Locus 9252

Sequence ID 3R_DroMel_CAF1
Location 24,672,516 – 24,672,702
Length 186
Max. P 0.959214
window14790 window14791 window14792 window14793

overview

Window 0

Location 24,672,516 – 24,672,629
Length 113
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 89.46
Mean single sequence MFE -26.72
Consensus MFE -20.18
Energy contribution -20.88
Covariance contribution 0.70
Combinations/Pair 1.07
Mean z-score -1.75
Structure conservation index 0.76
SVM decision value 0.35
SVM RNA-class probability 0.702275
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 24672516 113 + 27905053
UAAGCAGAAUAAAUAAACAGCAAAUAUAUUUUUGCCUGCACCACAGUCUACAUUUAAACGGUUACCACUG-------UGUAACCGGCGUGGAAAAUCAAGUUGCGUGUUGUGAUAACACA
...((((..........(((((((......)))).)))..((((.(....).......(((((((.....-------.)))))))..)))).........))))((((((...)))))). ( -26.70)
>DroSec_CAF1 13554 113 + 1
UUAGCGGAAUAAAUAAACAGCAAAUAUAUUUUCCCCUGCACUACAGUCUACAUUUCAACGGUUACCACUG-------UGUAACAGGCGUGGAAAAUCAAGUUGCGUGUUGUGAUAACACA
...................((((....(((((((((((...((((((..((.........))....))))-------))...))))...)))))))....))))((((((...)))))). ( -24.10)
>DroSim_CAF1 13548 113 + 1
UUAGCAGAAUAAAUAAACAGCAAAUAUAUUUUCCCCUGCACUACGGUCUACAUUUCAACGGUUACCACUG-------UGUAACCGGCGUGGAAAAUCAAGUUGCGUGUUGUGAUAACACA
...................((((....(((((((..(((((....))...........(((((((.....-------.)))))))))).)))))))....))))((((((...)))))). ( -28.60)
>DroEre_CAF1 15060 113 + 1
UUAGCAAAAUAAAUAGACAGAAAAUAUAUUUUUCUCUGCACAAUAGUCGACAUUUCAACGGUUACCACUG-------UGUAACCGGCAUGGAAAAUCAAGUUGCGUGUUUUGAUAACACA
...((((........(((((((((.....))))))..........)))((..(((((.(((((((.....-------.)))))))...)))))..))...))))(((((.....))))). ( -25.70)
>DroYak_CAF1 13850 120 + 1
UUAGCAAAAUAAAUAGACAGCAAGUAUAUUUUCCUCUGCACAAUAGUCGAGAUUUCAACGGUUACCAGUGUGUAGUGUGUAACCGGCGUGGAAAAUCAAGUUGCGUGUUUUGAUAACACA
...................((((.(..(((((((.(.((.........(......)..(((((((((.(....).)).)))))))))).)))))))..).))))(((((.....))))). ( -28.50)
>consensus
UUAGCAGAAUAAAUAAACAGCAAAUAUAUUUUCCCCUGCACAACAGUCUACAUUUCAACGGUUACCACUG_______UGUAACCGGCGUGGAAAAUCAAGUUGCGUGUUGUGAUAACACA
...................((((....(((((((..(((((....))...........(((((((.............)))))))))).)))))))....))))(((((.....))))). (-20.18 = -20.88 +   0.70)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 1

