))))))..................... (-14.21 = -14.38 +   0.17)

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 22:05:57 2011