Locus 4476

Sequence ID X_DroMel_CAF1
Location 11,847,319 – 11,847,419
Length 100
Max. P 0.933852
window7356 window7357

overview

Window 6

Location 11,847,319 – 11,847,419
Length 100
Sequences 3
Columns 114
Reading direction forward
Mean pairwise identity 72.59
Mean single sequence MFE -23.73
Consensus MFE -14.25
Energy contribution -14.37
Covariance contribution 0.12
Combinations/Pair 1.15
Mean z-score -1.55
Structure conservation index 0.60
SVM decision value 0.43
SVM RNA-class probability 0.734905
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 11847319 100 + 22224390
AUAAGCAAUCCAUC-UCUUGGACCGUUCAGAU-------------UCGGACUUGAAUUUGGAUUCUGUCCAGUCAUGGUUCCCAGUACCAUGCCCAUGCCCAUGCCCAAUUCCA
....(((.......-..((((((.((((((((-------------(((....)))))))))))...)))))).((((((.......))))))....)))............... ( -24.50)
>DroSec_CAF1 3173 91 + 1
AUAAGCAAUCCAUC---UUGGACCGUCCAGAU-------------UCGGAUUUGGACUUGGAUUCUGUCCAGUCAUGGCUCCCAAUCCCAUGCCCAUGCCCAAA------UCC-
...........(((---(.((.....))))))-------------..((((((((..((((((...)))))).((((((............).))))).)))))------)))- ( -22.50)
>DroEre_CAF1 3460 102 + 1
AUAAGCAGUCCAUCAUCUUGGACC-UCAAGUUUCGGCACUCGUAAUCGGAUUUGGAUUUGGAUUCUGUCCAGUCAUGAUUCCCAAUCCCAAGCCCAAGUCCAG-----------
.......(((((......))))).-......................((((((((..(((((((..(((.......)))....))).))))..))))))))..----------- ( -24.20)
>consensus
AUAAGCAAUCCAUC_UCUUGGACCGUCCAGAU_____________UCGGAUUUGGAUUUGGAUUCUGUCCAGUCAUGGUUCCCAAUCCCAUGCCCAUGCCCAA_______UCC_
....((..((((......)))).........................((....(((((.(((.((((......)).)).))).)))))....))...))............... (-14.25 = -14.37 +   0.12)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 7

Location 11,847,319 – 11,847,419
Length 100
Sequences 3
Columns 114
Reading direction reverse
Mean pairwise identity 72.59
Mean single sequence MFE -29.83
Consensus MFE -19.67
Energy contribution -18.90
Covariance contribution -0.77
Combinations/Pair 1.21
Mean z-score -1.58
Structure conservation index 0.66
SVM decision value 1.23
SVM RNA-class probability 0.933852
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 11847319 100 - 22224390
UGGAAUUGGGCAUGGGCAUGGGCAUGGUACUGGGAACCAUGACUGGACAGAAUCCAAAUUCAAGUCCGA-------------AUCUGAACGGUCCAAGA-GAUGGAUUGCUUAU
.(((.((((((.((((..((((((((((.......)))))).((....))..))))..)))).))))))-------------.)))...(((((((...-..)))))))..... ( -29.00)
>DroSec_CAF1 3173 91 - 1
-GGA------UUUGGGCAUGGGCAUGGGAUUGGGAGCCAUGACUGGACAGAAUCCAAGUCCAAAUCCGA-------------AUCUGGACGGUCCAA---GAUGGAUUGCUUAU
-(((------((((((..(((((...(((((..(..(((....))).)..)))))..)))))..)))))-------------))))((.((((((..---...))))))))... ( -32.40)
>DroEre_CAF1 3460 102 - 1
-----------CUGGACUUGGGCUUGGGAUUGGGAAUCAUGACUGGACAGAAUCCAAAUCCAAAUCCGAUUACGAGUGCCGAAACUUGA-GGUCCAAGAUGAUGGACUGCUUAU
-----------.....(((((((((.(((((.(((.((.((......)))).))).)))))...........(((((......))))))-))))))))................ ( -28.10)
>consensus
_GGA_______AUGGGCAUGGGCAUGGGAUUGGGAACCAUGACUGGACAGAAUCCAAAUCCAAAUCCGA_____________AUCUGGACGGUCCAAGA_GAUGGAUUGCUUAU
............((((..((((..(((..(((....(((....))).)))...)))..))))..)))).....................(((((((......)))))))..... (-19.67 = -18.90 +  -0.77)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:26:01 2006