Locus 650

Sequence ID	X_DroMel_CAF1
Location	1,822,902 – 1,823,017
Length	115
Max. P	0.982010

overview

Window 8

Location	1,822,902 – 1,823,017
Length	115
Sequences	3
Columns	115
Reading direction	forward
Mean pairwise identity	80.77
Mean single sequence MFE	-28.30
Consensus MFE	-23.57
Energy contribution	-23.13
Covariance contribution	-0.44
Combinations/Pair	1.17
Mean z-score	-1.13
Structure conservation index	0.83
SVM decision value	-0.03
SVM RNA-class probability	0.518408
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 1822902 115 + 22224390
CUGCCAGCAUGGCAAUAAAAUGUUAAAAGUGAAAAAGCCCGCGUGUGGGGCGGGGGCGGGGUGUGGUGGUUGCUGUUGUGUUAACAAAGGGGUGCACUGGCAAAAAAAAAACUCA
.((((.....))))......................((((.(((.....))).)))).((((....(..(((((..((..((........))..))..)))))..)....)))). ( -31.80)
>DroSec_CAF1 23659 108 + 1
CUGCCAGCAUGGCAAUAAAAUGUUAAAAGUGGAAAAGCCCGCGUGUGGGGCGGGGGCGGGGGGUGGGGCUUGG---UUUGUUAACAAAGGGGUGCACUGGCAAA----AAACUCA
.((((((....(((......((((((..........((((.(((.....))).))))...(((.....)))..---....))))))......))).))))))..----....... ( -30.00)
>DroEre_CAF1 23087 105 + 1
AUGCCAGCAUAGCAAUAAAAUGUUAAAAGUGAAAAAGCCCGCUUGAGGAGGAAGGGCGGGGGGAGAU---GGG---GGUGUUAAUGAAGGGGUGCACUGGCAGA----AAAUGCA
.((((((..(((((......)))))............(((((((.........))))))).......---...---.(..((........))..).))))))..----....... ( -23.10)
>consensus
CUGCCAGCAUGGCAAUAAAAUGUUAAAAGUGAAAAAGCCCGCGUGUGGGGCGGGGGCGGGGGGUGGUG_UUGG___UGUGUUAACAAAGGGGUGCACUGGCAAA____AAACUCA
.((((((....(((......((((((..........((((.(((.....))).))))..............((....)).))))))......))).))))))............. (-23.57 = -23.13 +  -0.44)

alignment

secondary structure

dotplot

Window 9

Location	1,822,902 – 1,823,017
Length	115
Sequences	3
Columns	115
Reading direction	reverse
Mean pairwise identity	80.77
Mean single sequence MFE	-22.31
Consensus MFE	-17.65
Energy contribution	-17.65
Covariance contribution	-0.00
Combinations/Pair	1.00
Mean z-score	-2.45
Structure conservation index	0.79
SVM decision value	1.90
SVM RNA-class probability	0.982010
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 1822902 115 - 22224390
UGAGUUUUUUUUUUGCCAGUGCACCCCUUUGUUAACACAACAGCAACCACCACACCCCGCCCCCGCCCCACACGCGGGCUUUUUCACUUUUAACAUUUUAUUGCCAUGCUGGCAG
.............((((((((((......((((((.......((..............)).(((((.......)))))...........))))))......)))...))))))). ( -24.54)
>DroSec_CAF1 23659 108 - 1
UGAGUUU----UUUGCCAGUGCACCCCUUUGUUAACAAA---CCAAGCCCCACCCCCCGCCCCCGCCCCACACGCGGGCUUUUCCACUUUUAACAUUUUAUUGCCAUGCUGGCAG
.......----..((((((((((......((((((....---..(((((((.......((....)).......).))))))........))))))......)))...))))))). ( -24.88)
>DroEre_CAF1 23087 105 - 1
UGCAUUU----UCUGCCAGUGCACCCCUUCAUUAACACC---CCC---AUCUCCCCCCGCCCUUCCUCCUCAAGCGGGCUUUUUCACUUUUAACAUUUUAUUGCUAUGCUGGCAU
.......----..((((((((((................---...---.......(((((.............)))))............(((....))).)))...))))))). ( -17.52)
>consensus
UGAGUUU____UUUGCCAGUGCACCCCUUUGUUAACACA___CCAA_CACCACCCCCCGCCCCCGCCCCACACGCGGGCUUUUUCACUUUUAACAUUUUAUUGCCAUGCUGGCAG
.............((((((((((................................(((((.............)))))............(((....))).)))...))))))). (-17.65 = -17.65 +  -0.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:50:18 2006