Locus 1755

Sequence ID	3R_DroMel_CAF1
Location	5,059,324 – 5,059,432
Length	108
Max. P	0.707585

overview

Window 2

Location	5,059,324 – 5,059,432
Length	108
Sequences	6
Columns	114
Reading direction	forward
Mean pairwise identity	76.31
Mean single sequence MFE	-45.00
Consensus MFE	-25.27
Energy contribution	-27.38
Covariance contribution	2.11
Combinations/Pair	1.20
Mean z-score	-1.68
Structure conservation index	0.56
SVM decision value	0.37
SVM RNA-class probability	0.707585
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 5059324 108 + 27905053
CGGCGGCGGCGGCCUCGUGCAAGGUCGAGCCUACGGCUCCGACCCCUGGCACACCGCCACCCACUCCGCCCACGCC------GACGCCAACCCCACCAGGCGAUGGACGCUGCU
.(((((((((((....((((..(((((((((...)))).)))))....)))).))))).........(.(((((((------................)))).))).))))))) ( -48.19)
>DroSec_CAF1 165684 108 + 1
CGGCGGCGGCGGCCUCGUGCAAGGUCGAGCCUACGGCUCCGACCCCUGGCACACCGCCACCCACUCCGCCCACGCC------GACGCCAACGCCACCAGGCGAUGGACGCUGCU
.(((((.((.(((...((((..(((((((((...)))).)))))....))))...))).))....)))))...((.------(.(((((.((((....)))).))).))).)). ( -51.80)
>DroSim_CAF1 171513 108 + 1
CGGCGGCGGCGGCCUCGUGCAAGGUCGAGCCUACGGCUCCGACUCCUGGCACACCGCCACCCACUCCGCCCACGCC------GACGCCAACGCCACCGGGCGAUGGACGCUGCU
.(((((.((.(((...((((..(((((((((...)))).)))))....))))...))).))....)))))...((.------(.(((((.((((....)))).))).))).)). ( -49.80)
>DroYak_CAF1 172476 114 + 1
CCGCGGCAGCGGCCUCGUGCAAGGUCGAGCCAACGGCUCCCACCCCUGGCACACCGCCACCCACUCCGCCCACGCCCACUCCGACGCCAACGCCACCGGGCGAUGGACGCUGCU
....(((((((((...((((.(((..(((((...))))).....))).))))...))).........(.((((((((....((.......)).....))))).))).))))))) ( -43.30)
>DroMoj_CAF1 206943 87 + 1
CAGCAGCCGCGGCGUCGUGCAAGUUGGAGCCAACGGGUCCGACGCCGA---CG---------------CCAGCGCC------GAUGC---CGCCGCCGGGUGAUGGGCGCUGCU
.((((((.(((((((((.((..((((((.((...)).)))))))))))---))---------------)).))(((------.((..---((((....)))))).))))))))) ( -49.50)
>DroAna_CAF1 160296 96 + 1
CGGCGGCAGCUGCAUCAUGCAAAUUGGAUCCAACUGCUCCAACACCCGGUACACCA------------CCCACACC------CACACCCACUCCUCCCGGAGAUGGGCGCUGCU
....(((((((((.....)))..(((((.(.....).))))).....((....)).------------........------....((((((((....)))).)))).)))))) ( -27.40)
>consensus
CGGCGGCGGCGGCCUCGUGCAAGGUCGAGCCAACGGCUCCGACCCCUGGCACACCGCCACCCACUCCGCCCACGCC______GACGCCAACGCCACCGGGCGAUGGACGCUGCU
....(((((((.....((((.(((..((((.....)))).....))).))))..................................(((.((((....)))).))).))))))) (-25.27 = -27.38 +   2.11)

alignment

secondary structure

dotplot

Window 3

Location	5,059,324 – 5,059,432
Length	108
Sequences	6
Columns	114
Reading direction	reverse
Mean pairwise identity	76.31
Mean single sequence MFE	-55.38
Consensus MFE	-30.36
Energy contribution	-32.90
Covariance contribution	2.54
Combinations/Pair	1.36
Mean z-score	-1.56
Structure conservation index	0.55
SVM decision value	-0.05
SVM RNA-class probability	0.508176
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 5059324 108 - 27905053
AGCAGCGUCCAUCGCCUGGUGGGGUUGGCGUC------GGCGUGGGCGGAGUGGGUGGCGGUGUGCCAGGGGUCGGAGCCGUAGGCUCGACCUUGCACGAGGCCGCCGCCGCCG
.((..((((((.((((.(..(.......)..)------))))))))))..)).((((((((((.(((.(((((((.((((...)))))))))))......))))))))))))). ( -59.50)
>DroSec_CAF1 165684 108 - 1
AGCAGCGUCCAUCGCCUGGUGGCGUUGGCGUC------GGCGUGGGCGGAGUGGGUGGCGGUGUGCCAGGGGUCGGAGCCGUAGGCUCGACCUUGCACGAGGCCGCCGCCGCCG
.((.(((.(((.((((....)))).)))))).------.))...(((((....((((((..(((((..(((((((.((((...))))))))))))))))..)))))).))))). ( -63.00)
>DroSim_CAF1 171513 108 - 1
AGCAGCGUCCAUCGCCCGGUGGCGUUGGCGUC------GGCGUGGGCGGAGUGGGUGGCGGUGUGCCAGGAGUCGGAGCCGUAGGCUCGACCUUGCACGAGGCCGCCGCCGCCG
.((.(((.(((.((((....)))).)))))).------.))...(((((....((((((..(((((.(((.((((.((((...))))))))))))))))..)))))).))))). ( -59.70)
>DroYak_CAF1 172476 114 - 1
AGCAGCGUCCAUCGCCCGGUGGCGUUGGCGUCGGAGUGGGCGUGGGCGGAGUGGGUGGCGGUGUGCCAGGGGUGGGAGCCGUUGGCUCGACCUUGCACGAGGCCGCUGCCGCGG
.((..((((((.((((((.(((((....)))))...)))))))))))).....((..(((((((((.((((....(((((...)))))..))))))))...)))))..)))).. ( -61.40)
>DroMoj_CAF1 206943 87 - 1
AGCAGCGCCCAUCACCCGGCGGCG---GCAUC------GGCGCUGG---------------CG---UCGGCGUCGGACCCGUUGGCUCCAACUUGCACGACGCCGCGGCUGCUG
((((((.........((((((.((---....)------).))))))---------------((---.((((((((..(..((((....))))..)..)))))))))))))))). ( -47.70)
>DroAna_CAF1 160296 96 - 1
AGCAGCGCCCAUCUCCGGGAGGAGUGGGUGUG------GGUGUGGG------------UGGUGUACCGGGUGUUGGAGCAGUUGGAUCCAAUUUGCAUGAUGCAGCUGCCGCCG
.((.(((((((.((((....))))))))))).------.))...((------------((((...((((.(((....))).)))).......((((.....))))..)))))). ( -41.00)
>consensus
AGCAGCGUCCAUCGCCCGGUGGCGUUGGCGUC______GGCGUGGGCGGAGUGGGUGGCGGUGUGCCAGGGGUCGGAGCCGUAGGCUCGACCUUGCACGAGGCCGCCGCCGCCG
.((.((((((..((((....))))...(((((......)))))))))......((((((..((((.(((((....((((.....))))..)))))))))..)))))))).)).. (-30.36 = -32.90 +   2.54)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:18:30 2006