Locus 2717

Sequence ID dm3.chr2L
Location 21,497,866 – 21,497,921
Length 55
Max. P 0.999855
window3729 window3730

overview

Window 9

Location 21,497,866 – 21,497,921
Length 55
Sequences 11
Columns 70
Reading direction forward
Mean pairwise identity 58.18
Shannon entropy 0.84926
G+C content 0.48075
Mean single sequence MFE -19.53
Consensus MFE -12.28
Energy contribution -13.32
Covariance contribution 1.04
Combinations/Pair 1.50
Mean z-score -2.09
Structure conservation index 0.63
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 4.59
SVM RNA-class probability 0.999855
Prediction RNA
WARNING Out of training range. z-scores are NOT reliable.

Download alignment: ClustalW | MAF

>dm3.chr2L 21497866 55 + 23011544
AUUGUGGCCCUGAAAAGGGCCGUUUUGGAUUA-UUGUCCGCA---UUCGCAGGAGAAAA-----------
.((((((((((....)))))).....((((..-..))))...---...)))).......----------- ( -20.10, z-score =  -2.58, R)
>droGri2.scaffold_14978 515427 60 + 1124632
UUUGUGGCCCUGAAAAGGGCCUUUUGCUGCUAGCUGCUCGCUGGUAUUUCUGCCUGCAAU----------
.((((((((((....))))))......(((((((.....))))))).........)))).---------- ( -23.60, z-score =  -2.79, R)
>droMoj3.scaffold_6540 26857080 64 - 34148556
UUUGUGGCCCUGAAAAGGGCCUUUUGCUUCU------UCUUUUGGAAUUCUGCAUACACCGAGGUAAGAU
.....((((((....))))))(((((((((.------.....((.(....).))......))))))))). ( -20.80, z-score =  -2.43, R)
>droVir3.scaffold_13047 1628952 66 + 19223366
UUUGUGGCCCUGAAAAGGGCCUUUUGCUUUU----GUUUGCUUCCCGUACAAUGCACAUCUAGCUGAAUU
.....((((((....))))))(((.(((...----((.(((............))).))..))).))).. ( -18.20, z-score =  -1.84, R)
>droAna3.scaffold_13030 44769 54 - 47400
GUUGUGGCCCUGAAAAGGGCCUUUUUGGAUCA-UUCUGCCCA----GCAAGCGAGCAAU-----------
((((.((((((....)))))).....(((...-.)))...))----))...........----------- ( -17.50, z-score =  -0.99, R)
>droEre2.scaffold_4845 19565920 55 - 22589142
AUUGUGGCCCUGAAGAGGGCCGUUUUGGAUUU-UUGUCCGCA---CUCGCAGGAGGAAA-----------
..(((((((((....)))))).....((((..-..)))))))---(((....)))....----------- ( -19.20, z-score =  -1.48, R)
>droYak2.chr2R_random 60460 58 - 67238
AUUGUGGCCCUGAAAAGGGCCGUUUUGGAUUA-AUGUCCGCAGCAUUCGUAGGAACAAA-----------
.((((((((((....))))))(((.(((((..-..))))).)))..........)))).----------- ( -23.20, z-score =  -3.62, R)
>droSec1.super_91 88087 55 + 125313
AUUGUGGCCCUGAAAAGGGCCGUUUUGGAUUG-UUGUCCGCA---CUCGCAGGAGCCAA-----------
.....((((((....))))))(((((((((..-..))))((.---...)).)))))...----------- ( -21.60, z-score =  -2.10, R)
>droSim1.chrU 5518301 55 - 15797150
AUUGUGGCCCUGAAAAGGGCCGUUUUGGAUUG-UUGUCCGCA---UUCGCAGGAGCCAA-----------
.....((((((....))))))(((((((((..-..))))((.---...)).)))))...----------- ( -21.60, z-score =  -2.34, R)
>anoGam1.chr2R 47876183 55 + 62725911
UUUGUGGUCCUGAAAAGGACCGAUUUGAGAGAACGAAGCCAAUC-AUUUCAGUGGC--------------
(((((((((((....))))))...((....)))))))((((...-.......))))-------------- ( -16.60, z-score =  -2.43, R)
>droWil1.scaffold_181036 6031 60 + 110856
AUUGUGGCCCUGAAAAGGGUUUUUUUUUUAAAAGGAAGCGUGUG-UUUAAGCUAGGGACAU---------
.((.(((((((....)))((((((((.....)))))))).....-.....)))).))....--------- ( -12.40, z-score =  -0.37, R)
>consensus
AUUGUGGCCCUGAAAAGGGCCGUUUUGGAUUA_UUGUCCGCA___UUCGCAGGAGCCAA___________
.....((((((....))))))................................................. (-12.28 = -13.32 +   1.04)

