Locus 5546

Sequence ID dm3.chr3LHet
Location 486,600 – 486,742
Length 142
Max. P 0.923076
window7616 window7617 window7618 window7619

overview

Window 6

Location 486,600 – 486,714
Length 114
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 59.11
Shannon entropy 0.69432
G+C content 0.51941
Mean single sequence MFE -37.80
Consensus MFE -8.65
Energy contribution -13.65
Covariance contribution 5.00
Combinations/Pair 1.35
Mean z-score -2.24
Structure conservation index 0.23
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.62
SVM RNA-class probability 0.762760
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3LHet 486600 114 + 2555491
UACCAGUAUUUAUUAACAUACGGCAGGCUUGCUCCUGCAAACCGUACUGUAGUGUGCCUACU-CUGGGCAAAAUGC-----AGCAGCAGCAUCGCCGUCUUGCUGGUGAGGACGGCAACG
((((((((...........(((((..(((.(((.(((((.....(((....)))(((((...-..)))))...)))-----)).))))))...)))))..))))))))....((....)) ( -40.12, z-score =  -1.22, R)
>droAna3.scaffold_13219 44901 114 - 86653
UACUUCACCUGUUUCGCAUACCUAAUGCUGGAGCCGUCGAGCCUGACAACGGGGGACCUG------GACAAGCUGCCUUUUAGCAGCAUUGUCACAGUCUUAUCCCUUGCCAAGCUGACU
..........(((((((((.....)))).))))).(((.(((.((.(((.(((((((.((------((((((((((......))))).))))).))))))...)))))).)).)))))). ( -40.60, z-score =  -2.94, R)
>droVir3.scaffold_12737 3614 120 - 48473
UAUUUCACCUCAGACGCAUACCUCACAUUCACUCCAUUCAGUCUGACAAUGGGUGGCCGACUAGCUGCCAAUCUGCCCUUGAGCAGCAUUGACACUGUCUUGUCCAUUGCAAGACUGACC
.....................................(((((((..(((((((..(..(((.((.((.((((((((......)))).)))).))))))))..)))))))..))))))).. ( -33.90, z-score =  -2.15, R)
>droGri2.scaffold_15040 117899 120 + 162499
UAUUUCACCUCCGACACAUAUCUCAGGCUGCCGCCAUUUAGCCUAACCAAUGGGGGUCGACUACGCGACAAUCUGCCCUUAAGCAGCAUUGUCACGGUCUUGUCCAUUGCCAGACUGACG
....((((((((((........))((((((........)))))).......)))))).))...((.((((((((((......)))).)))))).))(((..(((........))).))). ( -36.60, z-score =  -2.66, R)
>consensus
UACUUCACCUCAGACACAUACCUCAGGCUGGCGCCAUCAAGCCUGACAAUGGGGGGCCGACU_C__GACAAUCUGCCCUU_AGCAGCAUUGUCACAGUCUUGUCCAUUGCCAGACUGACG
.........................(((((((....))))))).......................((((((((((......)))).)))))).(((((((((.....)))))))))... ( -8.65 = -13.65 +   5.00)

