Locus 1857

Sequence ID dm3.chr2L
Location 14,425,904 – 14,426,057
Length 153
Max. P 0.991497
window2554 window2555 window2556 window2557

overview

Window 4

Location 14,425,904 – 14,425,997
Length 93
Sequences 10
Columns 110
Reading direction reverse
Mean pairwise identity 62.99
Shannon entropy 0.71148
G+C content 0.46272
Mean single sequence MFE -21.41
Consensus MFE -7.10
Energy contribution -7.02
Covariance contribution -0.08
Combinations/Pair 1.33
Mean z-score -1.74
Structure conservation index 0.33
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.04
SVM RNA-class probability 0.880286
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 14425904 93 - 23011544
GCACUUUCAAAAAUCCGUAUCCUUUGCGGAUUACA-AAACAGA-------------ACCAAUAUC---CCCAUUGUCAACUCGAAUGUGGCCUUUGAUGAAGGCGACACG
.(((.(((...((((((((.....))))))))...-.....((-------------..((((...---...)))))).....))).)))((((((...))))))...... ( -21.50, z-score =  -2.15, R)
>droGri2.scaffold_15126 740997 101 - 8399593
----GCUUCCCGCGUCAACGGGUCGAGUCCUUUGGAUUACAUGCACAUC---CAAUUCCAUUGUC-AGCUCGUCGUC-GUUGAAGUUUCGCCUUUGAUGAAGGCGACACG
----((.....)).((((((((.(((((.(..((((.............---....))))..)..-.))))).).))-))))).((.((((((((...)))))))).)). ( -31.63, z-score =  -1.77, R)
>droVir3.scaffold_12723 3039635 93 + 5802038
----GCUCCC----UCAAUGUGGCGAGU-CUUUGGAUUACAUACACAUU---CAAUUCCAUUGCC-AAC---UCAAC-GCUCGAGUUUCGCCUUUGAUGAAGGCGACACG
----.....(----((...(((..((((-(..((((.............---....))))..)..-.))---))..)-))..)))..((((((((...)))))))).... ( -22.13, z-score =  -1.30, R)
>droPer1.super_5 1741066 86 - 6813705
-----------UAUCCACUUUCACAAAUCCUUACACAAACAGA-------------ACGAAUAUCCAUCCCAUUGUCAAGUUGAAAGCGGCCUUUGAUGAAGGCGACACG
-----------................................-------------.................((((..((.....)).((((((...)))))))))).. ( -10.20, z-score =   0.53, R)
>dp4.chr4_group1 1800101 86 + 5278887
-----------UAUCCACUUUCACAAAUCCUUACACAAACAGA-------------ACGAAUAUCCAUCCCAUUGUCAAGUUGAAAGCGGCCUUUGAUGAAGGCGACACG
-----------................................-------------.................((((..((.....)).((((((...)))))))))).. ( -10.20, z-score =   0.53, R)
>droAna3.scaffold_12916 14786191 76 + 16180835
------------AAGCACUUUCGAAAAUCCGUAUCCUUUGCGG-------------------AUC---CCCAUUGUCAACUCGAAUGCGGCCUUUGAUGAAGGCGACACG
------------..(((..(((((..(((((((.....)))))-------------------)).---......(....))))))))).((((((...))))))...... ( -19.60, z-score =  -1.27, R)
>droEre2.scaffold_4929 6179254 93 - 26641161
--------------GCACUUUCGAAAAUCCGUAUCCUUUGCGGAUUACCAAACAGAACCAAUAUC---CCCAUUGUCAACUCGAAUGUGGCCUUUGAUGAAGGCGACACG
--------------.(((.(((((.((((((((.....))))))))........((..((((...---...))))))...))))).)))((((((...))))))...... ( -24.70, z-score =  -3.01, R)
>droYak2.chr2L 14530572 93 - 22324452
--------------GCACUUUCGAAAAUCCGUAUCCUUUGCGGAUUACAAAACAGAACCAAUAUC---CCCAUUGUCAACUCGAAUGUGGCCUUUGAUGAAGGCGACACG
--------------.(((.(((((.((((((((.....))))))))........((..((((...---...))))))...))))).)))((((((...))))))...... ( -24.70, z-score =  -2.98, R)
>droSec1.super_3 685333 93 - 7220098
--------------GCACUUUCGAAAAUCCGUAUCCUUUGCGGAUUACAAAACAGAACCAAUAUC---CCCAUUGUCAACUCGAAUGUGGCCUUUGAUGAAGGCGACACG
--------------.(((.(((((.((((((((.....))))))))........((..((((...---...))))))...))))).)))((((((...))))))...... ( -24.70, z-score =  -2.98, R)
>droSim1.chr2L 14174089 93 - 22036055
--------------GCACUUUCGAAAAUCCGUAUCCUUUGCGGAUUACAAAACAGAACCAAUAUC---CCCAUUGUCAACUCGAAUGUGGCCUUUGAUGAAGGCGACACG
--------------.(((.(((((.((((((((.....))))))))........((..((((...---...))))))...))))).)))((((((...))))))...... ( -24.70, z-score =  -2.98, R)
>consensus
______________GCACUUUCGAAAAUCCGUAUCCUUACAGG___A_____CA__ACCAAUAUC___CCCAUUGUCAACUCGAAUGUGGCCUUUGAUGAAGGCGACACG
.........................................................................((((....((....))((((((...)))))))))).. ( -7.10 =  -7.02 +  -0.08)

