Locus 8412

Sequence ID X_DroMel_CAF1
Location 20,884,131 – 20,884,324
Length 193
Max. P 0.951906
window13819 window13820 window13821 window13822

overview

Window 9

Location 20,884,131 – 20,884,244
Length 113
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 92.27
Mean single sequence MFE -40.38
Consensus MFE -31.65
Energy contribution -33.65
Covariance contribution 2.00
Combinations/Pair 1.00
Mean z-score -2.01
Structure conservation index 0.78
SVM decision value 0.48
SVM RNA-class probability 0.751985
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 20884131 113 + 22224390
AAUCCGCGGCAAUGUCCGACG-------ACCGACUGGCGACCGGCGACUGUUGCAAAUCGAAACGAUUCGCUGGAUCCGCUGGAUUCGCCAGCAAAACCUGCCCCGGAUCACAAUUUGUC
.(((((.((((..(((....)-------)).(.(((((((((((((......((.(((((...))))).))......))))))..))))))))......)))).)))))........... ( -41.90)
>DroSec_CAF1 4185 120 + 1
AAUCCGCGGCAAUGUCCGACGACCGACGACCGACUGGCGACCGGCGACUGUUGCAAAUCGAAACGAUUCGCUGGAUCCGCUGGAUUCGCCAGCAAAACCUGCCCCGGAUCACAAUUUGUC
.(((((.((((.((((........))))...(.(((((((((((((......((.(((((...))))).))......))))))..))))))))......)))).)))))........... ( -43.10)
>DroSim_CAF1 4787 113 + 1
AAUCCGCGGCAAUGUCCGACG-------ACCGACUGGCGACCGGCGACUGUUGCAAAUCGAAACGAUUCGCUGGAUCCGCUGGAUUCGCCAGCAAAACCUGCCCCGGAUCACAAUUUGUC
.(((((.((((..(((....)-------)).(.(((((((((((((......((.(((((...))))).))......))))))..))))))))......)))).)))))........... ( -41.90)
>DroYak_CAF1 5019 104 + 1
AAUCCGCGGCAAUGUCCGAUG-------ACCGACUGGCGACCGGCGACUGUUGCAAAUCGAAACGAUUCGCUGGAUCC---------GCCAGCAAAACCUGCACCGGAUCACAAUUUGUC
.(((((..(((..(((....)-------)).(.((((((.(((((((.((((.........))))..)))))))...)---------))))))......)))..)))))........... ( -34.60)
>consensus
AAUCCGCGGCAAUGUCCGACG_______ACCGACUGGCGACCGGCGACUGUUGCAAAUCGAAACGAUUCGCUGGAUCCGCUGGAUUCGCCAGCAAAACCUGCCCCGGAUCACAAUUUGUC
.(((((.((((.....((............)).(((((((((((((......((.(((((...))))).))......))))))..))))))).......)))).)))))........... (-31.65 = -33.65 +   2.00)

alignment

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secondary structure

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Window 0

Location 20,884,131 – 20,884,244
Length 113
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 92.27
Mean single sequence MFE -47.55
Consensus MFE -41.00
Energy contribution -41.75
Covariance contribution 0.75
Combinations/Pair 1.00
Mean z-score -2.26
Structure conservation index 0.86
SVM decision value 1.42
SVM RNA-class probability 0.951906
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 20884131 113 - 22224390
GACAAAUUGUGAUCCGGGGCAGGUUUUGCUGGCGAAUCCAGCGGAUCCAGCGAAUCGUUUCGAUUUGCAACAGUCGCCGGUCGCCAGUCGGU-------CGUCGGACAUUGCCGCGGAUU
..........((((((.(((((.....((((((((..((.((((.....((((((((...)))))))).....)))).))))))))))..((-------(....))).))))).)))))) ( -49.60)
>DroSec_CAF1 4185 120 - 1
GACAAAUUGUGAUCCGGGGCAGGUUUUGCUGGCGAAUCCAGCGGAUCCAGCGAAUCGUUUCGAUUUGCAACAGUCGCCGGUCGCCAGUCGGUCGUCGGUCGUCGGACAUUGCCGCGGAUU
..........((((((.(((((..((((((((.....))))))))(((.((((((((...))))))))....(.((((((..(((....)))..)))).)).))))..))))).)))))) ( -51.30)
>DroSim_CAF1 4787 113 - 1
GACAAAUUGUGAUCCGGGGCAGGUUUUGCUGGCGAAUCCAGCGGAUCCAGCGAAUCGUUUCGAUUUGCAACAGUCGCCGGUCGCCAGUCGGU-------CGUCGGACAUUGCCGCGGAUU
..........((((((.(((((.....((((((((..((.((((.....((((((((...)))))))).....)))).))))))))))..((-------(....))).))))).)))))) ( -49.60)
>DroYak_CAF1 5019 104 - 1
GACAAAUUGUGAUCCGGUGCAGGUUUUGCUGGC---------GGAUCCAGCGAAUCGUUUCGAUUUGCAACAGUCGCCGGUCGCCAGUCGGU-------CAUCGGACAUUGCCGCGGAUU
..........(((((((.((((((...((((((---------((.....((((((((...)))))))).....)))))))).))).(((.(.-------...).)))..)))).)))))) ( -39.70)
>consensus
GACAAAUUGUGAUCCGGGGCAGGUUUUGCUGGCGAAUCCAGCGGAUCCAGCGAAUCGUUUCGAUUUGCAACAGUCGCCGGUCGCCAGUCGGU_______CGUCGGACAUUGCCGCGGAUU
..........((((((.(((((((...((((((((.......(....).((((((((...)))))))).....)))))))).))).(((.(...........).)))..)))).)))))) (-41.00 = -41.75 +   0.75)

