Locus 5333

Sequence ID dm3.chr2R
Location 19,551,000 – 19,551,125
Length 125
Max. P 0.923535
window7311 window7312

overview

Window 1

Location 19,551,000 – 19,551,097
Length 97
Sequences 5
Columns 117
Reading direction reverse
Mean pairwise identity 63.12
Shannon entropy 0.61091
G+C content 0.42721
Mean single sequence MFE -31.74
Consensus MFE -9.48
Energy contribution -11.20
Covariance contribution 1.72
Combinations/Pair 1.43
Mean z-score -2.46
Structure conservation index 0.30
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.30
SVM RNA-class probability 0.923535
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 19551000 97 - 21146708
-------CCUUUGCACA-GGCACUUUAAUCUAUAUGCAGUGU--GACCUUGCUCUUAAAGUAAGGUC--CAAAUUAUUUUGCGAGCUAAG-GUCACGCUUAUUUUGAGCU-------
-------.....((.((-((((..(......)..)))(((((--((((((((((.((((((((....--....)))))))).)))).)))-))))))))....))).)).------- ( -32.70, z-score =  -3.97, R)
>droSec1.super_9 2830555 89 - 3197100
---------------CA-GGCCCUUUAAUCUAGGUGCAGUGU--GACCUUGCUCUCAAAGUAAGGUC--CAAAUUAGUUUGCCAGCUAAG-GUCACGCCUAUCUUGAGCU-------
---------------..-.(((((.......))).)).((((--(((((((((..((((.(((....--....))).))))..))).)))-)))))))............------- ( -28.90, z-score =  -2.47, R)
>droYak2.chr2R 19527282 104 - 21139217
-------CCUUUGCUUA-GGUCCUUUAAGCUGGCUGCAGUGU--GACCUUGCUCUCAAAGUAAGGUC--CAAAUUAUUUUGCGUGCUAUG-GUCACGCUUAGCUUGAGCUGAGGCAU
-------((((.(((((-(((....((((((((((..((..(--(((((((((.....)))))))))--((((....)))).)..))..)-)))).))))))))))))).))))... ( -40.90, z-score =  -3.47, R)
>droEre2.scaffold_4845 20913025 104 - 22589142
-------CCCUUGCAUA-GGCCCUUUAGGCUAGCUGCAGUGU--GACCUUGCUCUUAAAGUAGGGUC--CAAAUUAUUUCGCGAGCUAAG-GUCACGCUUAGCUUGAGCUAAGGCAC
-------.((((((...-((((.....))))(((((.(((((--((((((((((...((((((....--....))))))...)))).)))-)))))))))))))...)).))))... ( -41.40, z-score =  -2.83, R)
>droAna3.scaffold_13266 8184331 110 - 19884421
CCAUUGCCUCUAUCGUAUAACAAUAAAAUCUAAAUUUGUUUUUAAGAACUGACCUUUAGGUAUAAUCGGGAAAUUGGUAAGUAAAUUAAGUACUACCUCUUUAUUUACCA-------
...((.((.........(((.((((((.......)))))).))).((....(((....)))....)))).))..(((((((((((...((......)).)))))))))))------- ( -14.80, z-score =   0.43, R)
>consensus
_______CCCUUGCAUA_GGCCCUUUAAUCUAGAUGCAGUGU__GACCUUGCUCUUAAAGUAAGGUC__CAAAUUAUUUUGCGAGCUAAG_GUCACGCUUAUCUUGAGCU_______
...............................(((((.(((((..((((((((((.((((((((..........)))))))).)))).))).)))))))))))))............. ( -9.48 = -11.20 +   1.72)

alignment

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secondary structure

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dotplot

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Window 2

Location 19,551,032 – 19,551,125
Length 93
Sequences 5
Columns 117
Reading direction reverse
Mean pairwise identity 54.97
Shannon entropy 0.73007
G+C content 0.40394
Mean single sequence MFE -19.98
Consensus MFE -8.06
Energy contribution -8.14
Covariance contribution 0.08
Combinations/Pair 1.36
Mean z-score -1.15
Structure conservation index 0.40
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.82
SVM RNA-class probability 0.825836
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 19551032 93 - 21146708
-------------------GCUAACUUUUGCCAUGCCAAACUCCAAUCCUUUGCACA-GGCACUUUAAUCUAUAUGCAGUGU--GACCUUGCUCUUAAAGUAAGGUC--CAAAUUAU
-------------------.........((((.(((.(((.........))))))..-)))).................((.--(((((((((.....)))))))))--))...... ( -18.70, z-score =  -1.28, R)
>droSec1.super_9 2830587 74 - 3197100
-------------------------------------UGAUUUC-AUGCCAAACUCA-GGCCCUUUAAUCUAGGUGCAGUGU--GACCUUGCUCUCAAAGUAAGGUC--CAAAUUAG
-------------------------------------.((((..-..(((.......-))).....)))).........((.--(((((((((.....)))))))))--))...... ( -18.20, z-score =  -1.64, R)
>droYak2.chr2R 19527321 93 - 21139217
-------------------GCUUUUUUCGUCCAAGCCAAACUCCAAUCCUUUGCUUA-GGUCCUUUAAGCUGGCUGCAGUGU--GACCUUGCUCUCAAAGUAAGGUC--CAAAUUAU
-------------------..............(((((.........(((......)-))..........)))))....((.--(((((((((.....)))))))))--))...... ( -21.71, z-score =  -1.52, R)
>droEre2.scaffold_4845 20913064 93 - 22589142
-------------------GCUUUUUUUAUCCAUGCCAAACUCCAAUCCCUUGCAUA-GGCCCUUUAGGCUAGCUGCAGUGU--GACCUUGCUCUUAAAGUAGGGUC--CAAAUUAU
-------------------...............................(((((..-((((.....))))...)))))((.--(((((((((.....)))))))))--))...... ( -21.80, z-score =  -0.64, R)
>droAna3.scaffold_13266 8184364 117 - 19884421
GUUUGAUAUAAAUAAGUCCAAUUCACCCUGAUAUGAUAAGCCAUUGCCUCUAUCGUAUAACAAUAAAAUCUAAAUUUGUUUUUAAGAACUGACCUUUAGGUAUAAUCGGGAAAUUGG
.................((((((..(((..((((((((.((....))...)))))))).........(((((((...((((....)))).....)))))))......))).)))))) ( -19.50, z-score =  -0.68, R)
>consensus
___________________GCUUUUUUCUGCCAUGCCAAACUCCAAUCCCUUGCAUA_GGCCCUUUAAUCUAGAUGCAGUGU__GACCUUGCUCUUAAAGUAAGGUC__CAAAUUAU
...............................................................................((...(((((((((.....)))))))))..))...... ( -8.06 =  -8.14 +   0.08)

alignment

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secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:46:14 2011