Locus 8957

Sequence ID 3R_DroMel_CAF1
Location 24,030,886 – 24,031,026
Length 140
Max. P 0.988496
window14358 window14359 window14360

overview

Window 8

Location 24,030,886 – 24,030,996
Length 110
Sequences 5
Columns 115
Reading direction forward
Mean pairwise identity 72.29
Mean single sequence MFE -18.44
Consensus MFE -5.04
Energy contribution -4.72
Covariance contribution -0.32
Combinations/Pair 1.22
Mean z-score -1.67
Structure conservation index 0.27
SVM decision value 0.08
SVM RNA-class probability 0.575759
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 24030886 110 + 27905053
GCUUCAAAUUAAAAAGCAAUAUAACAAAUUCAAUACAAAAGUUUGGAAAAUGAGGACCAGAAAGUCGAAUUUAUUCCUAUAAUCCUACUUUCCAGCUCUGGCC-----AAACUUU
((((.........))))....................(((((((((.....(((.....((((((.(...((((....))))..).))))))...)))...))-----))))))) ( -18.30)
>DroSec_CAF1 226160 110 + 1
GCUUUAAAUUAAAAAGCAAUAUAACAUAAGCAAUACAAAAGUUUGGAUAUUGAGGACCGGAAAGCCGAAUUUAUUCCUAUAAUCCUACUUUCCAGCUUUGACA-----AAACUUU
(((((.......)))))....................((((((.(((.....((((.(((....)))...((((....))))))))....)))))))))....-----....... ( -17.70)
>DroSim_CAF1 223693 110 + 1
GCUUUAAAUUAAAAAGCAAUAUAACAUAAGCAAUACAAAAGUUUGGAUAUUGAGGACCGGAAAGCCGAAUUUAUUCCUAUAAUCCUACUUUCCAGCUUUGACC-----AAACUUU
(((((.......)))))....................(((((((((...(..(((.(.((((((......((((....)))).....)))))).))))..)))-----))))))) ( -22.80)
>DroEre_CAF1 237584 92 + 1
GCUUUCAACUUA--------------UAAGCAAUGCAAAAGUUUGG---------CCCAGAAUGUCGUAUUUACUGCUGUAAUCCUUCUUUCCACAUUUGGGCAUUUGGAACUUU
((((........--------------.))))......(((((((.(---------((((((.(((.(...((((....)))).........).)))))))))).....))))))) ( -17.30)
>DroYak_CAF1 236203 87 + 1
GCUUUAAAUUUA--------------UAAGCAAUACAAAAGUUUGG---------UUCAGAAAGUCGUUUUUCUUUCUGUAAUCCUUCUUUCACCAUUUGGCA-----AAACUUU
((((........--------------.))))......(((((((((---------(((((((((........))))))).)))).........((....))..-----))))))) ( -16.10)
>consensus
GCUUUAAAUUAAAAAGCAAUAUAACAUAAGCAAUACAAAAGUUUGGA_A_UGAGGACCAGAAAGUCGAAUUUAUUCCUAUAAUCCUACUUUCCAGCUUUGGCC_____AAACUUU
.....................................(((((((((..........)).(((((......((((....)))).....)))))................))))))) ( -5.04 =  -4.72 +  -0.32)