Location 24,672,556 – 24,672,667
Length 111
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 90.02
Mean single sequence MFE -30.56
Consensus MFE -23.70
Energy contribution -23.90
Covariance contribution 0.20
Combinations/Pair 1.06
Mean z-score -1.48
Structure conservation index 0.78
SVM decision value 0.05
SVM RNA-class probability 0.559341
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 24672556 111 + 27905053
CCACAGUCUACAUUUAAACGGUUACCACUG-------UGUAACCGGCGUGGAAAAUCAAGUUGCGUGUUGUGAUAACACACAUGCGAAUAAUACAAG--UGAAUCUUGGAUAUUCUUUGG
((((.(....).......(((((((.....-------.)))))))..)))).....((((..((((((.(((....)))))))))(((((...((((--.....))))..))))))))). ( -31.00)
>DroSec_CAF1 13594 113 + 1
CUACAGUCUACAUUUCAACGGUUACCACUG-------UGUAACAGGCGUGGAAAAUCAAGUUGCGUGUUGUGAUAACACACAUGCGAACAAUACAAGUGUGGAUCUUGGGUAUUCUUUGG
(((..((((((((((....((((.((((.(-------(.......))))))..))))..(((((((((.(((....))))))))).))).....))))))))))..)))........... ( -29.40)
>DroSim_CAF1 13588 113 + 1
CUACGGUCUACAUUUCAACGGUUACCACUG-------UGUAACCGGCGUGGAAAAUCAAGUUGCGUGUUGUGAUAACACACAUGCGAACAAUACAAGAGUGGAUCUUGGGUAUUCUUUGG
(((.(((((((.(((((.(((((((.....-------.)))))))...)))))......(((((((((.(((....))))))))).))).........))))))).)))........... ( -36.00)
>DroEre_CAF1 15100 111 + 1
CAAUAGUCGACAUUUCAACGGUUACCACUG-------UGUAACCGGCAUGGAAAAUCAAGUUGCGUGUUUUGAUAACACACAUGCGAACAACACAAG--UGGAUCUUGGAUAUUCUUUGU
..................(((((((.....-------.)))))))(((.((((.(((..(((((((((..((....)).)))))).)))....((((--.....))))))).)))).))) ( -27.10)
>DroYak_CAF1 13890 118 + 1
CAAUAGUCGAGAUUUCAACGGUUACCAGUGUGUAGUGUGUAACCGGCGUGGAAAAUCAAGUUGCGUGUUUUGAUAACACACAUGCGAACAAUACAAG--UGGAUCUUGGAUAUUCUUUGU
.((((..((((((((...(((((((((.(....).)).)))))))((((((.....).......(((((.....))))).)))))............--.))))))))..))))...... ( -29.30)
>consensus
CAACAGUCUACAUUUCAACGGUUACCACUG_______UGUAACCGGCGUGGAAAAUCAAGUUGCGUGUUGUGAUAACACACAUGCGAACAAUACAAG__UGGAUCUUGGAUAUUCUUUGG
..................(((((((.............))))))).((.((((.(((...((((((((.(((....)))))))))))......((((.......))))))).)))).)). (-23.70 = -23.90 +   0.20)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 2

Location 24,672,556 – 24,672,667
Length 111
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 90.02
Mean single sequence MFE -26.74
Consensus MFE -20.98
Energy contribution -21.02
Covariance contribution 0.04
Combinations/Pair 1.04
Mean z-score -1.44
Structure conservation index 0.78
SVM decision value 0.03
SVM RNA-class probability 0.548332
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 24672556 111 - 27905053
CCAAAGAAUAUCCAAGAUUCA--CUUGUAUUAUUCGCAUGUGUGUUAUCACAACACGCAACUUGAUUUUCCACGCCGGUUACA-------CAGUGGUAACCGUUUAAAUGUAGACUGUGG
.(((.(((((..((((.....--))))...)))))...((((((((.....))))))))..))).....((((...((((((.-------.....))))))(((((....))))).)))) ( -29.10)
>DroSec_CAF1 13594 113 - 1
CCAAAGAAUACCCAAGAUCCACACUUGUAUUGUUCGCAUGUGUGUUAUCACAACACGCAACUUGAUUUUCCACGCCUGUUACA-------CAGUGGUAACCGUUGAAAUGUAGACUGUAG
.....(((((..((((.......))))...)))))(((((((((((.....)))))))).((....((((.(((...(((((.-------.....)))))))).))))...))..))).. ( -22.40)
>DroSim_CAF1 13588 113 - 1
CCAAAGAAUACCCAAGAUCCACUCUUGUAUUGUUCGCAUGUGUGUUAUCACAACACGCAACUUGAUUUUCCACGCCGGUUACA-------CAGUGGUAACCGUUGAAAUGUAGACCGUAG
............(((((.....)))))(((.(((..((((((((((.....)))))))..............((.(((((((.-------.....))))))).))..)))..))).))). ( -27.20)
>DroEre_CAF1 15100 111 - 1
ACAAAGAAUAUCCAAGAUCCA--CUUGUGUUGUUCGCAUGUGUGUUAUCAAAACACGCAACUUGAUUUUCCAUGCCGGUUACA-------CAGUGGUAACCGUUGAAAUGUCGACUAUUG
.....(((((.(((((.....--)))).).)))))...((((((((.....))))))))..(((((.((.((...(((((((.-------.....))))))).)).)).)))))...... ( -28.00)
>DroYak_CAF1 13890 118 - 1
ACAAAGAAUAUCCAAGAUCCA--CUUGUAUUGUUCGCAUGUGUGUUAUCAAAACACGCAACUUGAUUUUCCACGCCGGUUACACACUACACACUGGUAACCGUUGAAAUCUCGACUAUUG
.(((.(((((..((((.....--))))...)))))...((((((((.....))))))))..)))............((((((.((........))))))))(((((....)))))..... ( -27.00)
>consensus
CCAAAGAAUAUCCAAGAUCCA__CUUGUAUUGUUCGCAUGUGUGUUAUCACAACACGCAACUUGAUUUUCCACGCCGGUUACA_______CAGUGGUAACCGUUGAAAUGUAGACUGUAG
.(((.(((((..((((.......))))...)))))...((((((((.....))))))))..)))...........(((((((.............))))))).................. (-20.98 = -21.02 +   0.04)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 3

