Locus 2009

Sequence ID	X_DroMel_CAF1
Location	5,514,857 – 5,514,950
Length	93
Max. P	0.996230

overview

Window 8

Location	5,514,857 – 5,514,950
Length	93
Sequences	6
Columns	96
Reading direction	forward
Mean pairwise identity	89.48
Mean single sequence MFE	-30.72
Consensus MFE	-24.11
Energy contribution	-24.08
Covariance contribution	-0.03
Combinations/Pair	1.12
Mean z-score	-2.43
Structure conservation index	0.78
SVM decision value	0.11
SVM RNA-class probability	0.590766
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5514857 93 + 22224390
GGCAGCUGCAUCUGCUGGCAG---UAGCGCAGAUGCUGCCGCUGCGAACAUCAAAAAGGAUGAGAAUGGUGCAAAGGUGUAUGAUGAAAAACGGCG
((((((...((((((..((..---..))))))))))))))((((....((((......))))...((.(((((....))))).))......)))). ( -32.00)
>DroVir_CAF1 6988 90 + 1
UGCAGCCGCAUCUGCGGGCAG------CGCAGAUGCUGCCGCGACAAACACCAAAAAGGAUGAGAAUGGUGCAAAGGUGCAUGAUGAAAAACGCCG
.((.((.(((((((((.....------))))))))).)).))...............((......((.(((((....))))).))........)). ( -30.54)
>DroYak_CAF1 4882 93 + 1
GGCAGCUGCAUCUGCCGGCGG---UAGCGGAGAUGCUGCCGCUGCAAACACCAAAAAGGAUGAGAAUGGUGCAAAGGUGUAUGAUGAAAAACGGCG
(((((......)))))(((((---(((((....))))))))))((...((((.....)).))...((.(((((....))))).))........)). ( -32.30)
>DroMoj_CAF1 5872 90 + 1
UGCAGCUGCAUCUGCGGGUGG------CGCAGAUGCCGCCGCGUCAAACACCAAAAAGGAUGAGAAUGGUGCAAAGGUGCAUGAUGAAAAACGGCG
.((.((.(((((((((.....------))))))))).)).))(((...((((.....)).))...((.(((((....))))).)).......))). ( -32.90)
>DroAna_CAF1 4667 96 + 1
UGCAGCUGCAUCUGCGAGCAGUAGUAGCGCAGAUGCUGCCGCUACAAACACCAAAAAGGAUGAGAAUGGUGCAAAGGUGUAUGAUGAAAAACGGCG
.......(((((((((.((....))..))))))))).((((.......((((.....)).))...((.(((((....))))).))......)))). ( -28.30)
>DroPer_CAF1 22250 93 + 1
UGCAGCUGCAUCUGCGACCAA---CAGCGCAGAUGCUGCCGCGACAAACACCAAAAAGGAUGAGAAUGGUGCAAAGGUGUAUGAUGAAAAACGGCG
.((.((.(((((((((.....---...))))))))).)).))..((.(((((.......................))))).))............. ( -28.30)
>consensus
UGCAGCUGCAUCUGCGGGCAG___UAGCGCAGAUGCUGCCGCGACAAACACCAAAAAGGAUGAGAAUGGUGCAAAGGUGUAUGAUGAAAAACGGCG
(((.((.(((((((((...........))))))))).)).))).....((((.....)).))...((.(((((....))))).))........... (-24.11 = -24.08 +  -0.03)

alignment

secondary structure

dotplot

Window 9

Location	5,514,857 – 5,514,950
Length	93
Sequences	6
Columns	96
Reading direction	reverse
Mean pairwise identity	89.48
Mean single sequence MFE	-31.38
Consensus MFE	-27.02
Energy contribution	-27.36
Covariance contribution	0.33
Combinations/Pair	1.00
Mean z-score	-3.58
Structure conservation index	0.86
SVM decision value	2.67
SVM RNA-class probability	0.996230
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5514857 93 - 22224390
CGCCGUUUUUCAUCAUACACCUUUGCACCAUUCUCAUCCUUUUUGAUGUUCGCAGCGGCAGCAUCUGCGCUA---CUGCCAGCAGAUGCAGCUGCC
.((((((...(((((............................))))).....)))))).((((((((((..---..))..))))))))....... ( -27.59)
>DroVir_CAF1 6988 90 - 1
CGGCGUUUUUCAUCAUGCACCUUUGCACCAUUCUCAUCCUUUUUGGUGUUUGUCGCGGCAGCAUCUGCG------CUGCCCGCAGAUGCGGCUGCA
..((((........))))......((((((.............)))))).....(((((.(((((((((------.....))))))))).))))). ( -34.72)
>DroYak_CAF1 4882 93 - 1
CGCCGUUUUUCAUCAUACACCUUUGCACCAUUCUCAUCCUUUUUGGUGUUUGCAGCGGCAGCAUCUCCGCUA---CCGCCGGCAGAUGCAGCUGCC
.((.((..........))......((((((.............))))))..)).(((((.((((((((((..---..).))).)))))).))))). ( -27.42)
>DroMoj_CAF1 5872 90 - 1
CGCCGUUUUUCAUCAUGCACCUUUGCACCAUUCUCAUCCUUUUUGGUGUUUGACGCGGCGGCAUCUGCG------CCACCCGCAGAUGCAGCUGCA
............(((.(((((.......................))))).))).(((((.(((((((((------.....))))))))).))))). ( -33.80)
>DroAna_CAF1 4667 96 - 1
CGCCGUUUUUCAUCAUACACCUUUGCACCAUUCUCAUCCUUUUUGGUGUUUGUAGCGGCAGCAUCUGCGCUACUACUGCUCGCAGAUGCAGCUGCA
...............((((.....((((((.............)))))).))))(((((.((((((((((.......))..)))))))).))))). ( -32.42)
>DroPer_CAF1 22250 93 - 1
CGCCGUUUUUCAUCAUACACCUUUGCACCAUUCUCAUCCUUUUUGGUGUUUGUCGCGGCAGCAUCUGCGCUG---UUGGUCGCAGAUGCAGCUGCA
........................((((((.............)))))).....(((((.((((((((((..---...).))))))))).))))). ( -32.32)
>consensus
CGCCGUUUUUCAUCAUACACCUUUGCACCAUUCUCAUCCUUUUUGGUGUUUGUAGCGGCAGCAUCUGCGCUA___CUGCCCGCAGAUGCAGCUGCA
........................((((((.............)))))).....(((((.((((((((.............)))))))).))))). (-27.02 = -27.36 +   0.33)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:24:03 2006