Locus 2274

Sequence ID dm3.chr2L
Location 17,538,825 – 17,538,936
Length 111
Max. P 0.998583
window3132 window3133 window3134 window3135

overview

Window 2

Location 17,538,825 – 17,538,933
Length 108
Sequences 5
Columns 108
Reading direction forward
Mean pairwise identity 94.35
Shannon entropy 0.10190
G+C content 0.35196
Mean single sequence MFE -24.37
Consensus MFE -22.24
Energy contribution -23.28
Covariance contribution 1.04
Combinations/Pair 1.06
Mean z-score -2.43
Structure conservation index 0.91
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.91
SVM RNA-class probability 0.974307
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 17538825 108 + 23011544
CAAAUGGAAUAGAUGGAAAAAUCGAAUUUAAUUCGCUUGACUUGGUCAACCGAAAAUGCCGAAAAUUAAGUCAUAUGUUUCAGUUCCCACCUAUUGAACCCAUUUGUA
((((((((((((.(((......(((((...)))))..(((((((((....((.......))...))))))))).............))).)))))....))))))).. ( -22.00, z-score =  -1.41, R)
>droEre2.scaffold_4845 15880465 102 - 22589142
CAAAUGGAAUAGAUGGAAAAAUCGAAUUUAAUUCACUUGACUUAGUCAACCGAAAAUGCCGAAAAUUAAGUCAUAUGUUUCGGUUCCCACCUAUUCAAACCA------
......((((((.(((...(((((((.......((..(((((((((....((.......))...)))))))))..)).))))))).))).))))))......------ ( -23.60, z-score =  -2.91, R)
>droYak2.chr2R 17579705 108 - 21139217
CAAAUGGAAUAGAUGGAAAAAUCGAAUUUAAUUCACUUGACUUAGUCAACCGAAAAUGCCGAAAAUGAAGUCAUAUGUUUCGGUUCCCACCUAUUGAACCCAUUUGCA
((((((((((((.(((...............(((..(((((...)))))..)))...((((((((((....)))...)))))))..))).)))))....))))))).. ( -24.60, z-score =  -2.28, R)
>droSec1.super_7 1180450 108 + 3727775
CAAAUGGAAUAGAUGGAAAAAUCGAAUUUAAUUCGCGUGACUUAGUCAACCGAAAAUGCCGAAAAUUAAGUCAUAUAUUUCGGUUCCCACCUAUUGAACCCAUUUGUA
((((((((((((.(((...(((((((..........((((((((((....((.......))...))))))))))....))))))).))).)))))....))))))).. ( -25.14, z-score =  -2.54, R)
>droSim1.chr2L 17242876 108 + 22036055
CAAAUGGAAUAGAUGGAAAAAUCGAAUUUAAUUCGCUUGACUUAGUCAACCGAAAAUGCCGAAAAUUAAGUCAUAUGUUUCGGUUCCCACCUAUUGAACCCAUUUGUA
((((((((((((.(((...............((((.(((((...))))).))))...(((((((..((.....))..)))))))..))).)))))....))))))).. ( -26.50, z-score =  -3.02, R)
>consensus
CAAAUGGAAUAGAUGGAAAAAUCGAAUUUAAUUCGCUUGACUUAGUCAACCGAAAAUGCCGAAAAUUAAGUCAUAUGUUUCGGUUCCCACCUAUUGAACCCAUUUGUA
((((((((((((.(((...(((((((.......((..(((((((((....((.......))...)))))))))..)).))))))).))).)))))....))))))).. (-22.24 = -23.28 +   1.04)