Location 24,672,589 – 24,672,702
Length 113
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 90.79
Mean single sequence MFE -30.86
Consensus MFE -25.34
Energy contribution -25.22
Covariance contribution -0.12
Combinations/Pair 1.06
Mean z-score -1.98
Structure conservation index 0.82
SVM decision value 1.50
SVM RNA-class probability 0.959214
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 24672589 113 - 27905053
GUCGAGGAGAAACCAAGACC-----AGCACAUUGUGCUGCCCAAAGAAUAUCCAAGAUUCA--CUUGUAUUAUUCGCAUGUGUGUUAUCACAACACGCAACUUGAUUUUCCACGCCGGUU
(.((.((((((..((((..(-----(((((...))))))......(((((..((((.....--))))...)))))...((((((((.....)))))))).)))).)))))).)).).... ( -32.00)
>DroSec_CAF1 13627 115 - 1
GUCGAGGAGAAACCAAAACC-----AGCACAUUGUGCUGCCCAAAGAAUACCCAAGAUCCACACUUGUAUUGUUCGCAUGUGUGUUAUCACAACACGCAACUUGAUUUUCCACGCCUGUU
(.((.((((((........(-----(((((...))))))..(((.(((((..((((.......))))...)))))...((((((((.....))))))))..))).)))))).)).).... ( -28.00)
>DroSim_CAF1 13621 115 - 1
GACGAGGAGAAACCAAAACC-----AGCACAUUGUGCUGCCCAAAGAAUACCCAAGAUCCACUCUUGUAUUGUUCGCAUGUGUGUUAUCACAACACGCAACUUGAUUUUCCACGCCGGUU
(.((.((((((........(-----(((((...))))))..(((.(((((..(((((.....)))))...)))))...((((((((.....))))))))..))).)))))).)).).... ( -30.40)
>DroEre_CAF1 15133 111 - 1
GCCGAGGAGAAACCAA--CC-----AGCACAAUGUGCUGCACAAAGAAUAUCCAAGAUCCA--CUUGUGUUGUUCGCAUGUGUGUUAUCAAAACACGCAACUUGAUUUUCCAUGCCGGUU
((((.((((((.....--.(-----(((((...))))))..(((.(((((.(((((.....--)))).).)))))...((((((((.....))))))))..))).))))))....)))). ( -31.90)
>DroYak_CAF1 13930 116 - 1
GCCGAGGAGAAACCAA--CUGGUGGAGCUCAAUGUGCUGCACAAAGAAUAUCCAAGAUCCA--CUUGUAUUGUUCGCAUGUGUGUUAUCAAAACACGCAACUUGAUUUUCCACGCCGGUU
((((.((((((.....--...(((.(((.......))).)))...(((((..((((.....--))))...)))))...((((((((.....))))))))......))))))....)))). ( -32.00)
>consensus
GCCGAGGAGAAACCAA_ACC_____AGCACAUUGUGCUGCCCAAAGAAUAUCCAAGAUCCA__CUUGUAUUGUUCGCAUGUGUGUUAUCACAACACGCAACUUGAUUUUCCACGCCGGUU
(.((.((((((..............(((((...)))))...(((.(((((..((((.......))))...)))))...((((((((.....))))))))..))).)))))).)).).... (-25.34 = -25.22 +  -0.12)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:29:57 2006