Locus 7639

Sequence ID 3R_DroMel_CAF1
Location 20,463,673 – 20,463,867
Length 194
Max. P 0.680156
window12331 window12332 window12333

overview

Window 1

Location 20,463,673 – 20,463,787
Length 114
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 78.62
Mean single sequence MFE -48.13
Consensus MFE -28.71
Energy contribution -29.22
Covariance contribution 0.51
Combinations/Pair 1.41
Mean z-score -1.64
Structure conservation index 0.60
SVM decision value 0.27
SVM RNA-class probability 0.661264
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 20463673 114 + 27905053
CUGUACCAUGGGCCGCGGUGGACGGGGUGAGUUCUUGGCUCCCAAUGGCCAAGGCGUAU------GCUUCGCACCGCGACGCGGAAAGUACGGUCCCAGAGGACCGAUCGCAUUGGGAGC
((((.((((.(....).))))))))............((((((((((((....))((((------..(((((........)))))..))))(((((....))))).....)))))))))) ( -47.20)
>DroVir_CAF1 14552 114 + 1
UUGCACCAUUGGCCUUGGGGGUCGAGGUGAAUUUUUGGCACCUAACGGCCAGGACGUCU------GCUUUGCACCGCGACGCGGAAAAUAAGGUCCUAACGGGCCUAUUGCAUUUGGUGC
..(((((((((((((((((.(((((((.....))))))).))))).))))))....(((------((.((((...)))).))))).....((((((....))))))........)))))) ( -50.30)
>DroGri_CAF1 18144 114 + 1
CUGCACCAUCGGCCUGGGUGGUCGUGGCGAGUUCUUGGCACCCAGUGGCCACGGCGUUU------GUUUGGCACCGCGACGUGGAAAAUAGGGUCCCAAGGGGCCAAUUGCGUUGGGUGC
..(((((..(((((.....)))))((((...(((((((.((((.((..(((((.(((.(------(.....))..))).)))))...)).)))).))))))))))).........))))) ( -47.60)
>DroWil_CAF1 16031 120 + 1
CUGCACCAUUGGUCUUGGUGGCCGAGGUGAAUUCUUGGAACCCAAUGGCCAAGGUGUGUGCUGGUGCUUGGCUCCACGACGUGGAAAGUAUGGACCCAAUGGUCCAAUGGCAUUCGGGGC
..(((((.((((((((((...((((((.....))))))...)))).)))))))))))((.((((((((....(((((...))))).....((((((....))))))..)))).)))).)) ( -50.60)
>DroMoj_CAF1 16519 114 + 1
UUGCACCAUUGGCCUCGGGGGACGAGGCGAGUUCUUAGCACCUAAAGGCCAGGGCGUCU------GCUUGGCACCGCGACGUGGAAAAUAUGGUCCUAAUGGGCCAAUUGCAUUGGGCGC
..((.(((((.((((((.....)))))).))).....(((.......((((((......------.)))))).((((...))))......((((((....))))))..)))...)))).. ( -42.40)
>DroAna_CAF1 13275 114 + 1
CUGGACCAUCGGACGCGGUGGUCUUGGUGAAUUCUUAGCCCCCAAUGGCCAUGGCGAGU------GCUUUGCACCGCGACGUGGAAAAUAGGGUCCCAAGGGACCAAUGGCAUUGGGAGC
(.(((((((((....))))))))).)...........((.(((((((.((((.(((.((------((...)))))))..............(((((....))))).))))))))))).)) ( -50.70)
>consensus
CUGCACCAUUGGCCUCGGUGGUCGAGGUGAAUUCUUGGCACCCAAUGGCCAAGGCGUCU______GCUUGGCACCGCGACGUGGAAAAUAGGGUCCCAAGGGGCCAAUUGCAUUGGGAGC
..((.((...((((..((..(((((((.....)))))))..))...))))....................((.((((...))))......((((((....))))))...))....)).)) (-28.71 = -29.22 +   0.51)

