Locus 7694

Sequence ID dm3.chr3L
Location 16,642,446 – 16,642,573
Length 127
Max. P 0.998710
window10586 window10587 window10588 window10589

overview

Window 6

Location 16,642,446 – 16,642,546
Length 100
Sequences 4
Columns 100
Reading direction forward
Mean pairwise identity 88.50
Shannon entropy 0.18547
G+C content 0.39750
Mean single sequence MFE -26.90
Consensus MFE -25.04
Energy contribution -26.85
Covariance contribution 1.81
Combinations/Pair 1.10
Mean z-score -3.74
Structure conservation index 0.93
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 3.46
SVM RNA-class probability 0.998710
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 16642446 100 + 24543557
AACAGUUCUCCAGUAAAUCAAAUUCAAUUUCAACCAAAAAUGCCUGUCGUUCAAGUAUCGCAAACUGUGCGAUAUCCAAACUGAAGGCAGGAGUCUGAUC
..(((..((((.(.((((........))))).........(((((...(((...((((((((.....))))))))...)))...))))))))).)))... ( -26.10, z-score =  -3.96, R)
>droSim1.chr3L 15973226 100 + 22553184
AACAGUUCUCCAGCAAAUCAAAUUCAAUUUCAACCAAAAAUGCCUGUCGUUCGAGUAUCGCAUACUGUGUGAUAUCCAAACUGAAGGCAGGAGUCUGAUC
..(((..((((.(.((((........))))).........(((((...(((.(..((((((((...))))))))..).)))...))))))))).)))... ( -26.20, z-score =  -3.08, R)
>droYak2.chr3L 6769365 100 - 24197627
AACAGUUUUCCAGCAAAUCAAAUUCUAUUUCAACCAAGAAUGCCCGACGUUUGAUUAUCGCAUACAAAGCGAUAUUGAAACUUUAGGCAGGAGUCUGAUC
..(((..((((..........(((((..........)))))(((..(.((((.(.((((((.......)))))).).)))).)..))).)))).)))... ( -26.00, z-score =  -3.58, R)
>droEre2.scaffold_4784 8576260 100 - 25762168
AACAGUUCUCCAGCAAAUCAAAUUCAAUUUCAACCAAGAUUGCCUGUCGUUUGAGUAUCGCAUACAGAGCGAUAUUUACACUAAAGGCAGGAGUCUGAUC
..(((..((((..................((......)).(((((...((.((((((((((.......)))))))))).))...))))))))).)))... ( -29.30, z-score =  -4.33, R)
>consensus
AACAGUUCUCCAGCAAAUCAAAUUCAAUUUCAACCAAAAAUGCCUGUCGUUCGAGUAUCGCAUACAGAGCGAUAUCCAAACUGAAGGCAGGAGUCUGAUC
..(((..((((.(.((((........))))).........(((((...(((((((((((((.......)))))))))))))...))))))))).)))... (-25.04 = -26.85 +   1.81)

alignment

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secondary structure

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dotplot

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Window 7

Location 16,642,446 – 16,642,546
Length 100
Sequences 4
Columns 100
Reading direction reverse
Mean pairwise identity 88.50
Shannon entropy 0.18547
G+C content 0.39750
Mean single sequence MFE -25.05
Consensus MFE -23.02
Energy contribution -23.52
Covariance contribution 0.50
Combinations/Pair 1.14
Mean z-score -1.66
Structure conservation index 0.92
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.23
SVM RNA-class probability 0.913581
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 16642446 100 - 24543557
GAUCAGACUCCUGCCUUCAGUUUGGAUAUCGCACAGUUUGCGAUACUUGAACGACAGGCAUUUUUGGUUGAAAUUGAAUUUGAUUUACUGGAGAACUGUU
...(((.(((((((((...(((..(.(((((((.....))))))).)..)))...))))).....(((..((......))..)))....))))..))).. ( -28.40, z-score =  -2.78, R)
>droSim1.chr3L 15973226 100 - 22553184
GAUCAGACUCCUGCCUUCAGUUUGGAUAUCACACAGUAUGCGAUACUCGAACGACAGGCAUUUUUGGUUGAAAUUGAAUUUGAUUUGCUGGAGAACUGUU
...(((.(((((((((...(((((..((((.((.....)).))))..)))))...))))).....(((..(((((......))))))))))))..))).. ( -25.60, z-score =  -1.47, R)
>droYak2.chr3L 6769365 100 + 24197627
GAUCAGACUCCUGCCUAAAGUUUCAAUAUCGCUUUGUAUGCGAUAAUCAAACGUCGGGCAUUCUUGGUUGAAAUAGAAUUUGAUUUGCUGGAAAACUGUU
(((((((.((.(((((...((((.(.((((((.......)))))).).))))...)))))(((......)))...)).)))))))............... ( -22.80, z-score =  -1.18, R)
>droEre2.scaffold_4784 8576260 100 + 25762168
GAUCAGACUCCUGCCUUUAGUGUAAAUAUCGCUCUGUAUGCGAUACUCAAACGACAGGCAAUCUUGGUUGAAAUUGAAUUUGAUUUGCUGGAGAACUGUU
...(((.(((((((((...((.....((((((.......)))))).....))...))))).....(((..(((((......))))))))))))..))).. ( -23.40, z-score =  -1.20, R)
>consensus
GAUCAGACUCCUGCCUUCAGUUUGAAUAUCGCACAGUAUGCGAUACUCAAACGACAGGCAUUCUUGGUUGAAAUUGAAUUUGAUUUGCUGGAGAACUGUU
...(((.(((((((((...((((((.((((((.......)))))).))))))...))))).....(((..((......))..)))....))))..))).. (-23.02 = -23.52 +   0.50)

