Locus 7816

Sequence ID dm3.chr3L
Location 17,525,055 – 17,525,193
Length 138
Max. P 0.979714
window10752 window10753 window10754 window10755

overview

Window 2

Location 17,525,055 – 17,525,163
Length 108
Sequences 4
Columns 108
Reading direction forward
Mean pairwise identity 83.33
Shannon entropy 0.27165
G+C content 0.37318
Mean single sequence MFE -26.66
Consensus MFE -19.26
Energy contribution -19.82
Covariance contribution 0.56
Combinations/Pair 1.18
Mean z-score -2.16
Structure conservation index 0.72
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.16
SVM RNA-class probability 0.902150
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 17525055 108 + 24543557
UAAAGAAAAAGUAGCUUUUUUGCGGAUUUUUUAAAAUCGAAUAACAUUUCUUGACUUGCACUUUCCGAAGAGCAGAAAAGUGCCAAGAAAAGUAUUAGGAAGCCGCCA
..........(..((((((((((.(((((....)))))........(((((((....(((((((.(........).)))))))))))))).)))..)))))))..).. ( -23.80, z-score =  -1.32, R)
>droYak2.chr3L 7649750 103 - 24197627
UAAAGAAGAAAUAGCCUUCUUGCGGAUUCUAUAAAAGCUAAACGCAACUCUUGGUUUGCACUUUUC-----GCAGAAGGGUGCCAAGAAAAGUAUUAUGAAGCCGCCA
..((((((.......))))))((((.(((.((((..((.....))...(((((....(((((((((-----...))))))))))))))......))))))).)))).. ( -28.10, z-score =  -1.69, R)
>droSim1.chr3L 16857099 108 + 22553184
UAAAGAAAAAGUAGCCUUUUUGCGGAUUUUUUAAAAUCCAAACACAUUUCUUGACUUGCACUUUCCGAAGAGCAGAAAAGUGCCAAGAAAAGUAUUUGGUAGCCGCCA
.....((((((....))))))((((............(((((.((.(((((((....(((((((.(........).)))))))))))))).)).)))))...)))).. ( -26.86, z-score =  -2.40, R)
>droSec1.super_0 9569783 102 + 21120651
------UAAAGUAGCCUUUUUGCGGAUUUUUUAAAAUCUAAACACAUUUCUUGACUUGCACUUUUCAAAGAGCCGAAAAGUGCCAAGAAAAGUAUUAGGUAGCCGCCA
------....((.((((...(((((((((....)))))).......(((((((....(((((((((........)))))))))))))))).)))..)))).))..... ( -27.90, z-score =  -3.21, R)
>consensus
UAAAGAAAAAGUAGCCUUUUUGCGGAUUUUUUAAAAUCUAAACACAUUUCUUGACUUGCACUUUCCGAAGAGCAGAAAAGUGCCAAGAAAAGUAUUAGGAAGCCGCCA
.....((((((....))))))((((....(((((.........((.(((((((....(((((((((........)))))))))))))))).)).)))))...)))).. (-19.26 = -19.82 +   0.56)

