Locus 3823

Sequence ID	2R_DroMel_CAF1
Location	12,613,867 – 12,613,977
Length	110
Max. P	0.879897

overview

Window 3

Location	12,613,867 – 12,613,977
Length	110
Sequences	6
Columns	119
Reading direction	forward
Mean pairwise identity	79.39
Mean single sequence MFE	-19.28
Consensus MFE	-10.12
Energy contribution	-11.07
Covariance contribution	0.95
Combinations/Pair	1.12
Mean z-score	-2.47
Structure conservation index	0.53
SVM decision value	0.91
SVM RNA-class probability	0.879897
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 12613867 110 + 20766785
GGACUCCUACAAUUUUCAUCUUGUACCCACACAAUCUUUGCUUCUACCCAAAUAA---CUACCAUAAAACGCAAUCGAAUUCACCAGCUUUUCGCAGCCAUGGGACUCCCACA------
(((.(((((.....(((...((((......))))...((((..............---............))))..))).......(((......)))..))))).)))....------ ( -12.37)
>DroSec_CAF1 6761 109 + 1
GGACUCCCACAAU-UUCAGCUUGUACCCACACAAUCUUUGGUUCUACCCAAAUAA---CUACCAUAUAACGCAAUCGAAUUCACUAGCUUUUCGCAACCAUGGGACUCCCACA------
(((.(((((....-....((((((......))))..(((((......)))))...---............))..............((.....)).....))))).)))....------ ( -18.20)
>DroSim_CAF1 6775 110 + 1
GGACUCCCACAAUUUUCAGCUUGUACCCACACAAUCUUUGGCUCUACCCAAAUAA---CUACCAUAAAACGCAAUCGAAUUCACCAGCUUUUCGCAACCAUGGGACUCCCACA------
(((.(((((.........((((((......))))..(((((......)))))...---............))..............((.....)).....))))).)))....------ ( -17.90)
>DroEre_CAF1 7029 107 + 1
GGACUCCCACA-UUUUCAGAUUGCACCUA--CAAUCUUUGGUUCUACCCAAAUAA---CUACCAUAAAACGCCAUCGAAUUCACCAGUUUUUCGCAAUCGUUGGACUCCCACA------
(((.(((.((.-......((((((.....--.....(((((......)))))...---.......(((((................)))))..)))))))).))).)))....------ ( -17.20)
>DroYak_CAF1 6874 110 + 1
GGACUCCCACAAUUUGCAGAUUGUACCUACACAAUCUUCGGUUCUACCCAAAUAA---CUGCCAUAAAACGCAAUCGAAUUCAGCAGUUUUUCGCAACCAUGGGACUCCCACA------
(((.(((((....(((((((((((......)))))))..((......))....((---((((.......((....))......))))))....))))...))))).)))....------ ( -26.22)
>DroAna_CAF1 7176 108 + 1
GGAUUCCCCUUCUUUU--UCUUAU-------CAU--UCUGGGACUACCCAAACAUUGCAUGCAAUAAAACUCCAUCGAUUUCACCAGCUUGCAAAACCCAUGGGAGUCCCCAAAAAGAC
((((((((........--......-------...--..((((....))))....(((((.((........................)).))))).......)))))))).......... ( -23.76)
>consensus
GGACUCCCACAAUUUUCAGCUUGUACCCACACAAUCUUUGGUUCUACCCAAAUAA___CUACCAUAAAACGCAAUCGAAUUCACCAGCUUUUCGCAACCAUGGGACUCCCACA______
(((.(((((...........................(((((......))))).......................((((...........))))......))))).))).......... (-10.12 = -11.07 +   0.95)

alignment

secondary structure

dotplot

Window 4

Location	12,613,867 – 12,613,977
Length	110
Sequences	6
Columns	119
Reading direction	reverse
Mean pairwise identity	79.39
Mean single sequence MFE	-30.53
Consensus MFE	-16.95
Energy contribution	-16.57
Covariance contribution	-0.38
Combinations/Pair	1.38
Mean z-score	-1.80
Structure conservation index	0.56
SVM decision value	0.08
SVM RNA-class probability	0.575418
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 12613867 110 - 20766785
------UGUGGGAGUCCCAUGGCUGCGAAAAGCUGGUGAAUUCGAUUGCGUUUUAUGGUAG---UUAUUUGGGUAGAAGCAAAGAUUGUGUGGGUACAAGAUGAAAAUUGUAGGAGUCC
------....(((.(((....((..((((...(....)..))))...))....((..((..---((((((..(((...(((.......)))...))).))))))..))..))))).))) ( -21.50)
>DroSec_CAF1 6761 109 - 1
------UGUGGGAGUCCCAUGGUUGCGAAAAGCUAGUGAAUUCGAUUGCGUUAUAUGGUAG---UUAUUUGGGUAGAACCAAAGAUUGUGUGGGUACAAGCUGAA-AUUGUGGGAGUCC
------....(((.(((((..(((......((((.(((....(((((((........))))---)).(((((......)))))......)....))).))))..)-))..))))).))) ( -32.20)
>DroSim_CAF1 6775 110 - 1
------UGUGGGAGUCCCAUGGUUGCGAAAAGCUGGUGAAUUCGAUUGCGUUUUAUGGUAG---UUAUUUGGGUAGAGCCAAAGAUUGUGUGGGUACAAGCUGAAAAUUGUGGGAGUCC
------....(((.(((((..(((......((((.(((....(((((((........))))---)).(((((......)))))......)....))).))))...)))..))))).))) ( -31.60)
>DroEre_CAF1 7029 107 - 1
------UGUGGGAGUCCAACGAUUGCGAAAAACUGGUGAAUUCGAUGGCGUUUUAUGGUAG---UUAUUUGGGUAGAACCAAAGAUUG--UAGGUGCAAUCUGAAAA-UGUGGGAGUCC
------....(((.(((..((((..(.(.....).)..)..)))...(((((((.......---....((((......))))((((((--(....))))))).))))-))).))).))) ( -26.20)
>DroYak_CAF1 6874 110 - 1
------UGUGGGAGUCCCAUGGUUGCGAAAAACUGCUGAAUUCGAUUGCGUUUUAUGGCAG---UUAUUUGGGUAGAACCGAAGAUUGUGUAGGUACAAUCUGCAAAUUGUGGGAGUCC
------....(((.(((((..(((((....((((((((((..((....))..)).))))))---))..((((......))))((((((((....)))))))))).)))..))))).))) ( -40.50)
>DroAna_CAF1 7176 108 - 1
GUCUUUUUGGGGACUCCCAUGGGUUUUGCAAGCUGGUGAAAUCGAUGGAGUUUUAUUGCAUGCAAUGUUUGGGUAGUCCCAGA--AUG-------AUAAGA--AAAAGAAGGGGAAUCC
(((.(((((((.(((((((......(((((.((.((((((((.......)))))))))).)))))....)))).)))))))))--).)-------))....--................ ( -31.20)
>consensus
______UGUGGGAGUCCCAUGGUUGCGAAAAGCUGGUGAAUUCGAUUGCGUUUUAUGGUAG___UUAUUUGGGUAGAACCAAAGAUUGUGUGGGUACAAGCUGAAAAUUGUGGGAGUCC
..........(((.((((((..((((.((((((...((....)).....))))).).))))......(((((......)))))..........................)))))).))) (-16.95 = -16.57 +  -0.38)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:04:50 2006