Locus 1365

Sequence ID X_DroMel_CAF1
Location 4,085,624 – 4,085,717
Length 93
Max. P 0.709458
window2171 window2172

overview

Window 1

Location 4,085,624 – 4,085,717
Length 93
Sequences 4
Columns 101
Reading direction forward
Mean pairwise identity 86.24
Mean single sequence MFE -17.50
Consensus MFE -12.34
Energy contribution -12.65
Covariance contribution 0.31
Combinations/Pair 1.06
Mean z-score -1.68
Structure conservation index 0.70
SVM decision value 0.25
SVM RNA-class probability 0.653579
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4085624 93 + 22224390
UGCAAACACUCACA--------CACACUAGUGUGCACUCUUGUUUCACACAGAUACUGGCACACACACGCAUGCACAGAAAGGUGAGUGCUUACAAACCAU
((.((.(((((((.--------....((.(((((.((....))..)))))))...((((((..(....)..))).)))....))))))).)).))...... ( -22.60)
>DroSim_CAF1 98873 97 + 1
UGCAAACACGCACACAC--GCACACACUAG--UGCACUCUUGUUUCACACAGAUACUGGCACACACACACAUGCACAGAAAGGUGAGUGCUUACAAACCAU
.........((((.(((--((((......)--)))....................((((((..........))).)))....))).))))........... ( -20.40)
>DroEre_CAF1 103564 97 + 1
UGCAAACACACAAACACACACACACACUAG--UACGCUCUUGUUUCACACAGAUACUGGCACAC--ACUCAUGCACAGAAAGGUGAGUGCUUACAAACCAU
.............................(--(((((((.(.((((...(((...)))(((...--.....)))...)))).).)))))..)))....... ( -13.30)
>DroYak_CAF1 96976 90 + 1
UGCAA-------AACACACACACACACUAG--UACACUCUUGUUUCACACAGAUACUGGCACAC--ACUCAUGCACAGAAAGGUGAGUGCUUACAAACCAU
.....-------.................(--(((((((.(.((((...(((...)))(((...--.....)))...)))).).)))))..)))....... ( -13.70)
>consensus
UGCAAACAC_CAAACAC__ACACACACUAG__UACACUCUUGUUUCACACAGAUACUGGCACAC__ACUCAUGCACAGAAAGGUGAGUGCUUACAAACCAU
.................................((((((.(.((((...(((...)))(((..........)))...)))).).))))))........... (-12.34 = -12.65 +   0.31)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 2

Location 4,085,624 – 4,085,717
Length 93
Sequences 4
Columns 101
Reading direction reverse
Mean pairwise identity 86.24
Mean single sequence MFE -29.25
Consensus MFE -19.45
Energy contribution -20.45
Covariance contribution 1.00
Combinations/Pair 1.00
Mean z-score -1.97
Structure conservation index 0.66
SVM decision value 0.37
SVM RNA-class probability 0.709458
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4085624 93 - 22224390
AUGGUUUGUAAGCACUCACCUUUCUGUGCAUGCGUGUGUGUGCCAGUAUCUGUGUGAAACAAGAGUGCACACUAGUGUG--------UGUGAGUGUUUGCA
......(((((((((((((........((((((..(((((..((.((.((.....)).))..).)..)))))..)))))--------)))))))))))))) ( -34.00)
>DroSim_CAF1 98873 97 - 1
AUGGUUUGUAAGCACUCACCUUUCUGUGCAUGUGUGUGUGUGCCAGUAUCUGUGUGAAACAAGAGUGCA--CUAGUGUGUGC--GUGUGUGCGUGUUUGCA
......((((((((((((((...(((.(((..(....)..)))))).....).)))).(((...(..((--(....)))..)--...)))..))))))))) ( -31.50)
>DroEre_CAF1 103564 97 - 1
AUGGUUUGUAAGCACUCACCUUUCUGUGCAUGAGU--GUGUGCCAGUAUCUGUGUGAAACAAGAGCGUA--CUAGUGUGUGUGUGUGUUUGUGUGUUUGCA
......((((((((((((((...(((.((((....--..))))))).....).)))).(((((.(((((--(........)))))).)))))))))))))) ( -27.60)
>DroYak_CAF1 96976 90 - 1
AUGGUUUGUAAGCACUCACCUUUCUGUGCAUGAGU--GUGUGCCAGUAUCUGUGUGAAACAAGAGUGUA--CUAGUGUGUGUGUGUGUU-------UUGCA
......(((((((((.((((...((((((((...(--((..(((((...))).))...)))...)))))--).))...).))).))).)-------))))) ( -23.90)
>consensus
AUGGUUUGUAAGCACUCACCUUUCUGUGCAUGAGU__GUGUGCCAGUAUCUGUGUGAAACAAGAGUGCA__CUAGUGUGUGU__GUGUGUG_GUGUUUGCA
......((((((((((((((...(((.((((........))))))).....).)))).(((..((......))..)))..............))))))))) (-19.45 = -20.45 +   1.00)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:07:26 2006