Locus 7004

Sequence ID X_DroMel_CAF1
Location 17,544,319 – 17,544,469
Length 150
Max. P 0.933291
window11443 window11444

overview

Window 3

Location 17,544,319 – 17,544,435
Length 116
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 87.48
Mean single sequence MFE -24.27
Consensus MFE -20.56
Energy contribution -21.62
Covariance contribution 1.06
Combinations/Pair 1.04
Mean z-score -1.44
Structure conservation index 0.85
SVM decision value 0.12
SVM RNA-class probability 0.592959
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 17544319 116 - 22224390
UUGUUAACACCAGAAACCAGUAAAGAAACUUUAUUUUGCACCUUACAUACGCG--UGUGUGUGUGCGUGCGCGUAUAUUUAAUUCUGGUGUUUUGUAUUAUUUUUAAAUCACGAACUC--
.....((((((((((....((((((........)))))).......(((((((--..(((....)))..)))))))......))))))))))..........................-- ( -31.80)
>DroSec_CAF1 36435 105 - 1
UUGUUAUCACCCGAAACCAGUAAAGAAACUUUAUUUUGCACCUUACAU------------GUGUGCGUGCGCGUAUAUUUAAUUCUGGUGUUUUGUAUUAUUUUUAAAUCACGA-CUC--
.......................(((((...(((...(((((......------------(((((((....)))))))........)))))...)))...))))).........-...-- ( -15.44)
>DroSim_CAF1 25952 107 - 1
UUGUUAUCACCCGAAACCAGUAAAGAAACUUUAUUUUGCACCUUACAU------------GUGUGCGUGCGCGUAUAUUUAAUUCUGGGGUUUUGUAUUAUUUUUAAAUCUUAA-AUCGU
...........(((((((.((((((........)))))).((......------------(((((((....)))))))........)))))))))...................-..... ( -18.24)
>DroYak_CAF1 33245 117 - 1
UUGUUAUCACCAGAAACCAGUAAAGAAACUUUAUUUUGCACCUUACAUACGCGCGCGUGUGUGUGUGUGUGCGUAUAUUUUAUUCUGGUGUUUUGUAUUAUUUUUAAAUCACGA-CUC--
.......((((((((...(((((((...)))))))..((((..((((((((((....)))))))))).))))..........))))))))........................-...-- ( -31.60)
>consensus
UUGUUAUCACCAGAAACCAGUAAAGAAACUUUAUUUUGCACCUUACAU____________GUGUGCGUGCGCGUAUAUUUAAUUCUGGUGUUUUGUAUUAUUUUUAAAUCACGA_CUC__
.......((((((((...(((((((...)))))))..((((..(((((((((....))))))))).))))............)))))))).............................. (-20.56 = -21.62 +   1.06)

alignment

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secondary structure

Postscript

dotplot

Postscript

Window 4

Location 17,544,357 – 17,544,469
Length 112
Sequences 4
Columns 117
Reading direction forward
Mean pairwise identity 87.32
Mean single sequence MFE -21.01
Consensus MFE -16.84
Energy contribution -17.40
Covariance contribution 0.56
Combinations/Pair 1.04
Mean z-score -2.21
Structure conservation index 0.80
SVM decision value 1.23
SVM RNA-class probability 0.933291
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 17544357 112 + 22224390
AAAUAUACGCGCACGCACACACACA--CGCGUAUGUAAGGUGCAAAAUAAAGUUUCUUUACUGGUUUCUGGUGUUAACAAC---AACAAAAAACAUGAAUAACUAAAGAAGAAACCG
..(((((((((..............--)))))))))...............((((((((..(((((..(.(((((......---.......))))).)..)))))..)))))))).. ( -24.16)
>DroSec_CAF1 36472 105 + 1
AAAUAUACGCGCACGCACAC------------AUGUAAGGUGCAAAAUAAAGUUUCUUUACUGGUUUCGGGUGAUAACAACAACAACAAAAAACGUGAAUAACUAAAGAAGAAACCG
........((((..(((...------------.)))...))))........((((((((..((((((((.((....................)).)))..)))))..)))))))).. ( -19.15)
>DroSim_CAF1 25991 105 + 1
AAAUAUACGCGCACGCACAC------------AUGUAAGGUGCAAAAUAAAGUUUCUUUACUGGUUUCGGGUGAUAACAACAACAACAAAAAACGUGAAUAACUAAAGAAGAAACCG
........((((..(((...------------.)))...))))........((((((((..((((((((.((....................)).)))..)))))..)))))))).. ( -19.15)
>DroYak_CAF1 33282 115 + 1
AAAUAUACGCACACACACACACACGCGCGCGUAUGUAAGGUGCAAAAUAAAGUUUCUUUACUGGUUUCUGGUGAUAACAACAAA--AAAAAAACAUGAAUAACUAAAGAAGAAACCA
........((((......(((.(((....))).)))...))))........((((((((..(((((..(.(((...........--.......))).)..)))))..)))))))).. ( -21.57)
>consensus
AAAUAUACGCGCACGCACAC____________AUGUAAGGUGCAAAAUAAAGUUUCUUUACUGGUUUCGGGUGAUAACAACAACAACAAAAAACAUGAAUAACUAAAGAAGAAACCG
........((((.(..(((.((........)).)))..)))))........((((((((..((((((((.((....................)).)))..)))))..)))))))).. (-16.84 = -17.40 +   0.56)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:27:52 2006