alignment

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secondary structure

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dotplot

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Window 7

Location 486,600 – 486,714
Length 114
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 59.11
Shannon entropy 0.69432
G+C content 0.51941
Mean single sequence MFE -43.60
Consensus MFE -13.26
Energy contribution -15.57
Covariance contribution 2.31
Combinations/Pair 1.44
Mean z-score -2.12
Structure conservation index 0.30
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.30
SVM RNA-class probability 0.923076
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3LHet 486600 114 - 2555491
CGUUGCCGUCCUCACCAGCAAGACGGCGAUGCUGCUGCU-----GCAUUUUGCCCAG-AGUAGGCACACUACAGUACGGUUUGCAGGAGCAAGCCUGCCGUAUGUUAAUAAAUACUGGUA
.(((((((((...........)))))))))((((((.((-----(((....(((...-.((((.....)))).....))).))))).))).))).((((((((........)))).)))) ( -40.90, z-score =  -1.41, R)
>droAna3.scaffold_13219 44901 114 + 86653
AGUCAGCUUGGCAAGGGAUAAGACUGUGACAAUGCUGCUAAAAGGCAGCUUGUC------CAGGUCCCCCGUUGUCAGGCUCGACGGCUCCAGCAUUAGGUAUGCGAAACAGGUGAAGUA
.((((((((((((((((....((((..(((((.((((((....)))))))))))------..)))).))).)))))))))).))).......((((.....))))............... ( -46.00, z-score =  -2.89, R)
>droVir3.scaffold_12737 3614 120 + 48473
GGUCAGUCUUGCAAUGGACAAGACAGUGUCAAUGCUGCUCAAGGGCAGAUUGGCAGCUAGUCGGCCACCCAUUGUCAGACUGAAUGGAGUGAAUGUGAGGUAUGCGUCUGAGGUGAAAUA
..(((((((.(((((((....((((((((((((.(((((....)))))))))))).)).)))......))))))).))))))).........((.(.(((......))).).))...... ( -41.00, z-score =  -1.36, R)
>droGri2.scaffold_15040 117899 120 - 162499
CGUCAGUCUGGCAAUGGACAAGACCGUGACAAUGCUGCUUAAGGGCAGAUUGUCGCGUAGUCGACCCCCAUUGGUUAGGCUAAAUGGCGGCAGCCUGAGAUAUGUGUCGGAGGUGAAAUA
(((((((((((((((((....((((((((((((.(((((....))))))))))))))..))).....))))).)))))))....)))))...((((..(((....)))..))))...... ( -46.50, z-score =  -2.82, R)
>consensus
CGUCAGCCUGGCAAUGGACAAGACAGUGACAAUGCUGCU_AAGGGCAGAUUGUC__G_AGUAGGCCCCCCAUUGUCAGGCUAAAUGGAGCCAGCCUGAGGUAUGCGAAUGAGGUGAAAUA
....((((((((((.((((......))((((((.(((((....)))))))))))..............)).))))))))))....................................... (-13.26 = -15.57 +   2.31)

alignment

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secondary structure

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dotplot

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Window 8

Location 486,640 – 486,742
Length 102
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 61.48
Shannon entropy 0.63229
G+C content 0.55689
Mean single sequence MFE -35.15
Consensus MFE -12.51
Energy contribution -16.32
Covariance contribution 3.81
Combinations/Pair 1.26
Mean z-score -1.72
Structure conservation index 0.36
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.74
SVM RNA-class probability 0.804715
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3LHet 486640 102 + 2555491
ACCGUACUGUAGUGUGCCUACU-CUGGGCAAAAUGC-----AGCAGCAGCAUCGCCGUCUUGC---UGGUGAG---GACGGCAACGCCGACUUCCCAUGCACCAACAACGGACA------
.((((.(((((...(((((...-..)))))...)))-----))..((((((.........)))---(((.(((---(.((((...)))).)))))))))).......))))...------ ( -36.40, z-score =  -1.01, R)
>droAna3.scaffold_13219 44941 114 - 86653
GCCUGACAACGGGGGACCUG------GACAAGCUGCCUUUUAGCAGCAUUGUCACAGUCUUAUCCCUUGCCAAGCUGACUCCCACACUGUCGCCCCACUGGCCAACAAUGCGCAAGCACU
((.((.(((.(((((((.((------((((((((((......))))).))))).))))))...)))))).)).)).(((.........)))(((.....)))......(((....))).. ( -38.80, z-score =  -2.19, R)
>droVir3.scaffold_12737 3654 114 - 48473
GUCUGACAAUGGGUGGCCGACUAGCUGCCAAUCUGCCCUUGAGCAGCAUUGACACUGUCUUGUCCAUUGCAAGACUGACCCCAACACUUUCACCCCACUCAUACACAGUGCGCA------
(((((...((((((((.......((((((((.......))).))))).........(((((((.....)))))))...................))))))))...))).))...------ ( -31.50, z-score =  -1.09, R)
>droGri2.scaffold_15040 117939 114 + 162499
GCCUAACCAAUGGGGGUCGACUACGCGACAAUCUGCCCUUAAGCAGCAUUGUCACGGUCUUGUCCAUUGCCAGACUGACGCCAACACUGAGACCCCACUCAUACACAACUCGCA------
............((((((......((((((((((((......)))).)))))).((((((.((.....)).))))))..))((....)).))))))..................------ ( -33.90, z-score =  -2.60, R)
>consensus
GCCUGACAAUGGGGGGCCGACU_C__GACAAUCUGCCCUU_AGCAGCAUUGUCACAGUCUUGUCCAUUGCCAGACUGACGCCAACACUGACACCCCACUCACAAACAACGCGCA______
...........((((...........((((((((((......)))).)))))).(((((((((.....)))))))))...............))))........................ (-12.51 = -16.32 +   3.81)

