Locus 173

Sequence ID 2R_DroMel_CAF1
Location 1,432,284 – 1,432,444
Length 160
Max. P 0.950141
window393 window394 window395 window396

overview

Window 3

Location 1,432,284 – 1,432,404
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 80.69
Mean single sequence MFE -37.70
Consensus MFE -20.24
Energy contribution -27.18
Covariance contribution 6.94
Combinations/Pair 1.07
Mean z-score -2.25
Structure conservation index 0.54
SVM decision value 0.19
SVM RNA-class probability 0.627977
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 1432284 120 + 20766785
ACGGCGAGGGACCAUCGAUAAUUCAUCCGGCUCCGCUAGCUGAGAGCCAUCCCGAUAAGAAUGUCCAAGACAUAGUGAACAGUGUGCAAAAUGUCUUGAAUAAGGAGAUGGCCUCCAGCU
..((((.(((.((...(((.....))).)))))))))(((((((.((((((((((((....))))((((((((..((.((...)).))..)))))))).....)).)))))))).))))) ( -42.80)
>DroSec_CAF1 50726 120 + 1
ACGGCGAGGGACCAUCGAUAAUCCAUCCGGCUCCGCUAGCUGAGAGCCAUCCCGAUAAGAAUGUCCAAGACAUAGUGAACAGUGUGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
.......((((.....(((.....))).(((((((.....)).))))).))))((((....))))....((((.(....).))))................................... ( -18.20)
>DroEre_CAF1 48833 120 + 1
ACGGCGAAGGACCGUCGAUAAUCCAUCCGGCUCCGCUGGCUGAGAGUCAUCCCGACAAAAAUGUCCAAGACAUAGUGAACAGUGUGCAAAAUGUCUUGAACAAGGAGAUGGCCUCUAGCU
.(((((..(..(((..(((.....))))))..))))))((((((.((((((((((((....))))((((((((..((.((...)).))..)))))))).....)).))))))))).))). ( -42.40)
>DroYak_CAF1 53899 120 + 1
ACGGCGAGGGACCGUCUAUUAUCCAUCCGGCUCCGCUGGCUGAGAGCCAUCCCGACAAGAAUGUUCAAGACAUAGUGAACAGUGUGCAAAAUGUCUUGAAUAAGGAGAUGGCCUCCAGCU
.(((((.(((.(((.............)))))))))))((((((.((((((((........((((((((((((..((.((...)).))..)))))))))))).)).)))))))).)))). ( -47.42)
>consensus
ACGGCGAGGGACCAUCGAUAAUCCAUCCGGCUCCGCUAGCUGAGAGCCAUCCCGACAAGAAUGUCCAAGACAUAGUGAACAGUGUGCAAAAUGUCUUGAAUAAGGAGAUGGCCUCCAGCU
.(((((.(((.(((..(((.....))))))))))))))((((((.((((((((((((....))))((((((((..((.((...)).))..)))))))).....)).))))))))).))). (-20.24 = -27.18 +   6.94)

alignment

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secondary structure

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dotplot

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Window 4

Location 1,432,284 – 1,432,404
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 80.69
Mean single sequence MFE -38.60
Consensus MFE -21.69
Energy contribution -28.25
Covariance contribution 6.56
Combinations/Pair 1.05
Mean z-score -2.09
Structure conservation index 0.56
SVM decision value 0.18
SVM RNA-class probability 0.621970
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 1432284 120 - 20766785
AGCUGGAGGCCAUCUCCUUAUUCAAGACAUUUUGCACACUGUUCACUAUGUCUUGGACAUUCUUAUCGGGAUGGCUCUCAGCUAGCGGAGCCGGAUGAAUUAUCGAUGGUCCCUCGCCGU
(((((..(((((((((..((((((((((((..((.((...)).))..))))))))))......))..)))))))))..))))).((((....((((.(........).))))....)))) ( -44.40)
>DroSec_CAF1 50726 120 - 1
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNCACACUGUUCACUAUGUCUUGGACAUUCUUAUCGGGAUGGCUCUCAGCUAGCGGAGCCGGAUGGAUUAUCGAUGGUCCCUCGCCGU
.......................................((((((........)))))).......(((..(((((((........)))))))((.((((((....)))))).)).))). ( -23.40)
>DroEre_CAF1 48833 120 - 1
AGCUAGAGGCCAUCUCCUUGUUCAAGACAUUUUGCACACUGUUCACUAUGUCUUGGACAUUUUUGUCGGGAUGACUCUCAGCCAGCGGAGCCGGAUGGAUUAUCGACGGUCCUUCGCCGU
.(((((((..((((((......((((((((..((.((...)).))..))))))))((((....)))))))))).)))).)))..((((...((((.(((((......))))))))))))) ( -40.60)
>DroYak_CAF1 53899 120 - 1
AGCUGGAGGCCAUCUCCUUAUUCAAGACAUUUUGCACACUGUUCACUAUGUCUUGAACAUUCUUGUCGGGAUGGCUCUCAGCCAGCGGAGCCGGAUGGAUAAUAGACGGUCCCUCGCCGU
.((((..(((((((((.....(((((((((..((.((...)).))..)))))))))(((....))).)))))))))..))))..((((....((((.(........).))))....)))) ( -46.00)
>consensus
AGCUGGAGGCCAUCUCCUUAUUCAAGACAUUUUGCACACUGUUCACUAUGUCUUGGACAUUCUUAUCGGGAUGGCUCUCAGCCAGCGGAGCCGGAUGGAUUAUCGACGGUCCCUCGCCGU
.(((((..((((((((......((((((((..((.((...)).))..))))))))((((....))))))))))))..)))))..((((....((((.(........).))))....)))) (-21.69 = -28.25 +   6.56)

