Locus 1634

Sequence ID dm3.chr2L
Location 12,715,903 – 12,716,018
Length 115
Max. P 0.924315
window2235 window2236 window2237

overview

Window 5

Location 12,715,903 – 12,715,999
Length 96
Sequences 4
Columns 96
Reading direction forward
Mean pairwise identity 90.97
Shannon entropy 0.14632
G+C content 0.50266
Mean single sequence MFE -31.95
Consensus MFE -29.20
Energy contribution -28.95
Covariance contribution -0.25
Combinations/Pair 1.16
Mean z-score -1.38
Structure conservation index 0.91
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.50
SVM RNA-class probability 0.720049
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 12715903 96 + 23011544
UUUCGCCAUGGCCGCGUUGAUCUUGGUUGCCUGUAGUUUCGGUUUGAUUACCGACUGACCAGGUUUGGAUGCACCAGGAUUGGUGUUCAUAGGUUU
....(((((((..(((..(((((((((.(((((..((((((((......)))))..))))))))........)))))))))..))))))).))).. ( -31.60, z-score =  -1.67, R)
>droEre2.scaffold_4929 13934892 94 - 26641161
UUUCGCCAUGGCCGCGUUGUUCUUAGUUGCCUGUGGUUUCGGUUUGAUUACCGGCUGGCCAAGUUUGGAUGCACCAGGAUUGGUGAUCAUAGGU--
....((....))................(((((((((((((((......)))))...(((((.(((((.....))))).)))))))))))))))-- ( -28.00, z-score =  -0.05, R)
>droYak2.chr2L 9154748 96 + 22324452
UUUCGCCAUGUCCGCGUUGUUCUUGGUUGCCUGUGGUUUAGGUUUGAUCACCGGCUGACCAGGUUUGGAUGCACCAGGAUUGGUGUUCACAGGUUU
...(((((.(((((((((...((((((((((.((((((.......)))))).))).)))))))....)))))....)))))))))........... ( -34.00, z-score =  -1.81, R)
>droSec1.super_16 900196 96 + 1878335
UUUUGCCGUGGCCGCGUUAAUCUUGGUUGCCUGUGGUUUUGGUUUGAUUACCGGCUGACCAGGUUUGGAUGCACCAGGAUUGGUGUUCACAGGUUU
....((((((..((((((...((((((((((.((((((.......)))))).))).)))))))....)))))(((......))))..))).))).. ( -34.20, z-score =  -2.00, R)
>consensus
UUUCGCCAUGGCCGCGUUGAUCUUGGUUGCCUGUGGUUUCGGUUUGAUUACCGGCUGACCAGGUUUGGAUGCACCAGGAUUGGUGUUCACAGGUUU
....((((((..((((((...((((((((((.((((((.......)))))).))).)))))))....)))))(((......))))..))).))).. (-29.20 = -28.95 +  -0.25)

alignment

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secondary structure

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dotplot

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Window 6

Location 12,715,923 – 12,716,018
Length 95
Sequences 5
Columns 99
Reading direction forward
Mean pairwise identity 67.18
Shannon entropy 0.59431
G+C content 0.46877
Mean single sequence MFE -27.42
Consensus MFE -13.48
Energy contribution -16.80
Covariance contribution 3.32
Combinations/Pair 1.22
Mean z-score -1.28
Structure conservation index 0.49
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.89
SVM RNA-class probability 0.845526
Prediction RNA
WARNING Out of training range. z-scores are NOT reliable.