alignment

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secondary structure

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dotplot

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Window 9

Location 24,030,922 – 24,031,026
Length 104
Sequences 5
Columns 109
Reading direction forward
Mean pairwise identity 78.69
Mean single sequence MFE -19.46
Consensus MFE -8.30
Energy contribution -8.14
Covariance contribution -0.16
Combinations/Pair 1.17
Mean z-score -2.19
Structure conservation index 0.43
SVM decision value 0.69
SVM RNA-class probability 0.822981
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 24030922 104 + 27905053
AAAAGUUUGGAAAAUGAGGACCAGAAAGUCGAAUUUAUUCCUAUAAUCCUACUUUCCAGCUCUGGCC-----AAACUUUUUUUUUCCUGUGUACCCACACAAAACUUAU
((((((((((.....(((.....((((((.(...((((....))))..).))))))...)))...))-----)))))))).......(((((....)))))........ ( -20.80)
>DroSec_CAF1 226196 102 + 1
AAAAGUUUGGAUAUUGAGGACCGGAAAGCCGAAUUUAUUCCUAUAAUCCUACUUUCCAGCUUUGACA-----AAACUUU--UUUUCCCGUGCACCCACACAAAACUUAU
((((((((.....(..(((.(.((((((......((((....)))).....)))))).))))..)..-----)))))))--)......(((......)))......... ( -16.20)
>DroSim_CAF1 223729 103 + 1
AAAAGUUUGGAUAUUGAGGACCGGAAAGCCGAAUUUAUUCCUAUAAUCCUACUUUCCAGCUUUGACC-----AAACUUUU-UUUUCCCGUGUACCCACACAAAACUUAU
((((((((((...(..(((.(.((((((......((((....)))).....)))))).))))..)))-----))))))))-.......((((....))))......... ( -23.10)
>DroEre_CAF1 237606 98 + 1
AAAAGUUUGG---------CCCAGAAUGUCGUAUUUACUGCUGUAAUCCUUCUUUCCACAUUUGGGCAUUUGGAACUUU--UUUUCCUGUGUAUCCACGCAAAACUUAU
..((((((.(---------((((((.(((.(...((((....)))).........).))))))))))....((((....--..))))(((((....))))))))))).. ( -20.90)
>DroYak_CAF1 236225 93 + 1
AAAAGUUUGG---------UUCAGAAAGUCGUUUUUCUUUCUGUAAUCCUUCUUUCACCAUUUGGCA-----AAACUUU--UUUUCCCGUGCAUCUACACAAAACUUAU
((((((((((---------(((((((((........))))))).)))).........((....))..-----)))))))--)......(((......)))......... ( -16.30)
>consensus
AAAAGUUUGGA_A_UGAGGACCAGAAAGUCGAAUUUAUUCCUAUAAUCCUACUUUCCAGCUUUGGCC_____AAACUUU__UUUUCCCGUGUACCCACACAAAACUUAU
..((((((...............(((((......((((....)))).....)))))................................(((......))).)))))).. ( -8.30 =  -8.14 +  -0.16)

alignment

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secondary structure

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dotplot

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Window 0

Location 24,030,922 – 24,031,026
Length 104
Sequences 5
Columns 109
Reading direction reverse
Mean pairwise identity 78.69
Mean single sequence MFE -25.66
Consensus MFE -15.80
Energy contribution -16.64
Covariance contribution 0.84
Combinations/Pair 1.17
Mean z-score -2.56
Structure conservation index 0.62
SVM decision value 2.12
SVM RNA-class probability 0.988496
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 24030922 104 - 27905053
AUAAGUUUUGUGUGGGUACACAGGAAAAAAAAAGUUU-----GGCCAGAGCUGGAAAGUAGGAUUAUAGGAAUAAAUUCGACUUUCUGGUCCUCAUUUUCCAAACUUUU
.....((((.((((....)))).))))..((((((((-----((..((..(..((((((.(((((.........))))).))))))..)..))......)))))))))) ( -30.80)
>DroSec_CAF1 226196 102 - 1
AUAAGUUUUGUGUGGGUGCACGGGAAAA--AAAGUUU-----UGUCAAAGCUGGAAAGUAGGAUUAUAGGAAUAAAUUCGGCUUUCCGGUCCUCAAUAUCCAAACUUUU
.....((((((((....))))))))..(--(((((((-----.(.....((((((((((.(((((.........))))).)))))))))).........).)))))))) ( -24.64)
>DroSim_CAF1 223729 103 - 1
AUAAGUUUUGUGUGGGUACACGGGAAAA-AAAAGUUU-----GGUCAAAGCUGGAAAGUAGGAUUAUAGGAAUAAAUUCGGCUUUCCGGUCCUCAAUAUCCAAACUUUU
.....((((.((((....)))).)))).-((((((((-----((.....((((((((((.(((((.........))))).)))))))))).........)))))))))) ( -31.54)
>DroEre_CAF1 237606 98 - 1
AUAAGUUUUGCGUGGAUACACAGGAAAA--AAAGUUCCAAAUGCCCAAAUGUGGAAAGAAGGAUUACAGCAGUAAAUACGACAUUCUGGG---------CCAAACUUUU
..((((((...(((....))).((((..--....))))....((((((((((.(.........((((....))))...).))))).))))---------).)))))).. ( -19.40)
>DroYak_CAF1 236225 93 - 1
AUAAGUUUUGUGUAGAUGCACGGGAAAA--AAAGUUU-----UGCCAAAUGGUGAAAGAAGGAUUACAGAAAGAAAAACGACUUUCUGAA---------CCAAACUUUU
.....((((((((....))))))))..(--(((((((-----..((....))..).....((.((.(((((((........)))))))))---------)).))))))) ( -21.90)
>consensus
AUAAGUUUUGUGUGGGUACACGGGAAAA__AAAGUUU_____GGCCAAAGCUGGAAAGUAGGAUUAUAGGAAUAAAUUCGACUUUCUGGUCCUCA_U_UCCAAACUUUU
.....((((((((....)))))))).....(((((((............(((((((((..(((((.........)))))..)))))))))...........))))))). (-15.80 = -16.64 +   0.84)

alignment

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secondary structure

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dotplot

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Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:23:34 2006