alignment

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secondary structure

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dotplot

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Window 2

Location 20,463,747 – 20,463,867
Length 120
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 82.83
Mean single sequence MFE -43.02
Consensus MFE -31.76
Energy contribution -32.43
Covariance contribution 0.67
Combinations/Pair 1.30
Mean z-score -1.81
Structure conservation index 0.74
SVM decision value 0.30
SVM RNA-class probability 0.680156
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 20463747 120 + 27905053
GCGGAAAGUACGGUCCCAGAGGACCGAUCGCAUUGGGAGCAUUCGCCACGGACAGAUGACAGUUGAUAAGAAUGGGCGCCAGAAUACUAAUGGUUUCCAGGCUGGGAUUGCGCACCAGCU
((((......((((((....)))))).)))).((((..(((.((.((...(((........)))....((..((((.((((.........)))).))))..)))))).)))...)))).. ( -36.30)
>DroVir_CAF1 14626 120 + 1
GCGGAAAAUAAGGUCCUAACGGGCCUAUUGCAUUUGGUGCAUUGGCCACGGACAAAUGGCAGUUGAUCAGAAUGGGCGCCAGAAUGAUGGUGGCCUCCAGGCUCGUGUUGCGCACUAGCU
..(((.....((((((....))))))..(((((...)))))..((((((.(.((..((((.(((.((....)).)))))))...)).).))))))))).((((.(((.....))).)))) ( -45.80)
>DroGri_CAF1 18218 120 + 1
GUGGAAAAUAGGGUCCCAAGGGGCCAAUUGCGUUGGGUGCAUUGGCCACAGACAAAUGGCAGUUGAUUAAAAUGGGCGCCAAAAUGCUGGUGGCCUCCAGGCUGGUGUUGCGCACCAGCU
.((((......(((((....)))))...((((.....))))..((((((((.((..((((.(((.((....)).)))))))...)))).))))))))))((((((((.....)))))))) ( -49.50)
>DroWil_CAF1 16111 120 + 1
GUGGAAAGUAUGGACCCAAUGGUCCAAUGGCAUUCGGGGCAUUGGCCACUGACAAAUGGCAGUUUAUCAGAAUGGGGGCUAAAAUGCUAGUGGCUUCCAGACUUGUGUUUCGCACCAGCU
((((((.((.((((((....))))))...)).)))(..((((.((.(.((((.((((....)))).))))..(((((((((.........)))))))))).)).))))..).)))..... ( -38.10)
>DroMoj_CAF1 16593 120 + 1
GUGGAAAAUAUGGUCCUAAUGGGCCAAUUGCAUUGGGCGCAUUGGCCACUGAUAAAUGGCAGUUGAUCAAAAUGGGCGCCAGAAUAGUGGUGGCCUCCAGGCUGGUGUUGCGCACCAGCU
.((((.....((((((....))))))..(((.......)))..((((((((.....((((.(((.((....)).)))))))......))))))))))))((((((((.....)))))))) ( -50.00)
>DroAna_CAF1 13349 120 + 1
GUGGAAAAUAGGGUCCCAAGGGACCAAUGGCAUUGGGAGCGUUCGCGACAGAAAGAUGACAAUUGAUCAGAAUGGGUGCCAAAAUGCUGGUGGCUUCUAGACUGGUGUUGCGCACCAGCU
...........(((((....)))))..(((((((.(..((....))..).((..(((....)))..))......)))))))....(((((((((.((......))....)).))))))). ( -38.40)
>consensus
GUGGAAAAUAGGGUCCCAAGGGGCCAAUUGCAUUGGGAGCAUUGGCCACAGACAAAUGGCAGUUGAUCAGAAUGGGCGCCAAAAUGCUGGUGGCCUCCAGGCUGGUGUUGCGCACCAGCU
((((..(((.((((((....))))))...((.......)))))..)))).......................(((..((((.........))))..)))((((((((.....)))))))) (-31.76 = -32.43 +   0.67)