Download alignment: ClustalW | MAF

>dm3.chr2L 12715923 95 + 23011544
UCUUGGUUGCCUGUAGUUUCGGUUUGAUUACCGACUGACCAGGUUUGGAUGCACCAG----GAUUGGUGUUCAUAGGUUUGUUUGGUUGCGGUGCACGA
.......(((((((((..(((((......)))))(..(.((((..((...(((((..----....)))))...))..)))).)..))))))).)))... ( -28.10, z-score =  -0.75, R)
>droEre2.scaffold_4929 13934912 74 - 26641161
UCUUAGUUGCCUGUGGUUUCGGUUUGAUUACCGGCUGGCCAAGUUUGGAUGCACCAG----GAUUGGUGAUCAUAGGU---------------------
........(((((((((((((((......)))))...(((((.(((((.....))))----).)))))))))))))))--------------------- ( -26.20, z-score =  -2.20, R)
>droYak2.chr2L 9154768 95 + 22324452
UCUUGGUUGCCUGUGGUUUAGGUUUGAUCACCGGCUGACCAGGUUUGGAUGCACCAG----GAUUGGUGUUCACAGGUUUGUUUGCAUGAGGUGCACGA
.((((((((((.((((((.......)))))).))).)))))))......((((((.(----(((....)))).((.((......)).)).))))))... ( -32.10, z-score =  -1.12, R)
>droSec1.super_16 900216 95 + 1878335
UCUUGGUUGCCUGUGGUUUUGGUUUGAUUACCGGCUGACCAGGUUUGGAUGCACCAG----GAUUGGUGUUCACAGGUUUGUUUGGUUGCGGUGCACGA
.((((((((((.((((((.......)))))).))).)))))))......((((((.(----(((....)))).((((....)))).....))))))... ( -29.40, z-score =  -0.63, R)
>droGri2.scaffold_15126 4526513 91 - 8399593
GCUCAAGUGCCU-----UAAGACUUUAUAAUAUACUUAUAAAGU---AAUUUACCAGUUCCGAAUGGUUUUAAUGGCAGCUUCUGUUGCUGCUGCCUAA
((......))..-----....(((((((((.....)))))))))---.....((((........))))......((((((..(....)..))))))... ( -21.30, z-score =  -1.69, R)
>consensus
UCUUGGUUGCCUGUGGUUUAGGUUUGAUUACCGGCUGACCAGGUUUGGAUGCACCAG____GAUUGGUGUUCAUAGGUUUGUUUGGUUGCGGUGCACGA
.((((((((((.((((((.......)))))).))).)))))))((((...(((((((......)))))))...))))...................... (-13.48 = -16.80 +   3.32)

alignment

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secondary structure

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dotplot

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Window 7

Location 12,715,923 – 12,716,018
Length 95
Sequences 5
Columns 99
Reading direction reverse
Mean pairwise identity 67.18
Shannon entropy 0.59431
G+C content 0.46877
Mean single sequence MFE -20.63
Consensus MFE -10.04
Energy contribution -10.16
Covariance contribution 0.12
Combinations/Pair 1.31
Mean z-score -1.49
Structure conservation index 0.49
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.31
SVM RNA-class probability 0.924315
Prediction RNA
WARNING Out of training range. z-scores are NOT reliable.

Download alignment: ClustalW | MAF

>dm3.chr2L 12715923 95 - 23011544
UCGUGCACCGCAACCAAACAAACCUAUGAACACCAAUC----CUGGUGCAUCCAAACCUGGUCAGUCGGUAAUCAAACCGAAACUACAGGCAACCAAGA
..((((((((............................----.)))))))).....((((.....(((((......))))).....))))......... ( -21.15, z-score =  -1.69, R)
>droEre2.scaffold_4929 13934912 74 + 26641161
---------------------ACCUAUGAUCACCAAUC----CUGGUGCAUCCAAACUUGGCCAGCCGGUAAUCAAACCGAAACCACAGGCAACUAAGA
---------------------......((((((((...----.))))).)))....(((((...((((((......)))(....)...)))..))))). ( -17.40, z-score =  -1.67, R)
>droYak2.chr2L 9154768 95 - 22324452
UCGUGCACCUCAUGCAAACAAACCUGUGAACACCAAUC----CUGGUGCAUCCAAACCUGGUCAGCCGGUGAUCAAACCUAAACCACAGGCAACCAAGA
...((((.....))))......((((((..(((((...----.))))).......(((.((....)))))..............))))))......... ( -22.10, z-score =  -0.97, R)
>droSec1.super_16 900216 95 - 1878335
UCGUGCACCGCAACCAAACAAACCUGUGAACACCAAUC----CUGGUGCAUCCAAACCUGGUCAGCCGGUAAUCAAACCAAAACCACAGGCAACCAAGA
...(((...)))..........((((((..(((((...----.))))).......(((.((....)))))..............))))))......... ( -19.80, z-score =  -0.76, R)
>droGri2.scaffold_15126 4526513 91 + 8399593
UUAGGCAGCAGCAACAGAAGCUGCCAUUAAAACCAUUCGGAACUGGUAAAUU---ACUUUAUAAGUAUAUUAUAAAGUCUUA-----AGGCACUUGAGC
...((((((..(....)..))))))......((((........)))).....---(((((((((.....)))))))))((((-----((...)))))). ( -22.70, z-score =  -2.38, R)
>consensus
UCGUGCACCGCAACCAAACAAACCUAUGAACACCAAUC____CUGGUGCAUCCAAACCUGGUCAGCCGGUAAUCAAACCGAAACCACAGGCAACCAAGA
..............................(((((........)))))........((((......((((......))))......))))......... (-10.04 = -10.16 +   0.12)

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 21:35:44 2011