Locus 6397

Sequence ID	3R_DroMel_CAF1
Location	16,772,913 – 16,773,026
Length	113
Max. P	0.927081

overview

Window 9

Location	16,772,913 – 16,773,026
Length	113
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	89.13
Mean single sequence MFE	-44.72
Consensus MFE	-36.92
Energy contribution	-37.67
Covariance contribution	0.75
Combinations/Pair	1.11
Mean z-score	-1.80
Structure conservation index	0.83
SVM decision value	0.69
SVM RNA-class probability	0.822490
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 16772913 113 + 27905053
GCAAAAGGAUGGGCAAAGUGGAAAGU-------GGGUUGCUCUGCAGCUGAGCGAAAAGUCGUUUCGCCUAAGCAACCGCAGCCCCUUUGGAGCUGCUUCCUUGUUUGUGCUCGUGUCGA
(((..((.((..((((...((((...-------.(((((((..(..((.((((((....)))))).)))..)))))))(((((((....)).)))))))))))))..)).))..)))... ( -42.30)
>DroSec_CAF1 4983 120 + 1
GCAAAAGGAUGGGCAAACUGGGAGGUGGGAAGUGGGUUGCUCUGCAGCUGAGCGAAAAGUCGUUUGGCCUAAGCAACCGCAGCCCCUUUGGAGCUGCUUCCUUGUUUGUGCUCGUGUCGA
......((((((((((((.((((((..(((((.(((((((..(((.((..(((((....)))))..))....)))...)))))))))))....)..)))))).)))..))))))).)).. ( -49.50)
>DroSim_CAF1 6439 113 + 1
ACAAAAGGAUGGGCAAACUGGGAGGU-------GGGUUGCUCUGCAGCUGAGCGAAAAGUCGUUUGGCCUAAGCAACCGCAGCCCCUUUGGAGCUGCUUCCUUGUUUGUGCUCGUGUCGA
......((((((((((((.(((((..-------.(((((((..(..((..(((((....)))))..)))..)))))))(((((((....)).)))))))))).)))..))))))).)).. ( -47.40)
>DroEre_CAF1 1177 112 + 1
GCAAAGCGAUGGGAAAACAGGGAAGC-------GGGGUGCUCUGCAGCUGAGGGAAAAGCCGUUUGGCC-AAGCAACCGCAGCCCGUUUGGAGCUACUUCCUCGCUUGUGCUCGUGUCGA
......(((((.((..(((((.((((-------(((.(((..(((.((..((((.....)).))..)).-..)))...))).)))))))((((....))))...)))))..)).))))). ( -39.70)
>consensus
GCAAAAGGAUGGGCAAACUGGGAAGU_______GGGUUGCUCUGCAGCUGAGCGAAAAGUCGUUUGGCCUAAGCAACCGCAGCCCCUUUGGAGCUGCUUCCUUGUUUGUGCUCGUGUCGA
(((..((.(..(((((...((((...........(((((((.....((..((((......))))..))...)))))))(((((((....)).))))))))))))))..).))..)))... (-36.92 = -37.67 +   0.75)

alignment

secondary structure

dotplot

Window 0

Location	16,772,913 – 16,773,026
Length	113
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	89.13
Mean single sequence MFE	-37.67
Consensus MFE	-32.67
Energy contribution	-32.93
Covariance contribution	0.25
Combinations/Pair	1.13
Mean z-score	-1.98
Structure conservation index	0.87
SVM decision value	1.18
SVM RNA-class probability	0.927081
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 16772913 113 - 27905053
UCGACACGAGCACAAACAAGGAAGCAGCUCCAAAGGGGCUGCGGUUGCUUAGGCGAAACGACUUUUCGCUCAGCUGCAGAGCAACCC-------ACUUUCCACUUUGCCCAUCCUUUUGC
.........(((.....(((((.((((((((...))))))))((((((((.(((....(((....)))....)))...)))))))).-------.................))))).))) ( -36.20)
>DroSec_CAF1 4983 120 - 1
UCGACACGAGCACAAACAAGGAAGCAGCUCCAAAGGGGCUGCGGUUGCUUAGGCCAAACGACUUUUCGCUCAGCUGCAGAGCAACCCACUUCCCACCUCCCAGUUUGCCCAUCCUUUUGC
.......((...(((((..(((.((((((((...))))))))((((((((.(((....(((....)))....)))...))))))))...........)))..)))))....))....... ( -37.70)
>DroSim_CAF1 6439 113 - 1
UCGACACGAGCACAAACAAGGAAGCAGCUCCAAAGGGGCUGCGGUUGCUUAGGCCAAACGACUUUUCGCUCAGCUGCAGAGCAACCC-------ACCUCCCAGUUUGCCCAUCCUUUUGU
...(((.(((..(((((..(((.((((((((...))))))))((((((((.(((....(((....)))....)))...)))))))).-------...)))..)))))......))).))) ( -38.10)
>DroEre_CAF1 1177 112 - 1
UCGACACGAGCACAAGCGAGGAAGUAGCUCCAAACGGGCUGCGGUUGCUU-GGCCAAACGGCUUUUCCCUCAGCUGCAGAGCACCCC-------GCUUCCCUGUUUUCCCAUCGCUUUGC
.........(((.(((((((((......)))((((((((((((((((...-((((....)))).......)))))))))(((.....-------)))..))))))).....))))))))) ( -38.70)
>consensus
UCGACACGAGCACAAACAAGGAAGCAGCUCCAAAGGGGCUGCGGUUGCUUAGGCCAAACGACUUUUCGCUCAGCUGCAGAGCAACCC_______ACCUCCCAGUUUGCCCAUCCUUUUGC
.......((...(((((..(((.(((((((.....)))))))((((((((.(((....(((....)))....)))...))))))))...........)))..)))))....))....... (-32.67 = -32.93 +   0.25)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:20:32 2006