Locus 5195

Sequence ID 3L_DroMel_CAF1
Location 14,316,865 – 14,316,996
Length 131
Max. P 0.717973
window8223 window8224

overview

Window 3

Location 14,316,865 – 14,316,964
Length 99
Sequences 6
Columns 114
Reading direction forward
Mean pairwise identity 86.30
Mean single sequence MFE -22.63
Consensus MFE -18.76
Energy contribution -18.26
Covariance contribution -0.50
Combinations/Pair 1.21
Mean z-score -1.94
Structure conservation index 0.83
SVM decision value 0.39
SVM RNA-class probability 0.717973
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 14316865 99 + 23771897
ACUAACCGCCACUUAUAACUAUUAU-----UUUAAGCAACGUGCAGCGAUGAGGCAACAAUUAAUUUU-CAACCGCCUUUCGCUGACGCAGACAUAAAAAAA--AGC-------
.........................-----..........(((((((((.(((((.............-.....))))))))))).))).............--...------- ( -19.17)
>DroSec_CAF1 141662 106 + 1
ACUAGCCGCCACUUAUAACUAUUAU-----UUUAAGCAACGUGCAGCGAUGAGGCAACAAUUAAUUUU-CAACCGCCUUUCGCUGACGCAGACAUGAAAAAA--AGCAGACACA
.((.((.((.....(((.....)))-----.....))...(((((((((.(((((.............-.....))))))))))).))).............--.))))..... ( -20.97)
>DroSim_CAF1 142313 106 + 1
ACUAGCCGCCACUUAUAACUAUUAU-----UUUAAGCAACGUGCAGCGAUGAGGCAACAAUUAAUUUG-CAACCGCCUUUCGCUGACGCAGACAUAAAAAAA--AGCAGGCACA
....(((((..((((..........-----..))))....(((((((((.(((((..(((.....)))-.....))))))))))).))).............--.)).)))... ( -26.20)
>DroEre_CAF1 141953 113 + 1
ACUAACCGCCACUUAUAACUAUUAUGUUAUAUUAAGCAACGUGCAGCGAUGAGGCAACAAUUAUUUUU-CAACGGCCUUUCGCUGAUGCAGACAAAAAAAAACAAACAAGCACA
.......((....((((((......))))))....))...(((((((((.(((((.............-.....))))))))))..((....))...............)))). ( -23.67)
>DroYak_CAF1 146166 108 + 1
ACUAACCGCCACUUAUAACUAUUAU-----UUUAAGCAACGUGCAGCGAUGAGGCAACAAUUAUUUUU-CAACCGCCUUUCGCUGACGCAGACACAAAAAAACUAGCAAGCGCG
......(((..((((..........-----..))))....(((((((((.(((((.............-.....))))))))))).)))....................))).. ( -21.67)
>DroAna_CAF1 135497 106 + 1
ACUAACCGCCACUUAUUACUAUUAU-----UUUAAGCAACGUGCAGCGAUGAGGCAACAAUUAUUGCUGGCACCGCCUCUCGUUGUUGCAGACACAACAAAAUU-GCA--CUCC
.........................-----.....((((..((((((((((((((((......)))).(((...))).))))))))))))(......)....))-)).--.... ( -24.10)
>consensus
ACUAACCGCCACUUAUAACUAUUAU_____UUUAAGCAACGUGCAGCGAUGAGGCAACAAUUAAUUUU_CAACCGCCUUUCGCUGACGCAGACAUAAAAAAA__AGCA_GCACA
........................................(((((((((.(((((...................))))))))))).)))......................... (-18.76 = -18.26 +  -0.50)

alignment

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secondary structure

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dotplot

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Window 4

Location 14,316,897 – 14,316,996
Length 99
Sequences 5
Columns 116
Reading direction forward
Mean pairwise identity 84.06
Mean single sequence MFE -20.96
Consensus MFE -18.79
Energy contribution -18.63
Covariance contribution -0.16
Combinations/Pair 1.07
Mean z-score -1.48
Structure conservation index 0.90
SVM decision value 0.14
SVM RNA-class probability 0.602977
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 14316897 99 + 23771897
AACGUGCAGCGAUGAGGCAACAAUUAAUUUUCAACCGCCUUUCGCUGACGCAGACAUAAAAAAA--AGC-----------GUUAA----AAAAUCACUCUUAAGUUCUUUUACUUU
...(((((((((.(((((..................)))))))))))((((.............--.))-----------))...----.....)))....((((......)))). ( -19.71)
>DroSec_CAF1 141694 110 + 1
AACGUGCAGCGAUGAGGCAACAAUUAAUUUUCAACCGCCUUUCGCUGACGCAGACAUGAAAAAA--AGCAGACACAGAC-GUUAA---AAAAAUCACUUUAAAGUUCUUUUACUUU
...(((((((((.(((((..................))))))))))).)))..........(((--((........(((-.((((---(........))))).))))))))..... ( -20.57)
>DroSim_CAF1 142345 110 + 1
AACGUGCAGCGAUGAGGCAACAAUUAAUUUGCAACCGCCUUUCGCUGACGCAGACAUAAAAAAA--AGCAGGCACAGAC-GUUAA---AAAAAUCACUUUAAAGUUCUUUUACUUU
...(((((((((.(((((..(((.....))).....))))))))))).)))..........(((--((........(((-.((((---(........))))).))))))))..... ( -21.00)
>DroEre_CAF1 141990 116 + 1
AACGUGCAGCGAUGAGGCAACAAUUAUUUUUCAACGGCCUUUCGCUGAUGCAGACAAAAAAAAACAAACAAGCACAGACAGUUAAAAAAAAAAUUACUUAUAUACUUUUUCACUUU
...(((((((((.(((((..................))))))))))..((....))...............))))......................................... ( -17.17)
>DroYak_CAF1 146198 116 + 1
AACGUGCAGCGAUGAGGCAACAAUUAUUUUUCAACCGCCUUUCGCUGACGCAGACACAAAAAAACUAGCAAGCGCGGACAGUUAAAGAAAAAAUCAUUUAAAAGUUUUUUUAUUUC
...(((((((((.(((((..................))))))))))).)))......(((((((((.((....))......(((((((.....)).))))).)))))))))..... ( -26.37)
>consensus
AACGUGCAGCGAUGAGGCAACAAUUAAUUUUCAACCGCCUUUCGCUGACGCAGACAUAAAAAAA__AGCAAGCACAGAC_GUUAA___AAAAAUCACUUUAAAGUUCUUUUACUUU
...(((((((((.(((((..................))))))))))).)))................................................................. (-18.79 = -18.63 +  -0.16)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:44:16 2006