Locus 12822

Sequence ID dm3.chrX
Location 2,441,957 – 2,442,104
Length 147
Max. P 0.992765
window17623 window17624 window17625

overview

Window 3

Location 2,441,957 – 2,442,064
Length 107
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 64.61
Shannon entropy 0.56477
G+C content 0.41270
Mean single sequence MFE -29.25
Consensus MFE -12.30
Energy contribution -16.43
Covariance contribution 4.12
Combinations/Pair 1.19
Mean z-score -1.97
Structure conservation index 0.42
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.30
SVM RNA-class probability 0.923754
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 2441957 107 + 22422827
------------AAUACACAGCGAAACAGCUUAUU-GGGGUAAAGUUUGCAAAAAAUAUAACUCAUACGCCCAGUGUAACAGGUCAAGUUGUGUUCAACAUGGCGUAUGAGCGAUAUUCC
------------........(((((...((((...-.))))....)))))....(((((..((((((((((..((((((((.(......).))))..))))))))))))))..))))).. ( -29.70, z-score =  -2.59, R)
>droSec1.super_10 2215583 93 + 3036183
-----------------------GAACAGCUUAUU-GUAGUAAAGUUGGCAG---AUAUUACCCAUACGCCCAGUGUUACAGGUCAAGUUGUGUUCAACAUGGCGUAUGAGCGAUAUUCC
-----------------------...((((((...-......))))))...(---((((..(.((((((((..((((((((.(......).)))..))))))))))))).)..))))).. ( -25.10, z-score =  -1.97, R)
>droYak2.chrX 15868011 117 - 21770863
AAUAUCUGGGAAAACAGCUUAUUGUGCAGCUAUCUUGGAGUAAAGCUUGCAG---AUAUAACUCAUCCGCCCCGUAUUGCUGAUGAAGUUUUGUUCAACGUGGCGUAUAAGCGAUAUUCC
((((((((......))(((...(((((.(((((.(((((.(((((((.....---.......(((((.((........)).))))))))))))))))).))))))))))))))))))).. ( -28.20, z-score =  -0.48, R)
>droEre2.scaffold_4644 2392346 110 + 2521924
AAUAACUAUGGAAAUAGCCUAUUGGGCAGCAAACUAAGAGUAAUGUUUGCAA---AUAUAACUCAUACGCCCAGUGUGGCUGGUGAUGUAUCAUC-------GCGUAUAUGCGAUAUUCC
.........((((.(((((((((((((.((((((..........))))))..---.(((.....))).)))))))).)))))..........(((-------(((....)))))).)))) ( -34.00, z-score =  -2.86, R)
>consensus
____________AAUAGCCUAUUGAACAGCUAACU_GGAGUAAAGUUUGCAA___AUAUAACUCAUACGCCCAGUGUUACAGGUCAAGUUGUGUUCAACAUGGCGUAUAAGCGAUAUUCC
............................(((((((........))))))).....((((..((((((((((......((((((......))))))......))))))))))..))))... (-12.30 = -16.43 +   4.12)

