Locus 3853

Sequence ID	2R_DroMel_CAF1
Location	12,739,134 – 12,739,234
Length	100
Max. P	0.999475

overview

Window 7

Location	12,739,134 – 12,739,234
Length	100
Sequences	5
Columns	110
Reading direction	forward
Mean pairwise identity	85.38
Mean single sequence MFE	-34.82
Consensus MFE	-30.30
Energy contribution	-30.54
Covariance contribution	0.24
Combinations/Pair	1.16
Mean z-score	-3.29
Structure conservation index	0.87
SVM decision value	3.64
SVM RNA-class probability	0.999475
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 12739134 100 + 20766785
GCUGUCAUGUUGCUGCAUUCACUCGUGCAUACAUGAAAGUCAAUUAAGCGUAUUAAGUGUGCAUGUGUGAAUGUACAGCGGUAUGUGU----------GUGUGUGAGCCU
((...((((..(((((((((((.(((((((((.(((..((.......))...))).))))))))).)))))))..))))..))))...----------)).......... ( -34.90)
>DroSec_CAF1 85457 98 + 1
GCUGUCAUGUUGCUGCAUUCACUCGUGCAUACAUGAAAGUCAAUUAAGCGUAUUAAGUGUGCAUGUGUGAAUGUACAGUGGUAUGUGU------------GUAUGAGCCU
((...((((..(((((((((((.(((((((((.(((..((.......))...))).))))))))).)))))))..))))..))))...------------))........ ( -33.60)
>DroSim_CAF1 92708 98 + 1
GCUGUCAUGUUGCUGCAUUCACUCGUGCAUACAUGAAAGUCAAUUAAGCGUAUUAAGUGUGCAUGUGUGAAUGUACAGCGGUAUGUGU------------GUGUGAGCCU
((...((((..(((((((((((.(((((((((.(((..((.......))...))).))))))))).)))))))..))))..))))...------------))........ ( -34.90)
>DroYak_CAF1 93135 110 + 1
GCUGUCAUGUCGCUGCAUUCACUCGUGCAUACAUGAAAGUCAAUUAAGCGUAUUAAGUGUGCAUGUGUGAAUGUACAGCGAUAUAUGUGAGUGUGUGUGUGUGGGAGCCU
(((.((((((((((((((((((.(((((((((.(((..((.......))...))).))))))))).)))))))..)))))))(((..(......)..))))))).))).. ( -41.30)
>DroAna_CAF1 79539 93 + 1
GCUGUCAUGUCGCUGCACUCACUCGUGCAUACAUGAAAGUCAAUUAAGCGUAUUAAGUGUGCCUGUGUGAGUGCACAUUCCCAUUUGAGG----------GUA-------
(((.(((......(((((((((.((.((((((.(((..((.......))...))).)))))).)).)))))))))..........))).)----------)).------- ( -29.39)
>consensus
GCUGUCAUGUUGCUGCAUUCACUCGUGCAUACAUGAAAGUCAAUUAAGCGUAUUAAGUGUGCAUGUGUGAAUGUACAGCGGUAUGUGU____________GUGUGAGCCU
.....(((((((((((((((((.(((((((((.(((..((.......))...))).))))))))).)))))))..))))))))))......................... (-30.30 = -30.54 +   0.24)

alignment

secondary structure

dotplot

Window 8

Location	12,739,134 – 12,739,234
Length	100
Sequences	5
Columns	110
Reading direction	reverse
Mean pairwise identity	85.38
Mean single sequence MFE	-21.15
Consensus MFE	-16.37
Energy contribution	-16.85
Covariance contribution	0.48
Combinations/Pair	1.05
Mean z-score	-1.62
Structure conservation index	0.77
SVM decision value	0.19
SVM RNA-class probability	0.627440
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 12739134 100 - 20766785
AGGCUCACACAC----------ACACAUACCGCUGUACAUUCACACAUGCACACUUAAUACGCUUAAUUGACUUUCAUGUAUGCACGAGUGAAUGCAGCAACAUGACAGC
............----------...(((...((((..(((((((.(.((((.((........(......)........)).)))).).)))))))))))...)))..... ( -19.69)
>DroSec_CAF1 85457 98 - 1
AGGCUCAUAC------------ACACAUACCACUGUACAUUCACACAUGCACACUUAAUACGCUUAAUUGACUUUCAUGUAUGCACGAGUGAAUGCAGCAACAUGACAGC
..........------------..........((((.(((((((.(.((((.((........(......)........)).)))).).)))))))((......)))))). ( -16.09)
>DroSim_CAF1 92708 98 - 1
AGGCUCACAC------------ACACAUACCGCUGUACAUUCACACAUGCACACUUAAUACGCUUAAUUGACUUUCAUGUAUGCACGAGUGAAUGCAGCAACAUGACAGC
..........------------...(((...((((..(((((((.(.((((.((........(......)........)).)))).).)))))))))))...)))..... ( -19.69)
>DroYak_CAF1 93135 110 - 1
AGGCUCCCACACACACACACUCACAUAUAUCGCUGUACAUUCACACAUGCACACUUAAUACGCUUAAUUGACUUUCAUGUAUGCACGAGUGAAUGCAGCGACAUGACAGC
.........................(((.((((((..(((((((.(.((((.((........(......)........)).)))).).))))))))))))).)))..... ( -23.39)
>DroAna_CAF1 79539 93 - 1
-------UAC----------CCUCAAAUGGGAAUGUGCACUCACACAGGCACACUUAAUACGCUUAAUUGACUUUCAUGUAUGCACGAGUGAGUGCAGCGACAUGACAGC
-------..(----------((......)))..(((((.((.....)))))))..................((.((((((.(((((......)))))...)))))).)). ( -26.90)
>consensus
AGGCUCACAC____________ACACAUACCGCUGUACAUUCACACAUGCACACUUAAUACGCUUAAUUGACUUUCAUGUAUGCACGAGUGAAUGCAGCAACAUGACAGC
...............................((((..(((((((.(.((((.((........(......)........)).)))).).)))))))))))........... (-16.37 = -16.85 +   0.48)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:05:41 2006