alignment

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secondary structure

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dotplot

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Window 3

Location 17,538,825 – 17,538,933
Length 108
Sequences 5
Columns 108
Reading direction reverse
Mean pairwise identity 94.35
Shannon entropy 0.10190
G+C content 0.35196
Mean single sequence MFE -31.26
Consensus MFE -29.56
Energy contribution -30.16
Covariance contribution 0.60
Combinations/Pair 1.06
Mean z-score -3.89
Structure conservation index 0.95
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 3.41
SVM RNA-class probability 0.998583
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 17538825 108 - 23011544
UACAAAUGGGUUCAAUAGGUGGGAACUGAAACAUAUGACUUAAUUUUCGGCAUUUUCGGUUGACCAAGUCAAGCGAAUUAAAUUCGAUUUUUCCAUCUAUUCCAUUUG
..((((((((....(((((((((((((((((..((.....))..))))))....((((.(((((...))))).))))............))))))))))))))))))) ( -31.10, z-score =  -3.89, R)
>droEre2.scaffold_4845 15880465 102 + 22589142
------UGGUUUGAAUAGGUGGGAACCGAAACAUAUGACUUAAUUUUCGGCAUUUUCGGUUGACUAAGUCAAGUGAAUUAAAUUCGAUUUUUCCAUCUAUUCCAUUUG
------......(((((((((((((((((((..((.....))..))))))....((((.(((((...))))).))))............)))))))))))))...... ( -28.00, z-score =  -2.93, R)
>droYak2.chr2R 17579705 108 + 21139217
UGCAAAUGGGUUCAAUAGGUGGGAACCGAAACAUAUGACUUCAUUUUCGGCAUUUUCGGUUGACUAAGUCAAGUGAAUUAAAUUCGAUUUUUCCAUCUAUUCCAUUUG
..((((((((....(((((((((((((((((...(((....)))))))))....((((.(((((...))))).))))............))))))))))))))))))) ( -33.20, z-score =  -4.12, R)
>droSec1.super_7 1180450 108 - 3727775
UACAAAUGGGUUCAAUAGGUGGGAACCGAAAUAUAUGACUUAAUUUUCGGCAUUUUCGGUUGACUAAGUCACGCGAAUUAAAUUCGAUUUUUCCAUCUAUUCCAUUUG
..((((((((....(((((((((((..........(((((((....(((((.......))))).)))))))..(((((...)))))...))))))))))))))))))) ( -30.70, z-score =  -3.79, R)
>droSim1.chr2L 17242876 108 - 22036055
UACAAAUGGGUUCAAUAGGUGGGAACCGAAACAUAUGACUUAAUUUUCGGCAUUUUCGGUUGACUAAGUCAAGCGAAUUAAAUUCGAUUUUUCCAUCUAUUCCAUUUG
..((((((((....(((((((((((((((((..((.....))..))))))....((((.(((((...))))).))))............))))))))))))))))))) ( -33.30, z-score =  -4.72, R)
>consensus
UACAAAUGGGUUCAAUAGGUGGGAACCGAAACAUAUGACUUAAUUUUCGGCAUUUUCGGUUGACUAAGUCAAGCGAAUUAAAUUCGAUUUUUCCAUCUAUUCCAUUUG
..(((((((....((((((((((((((((((.............))))))....((((.(((((...))))).))))............))))))))))))))))))) (-29.56 = -30.16 +   0.60)

alignment

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secondary structure

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dotplot

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Window 4

Location 17,538,828 – 17,538,936
Length 108
Sequences 5
Columns 108
Reading direction forward
Mean pairwise identity 93.24
Shannon entropy 0.12195
G+C content 0.36684
Mean single sequence MFE -21.38
Consensus MFE -18.98
Energy contribution -19.22
Covariance contribution 0.24
Combinations/Pair 1.06
Mean z-score -1.35
Structure conservation index 0.89
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.11
SVM RNA-class probability 0.548749
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 17538828 108 + 23011544
AUGGAAUAGAUGGAAAAAUCGAAUUUAAUUCGCUUGACUUGGUCAACCGAAAAUGCCGAAAAUUAAGUCAUAUGUUUCAGUUCCCACCUAUUGAACCCAUUUGUAGCC
..((.((((((((.....(((.((((...(((.(((((...))))).)))))))..)))................((((((........)))))).))))))))..)) ( -19.60, z-score =  -0.54, R)
>droEre2.scaffold_4845 15880468 99 - 22589142
AUGGAAUAGAUGGAAAAAUCGAAUUUAAUUCACUUGACUUAGUCAACCGAAAAUGCCGAAAAUUAAGUCAUAUGUUUCGGUUCCCACCUAUUCAAACCA---------
...((((((.(((...(((((((.......((..(((((((((....((.......))...)))))))))..)).))))))).))).))))))......--------- ( -23.60, z-score =  -2.91, R)
>droYak2.chr2R 17579708 108 - 21139217
AUGGAAUAGAUGGAAAAAUCGAAUUUAAUUCACUUGACUUAGUCAACCGAAAAUGCCGAAAAUGAAGUCAUAUGUUUCGGUUCCCACCUAUUGAACCCAUUUGCAGCC
(((((((((.(((...............(((..(((((...)))))..)))...((((((((((....)))...)))))))..))).)))))....))))........ ( -19.90, z-score =  -0.60, R)
>droSec1.super_7 1180453 108 + 3727775
AUGGAAUAGAUGGAAAAAUCGAAUUUAAUUCGCGUGACUUAGUCAACCGAAAAUGCCGAAAAUUAAGUCAUAUAUUUCGGUUCCCACCUAUUGAACCCAUUUGUAGCC
..((.(((((((((((...(((((...))))).((((((((((....((.......))...))))))))))...))))(((((.........))))))))))))..)) ( -22.20, z-score =  -1.44, R)
>droSim1.chr2L 17242879 108 + 22036055
AUGGAAUAGAUGGAAAAAUCGAAUUUAAUUCGCUUGACUUAGUCAACCGAAAAUGCCGAAAAUUAAGUCAUAUGUUUCGGUUCCCACCUAUUGAACCCAUUUGUAGCC
(((((((((.(((...............((((.(((((...))))).))))...(((((((..((.....))..)))))))..))).)))))....))))........ ( -21.60, z-score =  -1.26, R)
>consensus
AUGGAAUAGAUGGAAAAAUCGAAUUUAAUUCGCUUGACUUAGUCAACCGAAAAUGCCGAAAAUUAAGUCAUAUGUUUCGGUUCCCACCUAUUGAACCCAUUUGUAGCC
.((((((((.(((...(((((((.......((..(((((((((....((.......))...)))))))))..)).))))))).))).)))))....)))......... (-18.98 = -19.22 +   0.24)

