Locus 2852

Sequence ID 2R_DroMel_CAF1
Location 9,843,010 – 9,843,182
Length 172
Max. P 0.740543
window4717 window4718

overview

Window 7

Location 9,843,010 – 9,843,117
Length 107
Sequences 6
Columns 113
Reading direction forward
Mean pairwise identity 79.94
Mean single sequence MFE -36.25
Consensus MFE -24.97
Energy contribution -26.42
Covariance contribution 1.45
Combinations/Pair 1.11
Mean z-score -1.17
Structure conservation index 0.69
SVM decision value -0.01
SVM RNA-class probability 0.526709
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 9843010 107 + 20766785
------CAGAAUCCGAUGUUGGGACGAUCGGCUGGUCAGCAGCACAAGUCCAGCAUUUCCGUGACCAUUUCCAGCAGCGAGGCCGUGGUCACCAUUGCACCACAACCGCCAGC
------...........((((((((.....((((.....))))....)))).(((.....((((((((..((........))..))))))))...)))....))))....... ( -32.60)
>DroVir_CAF1 25142 96 + 1
------------GCGCAGCUGCUGCGU---CCGGCACAGCAGCACAAGUCGAGCAUAUCGGUGACCAUAUCCAGCAGCGAGGCGGUGGUCACCAUUGCGCCACAGCCGCCG--
------------((((((((((((.(.---....).)))))))................(((((((((..((........))..)))))))))..)))))...........-- ( -40.40)
>DroGri_CAF1 26969 102 + 1
------CCACAGUCACAGCUGCAUCGU---CCUGCACAGCAGCACAAGUCGAGCAUAUCGGUGACCAUAUCCAGCAGUGAGGCAGUCGUCACAAUUGCACCACAGCCGCCG--
------.....(((((.(((((.....---........)))))......(((.....))))))))........((.(((..(((((.......)))))..))).)).....-- ( -26.72)
>DroSec_CAF1 2124 107 + 1
------CAGAACCCGCUGCUGGGACGAUCGACUGGUCAGCAGCACAAGUCCAGCAUUUCGGUGACCAUUUCCAGCAGCGAGGCAGUGGUCACCAUUGCACCACAACCGCCAGC
------.......(((((((((((.((....((((.(..........).))))....))(....)...))))))))))).(((.(((((((....)).)))))....)))... ( -37.30)
>DroEre_CAF1 2361 107 + 1
------CAGAAUCAGCUUCUGGGACGAUCGGCUGGCCAGCAGCACAAGUCCAGCAUUUCGGUGACCAUUUCCAGCAGCGAGGCAGUGGUCACCAUUGCUCCACAGCCGCCGGC
------(((((.....)))))...((..((((((...((((((.........)).....((((((((((.((........)).))))))))))..))))...)))))).)).. ( -40.80)
>DroYak_CAF1 2252 113 + 1
CCGACUCAGAACCAGCUGCUGGGACGAUCUUCUGGCCAGCAGCACAAGUCCAGCAUUUCGGUGACCAUUUCCAGCAGCGAGGCAGUGGUCACCAUUGCUCCACAACCCCCAGC
..............((((((((..((......)).))))))))....((..((((....((((((((((.((........)).))))))))))..))))..)).......... ( -39.70)
>consensus
______CAGAACCCGCUGCUGGGACGAUCGCCUGGACAGCAGCACAAGUCCAGCAUUUCGGUGACCAUUUCCAGCAGCGAGGCAGUGGUCACCAUUGCACCACAACCGCCAGC
..............((.((((((((......(((.....))).....)))).(((....(((((((((..((........))..)))))))))..)))....)))).)).... (-24.97 = -26.42 +   1.45)

alignment

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secondary structure

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dotplot

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Window 8

Location 9,843,083 – 9,843,182
Length 99
Sequences 6
Columns 99
Reading direction forward
Mean pairwise identity 77.21
Mean single sequence MFE -34.85
Consensus MFE -17.81
Energy contribution -20.78
Covariance contribution 2.98
Combinations/Pair 1.17
Mean z-score -1.97
Structure conservation index 0.51
SVM decision value 0.45
SVM RNA-class probability 0.740543
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 9843083 99 + 20766785
AGGCCGUGGUCACCAUUGCACCACAACCGCCAGCUGGUAAGCCCAGCAAGCUGCAGUUGUCCCUGGGAAAGUCGGAGGCCCUCAGUUGCAGUACACCCA
.(((.(((((((....)).)))))....))).(((((.....)))))..((((((..((.((((((.....)))).))....))..))))))....... ( -33.40)
>DroGri_CAF1 27039 84 + 1
AGGCAGUCGUCACAAUUGCACCACAGCCGCCG---------CCCAGCAAGCCGCUGCUCAGC------AAACUGGAACUCCUCAGCUGCAGUGCACCCA
.(((....))).....(((((..((((.((.(---------..((((.....))))..).))------.....((....))...))))..))))).... ( -23.30)
>DroSec_CAF1 2197 99 + 1
AGGCAGUGGUCACCAUUGCACCACAACCGCCAGCUGGUAAGCCCAGCAAGCUGCAGUUGACCCUGGGAAAGUCGGAUGCCCUCAGCUGCAGUACACCCA
.(((.(((((((....)).)))))....))).(((((.....)))))..(((((((((((....(((...........))))))))))))))....... ( -38.20)
>DroEre_CAF1 2434 99 + 1
AGGCAGUGGUCACCAUUGCUCCACAGCCGCCGGCUGGCAAGCCGAGCAAGCUGCAGUUGUCCCAGGGAAAGUCCGAGGCCCUCAGCUGCAGUACACCCA
.(((.((((.((....))..)))).)))(((((((....))))).))..((((((((((.((..(((....)))..))....))))))))))....... ( -42.40)
>DroYak_CAF1 2331 99 + 1
AGGCAGUGGUCACCAUUGCUCCACAACCCCCAGCUGGUAAGCCCAGCAAGCUGCAGUUGUCCCAGGGAAAGACCGAGGCCCGCAGCUGCAGCACACCCA
.((((((((...))))))))............(((((.....)))))..(((((((((((((..((......))..))...)))))))))))....... ( -41.90)
>DroAna_CAF1 2439 84 + 1
AGGCGGUGGUCAGCAUAGCUCCUCAGCCCCCGGCCGGUAAGCCAAGCAAACUGCAG---------------ACUGACGCCCUCAGCUGCAGUGCACCCA
..(.((((....((...(((..((.(((...))).))..)))...))..(((((((---------------.((((.....))))))))))).))))). ( -29.90)
>consensus
AGGCAGUGGUCACCAUUGCACCACAACCGCCAGCUGGUAAGCCCAGCAAGCUGCAGUUGUCCC_GGGAAAGUCGGAGGCCCUCAGCUGCAGUACACCCA
..((((((.....)))))).............(((((....)).)))..((((((((((.....(((...........))).))))))))))....... (-17.81 = -20.78 +   2.98)

alignment

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secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:41:10 2006