Locus 3611

Sequence ID X_DroMel_CAF1
Location 9,668,679 – 9,668,795
Length 116
Max. P 0.602647
window5910 window5911

overview

Window 0

Location 9,668,679 – 9,668,795
Length 116
Sequences 4
Columns 116
Reading direction forward
Mean pairwise identity 83.76
Mean single sequence MFE -22.83
Consensus MFE -16.35
Energy contribution -17.48
Covariance contribution 1.12
Combinations/Pair 1.27
Mean z-score -1.58
Structure conservation index 0.72
SVM decision value 0.14
SVM RNA-class probability 0.602647
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 9668679 116 + 22224390
UAUUUCGUGAUAUAUAUACAAUAUUUUUAUCGCACAAAAUGCAAUGUUUGAAAGCUAAAAGCAAAUUCACGAGCUCUUUUCGAAUCCUUCGAGAUUUCUUUGCCUCUAUGAACACU
...(((((((.....................(((.....)))..(((((.........)))))...)))))))....((((((.....))))))...................... ( -15.80)
>DroSec_CAF1 4279 114 + 1
--UUUCGUGAUAAAUAUACAAUAUUUUUAUCGCACAAAAUGCAUUGUUUGAAAGCUAGAGGCAAAUUCAUGAGCUCUUUUUGAAUCCUUCGGGAUUUCUUUGCCUCUAUAAACACU
--....((((((((.(((...))).))))))))...........((((((.....((((((((((.....(....).....((((((....)))))).)))))))))))))))).. ( -29.30)
>DroSim_CAF1 17859 116 + 1
UAUUUCGUGAUAAAUAUACAAUAUUUUUAUCGCACAAAAUGCAAUGUUUGAAAGCUAGAGGCAAAUUCAUGAGCUCUUUUUGAAUCCUUCCGGAUUUCUUUGCCUCUAUGAACACU
......((((((((.(((...))).))))))))...........((((((.....((((((((((.....(....).....((((((....)))))).)))))))))))))))).. ( -25.10)
>DroEre_CAF1 11156 111 + 1
UA-----UUAUAUAUGCGCCAUAUUUGUAUUACCCAAAAUGCAAUGUUCGAAAUCUAAGAGCGAAUUCACGAGGUCAUUUCUAAUCCUGCGGGUUUUCUUUGCCUUUGUGAACACU
..-----.................(((((((......)))))))(((((.........)))))..(((((((((.((.....(((((...))))).....)).))))))))).... ( -21.10)
>consensus
UAUUUCGUGAUAAAUAUACAAUAUUUUUAUCGCACAAAAUGCAAUGUUUGAAAGCUAAAAGCAAAUUCACGAGCUCUUUUCGAAUCCUUCGGGAUUUCUUUGCCUCUAUGAACACU
......((((((((...........))))))))...........((((((.....((((((((((.....(((.....)))((((((....)))))).)))))))))))))))).. (-16.35 = -17.48 +   1.12)

alignment

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secondary structure

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dotplot

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Window 1

Location 9,668,679 – 9,668,795
Length 116
Sequences 4
Columns 116
Reading direction reverse
Mean pairwise identity 83.76
Mean single sequence MFE -24.08
Consensus MFE -18.56
Energy contribution -19.25
Covariance contribution 0.69
Combinations/Pair 1.25
Mean z-score -1.46
Structure conservation index 0.77
SVM decision value -0.00
SVM RNA-class probability 0.531171
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 9668679 116 - 22224390
AGUGUUCAUAGAGGCAAAGAAAUCUCGAAGGAUUCGAAAAGAGCUCGUGAAUUUGCUUUUAGCUUUCAAACAUUGCAUUUUGUGCGAUAAAAAUAUUGUAUAUAUAUCACGAAAUA
.(((....((((((((((....((.(((..(.(((.....))))))).)).))))))))))((...........))....(((((((((....))))))))).....)))...... ( -21.30)
>DroSec_CAF1 4279 114 - 1
AGUGUUUAUAGAGGCAAAGAAAUCCCGAAGGAUUCAAAAAGAGCUCAUGAAUUUGCCUCUAGCUUUCAAACAAUGCAUUUUGUGCGAUAAAAAUAUUGUAUAUUUAUCACGAAA--
.(((....(((((((((((((.(((....)))))).....(....).....))))))))))((...........))....(((((((((....))))))))).....)))....-- ( -25.70)
>DroSim_CAF1 17859 116 - 1
AGUGUUCAUAGAGGCAAAGAAAUCCGGAAGGAUUCAAAAAGAGCUCAUGAAUUUGCCUCUAGCUUUCAAACAUUGCAUUUUGUGCGAUAAAAAUAUUGUAUAUUUAUCACGAAAUA
.(((....(((((((((((((.(((....)))))).....(....).....))))))))))((...........))....(((((((((....))))))))).....)))...... ( -29.90)
>DroEre_CAF1 11156 111 - 1
AGUGUUCACAAAGGCAAAGAAAACCCGCAGGAUUAGAAAUGACCUCGUGAAUUCGCUCUUAGAUUUCGAACAUUGCAUUUUGGGUAAUACAAAUAUGGCGCAUAUAUAA-----UA
.((((((.(((((((((........((.(((.(((....))))))))((((.((.......)).))))....)))).))))).).)))))..(((((...)))))....-----.. ( -19.40)
>consensus
AGUGUUCAUAGAGGCAAAGAAAUCCCGAAGGAUUCAAAAAGAGCUCAUGAAUUUGCCUCUAGCUUUCAAACAUUGCAUUUUGUGCGAUAAAAAUAUUGUAUAUAUAUCACGAAAUA
(((((((.((((((((((..(((((....)))))......(....).....))))))))))......)))))))......(((((((((....))))))))).............. (-18.56 = -19.25 +   0.69)

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 11:03:43 2006