Locus 7531

Sequence ID 3L_DroMel_CAF1
Location 20,229,282 – 20,229,419
Length 137
Max. P 0.989149
window12240 window12241 window12242

overview

Window 0

Location 20,229,282 – 20,229,379
Length 97
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 73.59
Mean single sequence MFE -32.47
Consensus MFE -23.24
Energy contribution -23.13
Covariance contribution -0.11
Combinations/Pair 1.06
Mean z-score -1.79
Structure conservation index 0.72
SVM decision value 2.15
SVM RNA-class probability 0.989149
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 20229282 97 - 23771897
GCAGAUGCGG-----------------------GAUUUAAGCUGGCCAAGAGUUCAACUGGCCGGCAACAGCCUUUCCACCCCCUUUCGCCCGCCUUGCUGUAGUAAAACUAGCAGCAGA
......((((-----------------------(....(((..(((((..........)))))(((....)))..........)))...))))).(((((((((.....)).))))))). ( -31.40)
>DroSim_CAF1 121 90 - 1
GCAG------------------------------AUUUAAGCUGGCCAAGAGUUCAACUGGCCGGCAACAGCCUUUCCACCCCCUUUCGUCCGCCUGGCUGUAGUAAAACUAGCAGCAGA
((((------------------------------.((((.((((((((..........)))))))).((((((.......................))))))..)))).)).))...... ( -26.50)
>DroYak_CAF1 102 116 - 1
GCAGAAUUGAGAUUAAUUCGCUGCGAAUUGUUAGGUUUACGCUGGCCAAGGCUUCAACUGGCCGGCAAUAGCCUUUCCACCCCCUUUCG----CCUGGCUAUAGUAAUACUAGCAGCAGA
...((((((....)))))).((((....((((((..((((((((((((.(.......))))))))).((((((................----...)))))).))))..)))))))))). ( -39.51)
>consensus
GCAGA___G________________________GAUUUAAGCUGGCCAAGAGUUCAACUGGCCGGCAACAGCCUUUCCACCCCCUUUCG_CCGCCUGGCUGUAGUAAAACUAGCAGCAGA
((......................................((((((((..........)))))))).((((((.......................))))))..........))...... (-23.24 = -23.13 +  -0.11)

alignment

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secondary structure

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dotplot

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Window 1

Location 20,229,322 – 20,229,419
Length 97
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 72.11
Mean single sequence MFE -29.80
Consensus MFE -22.82
Energy contribution -24.27
Covariance contribution 1.45
Combinations/Pair 1.05
Mean z-score -1.18
Structure conservation index 0.77
SVM decision value 0.89
SVM RNA-class probability 0.874524
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 20229322 97 + 23771897
GUGGAAAGGCUGUUGCCGGCCAGUUGAACUCUUGGCCAGCUUAAAUC-----------------------CCGCAUCUGCAUGCUCAAAUCUGUGUGCUGCCUACAUAGAUUGAUAUUGA
((((...(((....)))((((((........))))))..........-----------------------)))).....((...((((.((((((((.....))))))))))))...)). ( -30.30)
>DroSim_CAF1 161 90 + 1
GUGGAAAGGCUGUUGCCGGCCAGUUGAACUCUUGGCCAGCUUAAAU------------------------------CUGCAUGCUCAAAUCUGUGUGCUGCCUACAUAGAUUGACAUUGA
(..((..(((....)))((((((........))))))........)------------------------------)..)(((.((((.((((((((.....)))))))))))))))... ( -29.90)
>DroYak_CAF1 138 116 + 1
GUGGAAAGGCUAUUGCCGGCCAGUUGAAGCCUUGGCCAGCGUAAACCUAACAAUUCGCAGCGAAUUAAUCUCAAUUCUGCUUGCCUAAGUCUGUGUGCUGCCU----AGAUUGAUAUUGG
..((...(((....)))((((((........))))))........))...(((((.((((((((((......))))).((((....))))......)))))..----.)))))....... ( -29.20)
>consensus
GUGGAAAGGCUGUUGCCGGCCAGUUGAACUCUUGGCCAGCUUAAAUC________________________C___UCUGCAUGCUCAAAUCUGUGUGCUGCCUACAUAGAUUGAUAUUGA
(..((..(((....)))((((((........))))))......................................))..).......((((((((((.....))))))))))........ (-22.82 = -24.27 +   1.45)

alignment

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secondary structure

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dotplot

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Window 2

Location 20,229,322 – 20,229,419
Length 97
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 72.11
Mean single sequence MFE -27.97
Consensus MFE -21.30
Energy contribution -21.63
Covariance contribution 0.33
Combinations/Pair 1.00
Mean z-score -1.30
Structure conservation index 0.76
SVM decision value 1.26
SVM RNA-class probability 0.936763
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 20229322 97 - 23771897
UCAAUAUCAAUCUAUGUAGGCAGCACACAGAUUUGAGCAUGCAGAUGCGG-----------------------GAUUUAAGCUGGCCAAGAGUUCAACUGGCCGGCAACAGCCUUUCCAC
.................((((.......((((((..((((....)))).)-----------------------)))))..((((((((..........))))))))....))))...... ( -26.20)
>DroSim_CAF1 161 90 - 1
UCAAUGUCAAUCUAUGUAGGCAGCACACAGAUUUGAGCAUGCAG------------------------------AUUUAAGCUGGCCAAGAGUUCAACUGGCCGGCAACAGCCUUUCCAC
.................((((.......(((((((......)))------------------------------))))..((((((((..........))))))))....))))...... ( -24.20)
>DroYak_CAF1 138 116 - 1
CCAAUAUCAAUCU----AGGCAGCACACAGACUUAGGCAAGCAGAAUUGAGAUUAAUUCGCUGCGAAUUGUUAGGUUUACGCUGGCCAAGGCUUCAACUGGCCGGCAAUAGCCUUUCCAC
.((((.((...((----((((........).)))))(((.((.((((((....)))))))))))))))))..(((((...((((((((.(.......)))))))))...)))))...... ( -33.50)
>consensus
UCAAUAUCAAUCUAUGUAGGCAGCACACAGAUUUGAGCAUGCAGA___G________________________GAUUUAAGCUGGCCAAGAGUUCAACUGGCCGGCAACAGCCUUUCCAC
.................((((.((.((......)).))..........................................((((((((..........))))))))....))))...... (-21.30 = -21.63 +   0.33)

alignment

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secondary structure

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dotplot

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Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:49:33 2006