Locus 3231

Sequence ID	3L_DroMel_CAF1
Location	9,451,452 – 9,451,547
Length	95
Max. P	0.821438

overview

Window 8

Location	9,451,452 – 9,451,547
Length	95
Sequences	6
Columns	95
Reading direction	forward
Mean pairwise identity	76.55
Mean single sequence MFE	-32.58
Consensus MFE	-14.37
Energy contribution	-14.98
Covariance contribution	0.61
Combinations/Pair	1.08
Mean z-score	-2.25
Structure conservation index	0.44
SVM decision value	0.68
SVM RNA-class probability	0.821438
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 9451452 95 + 23771897
AAUGGUUGUCUCCAAAGACAACAACAAGCGUCGCCGCAAGGAGACAGAGACGCCCCCACCGCCUCCGCCCGUACCGCCCGCUGGCUCCUCGCUGG
....(((((((....)))))))....((((((.((....)).))).(((..((.......))....(((.((.......)).)))..)))))).. ( -28.60)
>DroVir_CAF1 11343 83 + 1
AAUGGUUGUCUCAAAAGACA---ACAAGCGUCGCCGUAAGGAAACGGAGACACCGCCAACGUCAUCGUCGGUGGCGGC---------GGCGGUGA
....(((((((....)))))---))...(((..((....))..)))....(((((((..((((((.....))))))..---------))))))). ( -40.10)
>DroGri_CAF1 4556 83 + 1
AAUGGUUGUCUCAAAAGACA---ACAAGCGUCGCCGUAAGGAAACAGAUACGCCGCCAACGUCAUCGUCCGCGGCGUC---------GGCGGCGG
....(((((((....)))))---))...((((((((...(....)....(((((((..(((....)))..))))))))---------))))))). ( -41.00)
>DroSec_CAF1 5789 95 + 1
AAUGGUUGUCUCCAAAGACAACAACAAGCGUCGCCGCAAGGAGACGGAGACGCCCCCACCGCCUCCGCCCGCGCCGCCCACUGCCUCCUCGCUGG
....(((((((....))))))).....(((((.((....)).)))((((.((.......)).))))))(((((..((.....)).....))).)) ( -29.10)
>DroSim_CAF1 4102 95 + 1
AAUGGUUGUCUCCAAAGACAACAACAAGCGUCGCCGCAAGGAGACGGAGACGCCCCCACCGCCUCCGCCCGCCCCGCCCACUGCCUCCUCGCUGG
....(((((((....)))))))....((((((.((....)).)))((((.((.......)).))))........................))).. ( -27.80)
>DroAna_CAF1 4903 87 + 1
AAUGGUUGUCUCCAAAGACA---ACAAGCGUCGCCGCAAGGAGACGGAGACACCUCCCCCUCCACCACCAACGGCGUCCAAUGCU-----GCAGC
....(((((((....)))))---)).((((((((((...((((..((((....))))..))))........)))))....)))))-----..... ( -28.90)
>consensus
AAUGGUUGUCUCCAAAGACA___ACAAGCGUCGCCGCAAGGAGACGGAGACGCCCCCACCGCCACCGCCCGCGCCGCCCACUGCC__CUCGCUGG
...(((.(((((....(((..........))).((....)).....))))))))......................................... (-14.37 = -14.98 +   0.61)

alignment

secondary structure

dotplot

Window 9

Location	9,451,452 – 9,451,547
Length	95
Sequences	6
Columns	95
Reading direction	reverse
Mean pairwise identity	76.55
Mean single sequence MFE	-38.42
Consensus MFE	-20.70
Energy contribution	-20.95
Covariance contribution	0.25
Combinations/Pair	1.19
Mean z-score	-1.69
Structure conservation index	0.54
SVM decision value	0.17
SVM RNA-class probability	0.614939
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 9451452 95 - 23771897
CCAGCGAGGAGCCAGCGGGCGGUACGGGCGGAGGCGGUGGGGGCGUCUCUGUCUCCUUGCGGCGACGCUUGUUGUUGUCUUUGGAGACAACCAUU
...((((((((((....)))......((((((((((.......)))))))))))))))))(((((((.....))))))).(((....)))..... ( -40.50)
>DroVir_CAF1 11343 83 - 1
UCACCGCC---------GCCGCCACCGACGAUGACGUUGGCGGUGUCUCCGUUUCCUUACGGCGACGCUUGU---UGUCUUUUGAGACAACCAUU
.....((.---------(((((((.((.......)).)))))))(((.((((......)))).)))))..((---(((((....))))))).... ( -32.60)
>DroGri_CAF1 4556 83 - 1
CCGCCGCC---------GACGCCGCGGACGAUGACGUUGGCGGCGUAUCUGUUUCCUUACGGCGACGCUUGU---UGUCUUUUGAGACAACCAUU
.((.((((---------.(((((((.((((....)))).)))))))....((......)))))).))...((---(((((....))))))).... ( -36.20)
>DroSec_CAF1 5789 95 - 1
CCAGCGAGGAGGCAGUGGGCGGCGCGGGCGGAGGCGGUGGGGGCGUCUCCGUCUCCUUGCGGCGACGCUUGUUGUUGUCUUUGGAGACAACCAUU
...((((((((((.(((.....)))....(((((((.......)))))))))))))))))(((((((.....))))))).(((....)))..... ( -42.00)
>DroSim_CAF1 4102 95 - 1
CCAGCGAGGAGGCAGUGGGCGGGGCGGGCGGAGGCGGUGGGGGCGUCUCCGUCUCCUUGCGGCGACGCUUGUUGUUGUCUUUGGAGACAACCAUU
...((......))(((((((((((.(((((((((((.......)))))))))))))))))(((((((.....))))))).(((....)))))))) ( -43.20)
>DroAna_CAF1 4903 87 - 1
GCUGC-----AGCAUUGGACGCCGUUGGUGGUGGAGGGGGAGGUGUCUCCGUCUCCUUGCGGCGACGCUUGU---UGUCUUUGGAGACAACCAUU
(((((-----((.......((((...))))..(((((.((((....)))).)))))))))))).......((---(((((....))))))).... ( -36.00)
>consensus
CCAGCGAG__GGCAGUGGGCGCCGCGGGCGGAGGCGGUGGGGGCGUCUCCGUCUCCUUGCGGCGACGCUUGU___UGUCUUUGGAGACAACCAUU
...................................((((((((((((.((((......)))).))))))).....(((((....))))).))))) (-20.70 = -20.95 +   0.25)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:52:36 2006