Locus 5553

Sequence ID dm3.chr3LHet
Location 616,209 – 616,501
Length 292
Max. P 0.999619
window7628 window7629 window7630 window7631 window7632

overview

Window 8

Location 616,209 – 616,356
Length 147
Sequences 5
Columns 147
Reading direction reverse
Mean pairwise identity 56.73
Shannon entropy 0.79827
G+C content 0.52020
Mean single sequence MFE -52.70
Consensus MFE -13.12
Energy contribution -17.60
Covariance contribution 4.48
Combinations/Pair 1.61
Mean z-score -1.92
Structure conservation index 0.25
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.94
SVM RNA-class probability 0.858553
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3LHet 616209 147 - 2555491
GCCAGAGGCUAAUCCUGCUUGGAUGCCUUUCGGUAUGCCGAACAGUGUCCACAGUGGCACUGCAGGUACUUGGUGGAGCUCCCCCGCUUGAUCUGGCUGCUAAGUUAUUAGCGAUCAAAUACAAGCUAAAACGUGGAUUCCCGCUGG
(((((((((..((((.....)))))))))).))).((((...(((((((......)))))))..))))...((.((....)).))(((((((.((..((((((....))))))..)).)).)))))......((((....))))... ( -53.10, z-score =  -1.82, R)
>droAna3.scaffold_13082 239205 133 - 3919855
-----------GUGUGCAAAGGUUGAU--CUUGU-UGUCGCACUGUCUCUACGGAGGCAUUGCAAGUGUUGUUUGGAGCAGUUCCCCUUGACUUGGUGAUACGGCGUAGAGCCGUAAGCUACAAGCUCAAGAAGGGGCUGCCAUUGC
-----------(((((((((((.....--))).)-)).)))))((((((....))))))..((((..........(.((((((((.(((((((((....((((((.....)))))).....)))).)))))..))))))))).)))) ( -49.80, z-score =  -1.84, R)
>droVir3.scaffold_13050 451069 139 - 3426691
GCCAGAGAGUGCUUCUCUUAGGUUGUUUGCCUGUGUGCCGCACUGUCUCUACGGAGGCAA-GUAG-------UAGGAGUAGUCCCUCUUGACUUGGAAAUCAGGCGUCUAGCUUUGAUGUACAAGAUCAAGAGGCAGCUGCCAUUGC
(((.((.(((((..(.(.(((((.....))))).).)..))))).))((....)))))..-...(-------(((..(((((.((((((((((((...(((((((.....)).)))))...)))).))))))))..)))))..)))) ( -54.80, z-score =  -2.54, R)
>droGri2.scaffold_15040 117516 147 - 162499
GCCAGCGUGUGAUGUUGUUAGGGUGUCUGCCUGUAUGCCGCACUGUCUCCACGGAGGCAAUGCAGGUGUUGUUAGGAGUAGCCCCUCUGGACUUGGAGAUCAGGCGUCGUAGCCUGAUCUAUAAGAUCAAGAGGCGGUUGCCGUUGC
..(((((...((..((.....))..))..((((.((((((((.((((((....)))))).))).)))))...)))).(((((((((((.((((((.(((((((((......))))))))).)))).)).))))).))))))))))). ( -65.30, z-score =  -3.69, R)
>triCas2.chrUn_8 580423 147 - 609019
GUCAAAGAGUGUGCUUGUAUGGGUGCCUGCCAUUAUGUAAAACUGUCAGCACUGACGCAAUGUAAGUGCUCAUGGGGAGACUGCCGUGGGACCUAGAACUUCUGGGAAGAGGUGUGAAGUAUAGAAUUGAUAGAGGUGUAGCUCUCG
(((((....(((((((...(((((.((..(............((((.((((((.((.....)).)))))).))))(....)....)..)))))))..((((((....))))))...)))))))...))))).((((......)))). ( -40.50, z-score =   0.29, R)
>consensus
GCCAGAGAGUGAUCUUGUUAGGGUGCCUGCCUGUAUGCCGCACUGUCUCCACGGAGGCAAUGCAGGUGCUGUUAGGAGCAGUCCCGCUUGACUUGGAAAUCAGGCGUAGAGCCGUGAACUACAAGAUCAAGAGGGGGCUGCCAUUGC
..................((((.......))))......(((.((((((....)))))).)))..............((((((((((((((((((....(((((........)))))....)))).))))))).)))))))...... (-13.12 = -17.60 +   4.48)

