Locus 12108

Sequence ID dm3.chr3R
Location 25,691,585 – 25,691,721
Length 136
Max. P 0.978169
window16645 window16646 window16647 window16648

overview

Window 5

Location 25,691,585 – 25,691,692
Length 107
Sequences 5
Columns 107
Reading direction forward
Mean pairwise identity 91.48
Shannon entropy 0.14992
G+C content 0.29940
Mean single sequence MFE -23.36
Consensus MFE -19.94
Energy contribution -20.26
Covariance contribution 0.32
Combinations/Pair 1.10
Mean z-score -1.53
Structure conservation index 0.85
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.19
SVM RNA-class probability 0.585694
Prediction RNA
WARNING Out of training range. z-scores are NOT reliable.

Download alignment: ClustalW | MAF

>dm3.chr3R 25691585 107 + 27905053
AAUGCAGGUACUUAAAUGAUAAAUAUAUAUUUGCCAAUAUGGCUUGUUCGAGUUCGAGCAAUAAUUAAUUGGCUUUUUCCAUAAUUAAUAAGCAAUUUAGAUGCAGU
..((((((((..((.(((.....))).))..))))......(((((((((....)))))..((((((..(((......)))))))))..))))........)))).. ( -20.20, z-score =  -0.19, R)
>droEre2.scaffold_4820 8160794 105 - 10470090
AAUGCAGGUACUUAAAUGAU--UAAUAUCUUUGCCAAUUUCGAUUGUUCGAGUUCGAGCAAUAAUUAAUUGGCUUUUUCUAUAAUUUAUAAGCAAUUUAGAUGUAGU
..((((((((.((((....)--))))))))..(((((((...((((((((....))))))))....)))))))..................)))............. ( -23.80, z-score =  -2.36, R)
>droYak2.chr3R 8058817 105 - 28832112
AAUGCAGGUACUUAAAUGAU--UUAUAUCUUUGCCAAUUUUGUUUGCUCGCGUUCGAGCAAUAAUUAAUUGGCUUUUUCUAUAAUUCAUAAGCAAUUUAGACGCAGU
..(((..........((((.--(((((.....(((((((....(((((((....))))))).....)))))))......))))).))))((....)).....))).. ( -24.60, z-score =  -2.14, R)
>droSec1.super_4 4542599 107 + 6179234
AAUGCAGGUACUUAAAUGAUAAAUAUAUCUUUGCCAAUUUGGCUUGCUCGAGUUCGAGCAGUAAUUAAUUGGCUUUUUCCAUAAUUUAUAAGCAAUUAAGAUGAAGU
..(((..(((.......((((....))))...(((((((..(((.(((((....))))))))....))))))).............)))..)))............. ( -24.10, z-score =  -1.49, R)
>droSim1.chr3R 25367066 107 + 27517382
AAUGCAGGUACUUAAAUGAUAAAUAUAUCUUUGCCAAUUUGGCUUGCUCGAGUUCGAGCAGUAAUUAAUUGGCUUUUUCCAUAAUUUAUAAGCAAUUAAGAUGAAGU
..(((..(((.......((((....))))...(((((((..(((.(((((....))))))))....))))))).............)))..)))............. ( -24.10, z-score =  -1.49, R)
>consensus
AAUGCAGGUACUUAAAUGAUAAAUAUAUCUUUGCCAAUUUGGCUUGCUCGAGUUCGAGCAAUAAUUAAUUGGCUUUUUCCAUAAUUUAUAAGCAAUUUAGAUGAAGU
..(((............((((....))))...(((((((....(((((((....))))))).....)))))))..................)))............. (-19.94 = -20.26 +   0.32)

alignment

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secondary structure

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dotplot

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Window 6

Location 25,691,585 – 25,691,692
Length 107
Sequences 5
Columns 107
Reading direction reverse
Mean pairwise identity 91.48
Shannon entropy 0.14992
G+C content 0.29940
Mean single sequence MFE -22.14
Consensus MFE -19.12
Energy contribution -20.72
Covariance contribution 1.60
Combinations/Pair 1.00
Mean z-score -2.60
Structure conservation index 0.86
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.99
SVM RNA-class probability 0.978169
Prediction RNA
WARNING Out of training range. z-scores are NOT reliable.