alignment

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secondary structure

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Window 5

Location 14,425,934 – 14,426,036
Length 102
Sequences 5
Columns 103
Reading direction reverse
Mean pairwise identity 85.77
Shannon entropy 0.23887
G+C content 0.45403
Mean single sequence MFE -18.04
Consensus MFE -16.06
Energy contribution -15.90
Covariance contribution -0.16
Combinations/Pair 1.07
Mean z-score -1.80
Structure conservation index 0.89
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.46
SVM RNA-class probability 0.940026
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 14425934 102 - 23011544
UGUUCCAUCCAGCCACGUAGCUCUUCUUGCC-AGACUUGAGCACUUUCAAAAAUCCGUAUCCUUUGCGGAUUACAAAACAGAACCAAUAUCCCCAUUGUCAAC
.((((...........((.((((.(((....-)))...)))))).......((((((((.....))))))))........))))................... ( -18.50, z-score =  -2.08, R)
>droEre2.scaffold_4929 6179284 83 - 26641161
-------------------GCUCUUCUUGCC-GGAGCUGAGCACUUUCGAAAAUCCGUAUCCUUUGCGGAUUACCAAACAGAACCAAUAUCCCCAUUGUCAAC
-------------------((((..(((...-.)))..))))......((.((((((((.....))))))))............((((......))))))... ( -17.20, z-score =  -1.89, R)
>droYak2.chr2L 14530602 87 - 22324452
---------------UGCAGCUCUUCUUGCC-AGACUUGAGCACUUUCGAAAAUCCGUAUCCUUUGCGGAUUACAAAACAGAACCAAUAUCCCCAUUGUCAAC
---------------.(((((((.(((....-)))...)))).........((((((((.....))))))))........................))).... ( -16.00, z-score =  -1.61, R)
>droSec1.super_3 685363 103 - 7220098
UGUUCCCUCCAGCCACGUAGCUCUUCUUGCCAAGACUUGAGCACUUUCGAAAAUCCGUAUCCUUUGCGGAUUACAAAACAGAACCAAUAUCCCCAUUGUCAAC
.((((...........((.((((.(((.....)))...)))))).......((((((((.....))))))))........))))................... ( -18.70, z-score =  -1.87, R)
>droSim1.chr2L 14174119 103 - 22036055
UGUUCCCUCCAGCCACGUAGCUCUUCUGGCCAAGACUUGAGCACUUUCGAAAAUCCGUAUCCUUUGCGGAUUACAAAACAGAACCAAUAUCCCCAUUGUCAAC
.((((...........((.((((.(((.....)))...)))))).......((((((((.....))))))))........))))................... ( -19.80, z-score =  -1.53, R)
>consensus
UGUUCC_UCCAGCCACGUAGCUCUUCUUGCC_AGACUUGAGCACUUUCGAAAAUCCGUAUCCUUUGCGGAUUACAAAACAGAACCAAUAUCCCCAUUGUCAAC
...................((((.(((.....)))...)))).........((((((((.....))))))))............................... (-16.06 = -15.90 +  -0.16)

