Locus 7158

Sequence ID	3L_DroMel_CAF1
Location	19,206,059 – 19,206,198
Length	139
Max. P	0.999801

overview

Window 4

Location	19,206,059 – 19,206,158
Length	99
Sequences	5
Columns	111
Reading direction	forward
Mean pairwise identity	94.80
Mean single sequence MFE	-32.90
Consensus MFE	-25.37
Energy contribution	-25.37
Covariance contribution	-0.00
Combinations/Pair	1.00
Mean z-score	-1.70
Structure conservation index	0.77
SVM decision value	-0.04
SVM RNA-class probability	0.512906
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 19206059 99 + 23771897
GAAAGGCGUAGCACACUUUCGGGGCGUUUUUCCGGGCGCUGC------------GGAAAAGGCUGCAGCUGGAGGAAAAGCUAUAAAUCAGCGAAUGGCAAAAGUGGGCGA
..........((.((((((....((((((((((....(((((------------((......)))))))....)))))))).......((.....)))).)))))).)).. ( -31.90)
>DroSec_CAF1 34407 99 + 1
GAAAGGCGUAGCACACUUUCGGGGCGUUUUUCCGGGCGCUGC------------GGAAAAGGCUGCAGCUGGAGGAAAAGCUAUAAAUCAGCGAAUGGCAAAAGUGGGCGA
..........((.((((((....((((((((((....(((((------------((......)))))))....)))))))).......((.....)))).)))))).)).. ( -31.90)
>DroSim_CAF1 38733 99 + 1
GAAAGGCGUAGCACACUUUCGGGGCGUUUUUCCGGGCGCUGC------------GGAAAAGGCUGCAGCUGGAGGAAAAGCUAUAAAUCAGCGAAUGGCAAAAGUGGGCGA
..........((.((((((....((((((((((....(((((------------((......)))))))....)))))))).......((.....)))).)))))).)).. ( -31.90)
>DroEre_CAF1 37096 99 + 1
GAAAGGCGUAGCACACUUUCGGGGCGUUUUUCCGGGCGCUGC------------GGAAAAUGCUGCAGCUGGAGGAAAAGCUAUAAAUCAGCGAAUGGCAAAAGUGGGCGA
..........((.((((((....((((((((((....(((((------------((......)))))))....)))))))).......((.....)))).)))))).)).. ( -31.90)
>DroYak_CAF1 62079 111 + 1
GAAAGGCGUAGCACACUUUCGGGGCGUUUUUCCGGGCGCUGCGGAAAGUGCUGCGGAAAAUGCUGCAGCUGGAGGAAAAGCUAUAAAUCAGCGAAUGGCAAAAGUGGGCGA
......(((..(((.(((((((.(((.(((((((((((((......)))))).)))))))...)))..)))))))....(((((..........)))))....))).))). ( -36.90)
>consensus
GAAAGGCGUAGCACACUUUCGGGGCGUUUUUCCGGGCGCUGC____________GGAAAAGGCUGCAGCUGGAGGAAAAGCUAUAAAUCAGCGAAUGGCAAAAGUGGGCGA
..........((.((((((....((((((((((....(((((......................)))))....)))))))).......((.....)))).)))))).)).. (-25.37 = -25.37 +  -0.00)

