Locus 14179

Sequence ID dm3.chrX
Location 11,659,542 – 11,659,665
Length 123
Max. P 0.947080
window19522 window19523

overview

Window 2

Location 11,659,542 – 11,659,665
Length 123
Sequences 3
Columns 149
Reading direction forward
Mean pairwise identity 61.71
Shannon entropy 0.52386
G+C content 0.49167
Mean single sequence MFE -46.60
Consensus MFE -32.25
Energy contribution -31.16
Covariance contribution -1.09
Combinations/Pair 1.37
Mean z-score -1.26
Structure conservation index 0.69
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.53
SVM RNA-class probability 0.947080
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 11659542 123 + 22422827
UCCUGCAUUUCCAUUUUGGUCCGUUGUGGCGACGCCAGACAAUGUGGCACCAGCUAAGAUCGGAUGGUAUAUAGCCGGUUAUAUAUAUUCAACAUAUAUAUA-UAUAUGAAUACCCACUUGUUC-------------------------
.((.((((..((((((.(((((((((((((...)))..))))))((((....)))).))))))))))...)).)).))((((((((((...........)))-)))))))..............------------------------- ( -27.20, z-score =   0.38, R)
>droPer1.super_28 411842 146 - 1111753
UCCUGCGCCUGGAUCUUCGUCUGGCACUGAGAUGCCAGACAACGUGGCACCGCUUCAUGCU---UCAUAUAGGGGCAGGUAAACGCACUGCUCAUACGUGCAACAUGUUGCUUGGCAGGUGCAGUAACCAUUAGUGGAAGGAACUGUCG
(((((((((((.......((((((((......))))))))((((((((((.((.....)).---........((((((((....)).))))))....))))..))))))......))))))).....(((....))).))))....... ( -54.50, z-score =  -1.62, R)
>dp4.chrXL_group1a 6887464 146 - 9151740
UCCUGCGCCUGCAUCUUCGUCUGGCACUGAGAUGCCAGACAACGUGGCACCGCUUCAUGCU---UCAUAUAGGGGCAGGUAAACGCACUGCUCAUACGUGCAACAUGUUGCUUGGCAGGUGCAGUAACCAUUAGUGGAAGGAACUGUCG
((((((((((((......((((((((......))))))))((((((((((.((.....)).---........((((((((....)).))))))....))))..)))))).....)))))))).....(((....))).))))....... ( -58.10, z-score =  -2.55, R)
>consensus
UCCUGCGCCUGCAUCUUCGUCUGGCACUGAGAUGCCAGACAACGUGGCACCGCUUCAUGCU___UCAUAUAGGGGCAGGUAAACGCACUGCUCAUACGUGCAACAUGUUGCUUGGCAGGUGCAGUAACCAUUAGUGGAAGGAACUGUCG
..(((((((((.......((((((((......))))))))((((((..((((((((...............))))).)))....((((.........))))..))))))......)))))))))......................... (-32.25 = -31.16 +  -1.09)

alignment

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secondary structure

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dotplot

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Window 3

Location 11,659,542 – 11,659,665
Length 123
Sequences 3
Columns 149
Reading direction reverse
Mean pairwise identity 61.71
Shannon entropy 0.52386
G+C content 0.49167
Mean single sequence MFE -44.86
Consensus MFE -26.69
Energy contribution -23.93
Covariance contribution -2.76
Combinations/Pair 1.47
Mean z-score -1.31
Structure conservation index 0.59
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.07
SVM RNA-class probability 0.884610
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 11659542 123 - 22422827
-------------------------GAACAAGUGGGUAUUCAUAUA-UAUAUAUAUGUUGAAUAUAUAUAACCGGCUAUAUACCAUCCGAUCUUAGCUGGUGCCACAUUGUCUGGCGUCGCCACAACGGACCAAAAUGGAAAUGCAGGA
-------------------------..(((((((((((((((((((-(....))))).))))))).....((((((((...............)))))))).)))).))))((.((((..(((.............)))..)))).)). ( -31.98, z-score =  -0.84, R)
>droPer1.super_28 411842 146 + 1111753
CGACAGUUCCUUCCACUAAUGGUUACUGCACCUGCCAAGCAACAUGUUGCACGUAUGAGCAGUGCGUUUACCUGCCCCUAUAUGA---AGCAUGAAGCGGUGCCACGUUGUCUGGCAUCUCAGUGCCAGACGAAGAUCCAGGCGCAGGA
.(.((((.....(((....)))..))))).(((((...((..((((((.((..((.(.((((.(......))))).).))..)).---))))))..))...(((...(((((((((((....))))))))))).......)))))))). ( -51.30, z-score =  -1.74, R)
>dp4.chrXL_group1a 6887464 146 + 9151740
CGACAGUUCCUUCCACUAAUGGUUACUGCACCUGCCAAGCAACAUGUUGCACGUAUGAGCAGUGCGUUUACCUGCCCCUAUAUGA---AGCAUGAAGCGGUGCCACGUUGUCUGGCAUCUCAGUGCCAGACGAAGAUGCAGGCGCAGGA
.(.((((.....(((....)))..))))).(((((...((..((((((.((..((.(.((((.(......))))).).))..)).---))))))..))...(((...(((((((((((....))))))))))).......)))))))). ( -51.30, z-score =  -1.34, R)
>consensus
CGACAGUUCCUUCCACUAAUGGUUACUGCACCUGCCAAGCAACAUGUUGCACGUAUGAGCAGUGCGUUUACCUGCCCCUAUAUGA___AGCAUGAAGCGGUGCCACGUUGUCUGGCAUCUCAGUGCCAGACGAAGAUGCAGGCGCAGGA
..............................(((((...(((......(((((.........)))))......)))..............((.((.((((......))))(((((((((....))))))))).......)).))))))). (-26.69 = -23.93 +  -2.76)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 01:35:22 2011