alignment

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secondary structure

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dotplot

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Window 6

Location 14,425,964 – 14,426,056
Length 92
Sequences 7
Columns 95
Reading direction reverse
Mean pairwise identity 63.90
Shannon entropy 0.68874
G+C content 0.42045
Mean single sequence MFE -19.68
Consensus MFE -8.86
Energy contribution -9.90
Covariance contribution 1.04
Combinations/Pair 1.08
Mean z-score -1.89
Structure conservation index 0.45
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.48
SVM RNA-class probability 0.991497
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 14425964 92 - 23011544
-AUGCAAAUUGCAUUCAAGUAUGUUCCAUCCAGCCACGUAGCUCUUCUUGCC-AGACU-UGAGCACUUUCAAAAAUCCGUAUCCUUUGCGGAUUA
-.((.(((.(((..((((((.((........(((......)))........)-).)))-)))))).)))))..((((((((.....)))))))). ( -20.69, z-score =  -2.12, R)
>droWil1.scaffold_180764 2698624 84 - 3949147
AAUGCAAAUUAUAACGAUUGUUAUUGAAUU--------CGCUUCAACUGUCCGAUAGUCGGAUAA---UCCGAAAUCCUUUUUCUUAGUCGAAUG
..............((((((...(((((..--------...))))).((((((.....)))))).---...((((.....)))).)))))).... ( -14.60, z-score =  -0.86, R)
>droAna3.scaffold_12916 14786234 84 + 16180835
-AUGCAAAUGAUAUUAAGCUAUGGACCCUC--------UGGAACUUAUCGGAAAGGCUGAAAGCACUUUCGAAAAUCCGUAUCCUUUGCGGAU--
-.((((((.(((((((((...(((.....)--------))...))))((((((..((.....))..))))))......))))).))))))...-- ( -18.70, z-score =  -0.89, R)
>droEre2.scaffold_4929 6179314 69 - 26641161
----------------AUGCAAAUUGCAUU--------CAGCUCUUCUUGCC-GGAGC-UGAGCACUUUCGAAAAUCCGUAUCCUUUGCGGAUUA
----------------.(((.....)))((--------(((((((.......-)))))-))))..........((((((((.....)))))))). ( -23.40, z-score =  -3.32, R)
>droYak2.chr2L 14530632 77 - 22324452
----------------AUGCAAAUUGCAUUCAACUAUGCAGCUCUUCUUGCC-AGACU-UGAGCACUUUCGAAAAUCCGUAUCCUUUGCGGAUUA
----------------........(((((......)))))((((.(((....-)))..-.)))).........((((((((.....)))))))). ( -20.30, z-score =  -2.70, R)
>droSec1.super_3 685393 93 - 7220098
-AUGCAAAUUGCAUUCAACUAUGUUCCCUCCAGCCACGUAGCUCUUCUUGCCAAGACU-UGAGCACUUUCGAAAAUCCGUAUCCUUUGCGGAUUA
-.(((.....)))(((...(((((...........)))))((((.(((.....)))..-.))))......)))((((((((.....)))))))). ( -19.50, z-score =  -1.80, R)
>droSim1.chr2L 14174149 93 - 22036055
-AUGCAAAUUGCAUUCAACUAUGUUCCCUCCAGCCACGUAGCUCUUCUGGCCAAGACU-UGAGCACUUUCGAAAAUCCGUAUCCUUUGCGGAUUA
-.(((.....)))(((...(((((...........)))))((((.(((.....)))..-.))))......)))((((((((.....)))))))). ( -20.60, z-score =  -1.53, R)
>consensus
_AUGCAAAUUGCAUUCAACUAUGUUCCAUCCA_C_A_GUAGCUCUUCUUGCC_AGACU_UGAGCACUUUCGAAAAUCCGUAUCCUUUGCGGAUUA
........................................((((................)))).........((((((((.....)))))))). ( -8.86 =  -9.90 +   1.04)

