Locus 4717

Sequence ID	2L_DroMel_CAF1
Location	13,534,619 – 13,534,714
Length	95
Max. P	0.999870

overview

Window 5

Location	13,534,619 – 13,534,714
Length	95
Sequences	5
Columns	117
Reading direction	forward
Mean pairwise identity	73.74
Mean single sequence MFE	-23.76
Consensus MFE	-6.70
Energy contribution	-7.30
Covariance contribution	0.60
Combinations/Pair	1.00
Mean z-score	-2.69
Structure conservation index	0.28
SVM decision value	2.97
SVM RNA-class probability	0.997975
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 13534619 95 + 22407834
UUUAAAUACAAGCUUGCACAUUUUUUUCCUGGGCCCACACUCACACUCACACA-------------AGG----GGCAAUAUGCAAUGAUGGGUG-----GAGCAAAAAAAUAUGCAA
..............((((.((((((((.((..(((((((......(((.....-------------.))----)((.....))..)).))))).-----.)).)))))))).)))). ( -22.60)
>DroSec_CAF1 20645 93 + 1
UUUAAAUACAAGCUUGCACAUUUUUUUCCUGGGCCCACACACU--CACACACA-------------AGG----GGCAAUAUGCAAUGAUGGGUG-----GAGCAAAAAAAUAUGCAA
..............((((.((((((((.((..(((((((..((--(.......-------------.))----)((.....))..)).))))).-----.)).)))))))).)))). ( -22.40)
>DroSim_CAF1 17368 93 + 1
UUUAAAUACAAGCUUGCACAUUUUUUUCCUGAGCCCACACACC--CACACAGA-------------AGG----GGCAAUAUGCAAUGAUGGGUG-----GAGCAAAAAAAUAUGCAA
..............((((.((((((((.((..(((((((..((--(.......-------------.))----)((.....))..)).))))).-----.)).)))))))).)))). ( -25.80)
>DroEre_CAF1 20807 110 + 1
UUUAAAUACAAACUUGCACAUUU-UUUCCUGGGCUCACACUCACGCCCACACACACACACAAACACAGGAGCAGGCAAUAUGCAAUGAUGGGUG------AGCAAAAAAAUAUGCAA
..............((((.((((-(((.....((((((..(((.((((...................)).))..((.....))..)))...)))------))).))))))).)))). ( -22.71)
>DroAna_CAF1 22989 83 + 1
UUUAAAUACACAUAUGCAUAUUUUUUCACCGUCUCCCCA----------------------------------GCCAAUAUGCCAAGGAGAGUGGGAGGGCGCAAAAAAAUAUGCAA
..............((((((((((((...((((..((((----------------------------------.((..........))....))))..))))..)))))))))))). ( -25.30)
>consensus
UUUAAAUACAAGCUUGCACAUUUUUUUCCUGGGCCCACACACA__CACACACA_____________AGG____GGCAAUAUGCAAUGAUGGGUG_____GAGCAAAAAAAUAUGCAA
..............((((.((((((((...............................................((.....))........((........)))))))))).)))). ( -6.70 =  -7.30 +   0.60)

alignment

secondary structure

dotplot

Window 6

Location	13,534,619 – 13,534,714
Length	95
Sequences	5
Columns	117
Reading direction	reverse
Mean pairwise identity	73.74
Mean single sequence MFE	-30.42
Consensus MFE	-13.33
Energy contribution	-13.41
Covariance contribution	0.08
Combinations/Pair	1.24
Mean z-score	-3.33
Structure conservation index	0.44
SVM decision value	4.32
SVM RNA-class probability	0.999870
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 13534619 95 - 22407834
UUGCAUAUUUUUUUGCUC-----CACCCAUCAUUGCAUAUUGCC----CCU-------------UGUGUGAGUGUGAGUGUGGGCCCAGGAAAAAAAUGUGCAAGCUUGUAUUUAAA
((((((((((((((.((.-----..(((((..(..(((.(..(.----...-------------...)..))))..)..)))))...)).))))))))))))))............. ( -29.00)
>DroSec_CAF1 20645 93 - 1
UUGCAUAUUUUUUUGCUC-----CACCCAUCAUUGCAUAUUGCC----CCU-------------UGUGUGUG--AGUGUGUGGGCCCAGGAAAAAAAUGUGCAAGCUUGUAUUUAAA
((((((((((((((.((.-----..(((((((((((((((....----...-------------.)))))).--)))).)))))...)).))))))))))))))............. ( -30.80)
>DroSim_CAF1 17368 93 - 1
UUGCAUAUUUUUUUGCUC-----CACCCAUCAUUGCAUAUUGCC----CCU-------------UCUGUGUG--GGUGUGUGGGCUCAGGAAAAAAAUGUGCAAGCUUGUAUUUAAA
((((((((((((((.((.-----..((((.(((........(((----((.-------------.....).)--))))))))))...)).))))))))))))))............. ( -28.20)
>DroEre_CAF1 20807 110 - 1
UUGCAUAUUUUUUUGCU------CACCCAUCAUUGCAUAUUGCCUGCUCCUGUGUUUGUGUGUGUGUGUGGGCGUGAGUGUGAGCCCAGGAAA-AAAUGUGCAAGUUUGUAUUUAAA
(((((((((((((((((------((((((.(((.((((((.((..((......))..))))))))))))))((....))))))))....))))-))))))))))............. ( -34.60)
>DroAna_CAF1 22989 83 - 1
UUGCAUAUUUUUUUGCGCCCUCCCACUCUCCUUGGCAUAUUGGC----------------------------------UGGGGAGACGGUGAAAAAAUAUGCAUAUGUGUAUUUAAA
.((((((((((((..((......)..((((((..((......))----------------------------------..))))))..)..)))))))))))).............. ( -29.50)
>consensus
UUGCAUAUUUUUUUGCUC_____CACCCAUCAUUGCAUAUUGCC____CCU_____________UGUGUGUG__UGAGUGUGGGCCCAGGAAAAAAAUGUGCAAGCUUGUAUUUAAA
((((((((((((((.((........(((((.................................................)))))...)).))))))))))))))............. (-13.33 = -13.41 +   0.08)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:25:29 2006