Download alignment: ClustalW | MAF

>dm3.chr3R 25691585 107 - 27905053
ACUGCAUCUAAAUUGCUUAUUAAUUAUGGAAAAAGCCAAUUAAUUAUUGCUCGAACUCGAACAAGCCAUAUUGGCAAAUAUAUAUUUAUCAUUUAAGUACCUGCAUU
..(((((((((((((.....))))).))))....((((((......(((.(((....))).))).....)))))).......((((((.....))))))..)))).. ( -19.20, z-score =  -1.28, R)
>droEre2.scaffold_4820 8160794 105 + 10470090
ACUACAUCUAAAUUGCUUAUAAAUUAUAGAAAAAGCCAAUUAAUUAUUGCUCGAACUCGAACAAUCGAAAUUGGCAAAGAUAUUA--AUCAUUUAAGUACCUGCAUU
.............((((((...............(((((((....((((.(((....))).))))...)))))))...(((....--)))...))))))........ ( -17.80, z-score =  -2.25, R)
>droYak2.chr3R 8058817 105 + 28832112
ACUGCGUCUAAAUUGCUUAUGAAUUAUAGAAAAAGCCAAUUAAUUAUUGCUCGAACGCGAGCAAACAAAAUUGGCAAAGAUAUAA--AUCAUUUAAGUACCUGCAUU
..((((.......(((((((((.(((((......(((((((.....(((((((....)))))))....))))))).....)))))--.)))..))))))..)))).. ( -25.90, z-score =  -3.42, R)
>droSec1.super_4 4542599 107 - 6179234
ACUUCAUCUUAAUUGCUUAUAAAUUAUGGAAAAAGCCAAUUAAUUACUGCUCGAACUCGAGCAAGCCAAAUUGGCAAAGAUAUAUUUAUCAUUUAAGUACCUGCAUU
.............((((((...............(((((((......((((((....)))))).....)))))))...((((....))))...))))))........ ( -23.90, z-score =  -3.02, R)
>droSim1.chr3R 25367066 107 - 27517382
ACUUCAUCUUAAUUGCUUAUAAAUUAUGGAAAAAGCCAAUUAAUUACUGCUCGAACUCGAGCAAGCCAAAUUGGCAAAGAUAUAUUUAUCAUUUAAGUACCUGCAUU
.............((((((...............(((((((......((((((....)))))).....)))))))...((((....))))...))))))........ ( -23.90, z-score =  -3.02, R)
>consensus
ACUGCAUCUAAAUUGCUUAUAAAUUAUGGAAAAAGCCAAUUAAUUAUUGCUCGAACUCGAGCAAGCCAAAUUGGCAAAGAUAUAUUUAUCAUUUAAGUACCUGCAUU
.............((((((...............(((((((.....(((((((....)))))))....)))))))...((((....))))...))))))........ (-19.12 = -20.72 +   1.60)

alignment

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secondary structure

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dotplot

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Window 7

Location 25,691,614 – 25,691,721
Length 107
Sequences 5
Columns 111
Reading direction forward
Mean pairwise identity 89.18
Shannon entropy 0.19233
G+C content 0.33273
Mean single sequence MFE -27.96
Consensus MFE -23.48
Energy contribution -23.84
Covariance contribution 0.36
Combinations/Pair 1.10
Mean z-score -2.25
Structure conservation index 0.84
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.57
SVM RNA-class probability 0.951343
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 25691614 107 + 27905053
UUUGCCAAUAUGGCUUGUUCGAGUUCGAGCAAUAAUUAAUUGGCUUUUUCCAUAAUUAAUAAGCAAUUUAGAUGCAGUUAG----UUAGUUUGAAUGUGAUUGCUUUCCAG
...((((((.....(((((((....)))))))......))))))................((((((((.....(((.((((----.....)))).)))))))))))..... ( -22.80, z-score =  -1.04, R)
>droEre2.scaffold_4820 8160821 111 - 10470090
UUUGCCAAUUUCGAUUGUUCGAGUUCGAGCAAUAAUUAAUUGGCUUUUUCUAUAAUUUAUAAGCAAUUUAGAUGUAGUUAUAUGCUUAGUUUGAAUGUGAUUGCUAUUCUG
...(((((((...((((((((....))))))))....)))))))........................((((.((((((((((.(.......).))))))))))...)))) ( -28.60, z-score =  -3.21, R)
>droYak2.chr3R 8058844 111 - 28832112
UUUGCCAAUUUUGUUUGCUCGCGUUCGAGCAAUAAUUAAUUGGCUUUUUCUAUAAUUCAUAAGCAAUUUAGACGCAGUUAUAUGCUUAGUUUGAAUGUGAUUGCUACUCGG
...(((((((....(((((((....))))))).....)))))))....((((.(((((....).)))))))).((((((((((.(.......).))))))))))....... ( -28.50, z-score =  -2.32, R)
>droSec1.super_4 4542628 111 + 6179234
UUUGCCAAUUUGGCUUGCUCGAGUUCGAGCAGUAAUUAAUUGGCUUUUUCCAUAAUUUAUAAGCAAUUAAGAUGAAGUCAUGUGCUUAGUUUGAAUGUGAUUGCUUUCCAG
...(((((((..(((.(((((....))))))))....)))))))................(((((((((((((.((((.....)))).)))).....)))))))))..... ( -29.10, z-score =  -2.12, R)
>droSim1.chr3R 25367095 110 + 27517382
UUUGCCAAUUUGGCUUGCUCGAGUUCGAGCAGUAAUUAAUUGGCUUUUUCCAUAAUUUAUAAGCAAUUAAGAUGAAGUCAUG-GCUUAGUUUGAAUGUGAUUGCUUUCCAG
...(((((((..(((.(((((....))))))))....)))))))................(((((((((((((.((((....-)))).)))).....)))))))))..... ( -30.80, z-score =  -2.56, R)
>consensus
UUUGCCAAUUUGGCUUGCUCGAGUUCGAGCAAUAAUUAAUUGGCUUUUUCCAUAAUUUAUAAGCAAUUUAGAUGAAGUUAUAUGCUUAGUUUGAAUGUGAUUGCUUUCCAG
...(((((((....(((((((....))))))).....))))))).................((((((((((((..(((.....)))..))))).....)))))))...... (-23.48 = -23.84 +   0.36)