alignment

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secondary structure

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dotplot

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Window 7

Location 14,425,965 – 14,426,057
Length 92
Sequences 7
Columns 95
Reading direction reverse
Mean pairwise identity 67.77
Shannon entropy 0.61448
G+C content 0.41805
Mean single sequence MFE -19.26
Consensus MFE -7.76
Energy contribution -8.46
Covariance contribution 0.70
Combinations/Pair 1.15
Mean z-score -1.71
Structure conservation index 0.40
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.03
SVM RNA-class probability 0.876927
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 14425965 92 - 23011544
-AAUGCAAAUUGCAUUCAAGUAUGUUCCAUCCAGCCACGUAGCUCUUCUUGCC-AGACUUG-AGCACUUUCAAAAAUCCGUAUCCUUUGCGGAUU
-..((.(((.(((..((((((.((........(((......)))........)-).)))))-)))).)))))..((((((((.....)))))))) ( -19.99, z-score =  -1.84, R)
>droWil1.scaffold_180764 2698625 84 - 3949147
AAAUGCAAAUUAUAACGAUUGUUAUUGAAU---------UCGCUUCAACUGUCC--GAUAGUCGGAUAAUCCGAAAUCCUUUUUCUUAGUCGAAU
...............((((((...(((((.---------....))))).(((((--(.....))))))....((((.....)))).))))))... ( -14.60, z-score =  -0.91, R)
>droAna3.scaffold_12916 14786234 85 + 16180835
-AAUGCAAAUGAUAUUAAGCUAUGGACCCUC--------UGGAACUUAUCGGAAAGGCUGAAAGCACUUUCGAAAAUCCGUAUCCUUUGCGGAU-
-..((((((.(((((((((...(((.....)--------))...))))((((((..((.....))..))))))......))))).))))))...- ( -18.70, z-score =  -0.89, R)
>droEre2.scaffold_4929 6179315 69 - 26641161
-AAUGCAAAUUGCAUUCAGCUCU--------------------UCUUGCCGGA---GCUGA--GCACUUUCGAAAAUCCGUAUCCUUUGCGGAUU
-.((((.....))))((((((((--------------------.......)))---)))))--...........((((((((.....)))))))) ( -22.90, z-score =  -3.05, R)
>droYak2.chr2L 14530633 77 - 22324452
-AAUGCAAAUUGCAUUCAACUAUGC---------------AGCUCUUCUUGCC-AGACUUG-AGCACUUUCGAAAAUCCGUAUCCUUUGCGGAUU
-.........(((((......))))---------------)((((.(((....-)))...)-))).........((((((((.....)))))))) ( -19.60, z-score =  -2.36, R)
>droSec1.super_3 685394 93 - 7220098
-AAUGCAAAUUGCAUUCAACUAUGUUCCCUCCAGCCACGUAGCUCUUCUUGCCAAGACUUG-AGCACUUUCGAAAAUCCGUAUCCUUUGCGGAUU
-..(((.....)))(((...(((((...........)))))((((.(((.....)))...)-)))......)))((((((((.....)))))))) ( -18.80, z-score =  -1.51, R)
>droSim1.chr2L 14174150 93 - 22036055
-AAUGCAAAUUGCAUUCAACUAUGUUCCCUCCAGCCACGUAGCUCUUCUGGCCAAGACUUG-AGCACUUUCGAAAAUCCGUAUCCUUUGCGGAUU
-(((((.....)))))......(((((..((..((((.(........)))))...))...)-))))........((((((((.....)))))))) ( -20.20, z-score =  -1.37, R)
>consensus
_AAUGCAAAUUGCAUUCAACUAUGUUCCCUC________UAGCUCUUCUUGCC_AGACUUG_AGCACUUUCGAAAAUCCGUAUCCUUUGCGGAUU
.(((((.....)))))..........................................................((((((((.....)))))))) ( -7.76 =  -8.46 +   0.70)

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 21:40:11 2011