alignment

secondary structure

dotplot

Window 5

Location	19,206,059 – 19,206,158
Length	99
Sequences	5
Columns	111
Reading direction	reverse
Mean pairwise identity	94.80
Mean single sequence MFE	-27.64
Consensus MFE	-25.87
Energy contribution	-25.87
Covariance contribution	-0.00
Combinations/Pair	1.00
Mean z-score	-2.38
Structure conservation index	0.94
SVM decision value	4.11
SVM RNA-class probability	0.999801
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 19206059 99 - 23771897
UCGCCCACUUUUGCCAUUCGCUGAUUUAUAGCUUUUCCUCCAGCUGCAGCCUUUUCC------------GCAGCGCCCGGAAAAACGCCCCGAAAGUGUGCUACGCCUUUC
..((.((((((((......((((.....))))((((((....(((((..........------------)))))....))))))......)))))))).)).......... ( -27.20)
>DroSec_CAF1 34407 99 - 1
UCGCCCACUUUUGCCAUUCGCUGAUUUAUAGCUUUUCCUCCAGCUGCAGCCUUUUCC------------GCAGCGCCCGGAAAAACGCCCCGAAAGUGUGCUACGCCUUUC
..((.((((((((......((((.....))))((((((....(((((..........------------)))))....))))))......)))))))).)).......... ( -27.20)
>DroSim_CAF1 38733 99 - 1
UCGCCCACUUUUGCCAUUCGCUGAUUUAUAGCUUUUCCUCCAGCUGCAGCCUUUUCC------------GCAGCGCCCGGAAAAACGCCCCGAAAGUGUGCUACGCCUUUC
..((.((((((((......((((.....))))((((((....(((((..........------------)))))....))))))......)))))))).)).......... ( -27.20)
>DroEre_CAF1 37096 99 - 1
UCGCCCACUUUUGCCAUUCGCUGAUUUAUAGCUUUUCCUCCAGCUGCAGCAUUUUCC------------GCAGCGCCCGGAAAAACGCCCCGAAAGUGUGCUACGCCUUUC
..((.((((((((......((((.....))))((((((....(((((..........------------)))))....))))))......)))))))).)).......... ( -27.20)
>DroYak_CAF1 62079 111 - 1
UCGCCCACUUUUGCCAUUCGCUGAUUUAUAGCUUUUCCUCCAGCUGCAGCAUUUUCCGCAGCACUUUCCGCAGCGCCCGGAAAAACGCCCCGAAAGUGUGCUACGCCUUUC
..((.((((((((......((((.....(((((........))))))))).(((((((..((.((......)).)).)))))))......)))))))).)).......... ( -29.40)
>consensus
UCGCCCACUUUUGCCAUUCGCUGAUUUAUAGCUUUUCCUCCAGCUGCAGCCUUUUCC____________GCAGCGCCCGGAAAAACGCCCCGAAAGUGUGCUACGCCUUUC
..((.((((((((......((((.....))))((((((....(((((......................)))))....))))))......)))))))).)).......... (-25.87 = -25.87 +  -0.00)

alignment

secondary structure

dotplot

Window 6

Location	19,206,099 – 19,206,198
Length	99
Sequences	5
Columns	111
Reading direction	forward
Mean pairwise identity	92.29
Mean single sequence MFE	-33.06
Consensus MFE	-28.90
Energy contribution	-29.06
Covariance contribution	0.16
Combinations/Pair	1.04
Mean z-score	-1.62
Structure conservation index	0.87
SVM decision value	1.33
SVM RNA-class probability	0.942802
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 19206099 99 + 23771897
GC------------GGAAAAGGCUGCAGCUGGAGGAAAAGCUAUAAAUCAGCGAAUGGCAAAAGUGGGCGACAACGCGCUUUGUUGCAGCCACCAUGGAUGCAGUUUUCCU
..------------(((((((((((((((..........(((((..........))))).((((((.(......).))))))))))))))).(....)......)))))). ( -31.90)
>DroSec_CAF1 34447 99 + 1
GC------------GGAAAAGGCUGCAGCUGGAGGAAAAGCUAUAAAUCAGCGAAUGGCAAAAGUGGGCGACAACGCGCUUUGUUGCAGCCACCGUGGAUGCAGUUUGCCA
..------------((...(((((((((((........))))....(((.(((..((((........(((....)))((......)).)))).))).)))))))))).)). ( -32.10)
>DroSim_CAF1 38773 99 + 1
GC------------GGAAAAGGCUGCAGCUGGAGGAAAAGCUAUAAAUCAGCGAAUGGCAAAAGUGGGCGACAACGCGCUUUGUUGCAGCCACCGUGGAUGCAGUUUCCCU
((------------((....(((((((((..........(((((..........))))).((((((.(......).))))))))))))))).))))(((.......))).. ( -32.10)
>DroEre_CAF1 37136 99 + 1
GC------------GGAAAAUGCUGCAGCUGGAGGAAAAGCUAUAAAUCAGCGAAUGGCAAAAGUGGGCGACAACGCGCUUUGUUGCACCCACCAUGGAUGCAGUUUUCCG
.(------------(((((..(((((((((........))))....(((.((.....))....(((((.(.(((((.....)))))).)))))....)))))))))))))) ( -32.90)
>DroYak_CAF1 62119 111 + 1
GCGGAAAGUGCUGCGGAAAAUGCUGCAGCUGGAGGAAAAGCUAUAAAUCAGCGAAUGGCAAAAGUGGGCGACAACGCGCUUUGUUGCACCCACCGUGGAUGCAGUUUUCCU
((((......))))(((((..(((((((((........))))....(((.((.....))....(((((.(.(((((.....)))))).)))))....))))))))))))). ( -36.30)
>consensus
GC____________GGAAAAGGCUGCAGCUGGAGGAAAAGCUAUAAAUCAGCGAAUGGCAAAAGUGGGCGACAACGCGCUUUGUUGCAGCCACCGUGGAUGCAGUUUUCCU
..............(((((..((((((.((((.((....(((.......))).....((((....(.(((....))).)....))))..)).))).)..))))))))))). (-28.90 = -29.06 +   0.16)