alignment

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secondary structure

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dotplot

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Window 9

Location 616,356 – 616,462
Length 106
Sequences 4
Columns 106
Reading direction forward
Mean pairwise identity 55.03
Shannon entropy 0.76841
G+C content 0.49379
Mean single sequence MFE -26.11
Consensus MFE -9.43
Energy contribution -11.80
Covariance contribution 2.37
Combinations/Pair 1.38
Mean z-score -1.42
Structure conservation index 0.36
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.15
SVM RNA-class probability 0.900863
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3LHet 616356 106 + 2555491
AGGAGGCUAGUCGCCUCUGGGCAGCUACUUGUUCCGCGGUGUCAUACCAUACCGGGGCACCAAACAGCACACAAGGUGCCAUGAGUCCGUCAUAUAUGGUCCGCCU
.((((((.....))))))((((.((((..(((...((((..((((.((.....))((((((.............))))))))))..)))).)))..))))..)))) ( -38.12, z-score =  -1.01, R)
>droAna3.scaffold_13082 239338 103 + 3919855
---UUAAAAUUUUCAUUCUACCCCUAACGUCCAAGACUGCAUCGUACCACGCAGGUGAUCCGCUUGUUGCGCAAGUAACAAAAAGACCACCAUAUAUGGUGCGAGC
---.........................(((...))).((.((((((((....((((.((...(((((((....)))))))...)).)))).....)))))))))) ( -29.80, z-score =  -3.72, R)
>droVir3.scaffold_13050 451208 106 + 3426691
AAGCCAGCACUUUCUUUCUGCAAACCACAAUCGUGAACGCCUUGCACCAUACAUACGAUCCAUAUGCUGCACAUGCAGCAAACAGACCCUCAUAGAUGGUACGAAC
..((..(((.........)))....(((....)))...)).(((.(((((...((.((((....((((((....))))))....))...)).)).))))).))).. ( -19.60, z-score =  -0.77, R)
>droGri2.scaffold_15040 117663 106 + 162499
AAGCCAGCACAUUCUUUCUGCCUACAACAGUCGAAACUACUUUACACCAUACCGACGAUCCAUAAGUUGCACAGGCAACAAAUAGACCAUCGUAUACGGCGCGAGC
..(((.(((.........))).(((....((((...................)))).........(((((....)))))............)))...)))...... ( -16.91, z-score =  -0.18, R)
>consensus
AAGCCAGCACUUUCUUUCUGCCAACAACAUUCGAGACUGCAUCACACCAUACAGACGAUCCAUAUGUUGCACAAGCAACAAAAAGACCAUCAUAUAUGGUGCGAGC
.........................................((((((((((..((.(.((....((((((....))))))....)).).))...)))))))))).. ( -9.43 = -11.80 +   2.37)

