Locus 6949

Sequence ID	3R_DroMel_CAF1
Location	18,322,373 – 18,322,519
Length	146
Max. P	0.945601

overview

Window 9

Location	18,322,373 – 18,322,479
Length	106
Sequences	6
Columns	118
Reading direction	reverse
Mean pairwise identity	84.55
Mean single sequence MFE	-36.65
Consensus MFE	-29.87
Energy contribution	-30.30
Covariance contribution	0.43
Combinations/Pair	1.08
Mean z-score	-3.16
Structure conservation index	0.81
SVM decision value	1.35
SVM RNA-class probability	0.945601
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 18322373 106 - 27905053
AAAAGAAGUAACCAAAAUAGCAGCUGGGGCAACGGAGCCGACUGCGACUCC------------GUCUCCGUCUGAAAUAAAUCGCUAGUAGAUUAUUCGUGCUGGCACCCAGUUGCUC
..................(((((((((((..((((((.((....)).))))------------))..))..............(((((((((....)).)))))))..))))))))). ( -38.90)
>DroSec_CAF1 7993 106 - 1
AAAAGAAGUAACCAAAAUAGCAGCUGGGGCAGCGGAGCCGACUGCGACUCC------------GUCUCCGUCUGAAAUAAAUCGCUAGUAGAUUAUUCGUGCUGGCACCCAGUUGCUC
..................((((((((((.((((((((.((..........)------------).))))).))).........(((((((((....)).))))))).)))))))))). ( -41.10)
>DroSim_CAF1 8184 106 - 1
AAAAGAAGUAACCAAAAUAGCAGCUGGGGCAGCGGAGCCGACUGCGACUCC------------GUCUCCGUCUGAAAUAAAUCGCUAGUAGAUUAUUCGUGCUGGCACCCAGUUGCUC
..................((((((((((.((((((((.((..........)------------).))))).))).........(((((((((....)).))))))).)))))))))). ( -41.10)
>DroEre_CAF1 8320 99 - 1
AAAAGAAGUAACCAAAAUAGCAGCUGGGGCAGCGAAGCCGACUCCGUCUCC------------GUCU-------AAAUAAAUCGCUAGUAGAUUAUUCGUGCUGGCACCCAGUUGCUC
..................((((((((((...(((.((.((....)).)).)------------))..-------.........(((((((((....)).))))))).)))))))))). ( -32.50)
>DroYak_CAF1 8659 118 - 1
AAAAGAAGUUACCAAAAUAGCAGCUGGGGCAGCGGAGUCGACUCCGACUCCGUCACCGUCUCCGUCUCCGUCAGAAAUAAAUCGCUAGUAGAUUAUUCGUGCUGGCACCCAGUUGCUC
..................(((((((((((..(((((((((....)))))))))..))..........................(((((((((....)).)))))))..))))))))). ( -44.50)
>DroAna_CAF1 35045 85 - 1
-AAAGAAGUAACCAAAAUAGCAGUUGGGGC--------------------C------------GACUCCGUCUUAAAUAAAUCGCUAGUAGAUUAUUCGUGCUGGCACCCAGUUGUAC
-..................(((..((((..--------------------.------------(((...)))...........(((((((((....)).))))))).))))..))).. ( -21.80)
>consensus
AAAAGAAGUAACCAAAAUAGCAGCUGGGGCAGCGGAGCCGACUGCGACUCC____________GUCUCCGUCUGAAAUAAAUCGCUAGUAGAUUAUUCGUGCUGGCACCCAGUUGCUC
..................((((((((((.....((((.((....)).))))................................(((((((((....)).))))))).)))))))))). (-29.87 = -30.30 +   0.43)

alignment

secondary structure

dotplot

Window 0

Location	18,322,413 – 18,322,519
Length	106
Sequences	5
Columns	118
Reading direction	forward
Mean pairwise identity	87.18
Mean single sequence MFE	-34.72
Consensus MFE	-25.62
Energy contribution	-26.34
Covariance contribution	0.72
Combinations/Pair	1.07
Mean z-score	-1.63
Structure conservation index	0.74
SVM decision value	0.09
SVM RNA-class probability	0.579326
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 18322413 106 + 27905053
AUUUCAGACGGAGAC------------GGAGUCGCAGUCGGCUCCGUUGCCCCAGCUGCUAUUUUGGUUACUUCUUUUAUACACAAAUACCCAAAGAUUUGGGGGCAUGUUGGGUUCU
......(((((..((------------(((((((....)))))))))..))(((((((((..((((((............)).))))..(((((....))))))))).)))))))).. ( -37.00)
>DroSec_CAF1 8033 106 + 1
AUUUCAGACGGAGAC------------GGAGUCGCAGUCGGCUCCGCUGCCCCAGCUGCUAUUUUGGUUACUUCUUUUAUACACAAAUACCCACAGAUUUGGGGGCAUGUUGGGUUCU
.........(.((.(------------(((((((....)))))))))).)((((((((((..((((((............)).))))..((((......)))))))).)))))).... ( -35.20)
>DroSim_CAF1 8224 105 + 1
AUUUCAGACGGAGAC------------GGAGUCGCAGUCGGCUCCGCUGCCCCAGCUGCUAUUUUGGUUACUUCUUUUAUACACAAAUACCCACAGAUUUGG-GGCAUGUUGGGUUCU
.........(.((.(------------(((((((....)))))))))).)(((((((((...((((((............)).))))..((((......)))-)))).)))))).... ( -33.70)
>DroEre_CAF1 8360 98 + 1
AUUU-------AGAC------------GGAGACGGAGUCGGCUUCGCUGCCCCAGCUGCUAUUUUGGUUACUUCUUUUAUACACAAAUACCCACGGAAUU-GGGGCAUGUUGGGUUCU
...(-------((.(------------((((.((....)).)))))))).(((((((((...((((((............)).))))..((((......)-)))))).)))))).... ( -26.20)
>DroYak_CAF1 8699 118 + 1
AUUUCUGACGGAGACGGAGACGGUGACGGAGUCGGAGUCGACUCCGCUGCCCCAGCUGCUAUUUUGGUAACUUCUUUUAUACACAAAUACCCACAGCAUGAGGGGCAUGUUGGGUUUU
........((....))((((((((..((((((((....))))))))..)))((((((((...(((((((..........))).))))..(((.(.....).)))))).)))))))))) ( -41.50)
>consensus
AUUUCAGACGGAGAC____________GGAGUCGCAGUCGGCUCCGCUGCCCCAGCUGCUAUUUUGGUUACUUCUUUUAUACACAAAUACCCACAGAUUUGGGGGCAUGUUGGGUUCU
...........................(((((((....))))))).....((((((((((..((((((............)).))))..((((......)))))))).)))))).... (-25.62 = -26.34 +   0.72)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:33:57 2006