Locus 726

Sequence ID	X_DroMel_CAF1
Location	1,987,327 – 1,987,487
Length	160
Max. P	0.926085

overview

Window 9

Location	1,987,327 – 1,987,447
Length	120
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	97.08
Mean single sequence MFE	-36.88
Consensus MFE	-33.91
Energy contribution	-34.23
Covariance contribution	0.31
Combinations/Pair	1.04
Mean z-score	-2.37
Structure conservation index	0.92
SVM decision value	1.17
SVM RNA-class probability	0.926085
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 1987327 120 - 22224390
CACUCCGAACAGGCCCAGUGCUCCCAGCACACCCAACACUAACUGCAACUCAAUUGCCCGCCACACCAGCCUCACGCUGGAGAAGGCGCAGAAUCCCGGCCAGCAGGUGGCCGCCACCAC
...........((((..((((.....))))............((((..(......)...(((.(.(((((.....))))).)..)))))))......))))....(((((...))))).. ( -37.50)
>DroSec_CAF1 20865 119 - 1
CACUCCGAACAGGC-CAGUGCUCCCAGCACACCCAACACUAACUGCAACUCAAUUGCCCGCCACACCAGCCUCACGCUGGAGAAGGCGCAGAAUCCCGGCCAGCAGGUGGCCGCCAGCAC
...........(((-(.((((.....))))............((((..(......)...(((.(.(((((.....))))).)..)))))))......)))).((.(((....))).)).. ( -36.90)
>DroSim_CAF1 14630 120 - 1
CACUCCGAACAGGCCCAGUGCUCCCAGCACACCCAACACUAACUGCAACUCAAUUGCCCGCCACACCAGCCUCACGCUGGAGAAGGCGCAGAAUCCCGGCCAGCAGGUGGCCGCCACCAC
...........((((..((((.....))))............((((..(......)...(((.(.(((((.....))))).)..)))))))......))))....(((((...))))).. ( -37.50)
>DroEre_CAF1 10460 120 - 1
CACUCCAAACAGGCCCAGUGCACCCAGCACACCCAACACUAAUUGCAACUCCAUUGCCCGCCACACCAGCCUCACGCUGGAGAAGGCGCAGAAUCCCGGCCAGCAGGUGGCCACCACCAC
...........((((..((((.....))))..............((((.....)))).((((.(.(((((.....))))).)..)))).........))))....(((((...))))).. ( -35.60)
>consensus
CACUCCGAACAGGCCCAGUGCUCCCAGCACACCCAACACUAACUGCAACUCAAUUGCCCGCCACACCAGCCUCACGCUGGAGAAGGCGCAGAAUCCCGGCCAGCAGGUGGCCGCCACCAC
...........((((..((((.....))))............((((..(......)...(((.(.(((((.....))))).)..)))))))......))))....(((((...))))).. (-33.91 = -34.23 +   0.31)

alignment

secondary structure

dotplot

Window 0

Location	1,987,367 – 1,987,487
Length	120
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	96.25
Mean single sequence MFE	-28.01
Consensus MFE	-25.51
Energy contribution	-26.02
Covariance contribution	0.50
Combinations/Pair	1.00
Mean z-score	-2.09
Structure conservation index	0.91
SVM decision value	0.97
SVM RNA-class probability	0.892686
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 1987367 120 - 22224390
GAACUCCGCCCACGGGCCGCAGGCAAACCCACACCCCAAGCACUCCGAACAGGCCCAGUGCUCCCAGCACACCCAACACUAACUGCAACUCAAUUGCCCGCCACACCAGCCUCACGCUGG
.......(((....))).((.(((((............((((((((.....))...))))))....(((..............))).......))))).))....(((((.....))))) ( -30.34)
>DroSec_CAF1 20905 117 - 1
GAACUCCGC-CACGGGCCGCAGGCAAACCCACACC-CAAGCACUCCGAACAGGC-CAGUGCUCCCAGCACACCCAACACUAACUGCAACUCAAUUGCCCGCCACACCAGCCUCACGCUGG
.......((-(...))).((.(((((.........-..((((((((.....)).-.))))))....(((..............))).......))))).))....(((((.....))))) ( -27.74)
>DroSim_CAF1 14670 120 - 1
GAACUCCGCCCACGGGCCGCAGGCAAACCCACACCCCAAGCACUCCGAACAGGCCCAGUGCUCCCAGCACACCCAACACUAACUGCAACUCAAUUGCCCGCCACACCAGCCUCACGCUGG
.......(((....))).((.(((((............((((((((.....))...))))))....(((..............))).......))))).))....(((((.....))))) ( -30.34)
>DroEre_CAF1 10500 120 - 1
GAACUCCGCCCACGGUCCGCAGGCAAACCCACACCCCAAACACUCCAAACAGGCCCAGUGCACCCAGCACACCCAACACUAAUUGCAACUCCAUUGCCCGCCACACCAGCCUCACGCUGG
.....(((....)))...((.(((((..................((.....))....((((.....)))).......................))))).))....(((((.....))))) ( -23.60)
>consensus
GAACUCCGCCCACGGGCCGCAGGCAAACCCACACCCCAAGCACUCCGAACAGGCCCAGUGCUCCCAGCACACCCAACACUAACUGCAACUCAAUUGCCCGCCACACCAGCCUCACGCUGG
.....(((....)))...((.(((((............((((((((.....))...))))))....(((..............))).......))))).))....(((((.....))))) (-25.51 = -26.02 +   0.50)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:52:11 2006