alignment

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secondary structure

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dotplot

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Window 9

Location 486,640 – 486,742
Length 102
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 61.48
Shannon entropy 0.63229
G+C content 0.55689
Mean single sequence MFE -45.20
Consensus MFE -13.04
Energy contribution -15.47
Covariance contribution 2.44
Combinations/Pair 1.53
Mean z-score -2.09
Structure conservation index 0.29
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.63
SVM RNA-class probability 0.766251
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3LHet 486640 102 - 2555491
------UGUCCGUUGUUGGUGCAUGGGAAGUCGGCGUUGCCGUC---CUCACCA---GCAAGACGGCGAUGCUGCUGCU-----GCAUUUUGCCCAG-AGUAGGCACACUACAGUACGGU
------...((((..((((.(((..(..((((((((((((((((---.......---....)))))))))))))..)))-----...)..)))))))-.((((.....))))...)))). ( -39.20, z-score =  -0.76, R)
>droAna3.scaffold_13219 44941 114 + 86653
AGUGCUUGCGCAUUGUUGGCCAGUGGGGCGACAGUGUGGGAGUCAGCUUGGCAAGGGAUAAGACUGUGACAAUGCUGCUAAAAGGCAGCUUGUC------CAGGUCCCCCGUUGUCAGGC
...((((.((((((((((.((....)).)))))))))).))))..((((((((((((....((((..(((((.((((((....)))))))))))------..)))).))).))))))))) ( -58.50, z-score =  -4.95, R)
>droVir3.scaffold_12737 3654 114 + 48473
------UGCGCACUGUGUAUGAGUGGGGUGAAAGUGUUGGGGUCAGUCUUGCAAUGGACAAGACAGUGUCAAUGCUGCUCAAGGGCAGAUUGGCAGCUAGUCGGCCACCCAUUGUCAGAC
------..(.((((.......)))).).(((.((((..((((((.((((......))))..((((((((((((.(((((....)))))))))))).)).))))))).)))))).)))... ( -40.40, z-score =  -0.83, R)
>droGri2.scaffold_15040 117939 114 - 162499
------UGCGAGUUGUGUAUGAGUGGGGUCUCAGUGUUGGCGUCAGUCUGGCAAUGGACAAGACCGUGACAAUGCUGCUUAAGGGCAGAUUGUCGCGUAGUCGACCCCCAUUGGUUAGGC
------.....(((....((.((((((((((((.(((..((....).)..))).)))....((((((((((((.(((((....))))))))))))))..))))).))))))).))..))) ( -42.70, z-score =  -1.83, R)
>consensus
______UGCGCAUUGUGGAUGAGUGGGGUGACAGUGUUGGCGUCAGUCUGGCAAUGGACAAGACAGUGACAAUGCUGCU_AAGGGCAGAUUGUC__G_AGUAGGCCCCCCAUUGUCAGGC
.........((((((((.((.......))))))))))........(((((((((.((((......))((((((.(((((....)))))))))))..............)).))))))))) (-13.04 = -15.47 +   2.44)

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 22:50:33 2011