alignment

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secondary structure

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dotplot

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Window 8

Location 25,691,614 – 25,691,721
Length 107
Sequences 5
Columns 111
Reading direction reverse
Mean pairwise identity 89.18
Shannon entropy 0.19233
G+C content 0.33273
Mean single sequence MFE -21.33
Consensus MFE -18.03
Energy contribution -19.43
Covariance contribution 1.40
Combinations/Pair 1.00
Mean z-score -2.19
Structure conservation index 0.85
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.55
SVM RNA-class probability 0.949292
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 25691614 107 - 27905053
CUGGAAAGCAAUCACAUUCAAACUAA----CUAACUGCAUCUAAAUUGCUUAUUAAUUAUGGAAAAAGCCAAUUAAUUAUUGCUCGAACUCGAACAAGCCAUAUUGGCAAA
.....(((((((..............----..............)))))))................((((((......(((.(((....))).))).....))))))... ( -16.79, z-score =  -1.09, R)
>droEre2.scaffold_4820 8160821 111 + 10470090
CAGAAUAGCAAUCACAUUCAAACUAAGCAUAUAACUACAUCUAAAUUGCUUAUAAAUUAUAGAAAAAGCCAAUUAAUUAUUGCUCGAACUCGAACAAUCGAAAUUGGCAAA
..((((.(......)))))....((((((.................))))))...............(((((((....((((.(((....))).))))...)))))))... ( -18.13, z-score =  -2.55, R)
>droYak2.chr3R 8058844 111 + 28832112
CCGAGUAGCAAUCACAUUCAAACUAAGCAUAUAACUGCGUCUAAAUUGCUUAUGAAUUAUAGAAAAAGCCAAUUAAUUAUUGCUCGAACGCGAGCAAACAAAAUUGGCAAA
...............(((((...((((((.................)))))))))))..........(((((((.....(((((((....)))))))....)))))))... ( -24.33, z-score =  -2.49, R)
>droSec1.super_4 4542628 111 - 6179234
CUGGAAAGCAAUCACAUUCAAACUAAGCACAUGACUUCAUCUUAAUUGCUUAUAAAUUAUGGAAAAAGCCAAUUAAUUACUGCUCGAACUCGAGCAAGCCAAAUUGGCAAA
...........((.(((......((((((.(((....)))......))))))......)))))....(((((((......((((((....)))))).....)))))))... ( -23.70, z-score =  -2.49, R)
>droSim1.chr3R 25367095 110 - 27517382
CUGGAAAGCAAUCACAUUCAAACUAAGC-CAUGACUUCAUCUUAAUUGCUUAUAAAUUAUGGAAAAAGCCAAUUAAUUACUGCUCGAACUCGAGCAAGCCAAAUUGGCAAA
.....(((((((...........((((.-.(((....))))))))))))))................(((((((......((((((....)))))).....)))))))... ( -23.70, z-score =  -2.32, R)
>consensus
CUGGAAAGCAAUCACAUUCAAACUAAGCACAUAACUGCAUCUAAAUUGCUUAUAAAUUAUGGAAAAAGCCAAUUAAUUAUUGCUCGAACUCGAGCAAGCCAAAUUGGCAAA
.....(((((((................................)))))))................(((((((.....(((((((....)))))))....)))))))... (-18.03 = -19.43 +   1.40)

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 Wed Apr 20 00:55:54 2011