Locus 1261

Sequence ID	3R_DroMel_CAF1
Location	3,777,489 – 3,777,641
Length	152
Max. P	0.863756

overview

Window 8

Location	3,777,489 – 3,777,601
Length	112
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	85.80
Mean single sequence MFE	-27.75
Consensus MFE	-22.89
Energy contribution	-23.32
Covariance contribution	0.44
Combinations/Pair	1.07
Mean z-score	-1.76
Structure conservation index	0.82
SVM decision value	0.61
SVM RNA-class probability	0.797480
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3777489 112 - 27905053
AGCACACUCGAGCUUUAAUUGUGUGUAUAAAUUACAUUUGCUGUAUAAACCAUUCUAGUGGAUGUGGCGCUUCCUGUCAUAUCGCCAGAUGAUUUAGAUAGGACAC--------CAUGAU
(((((((.(((.......))).)))).....(((((((..(((.(........).)))..))))))).)))(((((((..((((.....))))...)))))))...--------...... ( -26.90)
>DroSec_CAF1 7072 97 - 1
---------------UAAUUGUGUGUAUAAAUUACAUUUGCUGGAUAAACCAUUCUAGUGGAUGUGGCGCUUCCUGUCAUAUCGCCAGAUGAUUUAGAUAGAACAC--------CAUGAU
---------------....((.((((.....(((((((..(((((........)))))..)))))))......(((((..((((.....))))...))))).))))--------)).... ( -25.20)
>DroSim_CAF1 10708 112 - 1
AGCACACUCGAGCUUUAAUUGUGUGUAUAAAUUACACUUGCUGGAUAAACCAUUCUAGUGGAUGUGGCGCUUCCUGUCAUAUCGCCAGAUGAUUUAGAUAGGACAC--------CAUGAU
(((((((.(((.......))).)))).....(((((.(..(((((........)))))..).))))).)))(((((((..((((.....))))...)))))))...--------...... ( -29.00)
>DroYak_CAF1 8819 114 - 1
AUCACAC------UUUAAUUAUGUGUAUAAAUUACAUUUGCUGGAUAAACAAUUUUAGUGGAUGUGGCGCUUCCUGUCAUAUCGCCAGAUGAUUUAGAUAGGAUACCAUGGUACCAUGAU
.......------....((((((.((((.....(((((..(((((........)))))..)))))((....(((((((..((((.....))))...)))))))..))...)))))))))) ( -29.90)
>consensus
AGCACAC______UUUAAUUGUGUGUAUAAAUUACAUUUGCUGGAUAAACCAUUCUAGUGGAUGUGGCGCUUCCUGUCAUAUCGCCAGAUGAUUUAGAUAGGACAC________CAUGAU
.................((((((........(((((((..(((((........)))))..)))))))....(((((((..((((.....))))...)))))))...........)))))) (-22.89 = -23.32 +   0.44)

alignment

secondary structure

dotplot

Window 9

Location	3,777,521 – 3,777,641
Length	120
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	88.80
Mean single sequence MFE	-31.50
Consensus MFE	-25.94
Energy contribution	-26.88
Covariance contribution	0.94
Combinations/Pair	1.07
Mean z-score	-1.90
Structure conservation index	0.82
SVM decision value	0.84
SVM RNA-class probability	0.863756
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3777521 120 - 27905053
AAAUAGCAGCUAAAUUGCGGCGCGCAAACUCGAGCAUUUGAGCACACUCGAGCUUUAAUUGUGUGUAUAAAUUACAUUUGCUGUAUAAACCAUUCUAGUGGAUGUGGCGCUUCCUGUCAU
..((((((((......)).((((((((....((((..(((((....)))))))))...))))))))............)))))).....((((....))))..((((((.....)))))) ( -30.90)
>DroSec_CAF1 7104 103 - 1
AAAUAGCAGCUAAAUUGCGGCGCGCAAACUCGAGCAUU-----------------UAAUUGUGUGUAUAAAUUACAUUUGCUGGAUAAACCAUUCUAGUGGAUGUGGCGCUUCCUGUCAU
.....((.((......)).))((((........((((.-----------------.....))))........((((((..(((((........)))))..)))))))))).......... ( -29.80)
>DroSim_CAF1 10740 120 - 1
AAAUAGCAGCUAAAUUGCGGCGCGCAAACUCGAGCAUUUGAGCACACUCGAGCUUUAAUUGUGUGUAUAAAUUACACUUGCUGGAUAAACCAUUCUAGUGGAUGUGGCGCUUCCUGUCAU
.....((((.......(((((((((((....((((..(((((....)))))))))...)))))))).....(((((.(..(((((........)))))..).))))))))...))))... ( -32.90)
>DroYak_CAF1 8859 114 - 1
AAAUAGCAGCUGAAUUGCUGCGCGCAAACUCGAGCAUUUGAUCACAC------UUUAAUUAUGUGUAUAAAUUACAUUUGCUGGAUAAACAAUUUUAGUGGAUGUGGCGCUUCCUGUCAU
.....(((((......)))))((((..................((((------.........))))......((((((..(((((........)))))..)))))))))).......... ( -32.40)
>consensus
AAAUAGCAGCUAAAUUGCGGCGCGCAAACUCGAGCAUUUGAGCACAC______UUUAAUUGUGUGUAUAAAUUACAUUUGCUGGAUAAACCAUUCUAGUGGAUGUGGCGCUUCCUGUCAU
.....((.((......)).))((((........((((..((((........)))).....))))........((((((..(((((........)))))..)))))))))).......... (-25.94 = -26.88 +   0.94)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:04:59 2006