Locus 2420

Sequence ID dm3.chr2L
Location 18,901,744 – 18,901,881
Length 137
Max. P 0.924770
window3329 window3330 window3331 window3332

overview

Window 9

Location 18,901,744 – 18,901,849
Length 105
Sequences 6
Columns 113
Reading direction forward
Mean pairwise identity 88.10
Shannon entropy 0.23116
G+C content 0.50816
Mean single sequence MFE -38.02
Consensus MFE -24.95
Energy contribution -26.38
Covariance contribution 1.43
Combinations/Pair 1.22
Mean z-score -2.27
Structure conservation index 0.66
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.61
SVM RNA-class probability 0.760295
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 18901744 105 + 23011544
UCUUCUCCCGCAAUUGCAAACUGCAGCGCUUGAGAGGCUGAAAAGCGGGACACAAUGGGGUAAACCUAAUGGAUUUCCGUUUCGGCCAAAA--------GCGGAAAACCAUUG
.......((((..((((.....)))).........(((((((..((((((..((.((((.....)))).))...)))))))))))))....--------)))).......... ( -34.70, z-score =  -2.04, R)
>droAna3.scaffold_12916 1914066 112 + 16180835
UCUUGGCCCACAAAUGCAAACUGCAGCGGUUAGGGGCUGGGGGAGCCCAGCACAAUGGGGUUAACCUAAUGGAUUUCCGUUUGGACCAAAA-GCCAGAGGCGGAAAACCAUCG
((((((((......(((.....)))..))))))))((((((....))))))....((((.....))))((((.(((((((((((.......-.))))..))))))).)))).. ( -42.20, z-score =  -1.72, R)
>droEre2.scaffold_4845 17213073 113 - 22589142
UCUUCUCCCUCAACUGCAAACUGCAUCGCUUGAGAGGCUGAAAAGCGGGACACAAUGGGGUAAACCUAAUGGACUUCCGUUUCGACCAAAAAGCCGAAGGCGGAAAACCAUUG
.....((((((((.(((.....)))....))))...(((....)))))))..((((((......((....))..((((((((((.(......).)))).))))))..)))))) ( -31.40, z-score =  -1.23, R)
>droYak2.chr2R 5418069 113 + 21139217
UCUUCUCCCUCAACUGCAAACUGCAGCGCUUGAGAGGAUGAAAAGCGGGACACAAUGGGGUAAACCUAAUGGAUUUCCGUUUCGGCCAAAAAGCCAAAGGCGGAAAACCAUUG
..(((((((((((((((.....))))...))))).))).)))..............(((.....)))(((((.(((((((((.(((......)))..))))))))).))))). ( -36.80, z-score =  -2.40, R)
>droSec1.super_7 2530538 112 + 3727775
UCUUCUCCCGCAACUGCAAACUGCAGCGCUGGAGAGGCUGAAAAGCGGGACACAAUGGGGUAAACCUAAUGGAUUUCCGUUUCGGCCAAAA-GCCAAAGGCGGAAAACCAUUG
...(((((.((..((((.....)))).)).)))))(((((((..((((((..((.((((.....)))).))...)))))))))))))....-(((...)))((....)).... ( -43.20, z-score =  -3.41, R)
>droSim1.chr2L 18591989 112 + 22036055
UCUUCUCCCGCAACUGCAAACUGCAGCACUGGAGAGGCUGAAAAGCGGGACACAAUGGGGUAAACCUAAUGGAUUUCCGUUUCGGCCAAAA-GCCAAAGGCGGAAAACCAUUG
...(((((.(...((((.....))))..).)))))(((((((..((((((..((.((((.....)))).))...)))))))))))))....-(((...)))((....)).... ( -39.80, z-score =  -2.84, R)
>consensus
UCUUCUCCCGCAACUGCAAACUGCAGCGCUUGAGAGGCUGAAAAGCGGGACACAAUGGGGUAAACCUAAUGGAUUUCCGUUUCGGCCAAAA_GCCAAAGGCGGAAAACCAUUG
...((((......((((.....)))).....))))(((((((..((((((..((.((((.....)))).))...))))))))))))).....(((...)))((....)).... (-24.95 = -26.38 +   1.43)

