Locus 6341

Sequence ID	3R_DroMel_CAF1
Location	16,593,804 – 16,593,900
Length	96
Max. P	0.966635

overview

Window 4

Location	16,593,804 – 16,593,900
Length	96
Sequences	6
Columns	108
Reading direction	forward
Mean pairwise identity	79.59
Mean single sequence MFE	-34.60
Consensus MFE	-25.28
Energy contribution	-25.37
Covariance contribution	0.08
Combinations/Pair	1.04
Mean z-score	-2.80
Structure conservation index	0.73
SVM decision value	1.60
SVM RNA-class probability	0.966635
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 16593804 96 + 27905053
CGACUGCCUGGCAUCCUGCUAGGCUGGACAUGCAAUUGCAUUGCAGUCGCUGCUACUGCUU------CU------GCUCCUGCCUUUGCUGCUGGCAUUGUUCCAGGC
.....(((((((.....)))))))(((((((((....(((..((((..((.((....))..------..------))..))))...))).....))).)).))))... ( -35.00)
>DroPse_CAF1 151647 78 + 1
CGACUGCCUGGCAUCCUGCUAGGCUGGACAUGCAAUUGCAUUGCAGUCGCUGUCGCUGU------------------------------CGCUGGCAUUGUUCCAGUC
.(((.(((((((.....)))))))..((((.((.(((((...))))).))))))...))------------------------------)(((((.......))))). ( -31.20)
>DroSec_CAF1 150130 96 + 1
CGACUGCCUGGCAUCCUGCUAGGCUGGACAUGCAAUUGCAUUGCAGUCGCUGCUACUGCUC------CU------GCUCCUGCCUUUGCUGCUGGCAUUGUUCCAGGC
.....(((((((.....)))))))(((((((((....(((..((((..((.((....))..------..------))..))))...))).....))).)).))))... ( -35.00)
>DroEre_CAF1 154076 78 + 1
CGACUGCCUGGCAUCCUGCUAGGCUGGACAUGCAAUUGCAUUGCAGUCGCUGCUCCUGCUU------------------------------CUGGCAUUGUUCCAGGC
.....((((((.((..((((((((.(((((.((.(((((...))))).)))).))).))..------------------------------))))))..)).)))))) ( -31.80)
>DroYak_CAF1 149734 108 + 1
CGACUGCCUGGCAUCCUGCUAGGCUGGACAUGCAAUUGCAUUGCAGUCGCUGCUCCUGUUUCUGCUUCUGCUCCUGCUCCUGCUCCAGCUCCUGGCAUUGUUCCAGGC
.....((((((.((..((((((((((((...(((...(((..((((..((.((....))....))..))))...)))...)))))))))..))))))..)).)))))) ( -43.40)
>DroPer_CAF1 158975 78 + 1
CGACUGCCUGGCAUCCUGCUAGGCUGGACAUGCAAUUGCAUUGCAGUCGCUGUCGCUGU------------------------------CGCUGGCAUUGUUCCAGUC
.(((.(((((((.....)))))))..((((.((.(((((...))))).))))))...))------------------------------)(((((.......))))). ( -31.20)
>consensus
CGACUGCCUGGCAUCCUGCUAGGCUGGACAUGCAAUUGCAUUGCAGUCGCUGCUACUGCUU____________________________UGCUGGCAUUGUUCCAGGC
.....((((((.((..((((((....(((.((((((...)))))))))((.......))................................))))))..)).)))))) (-25.28 = -25.37 +   0.08)

alignment

secondary structure

dotplot

Window 5

Location	16,593,804 – 16,593,900
Length	96
Sequences	6
Columns	108
Reading direction	reverse
Mean pairwise identity	79.59
Mean single sequence MFE	-33.80
Consensus MFE	-23.05
Energy contribution	-23.05
Covariance contribution	0.00
Combinations/Pair	1.00
Mean z-score	-2.57
Structure conservation index	0.68
SVM decision value	1.47
SVM RNA-class probability	0.956511
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 16593804 96 - 27905053
GCCUGGAACAAUGCCAGCAGCAAAGGCAGGAGC------AG------AAGCAGUAGCAGCGACUGCAAUGCAAUUGCAUGUCCAGCCUAGCAGGAUGCCAGGCAGUCG
((((((....((.((.((.....((((.(((((------((------..((.......))..)))).((((....)))).))).)))).)).)))).))))))..... ( -36.00)
>DroPse_CAF1 151647 78 - 1
GACUGGAACAAUGCCAGCG------------------------------ACAGCGACAGCGACUGCAAUGCAAUUGCAUGUCCAGCCUAGCAGGAUGCCAGGCAGUCG
..((((.......))))((------------------------------((.(.((((((((.(((...))).)))).))))).((((.((.....)).)))).)))) ( -28.10)
>DroSec_CAF1 150130 96 - 1
GCCUGGAACAAUGCCAGCAGCAAAGGCAGGAGC------AG------GAGCAGUAGCAGCGACUGCAAUGCAAUUGCAUGUCCAGCCUAGCAGGAUGCCAGGCAGUCG
((((((....((.((.((.....((((.(((((------((------..((.......))..)))).((((....)))).))).)))).)).)))).))))))..... ( -37.50)
>DroEre_CAF1 154076 78 - 1
GCCUGGAACAAUGCCAG------------------------------AAGCAGGAGCAGCGACUGCAAUGCAAUUGCAUGUCCAGCCUAGCAGGAUGCCAGGCAGUCG
((((((.....(((.((------------------------------..((.(((.((((((.(((...))).)))).))))).)))).))).....))))))..... ( -29.60)
>DroYak_CAF1 149734 108 - 1
GCCUGGAACAAUGCCAGGAGCUGGAGCAGGAGCAGGAGCAGAAGCAGAAACAGGAGCAGCGACUGCAAUGCAAUUGCAUGUCCAGCCUAGCAGGAUGCCAGGCAGUCG
((((((.....(((..((.((((((((((..(((...((((..((.............))..))))..)))..))))...)))))))).))).....))))))..... ( -43.52)
>DroPer_CAF1 158975 78 - 1
GACUGGAACAAUGCCAGCG------------------------------ACAGCGACAGCGACUGCAAUGCAAUUGCAUGUCCAGCCUAGCAGGAUGCCAGGCAGUCG
..((((.......))))((------------------------------((.(.((((((((.(((...))).)))).))))).((((.((.....)).)))).)))) ( -28.10)
>consensus
GCCUGGAACAAUGCCAGCA____________________________AAACAGCAGCAGCGACUGCAAUGCAAUUGCAUGUCCAGCCUAGCAGGAUGCCAGGCAGUCG
..((((.......))))..........................................(((((((.((((....))))((((.((...)).)))).....))))))) (-23.05 = -23.05 +   0.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:19:11 2006