Locus 7452

Sequence ID	3R_DroMel_CAF1
Location	19,869,499 – 19,869,688
Length	189
Max. P	0.940702

overview

Window 9

Location	19,869,499 – 19,869,619
Length	120
Sequences	3
Columns	120
Reading direction	forward
Mean pairwise identity	97.22
Mean single sequence MFE	-45.67
Consensus MFE	-43.11
Energy contribution	-43.00
Covariance contribution	-0.11
Combinations/Pair	1.05
Mean z-score	-1.69
Structure conservation index	0.94
SVM decision value	0.22
SVM RNA-class probability	0.641315
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 19869499 120 + 27905053
CAACGGCAUGGCCAGGAGCGGCUCCGACUUUGCUACUACUCGGUAUUGUACGUAACCUAAACGUGCGUAAUGCGCUUGCAACUGCUGCAGGUGCGGAAGCUGAUGCAGCAGAGGUGGUUG
((((.((..((((......))))....(((((((.(...(((((...((((((.......))))))....((((((((((.....))))))))))...))))).).))))))))).)))) ( -45.50)
>DroSec_CAF1 5278 120 + 1
CAACGGCAUGGCCAGGAGCGGCUCCGACGUUGUUACUACUCGGUAUUGUACGUAACCUAAACGUGCGUAAUGCGCUUGCAACUGCUGCAGGUGCGGAAGCUGAUGCAGCAGAGGUGGUUG
(((((....((((......))))....)))))..((((((..(((((((((((.......))))))..)))))........((((((((...((....))...)))))))).)))))).. ( -45.70)
>DroSim_CAF1 5280 118 + 1
CAACGGCAUGGCCAGGAGCGGCUCCGACUUUGUUACUACUCGGUA-UGUACGUAAC-UAAACGUGCGUAAUGCGCUUGCAACUGCUGCAGGUGCAGAAGCUGAUGCAGCAGAGGUGGUUG
((((.((..((((......))))....(((((((.(...((((((-(((((((...-...))))))))..((((((((((.....))))))))))...))))).).))))))))).)))) ( -45.80)
>consensus
CAACGGCAUGGCCAGGAGCGGCUCCGACUUUGUUACUACUCGGUAUUGUACGUAACCUAAACGUGCGUAAUGCGCUUGCAACUGCUGCAGGUGCGGAAGCUGAUGCAGCAGAGGUGGUUG
((((.((..((((......))))....(((((((.(...(((((...((((((.......))))))....((((((((((.....))))))))))...))))).).))))))))).)))) (-43.11 = -43.00 +  -0.11)

alignment

secondary structure

dotplot

Window 0

Location	19,869,539 – 19,869,659
Length	120
Sequences	3
Columns	120
Reading direction	forward
Mean pairwise identity	97.78
Mean single sequence MFE	-49.53
Consensus MFE	-47.82
Energy contribution	-47.60
Covariance contribution	-0.22
Combinations/Pair	1.03
Mean z-score	-1.91
Structure conservation index	0.97
SVM decision value	0.70
SVM RNA-class probability	0.827849
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 19869539 120 + 27905053
CGGUAUUGUACGUAACCUAAACGUGCGUAAUGCGCUUGCAACUGCUGCAGGUGCGGAAGCUGAUGCAGCAGAGGUGGUUGUGGCUGCGGCUGGGGGCGACUUCCCGGAUGCUGCAAACGG
(((((((((((((.......))))))..)))))..(..(..((((((((...((....))...))))))))..)..)(((..((.....(((((((....)))))))..))..))).)). ( -48.90)
>DroSec_CAF1 5318 120 + 1
CGGUAUUGUACGUAACCUAAACGUGCGUAAUGCGCUUGCAACUGCUGCAGGUGCGGAAGCUGAUGCAGCAGAGGUGGUUGUGGCUGCGGCUGGGGUCGACUUCCCGGAUGCUGCAAACGG
(((((((((((((.......))))))..)))))..(..(..((((((((...((....))...))))))))..)..)(((..((.....((((((......))))))..))..))).)). ( -49.50)
>DroSim_CAF1 5320 118 + 1
CGGUA-UGUACGUAAC-UAAACGUGCGUAAUGCGCUUGCAACUGCUGCAGGUGCAGAAGCUGAUGCAGCAGAGGUGGUUGUGGCUGCGGCUGGGGGCGACUUCCCGGAUGCUGCAAACGG
(((((-(((((((...-...))))))))..((((((((((.....))))))))))...)))).(((((((...(..((....))..)..(((((((....))))))).)))))))..... ( -50.20)
>consensus
CGGUAUUGUACGUAACCUAAACGUGCGUAAUGCGCUUGCAACUGCUGCAGGUGCGGAAGCUGAUGCAGCAGAGGUGGUUGUGGCUGCGGCUGGGGGCGACUUCCCGGAUGCUGCAAACGG
((((...((((((.......))))))....((((((((((.....))))))))))...)))).(((((((...(..((....))..)..((((((......)))))).)))))))..... (-47.82 = -47.60 +  -0.22)

alignment

secondary structure

dotplot

Window 1

Location	19,869,579 – 19,869,688
Length	109
Sequences	3
Columns	120
Reading direction	forward
Mean pairwise identity	92.78
Mean single sequence MFE	-53.07
Consensus MFE	-52.13
Energy contribution	-52.13
Covariance contribution	-0.00
Combinations/Pair	1.00
Mean z-score	-2.00
Structure conservation index	0.98
SVM decision value	1.31
SVM RNA-class probability	0.940702
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 19869579 109 + 27905053
ACUGCUGCAGGUGCGGAAGCUGAUGCAGCAGAGGUGGUUGUGGCUGCGGCUGGGGGCGACUUCCCGGAUGCUGCAAACGGCGUCGAAGCUGGCGUCACAUCUCAGCUCA-----------
..(((((((...((....))...)))))))(((.(((.((((((..((((((((((....))))).(((((((....)))))))..)))))..)))))).).)).))).----------- ( -53.50)
>DroSec_CAF1 5358 120 + 1
ACUGCUGCAGGUGCGGAAGCUGAUGCAGCAGAGGUGGUUGUGGCUGCGGCUGGGGUCGACUUCCCGGAUGCUGCAAACGGCGUCGAAGCUGGCGUCACAUCUCAGCUCAUUGGGUCUGGU
.((((((((...((....))...))))))))((((((((...((.(((.((((((......)))))).))).)).)))(((((((....))))))).)))))(((((.....)).))).. ( -55.00)
>DroSim_CAF1 5358 120 + 1
ACUGCUGCAGGUGCAGAAGCUGAUGCAGCAGAGGUGGUUGUGGCUGCGGCUGGGGGCGACUUCCCGGAUGCUGCAAACGGCGUCGAAGCUGGCGUCACAUCUCAGCUCAUUGGGUCUGGU
.((((((((...((....))...))))))))((((((((...((.(((.(((((((....))))))).))).)).)))(((((((....))))))).)))))(((((.....)).))).. ( -50.70)
>consensus
ACUGCUGCAGGUGCGGAAGCUGAUGCAGCAGAGGUGGUUGUGGCUGCGGCUGGGGGCGACUUCCCGGAUGCUGCAAACGGCGUCGAAGCUGGCGUCACAUCUCAGCUCAUUGGGUCUGGU
..(((((((...((....))...)))))))(((.(((.((((((..(((((((((......)))).(((((((....)))))))..)))))..)))))).).)).)))............ (-52.13 = -52.13 +  -0.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:46:25 2006