Locus 813

Sequence ID dm3.chr2L
Location 5,863,996 – 5,864,138
Length 142
Max. P 0.994862
window1097 window1098 window1099 window1100 window1101

overview

Window 7

Location 5,863,996 – 5,864,092
Length 96
Sequences 3
Columns 103
Reading direction reverse
Mean pairwise identity 78.41
Shannon entropy 0.29177
G+C content 0.38284
Mean single sequence MFE -22.60
Consensus MFE -12.93
Energy contribution -13.60
Covariance contribution 0.67
Combinations/Pair 1.00
Mean z-score -2.37
Structure conservation index 0.57
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.69
SVM RNA-class probability 0.789277
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 5863996 96 - 23011544
UGCCGGUUAGAUAUGGAUACGUGAGUAUCCACUUUCACCGAUUGCUUUCUGCUUAAAGCCCAAAAAACACGAUCCAU---AUAUGA----AUGCAAUAUCAUU
(((((((.(((..(((((((....))))))).))).))))...(((((......)))))..................---......----..)))........ ( -22.20, z-score =  -2.41, R)
>droYak2.chr2L 8990529 91 + 22324452
UUCCAGUUAGAUAUGGAUACGUGAGUCGCCAC-----------AAUUUCUGCUUUAAA-CCCAACAUCACGAUCCAUAUGAUAUGAUGAUGUGCAAUAUCAUU
..........((((((((.(((((........-----------...............-.......))))))))))))).....((((((((...)))))))) ( -18.01, z-score =  -0.86, R)
>droSim1.chr2L 5654530 95 - 22036055
UGCCGGUUAGAUAUGGAUACGUGAGUAUCCACUUUCACCGAUUGCUUUCUGCUUUAAG-CAGAACAACACGAUCCAU---AUAUGA----AUGCAAUAUCAUU
(((.(((.(((..(((((((....))))))).))).)))(((((..((((((.....)-))))).....)))))...---......----..)))........ ( -27.60, z-score =  -3.84, R)
>consensus
UGCCGGUUAGAUAUGGAUACGUGAGUAUCCACUUUCACCGAUUGCUUUCUGCUUUAAG_CCAAACAACACGAUCCAU___AUAUGA____AUGCAAUAUCAUU
.........(((((((((((....))))))...................(((........................................))))))))... (-12.93 = -13.60 +   0.67)

alignment

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secondary structure

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dotplot

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Window 8

Location 5,864,029 – 5,864,128
Length 99
Sequences 5
Columns 102
Reading direction forward
Mean pairwise identity 66.40
Shannon entropy 0.58660
G+C content 0.43834
Mean single sequence MFE -23.34
Consensus MFE -9.42
Energy contribution -10.50
Covariance contribution 1.08
Combinations/Pair 1.28
Mean z-score -1.37
Structure conservation index 0.40
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.08
SVM RNA-class probability 0.532141
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 5864029 99 + 23011544
UUGGGCUUUAAGCAGAAAGCAAUCGGUGAAAGUGGAUACUC-ACGUAUCCAUAU-CUAACCGGCACUUCUAGCAGGGCCUU-UCCGCAUCAAGAGUCAUAAA
...((((((..((.((((((...((((....((((((((..-..))))))))..-...))))((.......))...).)))-)).))....))))))..... ( -28.40, z-score =  -2.15, R)
>droAna3.scaffold_12916 11275690 99 + 16180835
-UCCGAUUAAAACGAGGUAUAAGCG--AAUCGUAACCUCUCGAAAGAAGCAUACAUUGUCUUGCAUGCACCGCUGAGAUUUAUCAGCUUAAAGGGCAAUAAA
-(((.........(((((....(((--...))).)))))((....)).((((.((......)).))))...(((((......))))).....)))....... ( -22.10, z-score =  -1.11, R)
>droYak2.chr2L 8990569 87 - 22324452
------------UGGGUUUAAAGCAGAAAUUGUGGCGACUC-ACGUAUCCAUAU-CUAACUGGAACUUCUAGCAAGGCUUU-UCCGCGUCAAGAGUCAUAAA
------------..........((((((...((((....))-))((.((((...-.....)))))))))).))..((((((-(.......)))))))..... ( -15.20, z-score =   0.87, R)
>droSec1.super_5 3933892 85 + 5866729
--------------GAAAGCAAUCGGUGAAAGUGGAUACUC-ACGUAUCCAUAU-CUAACCGGCACUUCUAGCAGGGCUUU-UCCGCGUCAAGAGUCAUAAA
--------------..........(((....((((((((..-..))))))))..-...)))(((.(((...((.(((....-)))))...))).)))..... ( -22.30, z-score =  -1.80, R)
>droSim1.chr2L 5654563 98 + 22036055
-UCUGCUUAAAGCAGAAAGCAAUCGGUGAAAGUGGAUACUC-ACGUAUCCAUAU-CUAACCGGCACUUCUAGCAGGGCUUU-UCCGCGUCAAGAGUCAUAAA
-(((((.....)))))........(((....((((((((..-..))))))))..-...)))(((.(((...((.(((....-)))))...))).)))..... ( -28.70, z-score =  -2.67, R)
>consensus
_U__G_UU_AA_CAGAAAGCAAUCGGUGAAAGUGGAUACUC_ACGUAUCCAUAU_CUAACCGGCACUUCUAGCAGGGCUUU_UCCGCGUCAAGAGUCAUAAA
...............................((((((((.....)))))))).........(((.(((...((.((......)).))...))).)))..... ( -9.42 = -10.50 +   1.08)

