Locus 5875

Sequence ID dm3.chr3L
Location 1,984,991 – 1,985,099
Length 108
Max. P 0.940853
window8079 window8080

overview

Window 9

Location 1,984,991 – 1,985,099
Length 108
Sequences 5
Columns 134
Reading direction forward
Mean pairwise identity 71.87
Shannon entropy 0.42706
G+C content 0.41377
Mean single sequence MFE -27.44
Consensus MFE -20.10
Energy contribution -20.46
Covariance contribution 0.36
Combinations/Pair 1.13
Mean z-score -1.59
Structure conservation index 0.73
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.47
SVM RNA-class probability 0.940853
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 1984991 108 + 24543557
--------------UGGUAAACUUAAAUUAUCCUAU------------UUAAAUUUGAAGUGAUCGUUUUCACCACGGCUGAAACUGCCACCAGCGAGGGGGUGGUCCAUUGUGGUGAGAUCAUCGAUGGACGA
--------------...((((.((((((......))------------)))).))))..((.((((.(((((((((((.((..((..((.((......))))..)).)))))))))))))....)))).).).. ( -29.80, z-score =  -0.71, R)
>droEre2.scaffold_4784 1974046 98 + 25762168
--------------UGGUAAAUUUAAAUUAUGUU---------------UAAAUUUUAAGUGAUCGUAUUCACCACAGCUGGAACUGCCACCGC-------GCUUUGCAUUGUGGUGAGAUUAUCGAUGGGCGA
--------------..((((((((((((...)))---------------)))))))....(.((((..((((((((((.((.((..((......-------)).)).)))))))))))).....)))).))).. ( -22.10, z-score =  -0.08, R)
>droYak2.chr3L 1939707 113 + 24197627
--------------UGGUAAACUUAAAUUAUCCUUUCCCGAAACCUGCUUAAAUUUUAAGUGAUCGUUUUCACCACAGCUGGAGCUGCUAGCUC------GGUU-UCCAUUGUGGUGAGAUUUUCGAUGAACGA
--------------.(((((.......)))))......((......(((((.....))))).((((.(((((((((((.((((((((......)------)).)-)))))))))))))))....))))...)). ( -29.10, z-score =  -1.84, R)
>droSec1.super_2 2010179 110 + 7591821
UGGUAAAUUUGAAUUAUCCGAUUUAACCUAUU-----------------UAAAUUUGAAGUGAUCGUUUUCACCACGCCUGGAACUGCCACCUC-------GCUUUCCAUUGUGGUGAGAUCAUCGAUAGACGA
.((((((((.((....)).))))).)))....-----------------..........((.((((.((((((((((..(((((..((......-------)).))))).))))))))))....))))..)).. ( -28.90, z-score =  -2.57, R)
>droSim1.chr3L 1554150 93 + 22553184
--------------UGGUAAAUUUGA---AUU-----------------UAAAUUUCAAGUGAUCGUUUUCACCACGCCUGGAACUGCCACCUC-------GCUUUCCAUUGUGGUGAGAUCAUCGAUAGACGA
--------------......((((((---(..-----------------.....))))))).((((.((((((((((..(((((..((......-------)).))))).))))))))))....))))...... ( -27.30, z-score =  -2.73, R)
>consensus
______________UGGUAAAUUUAAAUUAUC_U_______________UAAAUUUGAAGUGAUCGUUUUCACCACGGCUGGAACUGCCACCUC_______GCUUUCCAUUGUGGUGAGAUCAUCGAUGGACGA
...........................................................((.((((.(((((((((((.((((...((.............))..)))))))))))))))....))))..)).. (-20.10 = -20.46 +   0.36)

alignment

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secondary structure

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dotplot

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Window 0

Location 1,984,991 – 1,985,099
Length 108
Sequences 5
Columns 134
Reading direction reverse
Mean pairwise identity 71.87
Shannon entropy 0.42706
G+C content 0.41377
Mean single sequence MFE -25.86
Consensus MFE -13.75
Energy contribution -14.83
Covariance contribution 1.08
Combinations/Pair 1.05
Mean z-score -1.76
Structure conservation index 0.53
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.52
SVM RNA-class probability 0.728613
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 1984991 108 - 24543557
UCGUCCAUCGAUGAUCUCACCACAAUGGACCACCCCCUCGCUGGUGGCAGUUUCAGCCGUGGUGAAAACGAUCACUUCAAAUUUAA------------AUAGGAUAAUUUAAGUUUACCA--------------
(((.....)))((((((((((((..(((((((((........)))))....))))...)))))))....)))))....((((((((------------((......))))))))))....-------------- ( -28.80, z-score =  -2.10, R)
>droEre2.scaffold_4784 1974046 98 - 25762168
UCGCCCAUCGAUAAUCUCACCACAAUGCAAAGC-------GCGGUGGCAGUUCCAGCUGUGGUGAAUACGAUCACUUAAAAUUUA---------------AACAUAAUUUAAAUUUACCA--------------
.........(((....((((((((..((.....-------))(.(((.....))).))))))))).....))).....(((((((---------------((.....)))))))))....-------------- ( -21.10, z-score =  -1.69, R)
>droYak2.chr3L 1939707 113 - 24197627
UCGUUCAUCGAAAAUCUCACCACAAUGGA-AACC------GAGCUAGCAGCUCCAGCUGUGGUGAAAACGAUCACUUAAAAUUUAAGCAGGUUUCGGGAAAGGAUAAUUUAAGUUUACCA--------------
(((.....)))...((((..(.....)((-((((------..(((.(((((....)))))(((((......))))).........))).))))))))))..((.(((.......))))).-------------- ( -25.80, z-score =  -1.06, R)
>droSec1.super_2 2010179 110 - 7591821
UCGUCUAUCGAUGAUCUCACCACAAUGGAAAGC-------GAGGUGGCAGUUCCAGGCGUGGUGAAAACGAUCACUUCAAAUUUA-----------------AAUAGGUUAAAUCGGAUAAUUCAAAUUUACCA
(((.....)))((((((((((((..(((((.((-------......))..)))))...)))))))....)))))...........-----------------....(((.((((..((....))..))))))). ( -28.40, z-score =  -2.05, R)
>droSim1.chr3L 1554150 93 - 22553184
UCGUCUAUCGAUGAUCUCACCACAAUGGAAAGC-------GAGGUGGCAGUUCCAGGCGUGGUGAAAACGAUCACUUGAAAUUUA-----------------AAU---UCAAAUUUACCA--------------
.......((((((((((((((((..(((((.((-------......))..)))))...)))))))....))))).))))......-----------------...---............-------------- ( -25.20, z-score =  -1.90, R)
>consensus
UCGUCCAUCGAUGAUCUCACCACAAUGGAAAGC_______GAGGUGGCAGUUCCAGCCGUGGUGAAAACGAUCACUUAAAAUUUA_______________A_AAUAAUUUAAAUUUACCA______________
(((.....)))((((((((((((..(((((....................)))))...)))))))....)))))............................................................ (-13.75 = -14.83 +   1.08)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:56:53 2011