Locus 2431

Sequence ID 3R_DroMel_CAF1
Location 6,769,472 – 6,769,616
Length 144
Max. P 0.984588
window3964 window3965

overview

Window 4

Location 6,769,472 – 6,769,576
Length 104
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 82.73
Mean single sequence MFE -30.47
Consensus MFE -23.81
Energy contribution -25.18
Covariance contribution 1.38
Combinations/Pair 1.07
Mean z-score -2.52
Structure conservation index 0.78
SVM decision value 1.98
SVM RNA-class probability 0.984588
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6769472 104 + 27905053
AAGCAAUUAAGCGGCUUACAAAUGCCUGCCAUUGCAG--------------UGGGUAUCUAAAUAUCCCAGGACCAAGCACAGAUACAGAUACUCACACACACACUC--UCGCACAUGUG
..(((((...(((((........))).)).))))).(--------------(((((((((...((((....(......)...)))).))))))))))...((((...--.......)))) ( -25.50)
>DroSec_CAF1 33757 114 + 1
AAGCAAUUAAGCGGCUUACAAAUGCCAGACAUUGCAGUAUGUAGCCAAGUGUGGGUAUCUGAAUAUCCCAGGACCAAGCACAGAUACAGAUACUCACACACA--C----UCACACAUGGG
..((......))((((.(((..(((........)))...)))))))..(((((((((((((..((((....(......)...)))))))))))))))))...--(----(((....)))) ( -33.90)
>DroEre_CAF1 18629 120 + 1
AAGCAAUUAAGCGGCUUACAAAUGCCAGCCAUUGCAGAAUGUAGCUCAGUGGGGGUAUCUGAAUAUCCCAGGACCAACUACAGAUACAGAUACUCUCUCACACACACACGCACACAUGUG
..(((((...(((((........))).)).))))).............(.(((((((((((..((((..((......))...))))))))))))))).).....((((........)))) ( -30.70)
>DroYak_CAF1 30711 120 + 1
AAGCAAUUAAGCGGCUUACAAAUGCCAGCCAUUGCCAAAUGUAGCCGAGUGUGGGUAUCUGAAUAUCCCAGGACCAACUACAGAUACAGAUACUCCUACACACUUACACACACACAUGUG
..(((((...(((((........))).)).)))))....(((((..((((((..(((((((....((....)).......)))))))..)))))))))))......((((......)))) ( -31.80)
>consensus
AAGCAAUUAAGCGGCUUACAAAUGCCAGCCAUUGCAGAAUGUAGCC_AGUGUGGGUAUCUGAAUAUCCCAGGACCAACCACAGAUACAGAUACUCACACACACACAC__UCACACAUGUG
..(((((...(((((........))).)).))))).............(((((((((((((..((((...............)))))))))))))))))..................... (-23.81 = -25.18 +   1.38)

alignment

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secondary structure

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dotplot

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Window 5

Location 6,769,509 – 6,769,616
Length 107
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 84.40
Mean single sequence MFE -28.98
Consensus MFE -19.93
Energy contribution -21.31
Covariance contribution 1.38
Combinations/Pair 1.08
Mean z-score -1.88
Structure conservation index 0.69
SVM decision value 0.50
SVM RNA-class probability 0.759099
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6769509 107 + 27905053
-----------UGGGUAUCUAAAUAUCCCAGGACCAAGCACAGAUACAGAUACUCACACACACACUC--UCGCACAUGUGCAGAGCACAGACAGUUGGUGCAAACAACUCUGACAAGACU
-----------(((((((((...((((....(......)...)))).)))))))))........(((--(.(((....)))))))..((((..((((.......))))))))........ ( -23.60)
>DroSec_CAF1 33797 114 + 1
GUAGCCAAGUGUGGGUAUCUGAAUAUCCCAGGACCAAGCACAGAUACAGAUACUCACACACA--C----UCACACAUGGGCAGAGCACAGACAGUUGGUGCAAACAACUCUCACAAGACU
...(((..(((((((((((((..((((....(......)...))))))))))))))))).((--.----.......)))))........((.(((((.......))))).))........ ( -31.60)
>DroEre_CAF1 18669 120 + 1
GUAGCUCAGUGGGGGUAUCUGAAUAUCCCAGGACCAACUACAGAUACAGAUACUCUCUCACACACACACGCACACAUGUGGAAAGCACAGACAGUUGGUGCAAACAACUCUGACAAGACU
...(((..(.(((((((((((..((((..((......))...))))))))))))))).).....((((........))))...))).((((..((((.......))))))))........ ( -30.20)
>DroYak_CAF1 30751 120 + 1
GUAGCCGAGUGUGGGUAUCUGAAUAUCCCAGGACCAACUACAGAUACAGAUACUCCUACACACUUACACACACACAUGUGGAAAGCACAGACAGUUGGUGCAAACAACUCUGACAAGACU
...((.(((((((((((((((..((((..((......))...))))))))))))....))))))).((((......))))....)).((((..((((.......))))))))........ ( -30.50)
>consensus
GUAGCC_AGUGUGGGUAUCUGAAUAUCCCAGGACCAACCACAGAUACAGAUACUCACACACACACAC__UCACACAUGUGCAAAGCACAGACAGUUGGUGCAAACAACUCUGACAAGACU
........(((((((((((((..((((...............))))))))))))))))).................((((.....))))...(((((.......)))))........... (-19.93 = -21.31 +   1.38)

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 10:35:51 2006