alignment

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secondary structure

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dotplot

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Window 5

Location 1,432,324 – 1,432,444
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 92.78
Mean single sequence MFE -35.47
Consensus MFE -31.38
Energy contribution -30.83
Covariance contribution -0.55
Combinations/Pair 1.11
Mean z-score -1.99
Structure conservation index 0.88
SVM decision value 0.39
SVM RNA-class probability 0.718710
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 1432324 120 + 20766785
UGAGAGCCAUCCCGAUAAGAAUGUCCAAGACAUAGUGAACAGUGUGCAAAAUGUCUUGAAUAAGGAGAUGGCCUCCAGCUCAGCAAAGAAUAGCUCUGGGGAACUGCUUCUUCCUCUGUU
.(((.((((((((((((....))))((((((((..((.((...)).))..)))))))).....)).))))))((((((...(((........)))))))))............))).... ( -37.00)
>DroEre_CAF1 48873 120 + 1
UGAGAGUCAUCCCGACAAAAAUGUCCAAGACAUAGUGAACAGUGUGCAAAAUGUCUUGAACAAGGAGAUGGCCUCUAGCUCAGCAAAGAACAGCUCCGGGGAACUGCUUCCACCUCUGUU
.(((.((((((((((((....))))((((((((..((.((...)).))..)))))))).....)).))))))))).............(((((....((((((....)))).)).))))) ( -35.60)
>DroYak_CAF1 53939 120 + 1
UGAGAGCCAUCCCGACAAGAAUGUUCAAGACAUAGUGAACAGUGUGCAAAAUGUCUUGAAUAAGGAGAUGGCCUCCAGCUCAGCAAAGAACAACUCCGGCGAACUGCUUCCUCCUCUUUU
.(((.((((((((........((((((((((((..((.((...)).))..)))))))))))).)).)))))))))(((.((.((...((.....))..)))).))).............. ( -33.80)
>consensus
UGAGAGCCAUCCCGACAAGAAUGUCCAAGACAUAGUGAACAGUGUGCAAAAUGUCUUGAAUAAGGAGAUGGCCUCCAGCUCAGCAAAGAACAGCUCCGGGGAACUGCUUCCUCCUCUGUU
.(((.((((((((((((....))))((((((((..((.((...)).))..)))))))).....)).)))))))))............((((((.((....)).))).))).......... (-31.38 = -30.83 +  -0.55)

alignment

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secondary structure

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dotplot

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Window 6

Location 1,432,324 – 1,432,444
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 92.78
Mean single sequence MFE -41.47
Consensus MFE -36.14
Energy contribution -37.70
Covariance contribution 1.56
Combinations/Pair 1.05
Mean z-score -3.05
Structure conservation index 0.87
SVM decision value 1.40
SVM RNA-class probability 0.950141
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 1432324 120 - 20766785
AACAGAGGAAGAAGCAGUUCCCCAGAGCUAUUCUUUGCUGAGCUGGAGGCCAUCUCCUUAUUCAAGACAUUUUGCACACUGUUCACUAUGUCUUGGACAUUCUUAUCGGGAUGGCUCUCA
..(((..((((((..(((((....))))).)))))).))).....(((((((((((..((((((((((((..((.((...)).))..))))))))))......))..)))))))).))). ( -40.70)
>DroEre_CAF1 48873 120 - 1
AACAGAGGUGGAAGCAGUUCCCCGGAGCUGUUCUUUGCUGAGCUAGAGGCCAUCUCCUUGUUCAAGACAUUUUGCACACUGUUCACUAUGUCUUGGACAUUUUUGUCGGGAUGACUCUCA
...((.((..((((((((((....)))))))).))..))...))((((..((((((......((((((((..((.((...)).))..))))))))((((....)))))))))).)))).. ( -41.50)
>DroYak_CAF1 53939 120 - 1
AAAAGAGGAGGAAGCAGUUCGCCGGAGUUGUUCUUUGCUGAGCUGGAGGCCAUCUCCUUAUUCAAGACAUUUUGCACACUGUUCACUAUGUCUUGAACAUUCUUGUCGGGAUGGCUCUCA
..............(((((((.(((((.....))))).)))))))(((((((((((.....(((((((((..((.((...)).))..)))))))))(((....))).)))))))).))). ( -42.20)
>consensus
AACAGAGGAGGAAGCAGUUCCCCGGAGCUGUUCUUUGCUGAGCUGGAGGCCAUCUCCUUAUUCAAGACAUUUUGCACACUGUUCACUAUGUCUUGGACAUUCUUGUCGGGAUGGCUCUCA
..(((..((((((.((((((....)))))))))))).))).....(((((((((((......((((((((..((.((...)).))..))))))))((((....)))))))))))).))). (-36.14 = -37.70 +   1.56)

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 09:31:12 2006