Locus 3137

Sequence ID X_DroMel_CAF1
Location 8,356,574 – 8,356,673
Length 99
Max. P 0.896522
window5128 window5129

overview

Window 8

Location 8,356,574 – 8,356,673
Length 99
Sequences 4
Columns 113
Reading direction forward
Mean pairwise identity 83.81
Mean single sequence MFE -24.82
Consensus MFE -19.12
Energy contribution -20.00
Covariance contribution 0.88
Combinations/Pair 1.15
Mean z-score -1.74
Structure conservation index 0.77
SVM decision value 0.48
SVM RNA-class probability 0.754362
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 8356574 99 + 22224390
UCGUCUGGGAACUGAUCCUUAAUCCAAACCAAAUGCGGUAUAUGGAAUUUUUA--------UAAGCAUGUGUAUUUUAAUGAUACACACUGCUGUUUCAAGGAUCU------C
.............(((((((..((((.(((......)))...)))).......--------..((((((((((((.....)))))))).)))).....))))))).------. ( -28.10)
>DroSec_CAF1 21896 99 + 1
UCGUUUGGAAACUGAUCCUUAAUCCAAACCAAAUGCGGUAUAUAGGGUUUUUA--------UAAGCAUGUGUAUUUCAAUGAUACACAAUGCUGUUUCAGGGAUCU------C
......(....).((((((((((((..(((......))).....)))))....--------..((((((((((((.....))))))).))))).....))))))).------. ( -27.00)
>DroSim_CAF1 25091 99 + 1
UCGUCUGGAAACUGAUCCUUAAUCCAAACCAAAUGCGGUAUAUGGGGUUUUUA--------UAAGCAUGUGUAUUUUAAUGACACACAAUGCUGUUUCAGGGAUCU------C
......(....).((((((((((((..(((......))).....)))))....--------..(((((((((.((.....)).)))).))))).....))))))).------. ( -24.00)
>DroEre_CAF1 18958 113 + 1
UCGUCUGAGAACUGAUCCUUAAUCCAAGCCAAAUGCGGUAUAUAGAGUUCUUAAGGUUUGCUUAGCAUGUGUAUUUUUAUGAUAGACAAUGCUGUUUCAAUUAGUUAAAGUGC
.....(((((((((((.....)))...(((......)))......))))))))....(((..((((((((.((((.....)))).)).))))))...)))............. ( -20.20)
>consensus
UCGUCUGGAAACUGAUCCUUAAUCCAAACCAAAUGCGGUAUAUAGAGUUUUUA________UAAGCAUGUGUAUUUUAAUGAUACACAAUGCUGUUUCAAGGAUCU______C
.............(((((((..((((.(((......)))...)))).................((((((((((((.....)))))))).)))).....)))))))........ (-19.12 = -20.00 +   0.88)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 9

Location 8,356,574 – 8,356,673
Length 99
Sequences 4
Columns 113
Reading direction reverse
Mean pairwise identity 83.81
Mean single sequence MFE -22.68
Consensus MFE -19.05
Energy contribution -20.43
Covariance contribution 1.38
Combinations/Pair 1.10
Mean z-score -1.94
Structure conservation index 0.84
SVM decision value 0.99
SVM RNA-class probability 0.896522
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 8356574 99 - 22224390
G------AGAUCCUUGAAACAGCAGUGUGUAUCAUUAAAAUACACAUGCUUA--------UAAAAAUUCCAUAUACCGCAUUUGGUUUGGAUUAAGGAUCAGUUCCCAGACGA
.------.(((((((((...((((.(((((((.......)))))))))))..--------.......((((...((((....)))).)))))))))))))............. ( -29.40)
>DroSec_CAF1 21896 99 - 1
G------AGAUCCCUGAAACAGCAUUGUGUAUCAUUGAAAUACACAUGCUUA--------UAAAAACCCUAUAUACCGCAUUUGGUUUGGAUUAAGGAUCAGUUUCCAAACGA
.------.(((((.(((...(((((.((((((.......)))))))))))..--------........(((...((((....)))).))).))).)))))............. ( -21.70)
>DroSim_CAF1 25091 99 - 1
G------AGAUCCCUGAAACAGCAUUGUGUGUCAUUAAAAUACACAUGCUUA--------UAAAAACCCCAUAUACCGCAUUUGGUUUGGAUUAAGGAUCAGUUUCCAGACGA
.------.(((((.(((...(((((.((((((.......)))))))))))..--------........(((...((((....)))).))).))).))))).(((....))).. ( -24.40)
>DroEre_CAF1 18958 113 - 1
GCACUUUAACUAAUUGAAACAGCAUUGUCUAUCAUAAAAAUACACAUGCUAAGCAAACCUUAAGAACUCUAUAUACCGCAUUUGGCUUGGAUUAAGGAUCAGUUCUCAGACGA
...........((((((...(((((.((.(((.......))).))))))).......((((((....((((....(((....)))..)))))))))).))))))......... ( -15.20)
>consensus
G______AGAUCCCUGAAACAGCAUUGUGUAUCAUUAAAAUACACAUGCUUA________UAAAAACCCCAUAUACCGCAUUUGGUUUGGAUUAAGGAUCAGUUCCCAGACGA
........(((((((((...((((.(((((((.......)))))))))))..................(((...((((....)))).))).))))))))).(((....))).. (-19.05 = -20.43 +   1.38)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:51:49 2006