alignment

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secondary structure

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dotplot

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Window 4

Location 2,441,957 – 2,442,064
Length 107
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 64.61
Shannon entropy 0.56477
G+C content 0.41270
Mean single sequence MFE -27.75
Consensus MFE -13.53
Energy contribution -13.91
Covariance contribution 0.38
Combinations/Pair 1.13
Mean z-score -2.32
Structure conservation index 0.49
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.56
SVM RNA-class probability 0.992765
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 2441957 107 - 22422827
GGAAUAUCGCUCAUACGCCAUGUUGAACACAACUUGACCUGUUACACUGGGCGUAUGAGUUAUAUUUUUUGCAAACUUUACCCC-AAUAAGCUGUUUCGCUGUGUAUU------------
(((((((.(((((((((((......((((..........))))......))))))))))).)))))))...............(-(...(((......))).))....------------ ( -27.20, z-score =  -2.28, R)
>droSec1.super_10 2215583 93 - 3036183
GGAAUAUCGCUCAUACGCCAUGUUGAACACAACUUGACCUGUAACACUGGGCGUAUGGGUAAUAU---CUGCCAACUUUACUAC-AAUAAGCUGUUC-----------------------
((.((((..((((((((((.(((((....(.....).....)))))...))))))))))..))))---...))...........-............----------------------- ( -24.70, z-score =  -2.59, R)
>droYak2.chrX 15868011 117 + 21770863
GGAAUAUCGCUUAUACGCCACGUUGAACAAAACUUCAUCAGCAAUACGGGGCGGAUGAGUUAUAU---CUGCAAGCUUUACUCCAAGAUAGCUGCACAAUAAGCUGUUUUCCCAGAUAUU
..((((((((......))...(((((...........))))).....((((((((((.....)))---))))............(((((((((........)))))))))))).)))))) ( -28.60, z-score =  -1.55, R)
>droEre2.scaffold_4644 2392346 110 - 2521924
GGAAUAUCGCAUAUACGC-------GAUGAUACAUCACCAGCCACACUGGGCGUAUGAGUUAUAU---UUGCAAACAUUACUCUUAGUUUGCUGCCCAAUAGGCUAUUUCCAUAGUUAUU
((((((((((......))-------))))..........((((....((((((((.....)))..---..((((((..........)))))).)))))...))))..))))......... ( -30.50, z-score =  -2.89, R)
>consensus
GGAAUAUCGCUCAUACGCCAUGUUGAACAAAACUUCACCAGCAACACUGGGCGUAUGAGUUAUAU___CUGCAAACUUUACUCC_AAUAAGCUGCUCAAUAGGCUAUU____________
...((((.(((((((((((..............................))))))))))).))))....................................................... (-13.53 = -13.91 +   0.38)

alignment

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secondary structure

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dotplot

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Window 5

Location 2,441,984 – 2,442,104
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 77.78
Shannon entropy 0.35690
G+C content 0.41693
Mean single sequence MFE -30.15
Consensus MFE -20.13
Energy contribution -21.44
Covariance contribution 1.31
Combinations/Pair 1.18
Mean z-score -2.15
Structure conservation index 0.67
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.55
SVM RNA-class probability 0.949033
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 2441984 120 - 22422827
CCUGAAUGGCAGCGUUCUUCUUUUGAACAAUGGAAACCUUGGAAUAUCGCUCAUACGCCAUGUUGAACACAACUUGACCUGUUACACUGGGCGUAUGAGUUAUAUUUUUUGCAAACUUUA
........((((.((((.......))))...(....)...(((((((.(((((((((((......((((..........))))......))))))))))).)))))))))))........ ( -32.00, z-score =  -2.94, R)
>droSec1.super_10 2215599 109 - 3036183
--------GCAGCGUUCUUCUUUCGAACAAAGGAAUCGUUGGAAUAUCGCUCAUACGCCAUGUUGAACACAACUUGACCUGUAACACUGGGCGUAUGGGUAAUAU---CUGCCAACUUUA
--------.....((((.......)))).........(((((.((((..((((((((((.(((((....(.....).....)))))...))))))))))..))))---...))))).... ( -32.70, z-score =  -3.02, R)
>droYak2.chrX 15868051 117 + 21770863
CCUGAAUGGCAGCGUUCUUGAUUUGAACAAAGGAAUCCUUGGAAUAUCGCUUAUACGCCACGUUGAACAAAACUUCAUCAGCAAUACGGGGCGGAUGAGUUAUAU---CUGCAAGCUUUA
((((..(((((((((((.......)))).((((...))))........))).....)))).(((((...........)))))....))))(((((((.....)))---))))........ ( -27.90, z-score =  -0.56, R)
>droEre2.scaffold_4644 2392386 110 - 2521924
ACUGAAUGACAGCGUUCUCUAUGUGAACAAAGAAAUCCUUGGAAUAUCGCAUAUACGCGAUGAU-------ACAUCACCAGCCACACUGGGCGUAUGAGUUAUAU---UUGCAAACAUUA
....((((...((((((.......)))).............((((((.((.(((((((((((..-------.)))).((((.....))))))))))).)).))))---))))...)))). ( -28.00, z-score =  -2.10, R)
>consensus
CCUGAAUGGCAGCGUUCUUCAUUUGAACAAAGGAAUCCUUGGAAUAUCGCUCAUACGCCAUGUUGAACACAACUUCACCAGCAACACUGGGCGUAUGAGUUAUAU___CUGCAAACUUUA
........((((.((((.......))))...............((((.(((((((((((.(((((................)))))...))))))))))).))))...))))........ (-20.13 = -21.44 +   1.31)

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 01:09:25 2011