alignment

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secondary structure

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dotplot

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Window 8

Location 16,642,481 – 16,642,573
Length 92
Sequences 4
Columns 92
Reading direction forward
Mean pairwise identity 89.13
Shannon entropy 0.17514
G+C content 0.38315
Mean single sequence MFE -22.92
Consensus MFE -20.77
Energy contribution -22.77
Covariance contribution 2.00
Combinations/Pair 1.07
Mean z-score -2.21
Structure conservation index 0.91
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.92
SVM RNA-class probability 0.974941
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 16642481 92 + 24543557
AAAAAUGCCUGUCGUUCAAGUAUCGCAAACUGUGCGAUAUCCAAACUGAAGGCAGGAGUCUGAUCCUUCUUGAGAAUUUUAACUAAAAUUGG
.....(((((...(((...((((((((.....))))))))...)))...)))))(((......)))........((((((....)))))).. ( -21.40, z-score =  -1.82, R)
>droSim1.chr3L 15973261 92 + 22553184
AAAAAUGCCUGUCGUUCGAGUAUCGCAUACUGUGUGAUAUCCAAACUGAAGGCAGGAGUCUGAUCCUUCUUGAGAAUUUUAACUAAAAUUGG
.....(((((...(((.(..((((((((...))))))))..).)))...)))))(((......)))........((((((....)))))).. ( -21.50, z-score =  -1.69, R)
>droYak2.chr3L 6769400 92 - 24197627
AAGAAUGCCCGACGUUUGAUUAUCGCAUACAAAGCGAUAUUGAAACUUUAGGCAGGAGUCUGAUCCUUCUUGAGAAUUUUAACUAAAAUUGG
(((((((((..(.((((.(.((((((.......)))))).).)))).)..))))(((......))))))))...((((((....)))))).. ( -23.70, z-score =  -2.80, R)
>droEre2.scaffold_4784 8576295 92 - 25762168
AAGAUUGCCUGUCGUUUGAGUAUCGCAUACAGAGCGAUAUUUACACUAAAGGCAGGAGUCUGAUCCUUCUUGAGAAUUUUAACUAAAAUUGG
((((.(((((...((.((((((((((.......)))))))))).))...)))))(((......))).))))...((((((....)))))).. ( -25.10, z-score =  -2.51, R)
>consensus
AAAAAUGCCUGUCGUUCGAGUAUCGCAUACAGAGCGAUAUCCAAACUGAAGGCAGGAGUCUGAUCCUUCUUGAGAAUUUUAACUAAAAUUGG
.....(((((...(((((((((((((.......)))))))))))))...)))))(((......)))........((((((....)))))).. (-20.77 = -22.77 +   2.00)

alignment

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secondary structure

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dotplot

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Window 9

Location 16,642,481 – 16,642,573
Length 92
Sequences 4
Columns 92
Reading direction reverse
Mean pairwise identity 89.13
Shannon entropy 0.17514
G+C content 0.38315
Mean single sequence MFE -21.15
Consensus MFE -19.90
Energy contribution -19.90
Covariance contribution 0.00
Combinations/Pair 1.21
Mean z-score -2.22
Structure conservation index 0.94
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.14
SVM RNA-class probability 0.983590
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 16642481 92 - 24543557
CCAAUUUUAGUUAAAAUUCUCAAGAAGGAUCAGACUCCUGCCUUCAGUUUGGAUAUCGCACAGUUUGCGAUACUUGAACGACAGGCAUUUUU
.........................((((......))))((((...(((..(.(((((((.....))))))).)..)))...))))...... ( -23.70, z-score =  -2.60, R)
>droSim1.chr3L 15973261 92 - 22553184
CCAAUUUUAGUUAAAAUUCUCAAGAAGGAUCAGACUCCUGCCUUCAGUUUGGAUAUCACACAGUAUGCGAUACUCGAACGACAGGCAUUUUU
.........................((((......))))((((...(((((..((((.((.....)).))))..)))))...))))...... ( -20.60, z-score =  -2.02, R)
>droYak2.chr3L 6769400 92 + 24197627
CCAAUUUUAGUUAAAAUUCUCAAGAAGGAUCAGACUCCUGCCUAAAGUUUCAAUAUCGCUUUGUAUGCGAUAAUCAAACGUCGGGCAUUCUU
.....................((((((((......)))(((((...((((.(.((((((.......)))))).).))))...)))))))))) ( -20.90, z-score =  -2.52, R)
>droEre2.scaffold_4784 8576295 92 + 25762168
CCAAUUUUAGUUAAAAUUCUCAAGAAGGAUCAGACUCCUGCCUUUAGUGUAAAUAUCGCUCUGUAUGCGAUACUCAAACGACAGGCAAUCUU
.....................((((((((......))))((((...((.....((((((.......)))))).....))...))))..)))) ( -19.40, z-score =  -1.75, R)
>consensus
CCAAUUUUAGUUAAAAUUCUCAAGAAGGAUCAGACUCCUGCCUUCAGUUUGAAUAUCGCACAGUAUGCGAUACUCAAACGACAGGCAUUCUU
.....................((((((((......))))((((...((((((.((((((.......)))))).))))))...))))..)))) (-19.90 = -19.90 +   0.00)

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 23:31:42 2011