Locus 5618

Sequence ID X_DroMel_CAF1
Location 14,484,590 – 14,484,686
Length 96
Max. P 0.971226
window9130 window9131

overview

Window 0

Location 14,484,590 – 14,484,686
Length 96
Sequences 5
Columns 117
Reading direction forward
Mean pairwise identity 83.33
Mean single sequence MFE -34.80
Consensus MFE -27.40
Energy contribution -30.28
Covariance contribution 2.88
Combinations/Pair 1.11
Mean z-score -2.38
Structure conservation index 0.79
SVM decision value 1.67
SVM RNA-class probability 0.971226
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 14484590 96 + 22224390
UUAGAGGGUUAAUUGCGAGGGUUUAUCCCGGGGUUUCUGGAUUCUGGA---------------------UUCGGGAUUUGGCAAUCCGGACAUUGGACGCGGAAUAUCGCCCUCGAA
...((((((...(((((.(((.....))).(((((.(..(((((((..---------------------..)))))))..).)))))..........)))))......))))))... ( -34.80)
>DroSec_CAF1 9944 89 + 1
UUAGAGGGUUAAUUGCGAGGGUUUAUCCCGGGGUUUCUGGA----------------------------UUCGGGAUAUAGCAAUCCGGACAUUGGAAGCGGAAUAUCGCCCUCGAA
...((((((..(((.(..(((.....)))...(((((..(.----------------------------.((.((((......)))).))..)..)))))).)))...))))))... ( -30.80)
>DroSim_CAF1 16434 96 + 1
UUAGAGGGUUAAUUGCGAGGGUUUAUCCCGGGGUUUCUGGAUUCAGGA---------------------UUCGGGAUAUAGCAAUCCGGACAUUGGAAGCGGAAUAUCGCCCUCGAA
...((((((..(((.((...((((((((((((..(((((....)))))---------------------))))))))).)))..((((.....))))..)).)))...))))))... ( -32.50)
>DroEre_CAF1 8275 96 + 1
UUAGAGGGUUAAUUGCGAGGGUUUAUCCCGGGGUUUCUGGAUUCAGAA---------------------CUUAGAAUUCGGCAAUCCGGACAUCGGACGCGGCAUAUCGCCCUCGAA
...((((((....(((..(((.....))).(((((.((((((((....---------------------....)))))))).)))))..............)))....))))))... ( -33.80)
>DroYak_CAF1 13280 117 + 1
UUAGAGGGUUAAUUGCGAGGGUUUAUCCCGGGGUUUCUGGAUUCAGGAUUCUGAAUUCAGGAUUCAAGAUUUGGAAUUCGGCAAUCCGGACAUUGGUAGCGGAAUAUCGCCCUCGAA
...((((((...((((..(((.....)))..(..(((..((((..((((((((....))))))))..))))..)))..).))))((((.((....))..)))).....))))))... ( -42.10)
>consensus
UUAGAGGGUUAAUUGCGAGGGUUUAUCCCGGGGUUUCUGGAUUCAGGA_____________________UUCGGGAUUUGGCAAUCCGGACAUUGGAAGCGGAAUAUCGCCCUCGAA
...((((((..(((.((.(((.....))).(((((.((((((((.(((((((((((.....))))))))))).)))))))).)))))............)).)))...))))))... (-27.40 = -30.28 +   2.88)

alignment

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secondary structure

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dotplot

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Window 1

Location 14,484,590 – 14,484,686
Length 96
Sequences 5
Columns 117
Reading direction reverse
Mean pairwise identity 83.33
Mean single sequence MFE -25.70
Consensus MFE -18.86
Energy contribution -19.86
Covariance contribution 1.00
Combinations/Pair 1.00
Mean z-score -2.26
Structure conservation index 0.73
SVM decision value 1.21
SVM RNA-class probability 0.931624
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 14484590 96 - 22224390
UUCGAGGGCGAUAUUCCGCGUCCAAUGUCCGGAUUGCCAAAUCCCGAA---------------------UCCAGAAUCCAGAAACCCCGGGAUAAACCCUCGCAAUUAACCCUCUAA
..((((((...(((((((..((.....((.(((((...........))---------------------))).)).....)).....)))))))..))))))............... ( -22.70)
>DroSec_CAF1 9944 89 - 1
UUCGAGGGCGAUAUUCCGCUUCCAAUGUCCGGAUUGCUAUAUCCCGAA----------------------------UCCAGAAACCCCGGGAUAAACCCUCGCAAUUAACCCUCUAA
..((((((.........((.(((.......)))..))..(((((((..----------------------------...........)))))))..))))))............... ( -23.62)
>DroSim_CAF1 16434 96 - 1
UUCGAGGGCGAUAUUCCGCUUCCAAUGUCCGGAUUGCUAUAUCCCGAA---------------------UCCUGAAUCCAGAAACCCCGGGAUAAACCCUCGCAAUUAACCCUCUAA
..((((((.........((.(((.......)))..))..(((((((..---------------------..(((....)))......)))))))..))))))............... ( -25.50)
>DroEre_CAF1 8275 96 - 1
UUCGAGGGCGAUAUGCCGCGUCCGAUGUCCGGAUUGCCGAAUUCUAAG---------------------UUCUGAAUCCAGAAACCCCGGGAUAAACCCUCGCAAUUAACCCUCUAA
...(((((.....(((.(((((((.....)))).))).((........---------------------(((((....))))).....(((.....)))))))).....)))))... ( -26.60)
>DroYak_CAF1 13280 117 - 1
UUCGAGGGCGAUAUUCCGCUACCAAUGUCCGGAUUGCCGAAUUCCAAAUCUUGAAUCCUGAAUUCAGAAUCCUGAAUCCAGAAACCCCGGGAUAAACCCUCGCAAUUAACCCUCUAA
..((((((...(((((((.........((.(((((...........))))).))...(((.((((((....)))))).)))......)))))))..))))))............... ( -30.10)
>consensus
UUCGAGGGCGAUAUUCCGCUUCCAAUGUCCGGAUUGCCAAAUCCCGAA_____________________UCCUGAAUCCAGAAACCCCGGGAUAAACCCUCGCAAUUAACCCUCUAA
...(((((.((((((........))))))..((((((..................................(((....))).......(((.....)))..))))))..)))))... (-18.86 = -19.86 +   1.00)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:52:29 2006