Locus 6199

Sequence ID	2R_DroMel_CAF1
Location	19,517,433 – 19,517,579
Length	146
Max. P	0.993516

overview

Window 4

Location	19,517,433 – 19,517,541
Length	108
Sequences	4
Columns	108
Reading direction	forward
Mean pairwise identity	92.75
Mean single sequence MFE	-47.05
Consensus MFE	-40.79
Energy contribution	-41.10
Covariance contribution	0.31
Combinations/Pair	1.11
Mean z-score	-3.75
Structure conservation index	0.87
SVM decision value	1.98
SVM RNA-class probability	0.984503
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 19517433 108 + 20766785
GCAACCUCUUUUACUGGUGAAGUAACCACUUGCGGUUGUGGUGGAGGAGUCGCUACCUUCGCAGGAGUAAUCUCCUUCGGAGGUGGUGGGGAAGACACUACCUUCACU
((((((.(......((((......))))...).))))))((((((((((((((((((((((.(((((....))))).)))))))))))(......)))).)))))))) ( -48.00)
>DroSec_CAF1 14043 108 + 1
GCAACCUCUUUUACUGGUGAAGUAACCACUUGCGGUUGUGGUGGAGGAGUCUUUACCUUCGCAGGAGUAAUCUCCUUCGGAGGUGGUGGGGAAGACACGACCUUCACU
((((((.(......((((......))))...).))))))((((((((......((((((((.(((((....))))).))))))))(((.......)))..)))))))) ( -43.70)
>DroSim_CAF1 14816 108 + 1
GCAACCUCUUUUACUGGUGAAGUAACCACUGGCGGUUGUGGUGGAGGAGUCACUACCUUCGCAGGAGUAAUCUCCUUCGGAGGUGGUGGGGAAGACACUACCUUCACU
((((((.((.....((((......))))..)).))))))((((((((((((((((((((((.(((((....))))).)))))))))))(......)))).)))))))) ( -50.00)
>DroYak_CAF1 14126 108 + 1
GCAACCUCCUUUACUGGAGAAGUAACCACUUGCGGCGGUGGUGGAGGAGUCACUACCUUCGCAGGAGUAACCUCCUUCGGUGGCGGUGGAGGUGUCACUACCUUCACU
.....((((......))))......((((((((((.((((((((.....)))))))).)))))((((....))))...))))).((((((((((....)))))))))) ( -46.50)
>consensus
GCAACCUCUUUUACUGGUGAAGUAACCACUUGCGGUUGUGGUGGAGGAGUCACUACCUUCGCAGGAGUAAUCUCCUUCGGAGGUGGUGGGGAAGACACUACCUUCACU
....(((((..((((.....))))(((((........))))))))))..((((((((((((.(((((....))))).)))))))))))).((((.......))))... (-40.79 = -41.10 +   0.31)