alignment

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secondary structure

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dotplot

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Window 0

Location 616,356 – 616,462
Length 106
Sequences 4
Columns 106
Reading direction reverse
Mean pairwise identity 55.03
Shannon entropy 0.76841
G+C content 0.49379
Mean single sequence MFE -36.91
Consensus MFE -20.33
Energy contribution -22.45
Covariance contribution 2.12
Combinations/Pair 1.54
Mean z-score -2.14
Structure conservation index 0.55
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 4.09
SVM RNA-class probability 0.999619
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3LHet 616356 106 - 2555491
AGGCGGACCAUAUAUGACGGACUCAUGGCACCUUGUGUGCUGUUUGGUGCCCCGGUAUGGUAUGACACCGCGGAACAAGUAGCUGCCCAGAGGCGACUAGCCUCCU
.((((((((((((((((.....))))((((((.............))))))...)))))))........((.......))..)))))..(((((.....))))).. ( -34.92, z-score =   0.22, R)
>droAna3.scaffold_13082 239338 103 - 3919855
GCUCGCACCAUAUAUGGUGGUCUUUUUGUUACUUGCGCAACAAGCGGAUCACCUGCGUGGUACGAUGCAGUCUUGGACGUUAGGGGUAGAAUGAAAAUUUUAA---
(((((.((((..((.((((((((.((((((........)))))).))))))))))..)))).))).)).(((...)))........((((((....)))))).--- ( -32.40, z-score =  -1.95, R)
>droVir3.scaffold_13050 451208 106 - 3426691
GUUCGUACCAUCUAUGAGGGUCUGUUUGCUGCAUGUGCAGCAUAUGGAUCGUAUGUAUGGUGCAAGGCGUUCACGAUUGUGGUUUGCAGAAAGAAAGUGCUGGCUU
.((((((((((.((((..(((((((.((((((....)))))).))))))).)))).)))))))...(((.((((....))))..))).)))............... ( -36.50, z-score =  -1.89, R)
>droGri2.scaffold_15040 117663 106 - 162499
GCUCGCGCCGUAUACGAUGGUCUAUUUGUUGCCUGUGCAACUUAUGGAUCGUCGGUAUGGUGUAAAGUAGUUUCGACUGUUGUAGGCAGAAAGAAUGUGCUGGCUU
(((.(((((((((.(((((((((((..(((((....)))))..))))))))))))))))))))..((((..(((..((((.....))))...)))..))))))).. ( -43.80, z-score =  -4.95, R)
>consensus
GCUCGCACCAUAUAUGAUGGUCUAUUUGCUGCUUGUGCAACAUAUGGAUCGCCGGUAUGGUACAAAGCAGUCUCGAAUGUUGUUGGCAGAAAGAAAGUGCUGGCUU
....(((((((((.(((((((((((.((((((....)))))).))))))))))))))))))))........................................... (-20.33 = -22.45 +   2.12)

alignment

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secondary structure

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dotplot

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Window 1

Location 616,385 – 616,501
Length 116
Sequences 4
Columns 116
Reading direction forward
Mean pairwise identity 59.77
Shannon entropy 0.67899
G+C content 0.51392
Mean single sequence MFE -29.90
Consensus MFE -11.46
Energy contribution -13.77
Covariance contribution 2.31
Combinations/Pair 1.46
Mean z-score -1.25
Structure conservation index 0.38
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.40
SVM RNA-class probability 0.680158
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3LHet 616385 116 + 2555491
UGUUCCGCGGUGUCAUACCAUACCGGGGCACCAAACAGCACACAAGGUGCCAUGAGUCCGUCAUAUAUGGUCCGCCUGGCUCGAGGACUGAAGCCCCAGUCGGCUCGAAGCACACU
......((((......((((((....((((((.............))))))((((.....)))).))))))))))...((((((((((((......)))))..)))).)))..... ( -37.22, z-score =   0.01, R)
>droAna3.scaffold_13082 239367 113 + 3919855
---AAGACUGCAUCGUACCACGCAGGUGAUCCGCUUGUUGCGCAAGUAACAAAAAGACCACCAUAUAUGGUGCGAGCAGCUUUUCUGCUGAGGCCCCAUUCACUUCUUAAAACUCG
---(((.((((.((((((((....((((.((...(((((((....)))))))...)).)))).....))))))))))))))).......(((....................))). ( -37.15, z-score =  -3.56, R)
>droVir3.scaffold_13050 451237 116 + 3426691
AUCGUGAACGCCUUGCACCAUACAUACGAUCCAUAUGCUGCACAUGCAGCAAACAGACCCUCAUAGAUGGUACGAACAGUACGUCUACUUAGCCCCCAGUCAGACCUCAAAAUACG
..((((.((...(((.(((((...((.((((....((((((....))))))....))...)).)).))))).)))...))..(((((((........))).)))).......)))) ( -22.40, z-score =  -1.14, R)
>droGri2.scaffold_15040 117692 116 + 162499
GUCGAAACUACUUUACACCAUACCGACGAUCCAUAAGUUGCACAGGCAACAAAUAGACCAUCGUAUACGGCGCGAGCAGCAGUUCUGCUGAGGCCCCAGUCACUUCUCAAAAUCCG
((((...................)))).........(((((....))))).....(((....(....)((.((...(((((....)))))..)).)).)))............... ( -22.81, z-score =  -0.32, R)
>consensus
_UCGAGACUGCAUCACACCAUACAGACGAUCCAUAUGUUGCACAAGCAACAAAAAGACCAUCAUAUAUGGUGCGAGCAGCACGUCUACUGAGGCCCCAGUCACUUCUCAAAACACG
............((((((((((..((.(.((....((((((....))))))....)).).))...)))))))))).(((((....))))).......................... (-11.46 = -13.77 +   2.31)

