Locus 12718

Sequence ID dm3.chrX
Location 1,710,783 – 1,710,858
Length 75
Max. P 0.993439
window17488 window17489

overview

Window 8

Location 1,710,783 – 1,710,858
Length 75
Sequences 5
Columns 75
Reading direction forward
Mean pairwise identity 75.47
Shannon entropy 0.44658
G+C content 0.60368
Mean single sequence MFE -32.98
Consensus MFE -19.36
Energy contribution -20.64
Covariance contribution 1.28
Combinations/Pair 1.42
Mean z-score -2.59
Structure conservation index 0.59
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.61
SVM RNA-class probability 0.993439
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 1710783 75 + 22422827
GACAAACAGGAGCUUGGGGAGACCCAGGCCACGGAGCUUGUGCAGCUCCUGCUCGGUUACCGGGUAUCUGUGUGG
..((.(((((.(((((((....)))))))...((((((.....))))))(((((((...)))))))))))).)). ( -37.90, z-score =  -3.53, R)
>droPer1.super_11 880756 68 + 2846995
GACUCACCGAAGCCUCAGAGGACGUGAAGUCUGUGGACUGUGCACGUCGUCCUUAG-------CCAUCUGUGAGG
..(((((.((.((....((.((((((.((((....))))...)))))).))....)-------)..)).))))). ( -27.20, z-score =  -2.24, R)
>droEre2.scaffold_4644 1691576 71 + 2521924
GACAAACAGGAGU----GGAGACCCAAGCCAUGGAGCUUGUGCAGCUCCUGCUCGGUUACCGGCUACCUGUGUGG
..((.((((((((----((.((((..(((...((((((.....)))))).))).)))).)).))).))))).)). ( -30.00, z-score =  -2.37, R)
>droSec1.super_10 1505631 75 + 3036183
GACAAACAGGAGCUUGGGGAGACCCAGGCCACGGAGCUUGUGCAGCUCCUGCUCGGUUGCCGGCUAUCUGUGUGG
..((.(((((.(((((((....)))))))...((((((.....)))))).((.(((...)))))..))))).)). ( -34.70, z-score =  -2.13, R)
>droSim1.chrX 1203918 75 + 17042790
GACAAACAGGAGCUUGGGGAGACCCAGGCCACGGAGCUUGUGCAGCUCAUGCUCGGUUGCCGGCUAUCUGUGUGG
..((.(((((((((((((....))))(((.((.((((.((.......)).)))).)).))))))).))))).)). ( -35.10, z-score =  -2.66, R)
>consensus
GACAAACAGGAGCUUGGGGAGACCCAGGCCACGGAGCUUGUGCAGCUCCUGCUCGGUUACCGGCUAUCUGUGUGG
..((.(((((.(((((((....)))))))..(((...(((.((((...)))).)))...)))....))))).)). (-19.36 = -20.64 +   1.28)

alignment

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secondary structure

Postscript

dotplot

Postscript

Window 9

Location 1,710,783 – 1,710,858
Length 75
Sequences 5
Columns 75
Reading direction reverse
Mean pairwise identity 75.47
Shannon entropy 0.44658
G+C content 0.60368
Mean single sequence MFE -27.98
Consensus MFE -13.28
Energy contribution -15.04
Covariance contribution 1.76
Combinations/Pair 1.33
Mean z-score -1.98
Structure conservation index 0.47
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.65
SVM RNA-class probability 0.774364
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 1710783 75 - 22422827
CCACACAGAUACCCGGUAACCGAGCAGGAGCUGCACAAGCUCCGUGGCCUGGGUCUCCCCAAGCUCCUGUUUGUC
.......((.((((((...(((....((((((.....)))))).))).)))))).))..(((((....))))).. ( -26.70, z-score =  -1.54, R)
>droPer1.super_11 880756 68 - 2846995
CCUCACAGAUGG-------CUAAGGACGACGUGCACAGUCCACAGACUUCACGUCCUCUGAGGCUUCGGUGAGUC
.(((((.((.((-------((..(((.((((((...((((....)))).)))))).)))..)))))).))))).. ( -27.80, z-score =  -2.51, R)
>droEre2.scaffold_4644 1691576 71 - 2521924
CCACACAGGUAGCCGGUAACCGAGCAGGAGCUGCACAAGCUCCAUGGCUUGGGUCUCC----ACUCCUGUUUGUC
.((.(((((.((..((...((((((.((((((.....))))))...))))))....))----.))))))).)).. ( -31.40, z-score =  -3.16, R)
>droSec1.super_10 1505631 75 - 3036183
CCACACAGAUAGCCGGCAACCGAGCAGGAGCUGCACAAGCUCCGUGGCCUGGGUCUCCCCAAGCUCCUGUUUGUC
....((((((((((((...))).)).((((((.....))))))(..((.((((....)))).))..)))))))). ( -29.20, z-score =  -1.79, R)
>droSim1.chrX 1203918 75 - 17042790
CCACACAGAUAGCCGGCAACCGAGCAUGAGCUGCACAAGCUCCGUGGCCUGGGUCUCCCCAAGCUCCUGUUUGUC
....((((((((((((...))).))..(((((.....))))).(..((.((((....)))).))..)))))))). ( -24.80, z-score =  -0.90, R)
>consensus
CCACACAGAUAGCCGGCAACCGAGCAGGAGCUGCACAAGCUCCGUGGCCUGGGUCUCCCCAAGCUCCUGUUUGUC
....................((((((((((((.....((.((((.....)))).)).....)))))))))))).. (-13.28 = -15.04 +   1.76)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 01:07:31 2011