alignment

secondary structure

dotplot

Window 5

Location	19,517,469 – 19,517,579
Length	110
Sequences	4
Columns	110
Reading direction	forward
Mean pairwise identity	92.73
Mean single sequence MFE	-50.05
Consensus MFE	-45.79
Energy contribution	-46.48
Covariance contribution	0.69
Combinations/Pair	1.06
Mean z-score	-3.93
Structure conservation index	0.91
SVM decision value	2.40
SVM RNA-class probability	0.993516
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 19517469 110 + 20766785
UGUGGUGGAGGAGUCGCUACCUUCGCAGGAGUAAUCUCCUUCGGAGGUGGUGGGGAAGACACUACCUUCACUGGAGUAACCUCCUUGACUUGAGCUUGUGGUGGAGGAGG
...((((((((((((((((((((((.(((((....))))).)))))))))))(......)))).)))))))).......(((((((.(((.........))).))))))) ( -51.90)
>DroSec_CAF1 14079 110 + 1
UGUGGUGGAGGAGUCUUUACCUUCGCAGGAGUAAUCUCCUUCGGAGGUGGUGGGGAAGACACGACCUUCACUGGAGUAACCUCCUUCACUUGAGCUUGUGGCGGAGGAGG
...((((((((......((((((((.(((((....))))).))))))))(((.......)))..)))))))).......(((((.((((........)))).)))))... ( -47.30)
>DroSim_CAF1 14852 110 + 1
UGUGGUGGAGGAGUCACUACCUUCGCAGGAGUAAUCUCCUUCGGAGGUGGUGGGGAAGACACUACCUUCACUGGAGUAACCUCCUUCACUUGAGAUUGUGGCGGAGGAGG
...((((((((((((((((((((((.(((((....))))).)))))))))))(......)))).)))))))).......(((((.((((........)))).)))))... ( -52.00)
>DroYak_CAF1 14162 110 + 1
GGUGGUGGAGGAGUCACUACCUUCGCAGGAGUAACCUCCUUCGGUGGCGGUGGAGGUGUCACUACCUUCACUGGAGUAACCUCCUUCACUUGAGCUUGUGGUGGAGGAGA
((((((((.....)))))))).(((.(((((....))))).)))...(((((((((((....))))))))))).......((((((((((.........)))))))))). ( -49.00)
>consensus
UGUGGUGGAGGAGUCACUACCUUCGCAGGAGUAAUCUCCUUCGGAGGUGGUGGGGAAGACACUACCUUCACUGGAGUAACCUCCUUCACUUGAGCUUGUGGCGGAGGAGG
...((((((((...(((((((((((.(((((....))))).)))))))))))(......)....)))))))).......(((((.((((........)))).)))))... (-45.79 = -46.48 +   0.69)

alignment

secondary structure

dotplot

Window 6

Location	19,517,469 – 19,517,579
Length	110
Sequences	4
Columns	110
Reading direction	reverse
Mean pairwise identity	92.73
Mean single sequence MFE	-34.38
Consensus MFE	-31.35
Energy contribution	-31.72
Covariance contribution	0.37
Combinations/Pair	1.09
Mean z-score	-2.52
Structure conservation index	0.91
SVM decision value	2.10
SVM RNA-class probability	0.988010
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 19517469 110 - 20766785
CCUCCUCCACCACAAGCUCAAGUCAAGGAGGUUACUCCAGUGAAGGUAGUGUCUUCCCCACCACCUCCGAAGGAGAUUACUCCUGCGAAGGUAGCGACUCCUCCACCACA
..........................(((((...((((..((.((((.(((.......))).)))).))..)))).....((((((....)))).))..)))))...... ( -30.00)
>DroSec_CAF1 14079 110 - 1
CCUCCUCCGCCACAAGCUCAAGUGAAGGAGGUUACUCCAGUGAAGGUCGUGUCUUCCCCACCACCUCCGAAGGAGAUUACUCCUGCGAAGGUAAAGACUCCUCCACCACA
...(((((..(((........)))..)))))........(((..((..(.(((((.......((((.((.(((((....))))).)).)))).))))).)..))..))). ( -34.20)
>DroSim_CAF1 14852 110 - 1
CCUCCUCCGCCACAAUCUCAAGUGAAGGAGGUUACUCCAGUGAAGGUAGUGUCUUCCCCACCACCUCCGAAGGAGAUUACUCCUGCGAAGGUAGUGACUCCUCCACCACA
...(((((..(((........)))..)))))........(((.((((.(((.......))).))))..(.(((((.((((((((....))).)))))))))).)..))). ( -35.70)
>DroYak_CAF1 14162 110 - 1
UCUCCUCCACCACAAGCUCAAGUGAAGGAGGUUACUCCAGUGAAGGUAGUGACACCUCCACCGCCACCGAAGGAGGUUACUCCUGCGAAGGUAGUGACUCCUCCACCACC
.....................(((.(((((((((((((......)).)))))).....(((..((..((.(((((....))))).))..))..))).))))).))).... ( -37.60)
>consensus
CCUCCUCCACCACAAGCUCAAGUGAAGGAGGUUACUCCAGUGAAGGUAGUGUCUUCCCCACCACCUCCGAAGGAGAUUACUCCUGCGAAGGUAGUGACUCCUCCACCACA
((((((.(((...........))).))))))........(((..(((.(((.......))).)))...(.(((((.((((((((....))).)))))))))).)..))). (-31.35 = -31.72 +   0.37)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:05:17 2006