Locus 3553

Sequence ID	X_DroMel_CAF1
Location	9,527,263 – 9,527,404
Length	141
Max. P	0.922446

overview

Window 4

Location	9,527,263 – 9,527,370
Length	107
Sequences	5
Columns	107
Reading direction	reverse
Mean pairwise identity	94.11
Mean single sequence MFE	-49.90
Consensus MFE	-42.22
Energy contribution	-42.54
Covariance contribution	0.32
Combinations/Pair	1.09
Mean z-score	-1.69
Structure conservation index	0.85
SVM decision value	1.15
SVM RNA-class probability	0.922446
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 9527263 107 - 22224390
CGGCUCUGGCACAGGCGGAGUCGGUGUUGGAGUGAAUGUGGGUGUCGGCGGUGUUGUUGGCGUCGGCGUUGUGCCUUCCCAGAUGAACGGAGCCGGCGGCGGCAACG
..((((..((((.(((...))).))))..))))...(((.(.(((((((..((((.((((.(..(((.....)))..)))))...))))..))))))).).)))... ( -46.00)
>DroSec_CAF1 11013 107 - 1
CGGCUCUGGCACAGGCGGAGUCGGUGUUGGAGUCAAUGUGGGUGUCGGCGGUGUUGUUGGCGUCAGCGUUGUGCCUUCCCAGAUGAACGGAGCCGGCGGCGGCAACG
.(((((..((((.(((...))).))))..)))))..(((.(.(((((((((..((((((....)))))..)..)).(((.........)))))))))).).)))... ( -45.10)
>DroSim_CAF1 10501 107 - 1
CGGCUCUGGCACAGGCGGAGUCGGUGUUGGAGUCAAUGUGGGUGUCGGCGGUGUUGUUGGCGUCGGCGUUGUGCCUUCCCAGAUGAACGGAGCCGGCGGCGGCAACG
.(((((..((((.(((...))).))))..)))))..(((.(.(((((((..((((.((((.(..(((.....)))..)))))...))))..))))))).).)))... ( -48.90)
>DroEre_CAF1 11137 101 - 1
CGGCUCUGGCACUGGCGGAGUCGGUGUUGGAGUCAAUGUGACCGUCGGCGGUGUUGUCG------GCGUUGUGCCUUCCCAGAUGAACGGAGCCGGCGGCGGCAACG
.(((((..((((((((...))))))))..)))))......((((....))))(((((((------.(((((.((..(((.........)))))))))).))))))). ( -49.70)
>DroYak_CAF1 11318 107 - 1
UGGCUCUGGCACUGGCGGAGUCGGUGUUGGAGUCAAUGUGGCCGUCGGCGGUGUUGUCGGCGUCGGCGUUGUGCCUUCCCAGAUGAACGGAGCCGGCGGCGGCAACG
((((((..((((((((...))))))))..)))))).(((.(((((((((..(((((((((.(..(((.....)))..))).))).))))..))))))))).)))... ( -59.80)
>consensus
CGGCUCUGGCACAGGCGGAGUCGGUGUUGGAGUCAAUGUGGGUGUCGGCGGUGUUGUUGGCGUCGGCGUUGUGCCUUCCCAGAUGAACGGAGCCGGCGGCGGCAACG
.(((((..((((.(((...))).))))..)))))..(((.(.(((((((((..((((((....)))))..)..)).(((.........)))))))))).).)))... (-42.22 = -42.54 +   0.32)

alignment

secondary structure

dotplot

Window 5

Location	9,527,302 – 9,527,404
Length	102
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	80.05
Mean single sequence MFE	-50.35
Consensus MFE	-30.11
Energy contribution	-30.83
Covariance contribution	0.72
Combinations/Pair	1.19
Mean z-score	-1.75
Structure conservation index	0.60
SVM decision value	0.22
SVM RNA-class probability	0.637771
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 9527302 102 - 22224390
GUGGCGGACCCAACAAGCCGGCAGCCCAAGGACC------CGGCUCUGGCACAGGCGGAGUCGGUGUUGGAGUG------------AAUGUGGGUGUCGGCGGUGUUGUUGGCGUCGGCG
...((.(((((((((((((((((.((((..((((------((((((((.(...).))))))))).)))......------------....)))))))))))....))))))).))).)). ( -51.40)
>DroSec_CAF1 11052 102 - 1
GUGGAGGACCCAACAAGCCGGCAGCCCAAGGACC------CGGCUCUGGCACAGGCGGAGUCGGUGUUGGAGUC------------AAUGUGGGUGUCGGCGGUGUUGUUGGCGUCAGCG
...(..(((((((((((((((((.((((.(....------)(((((..((((.(((...))).))))..)))))------------....)))))))))))....))))))).)))..). ( -50.00)
>DroSim_CAF1 10540 102 - 1
GUGGAGGACCCAACAAGCCGGCAGCCCAAGGACC------CGGCUCUGGCACAGGCGGAGUCGGUGUUGGAGUC------------AAUGUGGGUGUCGGCGGUGUUGUUGGCGUCGGCG
((.((.(.(((((((.(((((((.((((.(....------)(((((..((((.(((...))).))))..)))))------------....)))))))))))..)))))..))).)).)). ( -50.90)
>DroEre_CAF1 11176 102 - 1
GUGGUGGACCCAAUAAACCGGCAGCCCAAGGACCCGGUCCCGGCUCUGGCACUGGCGGAGUCGGUGUUGGAGUC------------AAUGUGACCGUCGGCGGUGUUGUCG------GCG
.(((.....))).....((((((((((...(((..(((((.(((((..((((((((...))))))))..)))))------------...).)))))))...)).)))))))------).. ( -45.00)
>DroYak_CAF1 11357 102 - 1
GUGGCGGACCCAACAAACCGGCAGCCCAAGGACC------UGGCUCUGGCACUGGCGGAGUCGGUGUUGGAGUC------------AAUGUGGCCGUCGGCGGUGUUGUCGGCGUCGGCG
...((.(((((.((((.(((((.(((((......------((((((..((((((((...))))))))..)))))------------).)).))).))))).....)))).)).))).)). ( -48.60)
>DroAna_CAF1 16128 114 - 1
GCGGCGGACCAAAUAAGCCACCUGCCCAGGGACCUGGACCCGGUUCUGGACCCGGCGGUGUUGGUGUCGGAGUCGUCGGCGGCGUUAAUGUUGGCGUCG------UCGGCGGCGUCGGCG
..((....))......((((((((((..(((.((.((((...)))).)).)))))))).).))))((((..((((((((((((((((....))))))))------))))))))..)))). ( -56.20)
>consensus
GUGGCGGACCCAACAAGCCGGCAGCCCAAGGACC______CGGCUCUGGCACAGGCGGAGUCGGUGUUGGAGUC____________AAUGUGGGCGUCGGCGGUGUUGUCGGCGUCGGCG
......((((((((..((((((.(((..((..((.......))..))......)))...))))))))))).)))...............((.(((((((((......))))))))).)). (-30.11 = -30.83 +   0.72)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:02:15 2006