alignment

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secondary structure

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dotplot

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Window 9

Location 5,864,029 – 5,864,128
Length 99
Sequences 5
Columns 102
Reading direction reverse
Mean pairwise identity 66.40
Shannon entropy 0.58660
G+C content 0.43834
Mean single sequence MFE -26.07
Consensus MFE -10.62
Energy contribution -11.02
Covariance contribution 0.40
Combinations/Pair 1.47
Mean z-score -2.13
Structure conservation index 0.41
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.70
SVM RNA-class probability 0.962130
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 5864029 99 - 23011544
UUUAUGACUCUUGAUGCGGA-AAGGCCCUGCUAGAAGUGCCGGUUAG-AUAUGGAUACGU-GAGUAUCCACUUUCACCGAUUGCUUUCUGCUUAAAGCCCAA
.........(((...(((((-(((((.((......)).))((((.((-(..(((((((..-..))))))).))).))))....))))))))...)))..... ( -32.00, z-score =  -3.22, R)
>droAna3.scaffold_12916 11275690 99 - 16180835
UUUAUUGCCCUUUAAGCUGAUAAAUCUCAGCGGUGCAUGCAAGACAAUGUAUGCUUCUUUCGAGAGGUUACGAUU--CGCUUAUACCUCGUUUUAAUCGGA-
.......((..(((((((((......)))))((.(((((((......))))))).))......(((((.......--.......)))))...))))..)).- ( -23.74, z-score =  -1.10, R)
>droYak2.chr2L 8990569 87 + 22324452
UUUAUGACUCUUGACGCGGA-AAAGCCUUGCUAGAAGUUCCAGUUAG-AUAUGGAUACGU-GAGUCGCCACAAUUUCUGCUUUAAACCCA------------
..........((((.(((((-((...((.(((.(.....).))).))-...(((..((..-..))..)))...))))))).)))).....------------ ( -17.50, z-score =  -0.39, R)
>droSec1.super_5 3933892 85 - 5866729
UUUAUGACUCUUGACGCGGA-AAAGCCCUGCUAGAAGUGCCGGUUAG-AUAUGGAUACGU-GAGUAUCCACUUUCACCGAUUGCUUUC--------------
...............((((.-......))))..(((((..((((.((-(..(((((((..-..))))))).))).))))...))))).-------------- ( -23.80, z-score =  -2.13, R)
>droSim1.chr2L 5654563 98 - 22036055
UUUAUGACUCUUGACGCGGA-AAAGCCCUGCUAGAAGUGCCGGUUAG-AUAUGGAUACGU-GAGUAUCCACUUUCACCGAUUGCUUUCUGCUUUAAGCAGA-
.......(((((((.(((((-((.((...((.......))((((.((-(..(((((((..-..))))))).))).))))...))))))))).))))).)).- ( -33.30, z-score =  -3.81, R)
>consensus
UUUAUGACUCUUGACGCGGA_AAAGCCCUGCUAGAAGUGCCGGUUAG_AUAUGGAUACGU_GAGUAUCCACUUUCACCGAUUGCUUUCCG_UU_AA_C__A_
...............((((........)))).........((((.......(((((((.....))))))).....))))....................... (-10.62 = -11.02 +   0.40)

