Locus 6688

Sequence ID 2L_DroMel_CAF1
Location 18,723,849 – 18,724,049
Length 200
Max. P 0.995155
window10672 window10673

overview

Window 2

Location 18,723,849 – 18,723,969
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 95.25
Mean single sequence MFE -30.78
Consensus MFE -27.02
Energy contribution -26.86
Covariance contribution -0.16
Combinations/Pair 1.11
Mean z-score -2.12
Structure conservation index 0.88
SVM decision value 2.55
SVM RNA-class probability 0.995155
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 18723849 120 - 22407834
AAUAUAUGCACACGGGGAGAUAGUGAACUAUCGAGUUUGGCCUGGUCUAAAAGGCAGCUGGUGGGAACGGAGAAAGGUCGAGAGAAUGAUUAGCUCGAGCAAAGUUUAGAAACAAGCUCA
..................(((((....)))))(((((((((((........))))((((..((....))......(.(((((..(.....)..))))).)..))))......))))))). ( -31.10)
>DroSec_CAF1 16467 120 - 1
AAUAUAUGCGCACGGGGAGAUAGUGAACUAUCGAGUUUGGCCUGGUCUAAAAGGCAGCUGGUGGGAACAGAGAAAGGUCGAGAAAAUGAUUAGCUCGAGCAAAGUUUAGAAAUAAGCUCA
.........((.((((..(((((....)))))...((((((((.(((.....)))..(((.......)))....))))))))...........)))).))..((((((....)))))).. ( -32.20)
>DroSim_CAF1 14955 120 - 1
AAUAUAUGCACACGGGGAGAUAGUGAACUAUCGAGUUUGGCCUGGUCUAAAAGGCAGCUGGUGGGAACAGAGAAAGGUCGAGAGAAUGAUUAGCUCGAGCAAAGUUUAGAAAUAAGCUCA
......(((.(((.((..(((((....))))).......((((........))))..)).)))......(((..((.((....))....))..)))..))).((((((....)))))).. ( -32.00)
>DroEre_CAF1 16638 119 - 1
AAUAUAUGCACACGGAGAGAUAGUGAACUAUCGAGUUUGGUCUGGUCUAAAAGGCAGCUGGCGGGAACAGAGAAAGGUCGAGAAAAUGAUUACCUCGAGCAAAGUUUAGAAA-AAACUCA
..................(((((....)))))((((((..(((((.((.........(((.......))).....(.(((((...........))))).)..)).)))))..-)))))). ( -28.60)
>DroYak_CAF1 16684 120 - 1
AAUAUAUGCACACGGGGAGAUAGUGAACUAUCGAGUUUGGUCUGGUCUAAAAGGCAGCUUGUGGGAACAGAGAAAGGUCGAGAAAAUGAUUACCUCGAGCAAAGUUUAGAAAAAAACUCG
......(((...(((((.(((((....)))))((.(((..((((.(((..(((....)))...))).))))..))).)).............))))).))).(((((......))))).. ( -30.00)
>consensus
AAUAUAUGCACACGGGGAGAUAGUGAACUAUCGAGUUUGGCCUGGUCUAAAAGGCAGCUGGUGGGAACAGAGAAAGGUCGAGAAAAUGAUUAGCUCGAGCAAAGUUUAGAAAUAAGCUCA
..................(((((....)))))(((((((((((........))))((((...(....).......(.(((((...........))))).)..))))......))))))). (-27.02 = -26.86 +  -0.16)

alignment

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secondary structure

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dotplot

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Window 3

Location 18,723,929 – 18,724,049
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 98.67
Mean single sequence MFE -25.90
Consensus MFE -25.44
Energy contribution -25.28
Covariance contribution -0.16
Combinations/Pair 1.04
Mean z-score -1.24
Structure conservation index 0.98
SVM decision value 0.33
SVM RNA-class probability 0.691378
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 18723929 120 - 22407834
AAAUGGAUCGCCUCGGCAAAAAUAAAAACAAACACAAGCGCCGAAUGCUAAAUAGCUCCAGAUAUGCUAUUAGUACUUAUAAUAUAUGCACACGGGGAGAUAGUGAACUAUCGAGUUUGG
.........((....))...........(((((.....(.(((..(((..((((((.........)))))).(((.......)))..)))..))).).(((((....)))))..))))). ( -25.70)
>DroSec_CAF1 16547 120 - 1
AAAUGGAUCGCCUCGGCAAAAAUAAAAACAAACACAAGCGCCGAAUGCUAAAUAGCUCCAGAUAUGCUAUUAGUACUUAUAAUAUAUGCGCACGGGGAGAUAGUGAACUAUCGAGUUUGG
.........((....))...........(((((....((((.((.((((((.((((.........)))))))))).)).........)))).......(((((....)))))..))))). ( -26.50)
>DroSim_CAF1 15035 120 - 1
AAAUGGAUCGCCUCGGCAAAAAUAAAAACAAACACAUGCGCCGAAUGCUAAAUAGCUCCAGAUAUGCUAUUAGUACUUAUAAUAUAUGCACACGGGGAGAUAGUGAACUAUCGAGUUUGG
.........((....))...........(((((.....(.(((..(((..((((((.........)))))).(((.......)))..)))..))).).(((((....)))))..))))). ( -25.70)
>DroEre_CAF1 16717 120 - 1
AAAUGGAUCGCCUCGGCAAAAAUAAAAACAAACACAAGCGCCGAAUGCUAAAUAGCUCCAGAUAUGCUAUUAGUACUUAUAAUAUAUGCACACGGAGAGAUAGUGAACUAUCGAGUUUGG
.........((....))...........(((((.....(.(((..(((..((((((.........)))))).(((.......)))..)))..))).).(((((....)))))..))))). ( -24.10)
>DroYak_CAF1 16764 120 - 1
AAAUGGAUCGCCUCGGCAAAAAUAAAAACAAACACAAGCGCCGAAUGCUAAAUAGCUCCAGAUAUGCUAUUAGUAUUUAUAAUAUAUGCACACGGGGAGAUAGUGAACUAUCGAGUUUGG
.........((....))...........(((((.....(.(((..(((..((((((.........)))))).((((.......)))))))..))).).(((((....)))))..))))). ( -27.50)
>consensus
AAAUGGAUCGCCUCGGCAAAAAUAAAAACAAACACAAGCGCCGAAUGCUAAAUAGCUCCAGAUAUGCUAUUAGUACUUAUAAUAUAUGCACACGGGGAGAUAGUGAACUAUCGAGUUUGG
.........((....))...........(((((.....(.(((..(((..((((((.........)))))).(((.......)))..)))..))).).(((((....)))))..))))). (-25.44 = -25.28 +  -0.16)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:17:28 2006