alignment

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secondary structure

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dotplot

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Window 3

Location 17,525,055 – 17,525,163
Length 108
Sequences 4
Columns 108
Reading direction reverse
Mean pairwise identity 83.33
Shannon entropy 0.27165
G+C content 0.37318
Mean single sequence MFE -28.17
Consensus MFE -21.33
Energy contribution -22.70
Covariance contribution 1.37
Combinations/Pair 1.14
Mean z-score -2.55
Structure conservation index 0.76
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.03
SVM RNA-class probability 0.979714
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 17525055 108 - 24543557
UGGCGGCUUCCUAAUACUUUUCUUGGCACUUUUCUGCUCUUCGGAAAGUGCAAGUCAAGAAAUGUUAUUCGAUUUUAAAAAAUCCGCAAAAAAGCUACUUUUUCUUUA
.((..((((..(((((..((((((((((((((((........)))))))))....))))))))))))...(((((....))))).......))))..))......... ( -23.20, z-score =  -1.70, R)
>droYak2.chr3L 7649750 103 + 24197627
UGGCGGCUUCAUAAUACUUUUCUUGGCACCCUUCUGC-----GAAAAGUGCAAACCAAGAGUUGCGUUUAGCUUUUAUAGAAUCCGCAAGAAGGCUAUUUCUUCUUUA
..((((.(((....((((((((...(((......)))-----))))))))......((((((((....))))))))...))).))))(((((((.....))))))).. ( -26.60, z-score =  -1.28, R)
>droSim1.chr3L 16857099 108 - 22553184
UGGCGGCUACCAAAUACUUUUCUUGGCACUUUUCUGCUCUUCGGAAAGUGCAAGUCAAGAAAUGUGUUUGGAUUUUAAAAAAUCCGCAAAAAGGCUACUUUUUCUUUA
..((((...((((((((.((((((((((((((((........)))))))))....))))))).))))))))((((....))))))))((((((....))))))..... ( -34.90, z-score =  -4.55, R)
>droSec1.super_0 9569783 102 - 21120651
UGGCGGCUACCUAAUACUUUUCUUGGCACUUUUCGGCUCUUUGAAAAGUGCAAGUCAAGAAAUGUGUUUAGAUUUUAAAAAAUCCGCAAAAAGGCUACUUUA------
..((((....(((((((.((((((((((((((((((....)))))))))))....))))))).))).))))((((....))))))))..((((....)))).------ ( -28.00, z-score =  -2.68, R)
>consensus
UGGCGGCUACCUAAUACUUUUCUUGGCACUUUUCUGCUCUUCGAAAAGUGCAAGUCAAGAAAUGUGUUUAGAUUUUAAAAAAUCCGCAAAAAGGCUACUUUUUCUUUA
..(((.......(((((.((((((((((((((((........)))))))))....))))))).)))))..(((((....))))))))((((((....))))))..... (-21.33 = -22.70 +   1.37)

alignment

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secondary structure

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dotplot

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Window 4

Location 17,525,086 – 17,525,193
Length 107
Sequences 5
Columns 111
Reading direction forward
Mean pairwise identity 70.32
Shannon entropy 0.52614
G+C content 0.38951
Mean single sequence MFE -26.18
Consensus MFE -9.56
Energy contribution -9.24
Covariance contribution -0.32
Combinations/Pair 1.50
Mean z-score -2.12
Structure conservation index 0.37
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.71
SVM RNA-class probability 0.793824
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 17525086 107 + 24543557
UAAAAUCGAAUAACAUUUCUUGACUUGCACUUUCCGAAGAGCAGAAAAGUGCCAAGAAAAGUAUUAGGAAGCCGCCA-GAAAAUAAACUGGCAUCAUCGUUGUUUACU---
.......(((((((.(((((((....(((((((.(........).))))))))))))))..............((((-(........)))))......)))))))...--- ( -27.40, z-score =  -3.17, R)
>droYak2.chr3L 7649781 102 - 24197627
UAAAAGCUAAACGCAACUCUUGGUUUGCACUUUUC-----GCAGAAGGGUGCCAAGAAAAGUAUUAUGAAGCCGCCA-GAAAAUAAACUGGCAUCAUUGUUGUUUACU---
....((.(((((((((.(((((....(((((((((-----...))))))))))))))................((((-(........)))))....))).))))))))--- ( -25.60, z-score =  -1.32, R)
>droSim1.chr3L 16857130 107 + 22553184
UAAAAUCCAAACACAUUUCUUGACUUGCACUUUCCGAAGAGCAGAAAAGUGCCAAGAAAAGUAUUUGGUAGCCGCCA-GAAAAUAAACUGGCAUCAUCGUUGUUUGCU---
......(((((.((.(((((((....(((((((.(........).)))))))))))))).)).))))).....((((-(........)))))................--- ( -28.50, z-score =  -2.87, R)
>droSec1.super_0 9569808 107 + 21120651
UAAAAUCUAAACACAUUUCUUGACUUGCACUUUUCAAAGAGCCGAAAAGUGCCAAGAAAAGUAUUAGGUAGCCGCCA-GAAAAUAAACUGGCAUCAUUGUUGUUUGCU---
....((((((..((.(((((((....(((((((((........)))))))))))))))).)).))))))....((((-(........)))))................--- ( -30.00, z-score =  -3.60, R)
>droWil1.scaffold_181009 207336 106 - 3585778
CAAAGUUUAGUCA-ACCUCUUCGUUAAAGGAC----AGGCCCAAAAGAGUCCCCAAAAAAGUAUGCAACAUGCGUGAUGGUAAAAGAUUCGUGAGGUUUUCGUGACCAUGA
.........((((-(((((.........((..----....))....(((((..........(((((.....))))).........)))))..))))).....))))..... ( -19.41, z-score =   0.36, R)
>consensus
UAAAAUCUAAACACAUUUCUUGACUUGCACUUUCC_AAGAGCAGAAAAGUGCCAAGAAAAGUAUUAGGAAGCCGCCA_GAAAAUAAACUGGCAUCAUUGUUGUUUACU___
..................(((..((((((((((.(........).)))))).))))..)))............((((...........))))................... ( -9.56 =  -9.24 +  -0.32)

