Locus 6391

Sequence ID 3L_DroMel_CAF1
Location 17,116,846 – 17,116,959
Length 113
Max. P 0.977328
window10233 window10234

overview

Window 3

Location 17,116,846 – 17,116,959
Length 113
Sequences 4
Columns 119
Reading direction forward
Mean pairwise identity 89.80
Mean single sequence MFE -24.08
Consensus MFE -18.98
Energy contribution -19.23
Covariance contribution 0.25
Combinations/Pair 1.12
Mean z-score -2.26
Structure conservation index 0.79
SVM decision value 1.06
SVM RNA-class probability 0.908182
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17116846 113 + 23771897
UUUUCCUCGUCUUUCUGCCACUGGUUUUCCUUCGCCACAGCU------UCAGAUUCGGCUUCUCAGCGCAGCUCAACGCACAUUUUUAUGAGUUCAUUCGCUGCGCUCCUUUUAAUACU
........(((..((((....((((........)))).....------.))))...))).....((((((((.....((.(((....))).))......))))))))............ ( -23.50)
>DroSec_CAF1 1306 113 + 1
UUUUCCUCGCCUCUCUGCCACUGGUUUUCCAUUGCUUCAGCU------UGAGAUUCGGCUUCUCAGCGCAGCUCAACGCACAUUUUUAUGAGUUCAUUCGCUGCGCUCCUUUUAAUACU
........(((((((.((((.(((....))).)).....)).------.))))...))).....((((((((.....((.(((....))).))......))))))))............ ( -26.80)
>DroEre_CAF1 1178 119 + 1
UUUUCCUCGCUUUUCUGCCACUGGUUUUCCUUUGCUUCAGCUUCGACUUCAGAUUCGACUUCUCAGCGCAGCUCAACGCACAUUUUUAUGAGUUCAUUCGCUGAGCUGCUUUUUAUACU
........(((...(((.((..((....))..))...)))..((((........))))......)))((((((((.((...((((....)))).....)).)))))))).......... ( -22.10)
>DroYak_CAF1 1137 113 + 1
CUUUCCUCGCUUUUCUGCCACCGGGUUUCCUUUGCCUCAGCU------UUAGAUUCGGCUUCUUAGCGCAGCUCAACGCACAUUUUUAUGAGUUCAUUCGCUGCGCUCCUUUUUAUACU
........((......))..((((((((.....((....)).------..))))))))......((((((((.....((.(((....))).))......))))))))............ ( -23.90)
>consensus
UUUUCCUCGCCUUUCUGCCACUGGUUUUCCUUUGCCUCAGCU______UCAGAUUCGGCUUCUCAGCGCAGCUCAACGCACAUUUUUAUGAGUUCAUUCGCUGCGCUCCUUUUAAUACU
........(((..((((.....((....))...((....))........))))...))).....((((((((.....((.(((....))).))......))))))))............ (-18.98 = -19.23 +   0.25)

alignment

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secondary structure

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dotplot

Postscript

Window 4

Location 17,116,846 – 17,116,959
Length 113
Sequences 4
Columns 119
Reading direction reverse
Mean pairwise identity 89.80
Mean single sequence MFE -30.22
Consensus MFE -24.85
Energy contribution -24.72
Covariance contribution -0.13
Combinations/Pair 1.08
Mean z-score -2.75
Structure conservation index 0.82
SVM decision value 1.79
SVM RNA-class probability 0.977328
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17116846 113 - 23771897
AGUAUUAAAAGGAGCGCAGCGAAUGAACUCAUAAAAAUGUGCGUUGAGCUGCGCUGAGAAGCCGAAUCUGA------AGCUGUGGCGAAGGAAAACCAGUGGCAGAAAGACGAGGAAAA
............((((((((.((((....(((....)))..))))..))))))))......((...(((..------..((((.((...((....)).)).))))..)))...)).... ( -31.30)
>DroSec_CAF1 1306 113 - 1
AGUAUUAAAAGGAGCGCAGCGAAUGAACUCAUAAAAAUGUGCGUUGAGCUGCGCUGAGAAGCCGAAUCUCA------AGCUGAAGCAAUGGAAAACCAGUGGCAGAGAGGCGAGGAAAA
............((((((((.((((....(((....)))..))))..)))))))).....(((...((((.------.((....))..(((....)))......)))))))........ ( -30.50)
>DroEre_CAF1 1178 119 - 1
AGUAUAAAAAGCAGCUCAGCGAAUGAACUCAUAAAAAUGUGCGUUGAGCUGCGCUGAGAAGUCGAAUCUGAAGUCGAAGCUGAAGCAAAGGAAAACCAGUGGCAGAAAAGCGAGGAAAA
..........(((((((((((.....((..........)).)))))))))))(((..((..(((....)))..))..))).....((..((....))..))((......))........ ( -30.80)
>DroYak_CAF1 1137 113 - 1
AGUAUAAAAAGGAGCGCAGCGAAUGAACUCAUAAAAAUGUGCGUUGAGCUGCGCUAAGAAGCCGAAUCUAA------AGCUGAGGCAAAGGAAACCCGGUGGCAGAAAAGCGAGGAAAG
.((.........((((((((.((((....(((....)))..))))..))))))))..(..((((.......------.((....))...(....).))))..)......))........ ( -28.30)
>consensus
AGUAUAAAAAGGAGCGCAGCGAAUGAACUCAUAAAAAUGUGCGUUGAGCUGCGCUGAGAAGCCGAAUCUGA______AGCUGAAGCAAAGGAAAACCAGUGGCAGAAAAGCGAGGAAAA
.((.........((((((((.((((....(((....)))..))))..)))))))).....((((..............((....))...((....))..))))......))........ (-24.85 = -24.72 +  -0.13)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:17:14 2006