Locus 5845

Sequence ID X_DroMel_CAF1
Location 15,105,529 – 15,105,674
Length 145
Max. P 0.985671
window9483 window9484

overview

Window 3

Location 15,105,529 – 15,105,634
Length 105
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 60.37
Mean single sequence MFE -31.62
Consensus MFE -14.32
Energy contribution -15.24
Covariance contribution 0.92
Combinations/Pair 1.47
Mean z-score -2.00
Structure conservation index 0.45
SVM decision value 1.29
SVM RNA-class probability 0.938627
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 15105529 105 - 22224390
ACAUCAUUGGCGGAAACGGAAGCGGAAGCGGAAACGGUAACGGUAACGGUGAUGGUAACGGUAGUGGCAACACCGCCGGAA---------------ACGUCAGUAGCGGCACCCCCAGCA
.........(((....)((..((....))(....)(((..((.((....(((((....(((..(((....)))..)))...---------------.))))).)).))..))).)).)). ( -38.60)
>DroPse_CAF1 36177 87 - 1
------------GUGAAGGAAGCGGAGACGGAAAUGGUAACCAUAACUGG------AACAAUAACGGCAACAAUAAUGCAA---------------GCCACAUAACUGGCAUCUCGAACA
------------((...(((.(((....(((..((((...))))..))).------.........(....).....)))..---------------((((......)))).)))...)). ( -15.60)
>DroSec_CAF1 18275 99 - 1
ACAUCAUUGGCGGAAACGGAAGCGGAGGCGGAAACGGU------AACGGUGUUGUAAGCGGUAGUGGCAACACCGCCGGAA---------------ACGCCAGUGGCGUCACCUCCAGCA
..........((....))...(((((((((....))((------.((((((((.....(((..(((....)))..)))..)---------------))))).)).))....))))).)). ( -40.20)
>DroYak_CAF1 24546 114 - 1
GCAUCAUUGGCGGAAACGGAAACGGAGGCGGAAACGGUAACGGUAACGGU------AACGGCAGUGGCAACAUUGCUGGUGGUGGUGGUGCAAGUGGUGCAAGUGUUGGCGCCACCAGCA
(((((((((.((....((....((..(.((....)).)..))....))..------..((((((((....)))))))).)).)))))))))..(((((((........)))))))..... ( -47.60)
>DroPer_CAF1 64099 87 - 1
------------GUGAAGGAAGCGGAGACGGAAAUGGUAACCAUAACUGG------AACAAUAACGGCAACAAUAAUGCAA---------------GCCACAUAUCUGGCAUCUCGAACA
------------((...(((.(((....)(((.(((....(((....)))------.........(((.............---------------))).))).))).)).)))...)). ( -16.12)
>consensus
_CAUCAUUGGCGGAAACGGAAGCGGAGGCGGAAACGGUAACCAUAACGGU______AACGGUAGUGGCAACAAUGCUGGAA_______________GCGACAGUACUGGCACCUCCAGCA
.......................(((((((....))......................((((((((....)))))))).................................))))).... (-14.32 = -15.24 +   0.92)

alignment

Postscript

secondary structure

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dotplot

Postscript

Window 4

Location 15,105,554 – 15,105,674
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 80.17
Mean single sequence MFE -42.97
Consensus MFE -30.55
Energy contribution -30.00
Covariance contribution -0.55
Combinations/Pair 1.17
Mean z-score -2.57
Structure conservation index 0.71
SVM decision value 2.01
SVM RNA-class probability 0.985671
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 15105554 120 - 22224390
AACGGCGAUGGAAUGAGCAGCGCUGGGAGCCAGAGCGGCAACAUCAUUGGCGGAAACGGAAGCGGAAGCGGAAACGGUAACGGUAACGGUGAUGGUAACGGUAGUGGCAACACCGCCGGA
..(((((.((.......)).)))))...(((.....)))..((((((((.((....))....((..(.((....)).)..))....))))))))....(((..(((....)))..))).. ( -45.80)
>DroSec_CAF1 18300 111 - 1
---GGCGACGGAAUGAGCAGCGCCGGGAGCCAGAGCGGCAACAUCAUUGGCGGAAACGGAAGCGGAGGCGGAAACGGU------AACGGUGUUGUAAGCGGUAGUGGCAACACCGCCGGA
---((((((.(.....(((((((((...(((...(((....)........((....))...))...)))(....)...------..)))))))))...).)).(((....)))))))... ( -43.20)
>DroYak_CAF1 24586 108 - 1
A------GUGGCAUAAGCAGCGCCGGCAGCCAGAGCGGCAGCAUCAUUGGCGGAAACGGAAACGGAGGCGGAAACGGUAACGGUAACGGU------AACGGCAGUGGCAACAUUGCUGGU
.------((.((....)).))((((((.(((.....))).))........((....))....((..(.((....)).)..))....))))------..((((((((....)))))))).. ( -39.90)
>consensus
A__GGCGAUGGAAUGAGCAGCGCCGGGAGCCAGAGCGGCAACAUCAUUGGCGGAAACGGAAGCGGAGGCGGAAACGGUAACGGUAACGGUG_UG__AACGGUAGUGGCAACACCGCCGGA
....................(((((...((((((..(....).))..)))).....((....))....((....))..........))))).......((((.(((....))).)))).. (-30.55 = -30.00 +  -0.55)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:57:44 2006