alignment

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secondary structure

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dotplot

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Window 5

Location 17,538,828 – 17,538,936
Length 108
Sequences 5
Columns 108
Reading direction reverse
Mean pairwise identity 93.24
Shannon entropy 0.12195
G+C content 0.36684
Mean single sequence MFE -27.64
Consensus MFE -26.54
Energy contribution -26.54
Covariance contribution -0.00
Combinations/Pair 1.06
Mean z-score -2.45
Structure conservation index 0.96
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.39
SVM RNA-class probability 0.989820
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 17538828 108 - 23011544
GGCUACAAAUGGGUUCAAUAGGUGGGAACUGAAACAUAUGACUUAAUUUUCGGCAUUUUCGGUUGACCAAGUCAAGCGAAUUAAAUUCGAUUUUUCCAUCUAUUCCAU
........(((((....(((((((((((((((((..((.....))..))))))....((((.(((((...))))).))))............)))))))))))))))) ( -26.50, z-score =  -2.05, R)
>droEre2.scaffold_4845 15880468 99 + 22589142
---------UGGUUUGAAUAGGUGGGAACCGAAACAUAUGACUUAAUUUUCGGCAUUUUCGGUUGACUAAGUCAAGUGAAUUAAAUUCGAUUUUUCCAUCUAUUCCAU
---------......(((((((((((((((((((..((.....))..))))))....((((.(((((...))))).))))............)))))))))))))... ( -28.00, z-score =  -3.06, R)
>droYak2.chr2R 17579708 108 + 21139217
GGCUGCAAAUGGGUUCAAUAGGUGGGAACCGAAACAUAUGACUUCAUUUUCGGCAUUUUCGGUUGACUAAGUCAAGUGAAUUAAAUUCGAUUUUUCCAUCUAUUCCAU
........(((((....(((((((((((((((((...(((....)))))))))....((((.(((((...))))).))))............)))))))))))))))) ( -28.90, z-score =  -2.35, R)
>droSec1.super_7 1180453 108 - 3727775
GGCUACAAAUGGGUUCAAUAGGUGGGAACCGAAAUAUAUGACUUAAUUUUCGGCAUUUUCGGUUGACUAAGUCACGCGAAUUAAAUUCGAUUUUUCCAUCUAUUCCAU
........(((((....(((((((((((..........(((((((....(((((.......))))).)))))))..(((((...)))))...)))))))))))))))) ( -26.10, z-score =  -1.93, R)
>droSim1.chr2L 17242879 108 - 22036055
GGCUACAAAUGGGUUCAAUAGGUGGGAACCGAAACAUAUGACUUAAUUUUCGGCAUUUUCGGUUGACUAAGUCAAGCGAAUUAAAUUCGAUUUUUCCAUCUAUUCCAU
........(((((....(((((((((((((((((..((.....))..))))))....((((.(((((...))))).))))............)))))))))))))))) ( -28.70, z-score =  -2.87, R)
>consensus
GGCUACAAAUGGGUUCAAUAGGUGGGAACCGAAACAUAUGACUUAAUUUUCGGCAUUUUCGGUUGACUAAGUCAAGCGAAUUAAAUUCGAUUUUUCCAUCUAUUCCAU
........((((....((((((((((((((((((.............))))))....((((.(((((...))))).))))............)))))))))))))))) (-26.54 = -26.54 +  -0.00)

alignment

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secondary structure

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dotplot

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Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 21:48:10 2011