Locus 1561

Sequence ID	X_DroMel_CAF1
Location	4,468,869 – 4,469,006
Length	137
Max. P	0.964808

overview

Window 7

Location	4,468,869 – 4,468,970
Length	101
Sequences	3
Columns	113
Reading direction	forward
Mean pairwise identity	73.27
Mean single sequence MFE	-39.33
Consensus MFE	-21.37
Energy contribution	-22.27
Covariance contribution	0.89
Combinations/Pair	1.07
Mean z-score	-2.11
Structure conservation index	0.54
SVM decision value	1.08
SVM RNA-class probability	0.911292
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4468869 101 + 22224390
GCUGCAACAGUCAUGG------------CUGGCGGACCAGGAUCCUCCGGAUUCGGCUCCAAUCACCAUCAUGGCCAUGGCCAUGGUUCCCAUGGUUCCCAUGGUCAUGCUCC
...((..((((....)------------)))))(((((.((((((...)))))))).))).........(((((((((((((((((...))))))...))))))))))).... ( -41.70)
>DroSec_CAF1 70507 104 + 1
GCUGCAACAGUCAUGGGUCAGGUGCCGGUUGGCGGACCAGGAUCCUCCGGAUCGGGCUCCAAUCACCAUCAUGGCCACGGCCAUGGUUCCCA---------UGGUUAUGCUCC
...(((..(..((((((...((((((....)))(((((..(((((...))))).)).)))....)))((((((((....)))))))).))))---------))..).)))... ( -44.50)
>DroYak_CAF1 71387 83 + 1
GC------CGCCAUG---------------GGCGGACCAGGAUCCUCCGGUUCCGGCAGCAAUCACCAUCAUGGCCAUGGGCACGGUUCCCA---------UGGACAUGCUCC
((------((((...---------------)))(((((.((.....))))))).)))............((((.(((((((.......))))---------))).)))).... ( -31.80)
>consensus
GCUGCAACAGUCAUGG_____________UGGCGGACCAGGAUCCUCCGGAUCCGGCUCCAAUCACCAUCAUGGCCAUGGCCAUGGUUCCCA_________UGGUCAUGCUCC
.........(.((((...............(.((((((.((.....)))).)))).)..........((((((((....))))))))..(((((.....))))).)))))... (-21.37 = -22.27 +   0.89)

alignment

secondary structure

dotplot

Window 8

Location	4,468,897 – 4,469,006
Length	109
Sequences	3
Columns	109
Reading direction	forward
Mean pairwise identity	86.79
Mean single sequence MFE	-43.20
Consensus MFE	-33.98
Energy contribution	-34.54
Covariance contribution	0.56
Combinations/Pair	1.03
Mean z-score	-3.54
Structure conservation index	0.79
SVM decision value	1.57
SVM RNA-class probability	0.964808
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4468897 109 + 22224390
GAUCCUCCGGAUUCGGCUCCAAUCACCAUCAUGGCCAUGGCCAUGGUUCCCAUGGUUCCCAUGGUCAUGCUCCCAUUUCGGAGCAGGUCAAGUGCGCCAUUCUGGCGCA
(((((((((((...((.........))..(((((((((((((((((...))))))...))))))))))).......)))))))..))))...((((((.....)))))) ( -48.10)
>DroSec_CAF1 70547 100 + 1
GAUCCUCCGGAUCGGGCUCCAAUCACCAUCAUGGCCACGGCCAUGGUUCCCA---------UGGUUAUGCUCCCAUUUCGGAGCAGGUCAAGUGCGCCAUUCUGGCGCA
(((((...)))))((..........))....(((((..((((((((...)))---------))))).((((((......)))))))))))..((((((.....)))))) ( -43.30)
>DroYak_CAF1 71406 100 + 1
GAUCCUCCGGUUCCGGCAGCAAUCACCAUCAUGGCCAUGGGCACGGUUCCCA---------UGGACAUGCUCCCAUUUCGGAGCAGGUCAAGUACGCCAUACUGGCGCA
(((.(((((....))).))..))).(((..(((((((((((.......))))---------))(((.((((((......)))))).)))......)))))..))).... ( -38.20)
>consensus
GAUCCUCCGGAUCCGGCUCCAAUCACCAUCAUGGCCAUGGCCAUGGUUCCCA_________UGGUCAUGCUCCCAUUUCGGAGCAGGUCAAGUGCGCCAUUCUGGCGCA
....(.(((((...(((.......(((((((((((....))))))))..(((((.....)))))...((((((......))))))))).......)))..))))).).. (-33.98 = -34.54 +   0.56)

alignment

secondary structure

dotplot

Window 9

Location	4,468,897 – 4,469,006
Length	109
Sequences	3
Columns	109
Reading direction	reverse
Mean pairwise identity	86.79
Mean single sequence MFE	-44.43
Consensus MFE	-36.55
Energy contribution	-36.67
Covariance contribution	0.12
Combinations/Pair	1.09
Mean z-score	-2.73
Structure conservation index	0.82
SVM decision value	1.22
SVM RNA-class probability	0.932181
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4468897 109 - 22224390
UGCGCCAGAAUGGCGCACUUGACCUGCUCCGAAAUGGGAGCAUGACCAUGGGAACCAUGGGAACCAUGGCCAUGGCCAUGAUGGUGAUUGGAGCCGAAUCCGGAGGAUC
((((((.....)))))).....((((((((((.((.(...((((.((((((...((((((...)))))))))))).)))).).))..)))))))((....)).)))... ( -46.30)
>DroSec_CAF1 70547 100 - 1
UGCGCCAGAAUGGCGCACUUGACCUGCUCCGAAAUGGGAGCAUAACCA---------UGGGAACCAUGGCCGUGGCCAUGAUGGUGAUUGGAGCCCGAUCCGGAGGAUC
((((((.....)))))).....((((((((......)))))...((((---------((....)((((((....)))))))))))((((((...))))))...)))... ( -42.10)
>DroYak_CAF1 71406 100 - 1
UGCGCCAGUAUGGCGUACUUGACCUGCUCCGAAAUGGGAGCAUGUCCA---------UGGGAACCGUGCCCAUGGCCAUGAUGGUGAUUGCUGCCGGAACCGGAGGAUC
..(((((.((((((......(((.((((((......)))))).)))((---------((((.......)))))))))))).)))))....((.(((....))).))... ( -44.90)
>consensus
UGCGCCAGAAUGGCGCACUUGACCUGCUCCGAAAUGGGAGCAUGACCA_________UGGGAACCAUGGCCAUGGCCAUGAUGGUGAUUGGAGCCGGAUCCGGAGGAUC
((((((.....))))))(((.(((((((((......))))))...(((((.....)))))....((((((....))))))..)))...((((......))))))).... (-36.55 = -36.67 +   0.12)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:13:35 2006