alignment

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secondary structure

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dotplot

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Window 0

Location 18,901,744 – 18,901,849
Length 105
Sequences 6
Columns 113
Reading direction reverse
Mean pairwise identity 88.10
Shannon entropy 0.23116
G+C content 0.50816
Mean single sequence MFE -38.72
Consensus MFE -24.49
Energy contribution -25.52
Covariance contribution 1.03
Combinations/Pair 1.17
Mean z-score -2.31
Structure conservation index 0.63
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.46
SVM RNA-class probability 0.704792
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 18901744 105 - 23011544
CAAUGGUUUUCCGC--------UUUUGGCCGAAACGGAAAUCCAUUAGGUUUACCCCAUUGUGUCCCGCUUUUCAGCCUCUCAAGCGCUGCAGUUUGCAAUUGCGGGAGAAGA
.(((((.((((((.--------((((....)))))))))).))))).((..(((......)))..)).((((((.((.......)).(((((((.....))))))))))))). ( -31.20, z-score =  -0.91, R)
>droAna3.scaffold_12916 1914066 112 - 16180835
CGAUGGUUUUCCGCCUCUGGC-UUUUGGUCCAAACGGAAAUCCAUUAGGUUAACCCCAUUGUGCUGGGCUCCCCCAGCCCCUAACCGCUGCAGUUUGCAUUUGUGGGCCAAGA
.(((((.((((((....((((-.....).)))..)))))).))))).(((............((((((....))))))......(((((((.....)))...))))))).... ( -34.90, z-score =  -0.31, R)
>droEre2.scaffold_4845 17213073 113 + 22589142
CAAUGGUUUUCCGCCUUCGGCUUUUUGGUCGAAACGGAAGUCCAUUAGGUUUACCCCAUUGUGUCCCGCUUUUCAGCCUCUCAAGCGAUGCAGUUUGCAGUUGAGGGAGAAGA
.(((((.((((((..(((((((....))))))).)))))).))))).((..(((......)))..)).((((((..((((....((((......))))....)))))))))). ( -38.70, z-score =  -2.47, R)
>droYak2.chr2R 5418069 113 - 21139217
CAAUGGUUUUCCGCCUUUGGCUUUUUGGCCGAAACGGAAAUCCAUUAGGUUUACCCCAUUGUGUCCCGCUUUUCAUCCUCUCAAGCGCUGCAGUUUGCAGUUGAGGGAGAAGA
.(((((.((((((..(((((((....))))))).)))))).))))).((..(((......)))..))..(((((.(((.((((...(((((.....))))))))))))))))) ( -42.90, z-score =  -3.82, R)
>droSec1.super_7 2530538 112 - 3727775
CAAUGGUUUUCCGCCUUUGGC-UUUUGGCCGAAACGGAAAUCCAUUAGGUUUACCCCAUUGUGUCCCGCUUUUCAGCCUCUCCAGCGCUGCAGUUUGCAGUUGCGGGAGAAGA
.(((((.((((((..((((((-.....)))))).)))))).))))).((..(((......)))..))(((....))).(((((.(((((((.....)))).))).)))))... ( -43.40, z-score =  -3.38, R)
>droSim1.chr2L 18591989 112 - 22036055
CAAUGGUUUUCCGCCUUUGGC-UUUUGGCCGAAACGGAAAUCCAUUAGGUUUACCCCAUUGUGUCCCGCUUUUCAGCCUCUCCAGUGCUGCAGUUUGCAGUUGCGGGAGAAGA
.(((((.((((((..((((((-.....)))))).)))))).))))).((..(((......)))..))(((....))).(((((...(((((.....)))))....)))))... ( -41.20, z-score =  -2.95, R)
>consensus
CAAUGGUUUUCCGCCUUUGGC_UUUUGGCCGAAACGGAAAUCCAUUAGGUUUACCCCAUUGUGUCCCGCUUUUCAGCCUCUCAAGCGCUGCAGUUUGCAGUUGCGGGAGAAGA
.(((((.((((((..((((((......)))))).)))))).))))).......((((((((((..(.((....................)).)..))))).)).)))...... (-24.49 = -25.52 +   1.03)