alignment

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secondary structure

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dotplot

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Window 2

Location 616,385 – 616,501
Length 116
Sequences 4
Columns 116
Reading direction reverse
Mean pairwise identity 59.77
Shannon entropy 0.67899
G+C content 0.51392
Mean single sequence MFE -40.85
Consensus MFE -23.76
Energy contribution -26.57
Covariance contribution 2.81
Combinations/Pair 1.64
Mean z-score -1.66
Structure conservation index 0.58
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.95
SVM RNA-class probability 0.996546
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3LHet 616385 116 - 2555491
AGUGUGCUUCGAGCCGACUGGGGCUUCAGUCCUCGAGCCAGGCGGACCAUAUAUGACGGACUCAUGGCACCUUGUGUGCUGUUUGGUGCCCCGGUAUGGUAUGACACCGCGGAACA
.(((.(..(((.((((((((((((.((((((((((.....((....)).....))).))))..(((((((.....))))))).))).)))))))).)))).)))..))))...... ( -40.90, z-score =   0.32, R)
>droAna3.scaffold_13082 239367 113 - 3919855
CGAGUUUUAAGAAGUGAAUGGGGCCUCAGCAGAAAAGCUGCUCGCACCAUAUAUGGUGGUCUUUUUGUUACUUGCGCAACAAGCGGAUCACCUGCGUGGUACGAUGCAGUCUU---
.((((((((.........))))).))).........((((((((.((((..((.((((((((.((((((........)))))).))))))))))..)))).))).)))))...--- ( -35.10, z-score =  -0.87, R)
>droVir3.scaffold_13050 451237 116 - 3426691
CGUAUUUUGAGGUCUGACUGGGGGCUAAGUAGACGUACUGUUCGUACCAUCUAUGAGGGUCUGUUUGCUGCAUGUGCAGCAUAUGGAUCGUAUGUAUGGUGCAAGGCGUUCACGAU
..........(((((......)))))..((..((((.((....(((((((.((((..(((((((.((((((....)))))).))))))).)))).))))))).))))))..))... ( -40.00, z-score =  -1.83, R)
>droGri2.scaffold_15040 117692 116 - 162499
CGGAUUUUGAGAAGUGACUGGGGCCUCAGCAGAACUGCUGCUCGCGCCGUAUACGAUGGUCUAUUUGUUGCCUGUGCAACUUAUGGAUCGUCGGUAUGGUGUAAAGUAGUUUCGAC
......((((((....(((.((((...((((....))))))))(((((((((.(((((((((((..(((((....)))))..))))))))))))))))))))..)))..)))))). ( -47.40, z-score =  -4.27, R)
>consensus
CGUAUUUUGAGAACUGACUGGGGCCUCAGCAGAAGAGCUGCUCGCACCAUAUAUGAUGGUCUAUUUGCUGCUUGUGCAACAUAUGGAUCGCCGGUAUGGUACAAAGCAGUCUCGA_
....................................((((((((((((((((.(((((((((((.((((((....)))))).))))))))))))))))))))).))))))...... (-23.76 = -26.57 +   2.81)

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 22:50:44 2011