alignment

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secondary structure

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dotplot

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Window 1

Location 20,884,164 – 20,884,284
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 95.00
Mean single sequence MFE -41.35
Consensus MFE -35.59
Energy contribution -36.40
Covariance contribution 0.81
Combinations/Pair 1.03
Mean z-score -2.21
Structure conservation index 0.86
SVM decision value 0.94
SVM RNA-class probability 0.886029
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 20884164 120 - 22224390
AUAAAUAAAUAACAUAAUCAAGAGGCUUGCCCGGGCGUCGGACAAAUUGUGAUCCGGGGCAGGUUUUGCUGGCGAAUCCAGCGGAUCCAGCGAAUCGUUUCGAUUUGCAACAGUCGCCGG
.....................(((((((((((.((.((((.(.....).)))))).))))))))))).(((((((((((...))))...((((((((...)))))))).....))))))) ( -44.00)
>DroSec_CAF1 4225 120 - 1
AUAAAUAAAUAACAUAAUCAAGAGGCUUGCCCGGGCGUCGGACAAAUUGUGAUCCGGGGCAGGUUUUGCUGGCGAAUCCAGCGGAUCCAGCGAAUCGUUUCGAUUUGCAACAGUCGCCGG
.....................(((((((((((.((.((((.(.....).)))))).))))))))))).(((((((((((...))))...((((((((...)))))))).....))))))) ( -44.00)
>DroSim_CAF1 4820 120 - 1
AUAAAUAAAUAACAUAAUCAAGAGGCUUGCCCGGGCGUCGGACAAAUUGUGAUCCGGGGCAGGUUUUGCUGGCGAAUCCAGCGGAUCCAGCGAAUCGUUUCGAUUUGCAACAGUCGCCGG
.....................(((((((((((.((.((((.(.....).)))))).))))))))))).(((((((((((...))))...((((((((...)))))))).....))))))) ( -44.00)
>DroYak_CAF1 5052 111 - 1
AUAAAUAAAUAACAUAAUCAAGAGGUUUCCCCGGGCGUCGGACAAAUUGUGAUCCGGUGCAGGUUUUGCUGGC---------GGAUCCAGCGAAUCGUUUCGAUUUGCAACAGUCGCCGG
............((.((((....((.....))..((..((((((.....)).))))..)).)))).))(((((---------((.....((((((((...)))))))).....))))))) ( -33.40)
>consensus
AUAAAUAAAUAACAUAAUCAAGAGGCUUGCCCGGGCGUCGGACAAAUUGUGAUCCGGGGCAGGUUUUGCUGGCGAAUCCAGCGGAUCCAGCGAAUCGUUUCGAUUUGCAACAGUCGCCGG
.....................(((((((((((.((.((((.(.....).)))))).))))))))))).(((((((.......(....).((((((((...)))))))).....))))))) (-35.59 = -36.40 +   0.81)

alignment

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secondary structure

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dotplot

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Window 2

Location 20,884,204 – 20,884,324
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 95.00
Mean single sequence MFE -32.34
Consensus MFE -29.31
Energy contribution -29.68
Covariance contribution 0.37
Combinations/Pair 1.07
Mean z-score -1.56
Structure conservation index 0.91
SVM decision value 0.24
SVM RNA-class probability 0.648831
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 20884204 120 - 22224390
ACGCGCGGCAAUAACAUUAAACAUUAACGAGCAUGGCUAAAUAAAUAAAUAACAUAAUCAAGAGGCUUGCCCGGGCGUCGGACAAAUUGUGAUCCGGGGCAGGUUUUGCUGGCGAAUCCA
.(((.((((...................((..(((.................)))..))..(((((((((((.((.((((.(.....).)))))).))))))))))))))))))...... ( -35.13)
>DroSec_CAF1 4265 120 - 1
ACGCGCGGCAAUAACAUUAAACAUUAACGAGCAUGUCUAAAUAAAUAAAUAACAUAAUCAAGAGGCUUGCCCGGGCGUCGGACAAAUUGUGAUCCGGGGCAGGUUUUGCUGGCGAAUCCA
.(((.((((...................((..((((...............))))..))..(((((((((((.((.((((.(.....).)))))).))))))))))))))))))...... ( -35.26)
>DroSim_CAF1 4860 120 - 1
ACGCGCGGCAAUAACAUUAAACAUUAACGAGCAUGGCUAAAUAAAUAAAUAACAUAAUCAAGAGGCUUGCCCGGGCGUCGGACAAAUUGUGAUCCGGGGCAGGUUUUGCUGGCGAAUCCA
.(((.((((...................((..(((.................)))..))..(((((((((((.((.((((.(.....).)))))).))))))))))))))))))...... ( -35.13)
>DroYak_CAF1 5090 113 - 1
ACGCGCAGCAAUAACAUUAAACAUUAACGAGCAUGGCUAAAUAAAUAAAUAACAUAAUCAAGAGGUUUCCCCGGGCGUCGGACAAAUUGUGAUCCGGUGCAGGUUUUGCUGGC-------
..((.((((((.................((..(((.................)))..))...........((..((..((((((.....)).))))..)).))..))))))))------- ( -23.83)
>consensus
ACGCGCGGCAAUAACAUUAAACAUUAACGAGCAUGGCUAAAUAAAUAAAUAACAUAAUCAAGAGGCUUGCCCGGGCGUCGGACAAAUUGUGAUCCGGGGCAGGUUUUGCUGGCGAAUCCA
.(((.((((...................((..(((.................)))..))..(((((((((((.((.((((.(.....).)))))).))))))))))))))))))...... (-29.31 = -29.68 +   0.37)

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 13:03:24 2006