Locus 2331

Sequence ID dm3.chr2L
Location 18,022,506 – 18,022,661
Length 155
Max. P 0.781847
window3211 window3212

overview

Window 1

Location 18,022,506 – 18,022,661
Length 155
Sequences 6
Columns 157
Reading direction forward
Mean pairwise identity 73.56
Shannon entropy 0.51665
G+C content 0.53495
Mean single sequence MFE -57.07
Consensus MFE -32.78
Energy contribution -38.82
Covariance contribution 6.04
Combinations/Pair 1.27
Mean z-score -1.14
Structure conservation index 0.57
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.51
SVM RNA-class probability 0.725798
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 18022506 155 + 23011544
ACUGGGCCACAAAACCUUUAUGGCUGCCCAUACACACACUGGCAUACCGAAGUGUGCGGGUGCAAUGUGUGU--GUGCAUGUGGCUCUGCGUGUGUAUGGGUGCUUGUGGCUCUCAAGUGCAGCAGGGACAUACUUGGCUAGCCUUCCCUGGAAUCG
...(((((((((..((.....))..(((((((((((((((.((((((....)))))).)))((.((((((..--..)))))).)).....))))))))))))..)))))))))..........((((((.......((....)).))))))...... ( -63.90, z-score =  -1.37, R)
>droEre2.scaffold_4845 16348144 157 - 22589142
ACUGGGCCACAAAACCUUUAUGGCUGUCCAGACACACACUGGCAUACCGAAGUGUGCGGGUGCAAUGUGUGUAUGUGCAUGUGGCUCCGGGUGUGUAUGGUUGCCUGUGGCUCUUAAGUGCAGCAGGGACAUACUUGGCUAGCCUUCCCUGGAAUCG
.....((((((...((.....)).((..((.(((((((((.((((((....)))))).))).....)))))).))..))))))))((((((...(((((....(((((.((........)).)))))..)))))..((....))...)))))).... ( -57.80, z-score =   0.00, R)
>droYak2.chr2R 18071360 129 - 21139217
ACUGGGCCACAAAACCUUUAUGGCUGUCCGUACACACACUGGCAUACCGAAGUGUGCGGGUGCAAUGUGUGU----------------------------GUGCAUGUGGCUCUUAAGUGCAGCCGGGACAUACUUGGCUAGCCUUCCCUGGAAUCG
...((((((((...((.....))......((((((((((..((((.(((.......)))))))...))))))----------------------------)))).))))))))..(((.(((((((((.....))))))).)))))........... ( -52.60, z-score =  -2.28, R)
>droSec1.super_7 1657136 155 + 3727775
ACUGGGCCACAAAACCUUUAUGGCUGCCCAUGCACACACUAGCAUACCGAAGUGUGCGGGUGCAAUGUGUGU--GUGCAUGUGGCUCUGCGUGUGUAUGGGUGCUUGUGGCUCUCAAGUGCAGCAGGGACAUACUUGGCCAGCCUUCCCUGGAAUCG
...(((((((((.((((.((((((.((((((((((((((..((((.(((.......))))))).....))))--))))))).)))...)).))))...))))..)))))))))..........((((((.......((....)).))))))...... ( -64.10, z-score =  -1.05, R)
>droSim1.chr2L 17704347 155 + 22036055
ACUGGGCCACAAAACCUUUAUGGCUGCCCAUGCACACACUGGCAUACCGAAGUGUGCGGGUGCAAUGUGUGU--GUGCAUGUGGCUCUGCGUGUGUAUGGGUGCUUGUGGCUCUCAAGUGCAGCAGGGACAUACUUGGCUAGCCUUCCCUGGAAUCG
...(((((((((.((((.((((((.((((((((((((((..((((.(((.......))))))).....))))--))))))).)))...)).))))...))))..)))))))))..........((((((.......((....)).))))))...... ( -65.20, z-score =  -1.38, R)
>droVir3.scaffold_12963 17100687 139 + 20206255
ACCGCAUCACCAACUACAUACA-UUGUACAUAUACGAACCUCUAGAUGCAAUUUGGUGCAU-CGUUGCCUGU---UGGCAGGGGGGACGAGAGGGUAUUACGGGUUUUGGCAUUU--UUGUUGCAGGCACACAGGCGUUAAAAAUG-----------
.(((.(..(((..(((((....-.))).......((..(((((.((((((......)))))-)..((((...---.)))))))))..))))..)))..).))).......(((((--(((.(((..(....)..))).))))))))----------- ( -38.80, z-score =  -0.75, R)
>consensus
ACUGGGCCACAAAACCUUUAUGGCUGCCCAUACACACACUGGCAUACCGAAGUGUGCGGGUGCAAUGUGUGU__GUGCAUGUGGCUCUGCGUGUGUAUGGGUGCUUGUGGCUCUCAAGUGCAGCAGGGACAUACUUGGCUAGCCUUCCCUGGAAUCG
...((((((((..........(((.(((((((((((((((.((((((....)))))).)))((.((((((......)))))).)).....)))))))))))))))))))))))..........((((((.......((....)).))))))...... (-32.78 = -38.82 +   6.04)