alignment

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secondary structure

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dotplot

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Window 5

Location 17,525,086 – 17,525,193
Length 107
Sequences 5
Columns 111
Reading direction reverse
Mean pairwise identity 70.32
Shannon entropy 0.52614
G+C content 0.38951
Mean single sequence MFE -28.24
Consensus MFE -13.00
Energy contribution -14.92
Covariance contribution 1.92
Combinations/Pair 1.35
Mean z-score -2.27
Structure conservation index 0.46
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.89
SVM RNA-class probability 0.973409
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 17525086 107 - 24543557
---AGUAAACAACGAUGAUGCCAGUUUAUUUUC-UGGCGGCUUCCUAAUACUUUUCUUGGCACUUUUCUGCUCUUCGGAAAGUGCAAGUCAAGAAAUGUUAUUCGAUUUUA
---....((((..((...((((((........)-)))))...))........((((((((((((((((........)))))))))....)))))))))))........... ( -28.00, z-score =  -2.50, R)
>droYak2.chr3L 7649781 102 + 24197627
---AGUAAACAACAAUGAUGCCAGUUUAUUUUC-UGGCGGCUUCAUAAUACUUUUCUUGGCACCCUUCUGC-----GAAAAGUGCAAACCAAGAGUUGCGUUUAGCUUUUA
---..(((((....((((((((((........)-)))))...))))...(((((((...(((......)))-----)))))))((((........)))))))))....... ( -22.60, z-score =  -0.54, R)
>droSim1.chr3L 16857130 107 - 22553184
---AGCAAACAACGAUGAUGCCAGUUUAUUUUC-UGGCGGCUACCAAAUACUUUUCUUGGCACUUUUCUGCUCUUCGGAAAGUGCAAGUCAAGAAAUGUGUUUGGAUUUUA
---(((...((....)).((((((........)-)))))))).((((((((.((((((((((((((((........)))))))))....))))))).))))))))...... ( -38.20, z-score =  -4.91, R)
>droSec1.super_0 9569808 107 - 21120651
---AGCAAACAACAAUGAUGCCAGUUUAUUUUC-UGGCGGCUACCUAAUACUUUUCUUGGCACUUUUCGGCUCUUUGAAAAGUGCAAGUCAAGAAAUGUGUUUAGAUUUUA
---(((...((....)).((((((........)-))))))))..(((((((.((((((((((((((((((....)))))))))))....))))))).))).))))...... ( -32.50, z-score =  -3.60, R)
>droWil1.scaffold_181009 207336 106 + 3585778
UCAUGGUCACGAAAACCUCACGAAUCUUUUACCAUCACGCAUGUUGCAUACUUUUUUGGGGACUCUUUUGGGCCU----GUCCUUUAACGAAGAGGU-UGACUAAACUUUG
...((((((.....(((((...................((.....))...........(((.(((....))))))----.............)))))-))))))....... ( -19.90, z-score =   0.22, R)
>consensus
___AGCAAACAACAAUGAUGCCAGUUUAUUUUC_UGGCGGCUACCUAAUACUUUUCUUGGCACUUUUCUGCUCUU_GAAAAGUGCAAGUCAAGAAAUGUGUUUAGAUUUUA
..................(((((...........))))).......(((((.((((((((((((((((........)))))))))....))))))).)))))......... (-13.00 = -14.92 +   1.92)

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 23:34:00 2011