Locus 116

Sequence ID 2R_DroMel_CAF1
Location 1,371,671 – 1,371,790
Length 119
Max. P 0.800841
window250 window251

overview

Window 0

Location 1,371,671 – 1,371,790
Length 119
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 91.24
Mean single sequence MFE -20.73
Consensus MFE -16.73
Energy contribution -17.23
Covariance contribution 0.50
Combinations/Pair 1.00
Mean z-score -1.89
Structure conservation index 0.81
SVM decision value 0.62
SVM RNA-class probability 0.800841
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 1371671 119 + 20766785
AAAAUGUAAAGCCACAUUAAUCACAGUUGA-AGGACUAAAGUGCACACAAUAAAUUUGCAAAUACUUGCAAUAACUGUAAUCAACACACUUGCCAAUCCCAGGUGGCUAGAGCAAACAGC
....(((..((((((.......(((((((.-.(.((....)).)...........((((((....)))))))))))))...(((.....)))..........))))))...)))...... ( -22.60)
>DroSec_CAF1 3838 119 + 1
AAAAUGUAAAGCCACAUUAAUCACAGUUGA-AGGACUAAAGUGCACACAAUAAAUUUGCAAAUACUUGCAAUAACUGUAAUCAACACACUUGCCAAUCCCACGCGGCCAGAGCAAACAGC
..(((((......)))))....(((((((.-.(.((....)).)...........((((((....)))))))))))))..........((.(((..........))).)).......... ( -18.80)
>DroEre_CAF1 2007 108 + 1
AAAAUGUAAAGCCACAUUAAUCACAGUUGAAAAGACUAAAGUGCACACAAUAAAUUUGCAAAUACUUGCAAUAACUGUAAUCAACACACUUGCCAAUCCCACGUGGCU------------
.........((((((.......(((((((...........((....)).......((((((....)))))))))))))...(((.....)))..........))))))------------ ( -19.70)
>DroYak_CAF1 1097 120 + 1
AAAAUGUAAGGCCACAUUAAUCACAGUUGAAAGGACUAAAGUGCACAGAAUAAAUUUGCAAAUACUUGCAAUAACUGUAAUCAACACACUUGCCAAUCCCACAUGGCUUGAGCAAACAGC
..(((((......))))).......(((((..(.((....)).)((((.......((((((....))))))...))))..)))))....(((((((.((.....)).))).))))..... ( -21.80)
>consensus
AAAAUGUAAAGCCACAUUAAUCACAGUUGA_AGGACUAAAGUGCACACAAUAAAUUUGCAAAUACUUGCAAUAACUGUAAUCAACACACUUGCCAAUCCCACGUGGCUAGAGCAAACAGC
..(((((......)))))....(((((((...(.((....)).)...........((((((....))))))))))))).............((((........))))............. (-16.73 = -17.23 +   0.50)

alignment

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secondary structure

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dotplot

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Window 1

Location 1,371,671 – 1,371,790
Length 119
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 91.24
Mean single sequence MFE -28.45
Consensus MFE -25.96
Energy contribution -25.90
Covariance contribution -0.06
Combinations/Pair 1.09
Mean z-score -1.40
Structure conservation index 0.91
SVM decision value 0.24
SVM RNA-class probability 0.647543
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 1371671 119 - 20766785
GCUGUUUGCUCUAGCCACCUGGGAUUGGCAAGUGUGUUGAUUACAGUUAUUGCAAGUAUUUGCAAAUUUAUUGUGUGCACUUUAGUCCU-UCAACUGUGAUUAAUGUGGCUUUACAUUUU
((..(..((.((.((((........)))).)).))(((((((((((((.((((((....))))))..(((..((....))..)))....-..))))))))))))))..)).......... ( -28.40)
>DroSec_CAF1 3838 119 - 1
GCUGUUUGCUCUGGCCGCGUGGGAUUGGCAAGUGUGUUGAUUACAGUUAUUGCAAGUAUUUGCAAAUUUAUUGUGUGCACUUUAGUCCU-UCAACUGUGAUUAAUGUGGCUUUACAUUUU
((.....))...(((((((((((((((..(((((..(.....(((((..((((((....))))))....))))))..))))))))))))-(((....)))...))))))))......... ( -30.50)
>DroEre_CAF1 2007 108 - 1
------------AGCCACGUGGGAUUGGCAAGUGUGUUGAUUACAGUUAUUGCAAGUAUUUGCAAAUUUAUUGUGUGCACUUUAGUCUUUUCAACUGUGAUUAAUGUGGCUUUACAUUUU
------------((((((((.(((..(((.((.((((....((((((..((((((....))))))....)))))).)))).)).)))..)))...........))))))))......... ( -27.10)
>DroYak_CAF1 1097 120 - 1
GCUGUUUGCUCAAGCCAUGUGGGAUUGGCAAGUGUGUUGAUUACAGUUAUUGCAAGUAUUUGCAAAUUUAUUCUGUGCACUUUAGUCCUUUCAACUGUGAUUAAUGUGGCCUUACAUUUU
(((.(((((.(((.((.....)).)))))))).(..((((((((((((.((((((....)))))).........(..(......)..)....))))))))))))..)))).......... ( -27.80)
>consensus
GCUGUUUGCUCUAGCCACGUGGGAUUGGCAAGUGUGUUGAUUACAGUUAUUGCAAGUAUUUGCAAAUUUAUUGUGUGCACUUUAGUCCU_UCAACUGUGAUUAAUGUGGCUUUACAUUUU
.............((((((((((((((..(((((..(.....(((((..((((((....))))))....))))))..)))))))))))).(((....)))...))))))).......... (-25.96 = -25.90 +  -0.06)

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 09:27:49 2006