Locus 9958

Sequence ID	3R_DroMel_CAF1
Location	26,682,223 – 26,682,375
Length	152
Max. P	0.999992

overview

Window 7

Location	26,682,223 – 26,682,335
Length	112
Sequences	5
Columns	119
Reading direction	forward
Mean pairwise identity	96.34
Mean single sequence MFE	-29.70
Consensus MFE	-26.69
Energy contribution	-26.89
Covariance contribution	0.20
Combinations/Pair	1.00
Mean z-score	-1.42
Structure conservation index	0.90
SVM decision value	0.79
SVM RNA-class probability	0.850253
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 26682223 112 + 27905053
UAGAUUUUAAUGGGCAGGAUUACCCUUUUGCUAAAUA-------CCAAAAUCCUGGACGGGCGGUCUGCGCACCGCAGCUCCUUUGUUUUCAAAUGUAAUGAGAAUGUCUCUAAGCCAA
............(((((((((......((....))..-------....))))))(((((((.((.(((((...))))))))))..(((((((.......)))))))))))....))).. ( -25.40)
>DroSec_CAF1 272909 112 + 1
UAGAUUUUAAUGGGCAGGAUUACCCUUUUGCUAAAUA-------CCAAAAUCCUGGCCGGGCGGUCUGCGCACCGCAGCUCCUUUGUUUUCAAAUGUAAUGAGAAUGUCUCUAAGCCAA
..........(((.(((((((......((....))..-------....))))))).)))(((((.(((((...)))))..))...(((((((.......)))))))........))).. ( -29.60)
>DroSim_CAF1 269649 112 + 1
UAGAUUUUAAUGGGCAGGAUUACCCUUUUGCUAAAUA-------CCAAAAUCCUGGCCGGGCGGUCUGCGCACCGCAGCUCCUUUGUUUUCAAAUGUAAUGAGAAUGUCUCUAAGCCAA
..........(((.(((((((......((....))..-------....))))))).)))(((((.(((((...)))))..))...(((((((.......)))))))........))).. ( -29.60)
>DroEre_CAF1 288804 112 + 1
UAGAUUUUAAUGGCCAGGAUUACCCUUUUGCUAAAUA-------CCAAAAUCCUGGCCGGGCGGUCUGCUCACCGCAGCUCCUUUGUUUUCAAAUGUAAUGAGAAUGUCUCUAAGCCAA
..........(((((((((((......((....))..-------....)))))))))))(((((.((((.....))))..))...(((((((.......)))))))........))).. ( -33.30)
>DroYak_CAF1 277793 119 + 1
UAGAUUUUAAUGGGCAGGAUUACCCUUUUGCUAAAUACCAAAUACCAAAAUCCUGGCCGGGCGGUCUGCUCACCGCAGCUCCUUUGUUUUCAAAUGUAAUGAGAAUGUCUCUAAGCCAA
..........(((.(((((((.....((((........))))......))))))).)))(((((.((((.....))))..))...(((((((.......)))))))........))).. ( -30.60)
>consensus
UAGAUUUUAAUGGGCAGGAUUACCCUUUUGCUAAAUA_______CCAAAAUCCUGGCCGGGCGGUCUGCGCACCGCAGCUCCUUUGUUUUCAAAUGUAAUGAGAAUGUCUCUAAGCCAA
..........(((.(((((((...........................))))))).)))(((((.((((.....))))..))...(((((((.......)))))))........))).. (-26.69 = -26.89 +   0.20)

alignment

secondary structure

dotplot

Window 8

Location	26,682,260 – 26,682,375
Length	115
Sequences	5
Columns	119
Reading direction	forward
Mean pairwise identity	95.37
Mean single sequence MFE	-35.38
Consensus MFE	-35.08
Energy contribution	-35.28
Covariance contribution	0.20
Combinations/Pair	1.00
Mean z-score	-3.13
Structure conservation index	0.99
SVM decision value	5.71
SVM RNA-class probability	0.999992
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 26682260 115 + 27905053
----CCAAAAUCCUGGACGGGCGGUCUGCGCACCGCAGCUCCUUUGUUUUCAAAUGUAAUGAGAAUGUCUCUAAGCCAAAAUAUUAAACAUCCGUUUGAGCCUGGCCAGAACAUACCCA
----........((((.(((((((((((((...))))).......(((((((.......)))))))........)))......((((((....))))))))))).)))).......... ( -30.20)
>DroSec_CAF1 272946 115 + 1
----CCAAAAUCCUGGCCGGGCGGUCUGCGCACCGCAGCUCCUUUGUUUUCAAAUGUAAUGAGAAUGUCUCUAAGCCAAAAUAUUAAACAUCCGUUUGAGCCUGGCCAGAACACAACCA
----........((((((((((((((((((...))))).......(((((((.......)))))))........)))......((((((....)))))))))))))))).......... ( -37.30)
>DroSim_CAF1 269686 115 + 1
----CCAAAAUCCUGGCCGGGCGGUCUGCGCACCGCAGCUCCUUUGUUUUCAAAUGUAAUGAGAAUGUCUCUAAGCCAAAAUAUUAAACAUCCGUUUGAGCCUGGCCAGAACACAACCA
----........((((((((((((((((((...))))).......(((((((.......)))))))........)))......((((((....)))))))))))))))).......... ( -37.30)
>DroEre_CAF1 288841 115 + 1
----CCAAAAUCCUGGCCGGGCGGUCUGCUCACCGCAGCUCCUUUGUUUUCAAAUGUAAUGAGAAUGUCUCUAAGCCAAAAUAUUAAACAUCCGUUUGAGCCUGGCCAGCACAUACCCA
----........(((((((((((((((((.....)))).......(((((((.......)))))))........)))......((((((....)))))))))))))))).......... ( -35.70)
>DroYak_CAF1 277833 119 + 1
AAUACCAAAAUCCUGGCCGGGCGGUCUGCUCACCGCAGCUCCUUUGUUUUCAAAUGUAAUGAGAAUGUCUCUAAGCCAAAAUAUUAAACAUCCGUUUGAGCCUGGCCAGAACAUGCAUA
............(((((((((((((((((.....)))).......(((((((.......)))))))........)))......((((((....)))))))))))))))).......... ( -36.40)
>consensus
____CCAAAAUCCUGGCCGGGCGGUCUGCGCACCGCAGCUCCUUUGUUUUCAAAUGUAAUGAGAAUGUCUCUAAGCCAAAAUAUUAAACAUCCGUUUGAGCCUGGCCAGAACAUACCCA
............(((((((((((((((((.....)))).......(((((((.......)))))))........)))......((((((....)))))))))))))))).......... (-35.08 = -35.28 +   0.20)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:45:40 2006