alignment

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secondary structure

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dotplot

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Window 1

Location 18,901,773 – 18,901,881
Length 108
Sequences 6
Columns 116
Reading direction forward
Mean pairwise identity 84.72
Shannon entropy 0.29170
G+C content 0.51009
Mean single sequence MFE -38.53
Consensus MFE -28.74
Energy contribution -29.80
Covariance contribution 1.06
Combinations/Pair 1.34
Mean z-score -2.05
Structure conservation index 0.75
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.31
SVM RNA-class probability 0.924770
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 18901773 108 + 23011544
UUGAGAGGCUGAAAAGCGGGACACAAUGGGGUAAACCUAAUGGAUUUCCGUUUCGGCCAAAA-GC-------GGAAAACCAUUGGCACUUGAGGAGGCCAACAUCUCCUAACCAUC
..(((((((((((..((((((..((.((((.....)))).))...)))))))))))))....-..-------((....)).(((((.(((...))))))))..))))......... ( -35.10, z-score =  -2.13, R)
>droAna3.scaffold_12916 1914095 114 + 16180835
UUAGGGGCUGGGGGAGCCCAGCACAAUGGGGUUAACCUAAUGGAUUUCCGUUUGGACCAAAA-GCCAGAGGCGGAAAACCAUCGGUACUUGAGGAGGCCAGCCAUUCUCAGUUGC-
......((((((....))))))....((((.....))))((((.(((((((((((.......-.))))..))))))).))))..(((.(((((((((....)).))))))).)))- ( -42.80, z-score =  -1.61, R)
>droEre2.scaffold_4845 17213102 116 - 22589142
UUGAGAGGCUGAAAAGCGGGACACAAUGGGGUAAACCUAAUGGACUUCCGUUUCGACCAAAAAGCCGAAGGCGGAAAACCAUUGGCACUUGAGGAGACCGACUUCUCCUGGCCAUC
......((((...((((((((..((.((((.....)))).))...))))))))..........(((((.((.......)).))))).....((((((......))))))))))... ( -36.60, z-score =  -1.46, R)
>droYak2.chr2R 5418098 116 + 21139217
UUGAGAGGAUGAAAAGCGGGACACAAUGGGGUAAACCUAAUGGAUUUCCGUUUCGGCCAAAAAGCCAAAGGCGGAAAACCAUUGGCACUUGAGAAGACCGACAACUCCGGGCCAUC
.............((((((((..((.((((.....)))).))...)))))))).((((.....(((((.((.......)).)))))....(((..(.....)..)))..))))... ( -32.50, z-score =  -0.83, R)
>droSec1.super_7 2530567 115 + 3727775
UGGAGAGGCUGAAAAGCGGGACACAAUGGGGUAAACCUAAUGGAUUUCCGUUUCGGCCAAAA-GCCAAAGGCGGAAAACCAUUGGCACUUGAGGAGGCCAACAUCUCCUAACCAUC
(((...(((((((..((((((..((.((((.....)))).))...)))))))))))))....-(((((.((.......)).))))).....((((((......))))))..))).. ( -42.10, z-score =  -3.13, R)
>droSim1.chr2L 18592018 115 + 22036055
UGGAGAGGCUGAAAAGCGGGACACAAUGGGGUAAACCUAAUGGAUUUCCGUUUCGGCCAAAA-GCCAAAGGCGGAAAACCAUUGGCACUUGAGGAGGCCAACAUCUCCUAACCAUC
(((...(((((((..((((((..((.((((.....)))).))...)))))))))))))....-(((((.((.......)).))))).....((((((......))))))..))).. ( -42.10, z-score =  -3.13, R)
>consensus
UUGAGAGGCUGAAAAGCGGGACACAAUGGGGUAAACCUAAUGGAUUUCCGUUUCGGCCAAAA_GCCAAAGGCGGAAAACCAUUGGCACUUGAGGAGGCCAACAUCUCCUAACCAUC
(((((.(((((((..((((((..((.((((.....)))).))...))))))))))))).....(((((.((.......)).))))).)))))((((........))))........ (-28.74 = -29.80 +   1.06)