alignment

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secondary structure

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dotplot

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Window 3

Location 20,463,747 – 20,463,867
Length 120
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 82.83
Mean single sequence MFE -35.71
Consensus MFE -24.22
Energy contribution -24.53
Covariance contribution 0.31
Combinations/Pair 1.34
Mean z-score -1.80
Structure conservation index 0.68
SVM decision value 0.11
SVM RNA-class probability 0.586199
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 20463747 120 - 27905053
AGCUGGUGCGCAAUCCCAGCCUGGAAACCAUUAGUAUUCUGGCGCCCAUUCUUAUCAACUGUCAUCUGUCCGUGGCGAAUGCUCCCAAUGCGAUCGGUCCUCUGGGACCGUACUUUCCGC
.(((((.........)))))..((((((((((((((((((((...)))............(((((......))))))))))))...)))).)..((((((....))))))...))))).. ( -33.40)
>DroVir_CAF1 14626 120 - 1
AGCUAGUGCGCAACACGAGCCUGGAGGCCACCAUCAUUCUGGCGCCCAUUCUGAUCAACUGCCAUUUGUCCGUGGCCAAUGCACCAAAUGCAAUAGGCCCGUUAGGACCUUAUUUUCCGC
.((....))((...(((.(((((..((((((...((...(((((...............)))))..))...))))))..((((.....)))).))))).)))..(((........))))) ( -35.16)
>DroGri_CAF1 18218 120 - 1
AGCUGGUGCGCAACACCAGCCUGGAGGCCACCAGCAUUUUGGCGCCCAUUUUAAUCAACUGCCAUUUGUCUGUGGCCAAUGCACCCAACGCAAUUGGCCCCUUGGGACCCUAUUUUCCAC
.(((((((.....))))))).((((((((((..(((...(((((...............)))))..)))..))))))......(((((.((.....))...))))).........)))). ( -42.86)
>DroWil_CAF1 16111 120 - 1
AGCUGGUGCGAAACACAAGUCUGGAAGCCACUAGCAUUUUAGCCCCCAUUCUGAUAAACUGCCAUUUGUCAGUGGCCAAUGCCCCGAAUGCCAUUGGACCAUUGGGUCCAUACUUUCCAC
.((((((((....((......))...).)))))))......(..((((..((((((((......))))))))(((((((((.(......).)))))).))).))))..)........... ( -33.10)
>DroMoj_CAF1 16593 120 - 1
AGCUGGUGCGCAACACCAGCCUGGAGGCCACCACUAUUCUGGCGCCCAUUUUGAUCAACUGCCAUUUAUCAGUGGCCAAUGCGCCCAAUGCAAUUGGCCCAUUAGGACCAUAUUUUCCAC
.(((((((.....))))))).((((((((((........(((((...............))))).......))))))..((((.....))))..(((.((....)).))).....)))). ( -37.12)
>DroAna_CAF1 13349 120 - 1
AGCUGGUGCGCAACACCAGUCUAGAAGCCACCAGCAUUUUGGCACCCAUUCUGAUCAAUUGUCAUCUUUCUGUCGCGAACGCUCCCAAUGCCAUUGGUCCCUUGGGACCCUAUUUUCCAC
.(((((((.((..(.........)..)))))))))....(((((.......((((.....))))..........((....))......)))))..(((((....)))))........... ( -32.60)
>consensus
AGCUGGUGCGCAACACCAGCCUGGAAGCCACCAGCAUUCUGGCGCCCAUUCUGAUCAACUGCCAUUUGUCAGUGGCCAAUGCACCCAAUGCAAUUGGCCCAUUGGGACCAUAUUUUCCAC
.(((((((.....))))))).((((((((((..(((...(((((...............)))))..)))..)))))....((.......))...(((.((....)).)))....))))). (-24.22 = -24.53 +   0.31)

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 12:50:55 2006