alignment

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secondary structure

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dotplot

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Window 0

Location 21,497,866 – 21,497,921
Length 55
Sequences 11
Columns 70
Reading direction reverse
Mean pairwise identity 58.18
Shannon entropy 0.84926
G+C content 0.48075
Mean single sequence MFE -15.49
Consensus MFE -10.82
Energy contribution -10.84
Covariance contribution 0.02
Combinations/Pair 1.17
Mean z-score -1.64
Structure conservation index 0.70
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 4.06
SVM RNA-class probability 0.999595
Prediction RNA
WARNING Out of training range. z-scores are NOT reliable.

Download alignment: ClustalW | MAF

>dm3.chr2L 21497866 55 - 23011544
-----------UUUUCUCCUGCGAA---UGCGGACAA-UAAUCCAAAACGGCCCUUUUCAGGGCCACAAU
-----------.......((((...---.))))....-...........((((((....))))))..... ( -15.70, z-score =  -2.52, R)
>droGri2.scaffold_14978 515427 60 - 1124632
----------AUUGCAGGCAGAAAUACCAGCGAGCAGCUAGCAGCAAAAGGCCCUUUUCAGGGCCACAAA
----------.((((.((.(....).))(((.....)))....))))..((((((....))))))..... ( -20.30, z-score =  -2.35, R)
>droMoj3.scaffold_6540 26857080 64 + 34148556
AUCUUACCUCGGUGUAUGCAGAAUUCCAAAAGA------AGAAGCAAAAGGCCCUUUUCAGGGCCACAAA
....(((....)))..(((....(((.....))------)...)))...((((((....))))))..... ( -15.10, z-score =  -1.13, R)
>droVir3.scaffold_13047 1628952 66 - 19223366
AAUUCAGCUAGAUGUGCAUUGUACGGGAAGCAAAC----AAAAGCAAAAGGCCCUUUUCAGGGCCACAAA
......(((...(((((...)))))...)))....----..........((((((....))))))..... ( -18.30, z-score =  -1.74, R)
>droAna3.scaffold_13030 44769 54 + 47400
-----------AUUGCUCGCUUGC----UGGGCAGAA-UGAUCCAAAAAGGCCCUUUUCAGGGCCACAAC
-----------.(((((((.....----)))))))..-...........((((((....))))))..... ( -18.10, z-score =  -1.59, R)
>droEre2.scaffold_4845 19565920 55 + 22589142
-----------UUUCCUCCUGCGAG---UGCGGACAA-AAAUCCAAAACGGCCCUCUUCAGGGCCACAAU
-----------.......((((...---.))))....-...........((((((....))))))..... ( -15.70, z-score =  -1.91, R)
>droYak2.chr2R_random 60460 58 + 67238
-----------UUUGUUCCUACGAAUGCUGCGGACAU-UAAUCCAAAACGGCCCUUUUCAGGGCCACAAU
-----------(((((....)))))......(((...-...))).....((((((....))))))..... ( -15.40, z-score =  -2.01, R)
>droSec1.super_91 88087 55 - 125313
-----------UUGGCUCCUGCGAG---UGCGGACAA-CAAUCCAAAACGGCCCUUUUCAGGGCCACAAU
-----------...((((....)))---)..(((...-...))).....((((((....))))))..... ( -17.20, z-score =  -1.44, R)
>droSim1.chrU 5518301 55 + 15797150
-----------UUGGCUCCUGCGAA---UGCGGACAA-CAAUCCAAAACGGCCCUUUUCAGGGCCACAAU
-----------(((..(((.((...---.)))))...-)))........((((((....))))))..... ( -16.30, z-score =  -1.62, R)
>anoGam1.chr2R 47876183 55 - 62725911
--------------GCCACUGAAAU-GAUUGGCUUCGUUCUCUCAAAUCGGUCCUUUUCAGGACCACAAA
--------------((((.......-...))))................((((((....))))))..... ( -13.50, z-score =  -2.00, R)
>droWil1.scaffold_181036 6031 60 - 110856
---------AUGUCCCUAGCUUAAA-CACACGCUUCCUUUUAAAAAAAAAACCCUUUUCAGGGCCACAAU
---------.((.(((((((.....-.....)))...((((....))))..........)))).)).... (  -4.80, z-score =   0.27, R)
>consensus
___________UUGGCUCCUGCGAA___UGCGGACAA_UAAUCCAAAACGGCCCUUUUCAGGGCCACAAU
.................................................((((((....))))))..... (-10.82 = -10.84 +   0.02)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 21:56:30 2011