alignment

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secondary structure

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dotplot

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Window 0

Location 5,864,041 – 5,864,138
Length 97
Sequences 5
Columns 104
Reading direction forward
Mean pairwise identity 68.57
Shannon entropy 0.54786
G+C content 0.46568
Mean single sequence MFE -26.08
Consensus MFE -15.62
Energy contribution -17.82
Covariance contribution 2.20
Combinations/Pair 1.28
Mean z-score -2.10
Structure conservation index 0.60
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.74
SVM RNA-class probability 0.994862
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 5864041 97 + 23011544
-----CAGAAAGCAAUCGGUGAAAGUGGAUACUCACGUAUCCAUAUCUAACCGGCACUUCUAGCAGGGCCUUUCCGCAUCAAGAGUCAUAAAGCCUGCUACC--
-----.((((.((...((((....((((((((....)))))))).....))))))..))))((((((..((((..((.......))...))))))))))...-- ( -26.30, z-score =  -1.96, R)
>droAna3.scaffold_12916 11275701 100 + 16180835
CGAGGUAUAAGCGAAUCGUAACCUCUCGAAAGAAGCAUA-CAUUGUCUUGCAUGCACCGCUG---AGAUUUAUCAGCUUAAAGGGCAAUAAAAUUUUUUCAGCC
.(((((....(((...))).)))))((....)).((((.-((......)).))))...((((---((((((((..(((.....))).)))))....))))))). ( -23.80, z-score =  -1.37, R)
>droYak2.chr2L 8990580 86 - 22324452
----------------CAGAAAUUGUGGCGACUCACGUAUCCAUAUCUAACUGGAACUUCUAGCAAGGCUUUUCCGCGUCAAGAGUCAUAAAGCCUGCUUCC--
----------------.((((...((((....))))((.((((........))))))))))((((.((((((...((.......))...))))))))))...-- ( -19.50, z-score =  -0.86, R)
>droSec1.super_5 3933892 95 + 5866729
-------GAAAGCAAUCGGUGAAAGUGGAUACUCACGUAUCCAUAUCUAACCGGCACUUCUAGCAGGGCUUUUCCGCGUCAAGAGUCAUAAAGCCUGCUACC--
-------....((...((((....((((((((....)))))))).....)))))).....(((((((.((((...((.......))...)))))))))))..-- ( -30.40, z-score =  -3.24, R)
>droSim1.chr2L 5654574 97 + 22036055
-----CAGAAAGCAAUCGGUGAAAGUGGAUACUCACGUAUCCAUAUCUAACCGGCACUUCUAGCAGGGCUUUUCCGCGUCAAGAGUCAUAAAGCCUGCUACC--
-----.((((.((...((((....((((((((....)))))))).....))))))..))))((((((.((((...((.......))...))))))))))...-- ( -30.40, z-score =  -3.07, R)
>consensus
______AGAAAGCAAUCGGUGAAAGUGGAUACUCACGUAUCCAUAUCUAACCGGCACUUCUAGCAGGGCUUUUCCGCGUCAAGAGUCAUAAAGCCUGCUACC__
................((((....((((((((....)))))))).....)))).......((((.(((((((...((.......))...))))))))))).... (-15.62 = -17.82 +   2.20)

alignment

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secondary structure

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dotplot

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Window 1

Location 5,864,041 – 5,864,138
Length 97
Sequences 5
Columns 104
Reading direction reverse
Mean pairwise identity 68.57
Shannon entropy 0.54786
G+C content 0.46568
Mean single sequence MFE -28.39
Consensus MFE -15.45
Energy contribution -15.37
Covariance contribution -0.08
Combinations/Pair 1.50
Mean z-score -1.84
Structure conservation index 0.54
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.94
SVM RNA-class probability 0.975906
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 5864041 97 - 23011544
--GGUAGCAGGCUUUAUGACUCUUGAUGCGGAAAGGCCCUGCUAGAAGUGCCGGUUAGAUAUGGAUACGUGAGUAUCCACUUUCACCGAUUGCUUUCUG-----
--..(((((((((((.((.(.......)))..)))).)))))))((((.((((((.(((..(((((((....))))))).))).))))...))))))..----- ( -32.50, z-score =  -2.34, R)
>droAna3.scaffold_12916 11275701 100 - 16180835
GGCUGAAAAAAUUUUAUUGCCCUUUAAGCUGAUAAAUCU---CAGCGGUGCAUGCAAGACAAUG-UAUGCUUCUUUCGAGAGGUUACGAUUCGCUUAUACCUCG
(((..(((....)))...)))......(((((......)---))))((.(((((((......))-))))).))......(((((..............))))). ( -24.44, z-score =  -1.37, R)
>droYak2.chr2L 8990580 86 + 22324452
--GGAAGCAGGCUUUAUGACUCUUGACGCGGAAAAGCCUUGCUAGAAGUUCCAGUUAGAUAUGGAUACGUGAGUCGCCACAAUUUCUG----------------
--...((((((((((.....(((......))))))))).))))((((((((((........))))...(((......))).)))))).---------------- ( -20.30, z-score =  -0.06, R)
>droSec1.super_5 3933892 95 - 5866729
--GGUAGCAGGCUUUAUGACUCUUGACGCGGAAAAGCCCUGCUAGAAGUGCCGGUUAGAUAUGGAUACGUGAGUAUCCACUUUCACCGAUUGCUUUC-------
--..(((((((((((.....(((......))))))).)))))))(((((..((((.(((..(((((((....))))))).))).))))...))))).------- ( -32.30, z-score =  -2.80, R)
>droSim1.chr2L 5654574 97 - 22036055
--GGUAGCAGGCUUUAUGACUCUUGACGCGGAAAAGCCCUGCUAGAAGUGCCGGUUAGAUAUGGAUACGUGAGUAUCCACUUUCACCGAUUGCUUUCUG-----
--..(((((((((((.....(((......))))))).)))))))((((.((((((.(((..(((((((....))))))).))).))))...))))))..----- ( -32.40, z-score =  -2.63, R)
>consensus
__GGUAGCAGGCUUUAUGACUCUUGACGCGGAAAAGCCCUGCUAGAAGUGCCGGUUAGAUAUGGAUACGUGAGUAUCCACUUUCACCGAUUGCUUUCU______
..(((((((((((((.................))))).)))))..................(((((((....))))))).....)))................. (-15.45 = -15.37 +  -0.08)

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 21:19:59 2011