alignment

secondary structure

dotplot

Window 7

Location	19,206,099 – 19,206,198
Length	99
Sequences	5
Columns	111
Reading direction	reverse
Mean pairwise identity	92.29
Mean single sequence MFE	-30.72
Consensus MFE	-24.32
Energy contribution	-24.16
Covariance contribution	-0.16
Combinations/Pair	1.07
Mean z-score	-2.05
Structure conservation index	0.79
SVM decision value	1.19
SVM RNA-class probability	0.928729
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 19206099 99 - 23771897
AGGAAAACUGCAUCCAUGGUGGCUGCAACAAAGCGCGUUGUCGCCCACUUUUGCCAUUCGCUGAUUUAUAGCUUUUCCUCCAGCUGCAGCCUUUUCC------------GC
.(((((((((((...((((((((.(((((.......))))).))).......)))))..((((.................)))))))))..))))))------------.. ( -28.54)
>DroSec_CAF1 34447 99 - 1
UGGCAAACUGCAUCCACGGUGGCUGCAACAAAGCGCGUUGUCGCCCACUUUUGCCAUUCGCUGAUUUAUAGCUUUUCCUCCAGCUGCAGCCUUUUCC------------GC
((((((((((......))))(((.(((((.......))))).))).....))))))...((((.....(((((........))))))))).......------------.. ( -26.70)
>DroSim_CAF1 38773 99 - 1
AGGGAAACUGCAUCCACGGUGGCUGCAACAAAGCGCGUUGUCGCCCACUUUUGCCAUUCGCUGAUUUAUAGCUUUUCCUCCAGCUGCAGCCUUUUCC------------GC
.(((((((((((.....((((((.(((((.......))))).))).......)))....((((.................)))))))))..))))))------------.. ( -26.94)
>DroEre_CAF1 37136 99 - 1
CGGAAAACUGCAUCCAUGGUGGGUGCAACAAAGCGCGUUGUCGCCCACUUUUGCCAUUCGCUGAUUUAUAGCUUUUCCUCCAGCUGCAGCAUUUUCC------------GC
(((((((..(((.....((((((((((((.......)))).))))))))..))).....((((.....(((((........))))))))).))))))------------). ( -35.00)
>DroYak_CAF1 62119 111 - 1
AGGAAAACUGCAUCCACGGUGGGUGCAACAAAGCGCGUUGUCGCCCACUUUUGCCAUUCGCUGAUUUAUAGCUUUUCCUCCAGCUGCAGCAUUUUCCGCAGCACUUUCCGC
.(((((.((((......((((((((((((.......)))).))))))))..........((((.....(((((........))))))))).......))))...))))).. ( -36.40)
>consensus
AGGAAAACUGCAUCCACGGUGGCUGCAACAAAGCGCGUUGUCGCCCACUUUUGCCAUUCGCUGAUUUAUAGCUUUUCCUCCAGCUGCAGCCUUUUCC____________GC
.((((((((((.....(((((..(((((......(((....)))......))).))..)))))......((((........))))))))..)))))).............. (-24.32 = -24.16 +  -0.16)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:39:36 2006