Locus 6288

Sequence ID 3L_DroMel_CAF1
Location 16,748,240 – 16,748,409
Length 169
Max. P 0.944609
window10086 window10087 window10088

overview

Window 6

Location 16,748,240 – 16,748,351
Length 111
Sequences 3
Columns 111
Reading direction forward
Mean pairwise identity 95.50
Mean single sequence MFE -26.07
Consensus MFE -24.02
Energy contribution -23.80
Covariance contribution -0.22
Combinations/Pair 1.04
Mean z-score -1.80
Structure conservation index 0.92
SVM decision value 0.27
SVM RNA-class probability 0.662318
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 16748240 111 + 23771897
CGGUUUAUAGCAACUGCAUGCGUAGUGCGACAGAGAGUUGCUAUAAAAAUAUAUUGGAACGUCAACAAACAUAUGCCACGAAAGAAAAUAUUCCGAUUCAACGGAAAAUGA
.((((((((((((((...((((.....)).))...))))))))))).......(((.........)))......))).(....)......(((((......)))))..... ( -25.40)
>DroSim_CAF1 1085 111 + 1
CGGUUUAUAGCAACUGCAUGCGUAGUGCGACAGAGAGUUGCUAUAAAAGUAUAUUGGAACGUCAACAAACAUAUGCCACGAAAGAAAAUAUUCCGAUUCGACGGAAUAUGA
.((((((((((((((...((((.....)).))...)))))))))))..((.(.((((....)))).).))....))).(....)...((((((((......)))))))).. ( -29.10)
>DroYak_CAF1 1100 111 + 1
CGCUUUAUAGCAGCUGCAUGCGUAGUGCGACACCGAGUUGCUAUAAAAAUAUAUUGGAACGUCAACAAACAUAUGCCACGAAAGAAAAUAUUCCGAUUCGACGGAACAUGA
...((((((((((((((((.....))))(....).))))))))))))........................((((...(....)......(((((......))))))))). ( -23.70)
>consensus
CGGUUUAUAGCAACUGCAUGCGUAGUGCGACAGAGAGUUGCUAUAAAAAUAUAUUGGAACGUCAACAAACAUAUGCCACGAAAGAAAAUAUUCCGAUUCGACGGAAAAUGA
...((((((((((((...((((.....)).))...))))))))))))......................(((......(....)......(((((......))))).))). (-24.02 = -23.80 +  -0.22)

alignment

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secondary structure

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dotplot

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Window 7

Location 16,748,240 – 16,748,351
Length 111
Sequences 3
Columns 111
Reading direction reverse
Mean pairwise identity 95.50
Mean single sequence MFE -26.60
Consensus MFE -25.61
Energy contribution -26.17
Covariance contribution 0.56
Combinations/Pair 1.03
Mean z-score -1.89
Structure conservation index 0.96
SVM decision value 0.74
SVM RNA-class probability 0.838754
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 16748240 111 - 23771897
UCAUUUUCCGUUGAAUCGGAAUAUUUUCUUUCGUGGCAUAUGUUUGUUGACGUUCCAAUAUAUUUUUAUAGCAACUCUCUGUCGCACUACGCAUGCAGUUGCUAUAAACCG
.....(((((......)))))............(((...(((((....))))).))).......((((((((((((.(.((.((.....)))).).))))))))))))... ( -24.80)
>DroSim_CAF1 1085 111 - 1
UCAUAUUCCGUCGAAUCGGAAUAUUUUCUUUCGUGGCAUAUGUUUGUUGACGUUCCAAUAUACUUUUAUAGCAACUCUCUGUCGCACUACGCAUGCAGUUGCUAUAAACCG
..((((((((......)))))))).........(((...(((((....))))).))).......((((((((((((.(.((.((.....)))).).))))))))))))... ( -27.90)
>DroYak_CAF1 1100 111 - 1
UCAUGUUCCGUCGAAUCGGAAUAUUUUCUUUCGUGGCAUAUGUUUGUUGACGUUCCAAUAUAUUUUUAUAGCAACUCGGUGUCGCACUACGCAUGCAGCUGCUAUAAAGCG
..((((((((......)))))))).........(((...(((((....))))).)))......((((((((((.((((((((......)))).)).)).)))))))))).. ( -27.10)
>consensus
UCAUAUUCCGUCGAAUCGGAAUAUUUUCUUUCGUGGCAUAUGUUUGUUGACGUUCCAAUAUAUUUUUAUAGCAACUCUCUGUCGCACUACGCAUGCAGUUGCUAUAAACCG
..((((((((......)))))))).........(((...(((((....))))).))).......((((((((((((...((.((.....))))...))))))))))))... (-25.61 = -26.17 +   0.56)

alignment

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secondary structure

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dotplot

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Window 8

Location 16,748,319 – 16,748,409
Length 90
Sequences 3
Columns 90
Reading direction reverse
Mean pairwise identity 88.89
Mean single sequence MFE -21.51
Consensus MFE -20.76
Energy contribution -20.99
Covariance contribution 0.23
Combinations/Pair 1.15
Mean z-score -1.89
Structure conservation index 0.96
SVM decision value 1.35
SVM RNA-class probability 0.944609
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 16748319 90 - 23771897
GGUUAAAUGUACGAUCGAAUGGCUUUCUGAAUAUCUGCCAGUUCGGUCUUUAAUUAAUUCAUUUUCCGUUGAAUCGGAAUAUUUUCUUUC
....((((((..(((((((((((.............)))).)))))))................((((......))))))))))...... ( -19.52)
>DroSim_CAF1 1164 90 - 1
AGUUAAAUGUACGAUCGAAUGGCUUUCUGGAUGUUUGCCAGUUCGGUCUUUAAUUAAUUCAUAUUCCGUCGAAUCGGAAUAUUUUCUUUC
(((((((.....(((((((((((...(.....)...)))).)))))))))))))).....((((((((......))))))))........ ( -23.10)
>DroYak_CAF1 1179 90 - 1
GGUUAAAUGGCUGAUCGAAUGGCUGUCUGAAUCUCUGCCAGUCCGAUCUGUAAUCAAUUCAUGUUCCGUCGAAUCGGAAUAUUUUCUUUC
(((((.......(((((..((((.............))))...)))))..))))).....((((((((......))))))))........ ( -21.92)
>consensus
GGUUAAAUGUACGAUCGAAUGGCUUUCUGAAUAUCUGCCAGUUCGGUCUUUAAUUAAUUCAUAUUCCGUCGAAUCGGAAUAUUUUCUUUC
(((((((.....(((((((((((.............)))).)))))))))))))).....((((((((......))))))))........ (-20.76 = -20.99 +   0.23)

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 12:14:47 2006