alignment

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secondary structure

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dotplot

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Window 2

Location 18,901,773 – 18,901,881
Length 108
Sequences 6
Columns 116
Reading direction reverse
Mean pairwise identity 84.72
Shannon entropy 0.29170
G+C content 0.51009
Mean single sequence MFE -35.88
Consensus MFE -24.52
Energy contribution -25.75
Covariance contribution 1.23
Combinations/Pair 1.27
Mean z-score -1.79
Structure conservation index 0.68
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.36
SVM RNA-class probability 0.661355
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 18901773 108 - 23011544
GAUGGUUAGGAGAUGUUGGCCUCCUCAAGUGCCAAUGGUUUUCC-------GC-UUUUGGCCGAAACGGAAAUCCAUUAGGUUUACCCCAUUGUGUCCCGCUUUUCAGCCUCUCAA
((.((((.(((((.((.(((((.....)).)))(((((.(((((-------(.-((((....)))))))))).))))).((..(((......)))..))))))))))))))).... ( -29.50, z-score =  -0.71, R)
>droAna3.scaffold_12916 1914095 114 - 16180835
-GCAACUGAGAAUGGCUGGCCUCCUCAAGUACCGAUGGUUUUCCGCCUCUGGC-UUUUGGUCCAAACGGAAAUCCAUUAGGUUAACCCCAUUGUGCUGGGCUCCCCCAGCCCCUAA
-((((.((((...((....))..))))...((((((((.((((((....((((-.....).)))..)))))).))))).)))........))))((((((....))))))...... ( -34.10, z-score =  -0.52, R)
>droEre2.scaffold_4845 17213102 116 + 22589142
GAUGGCCAGGAGAAGUCGGUCUCCUCAAGUGCCAAUGGUUUUCCGCCUUCGGCUUUUUGGUCGAAACGGAAGUCCAUUAGGUUUACCCCAUUGUGUCCCGCUUUUCAGCCUCUCAA
((.(((...(((((((.((.(....(((..((((((((.((((((..(((((((....))))))).)))))).))))).)))........))).).)).))))))).))))).... ( -40.20, z-score =  -2.82, R)
>droYak2.chr2R 5418098 116 - 21139217
GAUGGCCCGGAGUUGUCGGUCUUCUCAAGUGCCAAUGGUUUUCCGCCUUUGGCUUUUUGGCCGAAACGGAAAUCCAUUAGGUUUACCCCAUUGUGUCCCGCUUUUCAUCCUCUCAA
(((((.((((.....)))).......((((...(((((.((((((..(((((((....))))))).)))))).))))).((..(((......)))..)))))).)))))....... ( -33.50, z-score =  -1.44, R)
>droSec1.super_7 2530567 115 - 3727775
GAUGGUUAGGAGAUGUUGGCCUCCUCAAGUGCCAAUGGUUUUCCGCCUUUGGC-UUUUGGCCGAAACGGAAAUCCAUUAGGUUUACCCCAUUGUGUCCCGCUUUUCAGCCUCUCCA
........(((((.((((((((.....)).)))(((((.((((((..((((((-.....)))))).)))))).))))).((..(((......)))..)).......))).))))). ( -39.00, z-score =  -2.62, R)
>droSim1.chr2L 18592018 115 - 22036055
GAUGGUUAGGAGAUGUUGGCCUCCUCAAGUGCCAAUGGUUUUCCGCCUUUGGC-UUUUGGCCGAAACGGAAAUCCAUUAGGUUUACCCCAUUGUGUCCCGCUUUUCAGCCUCUCCA
........(((((.((((((((.....)).)))(((((.((((((..((((((-.....)))))).)))))).))))).((..(((......)))..)).......))).))))). ( -39.00, z-score =  -2.62, R)
>consensus
GAUGGCUAGGAGAUGUUGGCCUCCUCAAGUGCCAAUGGUUUUCCGCCUUUGGC_UUUUGGCCGAAACGGAAAUCCAUUAGGUUUACCCCAUUGUGUCCCGCUUUUCAGCCUCUCAA
(((((..(((((........))))).....((((((((.((((((..((((((......)))))).)))))).))))).))).....)))))........................ (-24.52 = -25.75 +   1.23)

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 21:50:55 2011