alignment

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secondary structure

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dotplot

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Window 2

Location 18,022,506 – 18,022,661
Length 155
Sequences 6
Columns 157
Reading direction reverse
Mean pairwise identity 73.56
Shannon entropy 0.51665
G+C content 0.53495
Mean single sequence MFE -50.95
Consensus MFE -26.07
Energy contribution -29.30
Covariance contribution 3.23
Combinations/Pair 1.22
Mean z-score -1.46
Structure conservation index 0.51
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.67
SVM RNA-class probability 0.781847
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 18022506 155 - 23011544
CGAUUCCAGGGAAGGCUAGCCAAGUAUGUCCCUGCUGCACUUGAGAGCCACAAGCACCCAUACACACGCAGAGCCACAUGCAC--ACACACAUUGCACCCGCACACUUCGGUAUGCCAGUGUGUGUAUGGGCAGCCAUAAAGGUUUUGUGGCCCAGU
......((((((..(((.....)))...))))))......(((.(.(((((((...(((((((((((((.........((((.--........))))...(((.((....)).)))..))))))))))))).((((.....))))))))))))))). ( -57.90, z-score =  -2.12, R)
>droEre2.scaffold_4845 16348144 157 + 22589142
CGAUUCCAGGGAAGGCUAGCCAAGUAUGUCCCUGCUGCACUUAAGAGCCACAGGCAACCAUACACACCCGGAGCCACAUGCACAUACACACAUUGCACCCGCACACUUCGGUAUGCCAGUGUGUGUCUGGACAGCCAUAAAGGUUUUGUGGCCCAGU
........(((..((....))..(((((..((((..((........))..))))....)))))...)))((.((((((((..((.((((((((((.....(((.((....)).))))))))))))).))..))(((.....)))..))))))))... ( -56.00, z-score =  -1.94, R)
>droYak2.chr2R 18071360 129 + 21139217
CGAUUCCAGGGAAGGCUAGCCAAGUAUGUCCCGGCUGCACUUAAGAGCCACAUGCAC----------------------------ACACACAUUGCACCCGCACACUUCGGUAUGCCAGUGUGUGUACGGACAGCCAUAAAGGUUUUGUGGCCCAGU
....(((.((((..(((.....)))...))))((((.(......)))))........----------------------------((((((((((.....(((.((....)).)))))))))))))..)))..(((((((.....)))))))..... ( -43.80, z-score =  -1.01, R)
>droSec1.super_7 1657136 155 - 3727775
CGAUUCCAGGGAAGGCUGGCCAAGUAUGUCCCUGCUGCACUUGAGAGCCACAAGCACCCAUACACACGCAGAGCCACAUGCAC--ACACACAUUGCACCCGCACACUUCGGUAUGCUAGUGUGUGCAUGGGCAGCCAUAAAGGUUUUGUGGCCCAGU
......((((((..(((.....)))...))))))......(((.(.(((((((...................(((.(((((((--((((.....(....)(((.((....)).)))..))))))))))))))((((.....))))))))))))))). ( -57.30, z-score =  -1.26, R)
>droSim1.chr2L 17704347 155 - 22036055
CGAUUCCAGGGAAGGCUAGCCAAGUAUGUCCCUGCUGCACUUGAGAGCCACAAGCACCCAUACACACGCAGAGCCACAUGCAC--ACACACAUUGCACCCGCACACUUCGGUAUGCCAGUGUGUGCAUGGGCAGCCAUAAAGGUUUUGUGGCCCAGU
......((((((..(((.....)))...))))))......(((.(.(((((((...................(((.(((((((--((((....(((....))).((....))......))))))))))))))((((.....))))))))))))))). ( -56.40, z-score =  -1.59, R)
>droVir3.scaffold_12963 17100687 139 - 20206255
-----------CAUUUUUAACGCCUGUGUGCCUGCAACAA--AAAUGCCAAAACCCGUAAUACCCUCUCGUCCCCCCUGCCA---ACAGGCAACG-AUGCACCAAAUUGCAUCUAGAGGUUCGUAUAUGUACAA-UGUAUGUAGUUGGUGAUGCGGU
-----------(((((((...((..(....)..))...))--))))).......(((((.((((.((((........((((.---...))))..(-(((((......))))))..))))..(((((((.....)-)))))).....)))).))))). ( -34.30, z-score =  -0.84, R)
>consensus
CGAUUCCAGGGAAGGCUAGCCAAGUAUGUCCCUGCUGCACUUAAGAGCCACAAGCACCCAUACACACGCAGAGCCACAUGCAC__ACACACAUUGCACCCGCACACUUCGGUAUGCCAGUGUGUGUAUGGACAGCCAUAAAGGUUUUGUGGCCCAGU
......((((((..(((.....)))...))))))............(((((((((...............................(((((((((.....(((.((....)).))))))))))))(((((....)))))...)))).)))))..... (-26.07 = -29.30 +   3.23)

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 21:49:15 2011