Locus 2173

Sequence ID	X_DroMel_CAF1
Location	5,897,916 – 5,898,046
Length	130
Max. P	0.938579

overview

Window 2

Location	5,897,916 – 5,898,006
Length	90
Sequences	4
Columns	90
Reading direction	reverse
Mean pairwise identity	97.78
Mean single sequence MFE	-27.33
Consensus MFE	-26.00
Energy contribution	-26.25
Covariance contribution	0.25
Combinations/Pair	1.00
Mean z-score	-2.10
Structure conservation index	0.95
SVM decision value	0.89
SVM RNA-class probability	0.875520
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5897916 90 - 22224390
UUGUGUAUCUAUGAGAUACGCGCAACGUGAAUUGGCAUUUUCCAUUUGGCAAUUUGCAUGUGCAAUGCAAUGCGGGCUCCAAGAUCUGCA
(((((((((.....)))))(((((..(..(((((.((.........)).)))))..).)))))...))))(((((((.....).)))))) ( -27.50)
>DroSec_CAF1 14659 90 - 1
UUGUGUAUCUAUGAGAUACGCGCAACGUGAAUUGGCAUUUUCCAUUUGGCAAUUUGCAUGUGCAAUGUAAUGCGGGCUCCAAGAUCUGCA
..(((((((.....)))))))(((..(..(((((.((.........)).)))))..)...))).......(((((((.....).)))))) ( -27.20)
>DroEre_CAF1 14755 90 - 1
UUGUGUAUCUAUGAGAUACGCGCAACGUGAAUUGGCAUUUUCCAUUUGGCAAUUUGCAUGUGCAAUGCAAUGCGGGCUCCAAGAUCUGCA
(((((((((.....)))))(((((..(..(((((.((.........)).)))))..).)))))...))))(((((((.....).)))))) ( -27.50)
>DroYak_CAF1 14860 90 - 1
UUGUGUAUCUAUGAGAUACGCGCAACGUGAAUUGGCAUUUUCCAUUUGGCAAUUUGCAUGUGCAAUGCAAUGCGGGCAGCAAGAUAUGCA
.(((((((((.........(((((..(..(((((.((.........)).)))))..).))))).......(((.....)))))))))))) ( -27.10)
>consensus
UUGUGUAUCUAUGAGAUACGCGCAACGUGAAUUGGCAUUUUCCAUUUGGCAAUUUGCAUGUGCAAUGCAAUGCGGGCUCCAAGAUCUGCA
..(((((((.....)))))))(((..(..(((((.((.........)).)))))..)...))).......(((((((.....).)))))) (-26.00 = -26.25 +   0.25)

alignment

secondary structure

dotplot

Window 3

Location	5,897,948 – 5,898,046
Length	98
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	84.27
Mean single sequence MFE	-22.44
Consensus MFE	-14.14
Energy contribution	-15.74
Covariance contribution	1.60
Combinations/Pair	1.00
Mean z-score	-2.85
Structure conservation index	0.63
SVM decision value	1.27
SVM RNA-class probability	0.938579
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5897948 98 + 22224390
UGCA---------------------AAUUGCCAAAUGGAAAAUGCCAAUUCACGUUGCGCGUAUCUCAUAGAUACACAA-AAUUGAAAUUAUAAUAAAAAGCAAUGAGGCAAAAAACGGU
....---------------------..(((((...(((......))).....((((((..(((((.....))))).((.-...))...............)))))).)))))........ ( -21.10)
>DroSec_CAF1 14691 98 + 1
UGCA---------------------AAUUGCCAAAUGGAAAAUGCCAAUUCACGUUGCGCGUAUCUCAUAGAUACACAA-AAUUGAAAUUAUAAUAAAAAGCAAUGAGGCAAAAAACGGU
....---------------------..(((((...(((......))).....((((((..(((((.....))))).((.-...))...............)))))).)))))........ ( -21.10)
>DroEre_CAF1 14787 97 + 1
UGCA---------------------AAUUGCCAAAUGGAAAAUGCCAAUUCACGUUGCGCGUAUCUCAUAGAUACACAA-AAUUGAAAUUAUAAUAAAAAGCAAUGAGGCAA-AAACGGU
....---------------------..(((((...(((......))).....((((((..(((((.....))))).((.-...))...............)))))).)))))-....... ( -21.10)
>DroWil_CAF1 14757 118 + 1
UGCAAAUUGCAAAUUACGAUUGGCGAAUUGCAAAAUGCAAAAUGCCAAUUCACCUAGCGCGUAUCUCAUAGAUACACAAAAAUUGAAAUUAUAAGACUGCCCCCUGAGGCUCAUAG-GC-
(((.....)))......((((((((..((((.....))))..))))))))..((((..(.(((((.....))))).).....................(((......)))...)))-).- ( -27.80)
>DroYak_CAF1 14892 98 + 1
UGCA---------------------AAUUGCCAAAUGGAAAAUGCCAAUUCACGUUGCGCGUAUCUCAUAGAUACACAA-AAUUGAAAUUAUAAUAAAAAGCAAUGAGGCAAAAAACGGU
....---------------------..(((((...(((......))).....((((((..(((((.....))))).((.-...))...............)))))).)))))........ ( -21.10)
>consensus
UGCA_____________________AAUUGCCAAAUGGAAAAUGCCAAUUCACGUUGCGCGUAUCUCAUAGAUACACAA_AAUUGAAAUUAUAAUAAAAAGCAAUGAGGCAAAAAACGGU
...........................(((((...(((......))).....((((((..(((((.....))))).((.....))...............)))))).)))))........ (-14.14 = -15.74 +   1.60)

alignment

secondary structure

dotplot

Window 4

Location	5,897,948 – 5,898,046
Length	98
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	84.27
Mean single sequence MFE	-23.32
Consensus MFE	-15.34
Energy contribution	-16.14
Covariance contribution	0.80
Combinations/Pair	1.00
Mean z-score	-2.09
Structure conservation index	0.66
SVM decision value	0.47
SVM RNA-class probability	0.748424
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5897948 98 - 22224390
ACCGUUUUUUGCCUCAUUGCUUUUUAUUAUAAUUUCAAUU-UUGUGUAUCUAUGAGAUACGCGCAACGUGAAUUGGCAUUUUCCAUUUGGCAAUU---------------------UGCA
...((...(((((....................((((...-.((((((((.....)))))))).....)))).(((......)))...)))))..---------------------.)). ( -20.50)
>DroSec_CAF1 14691 98 - 1
ACCGUUUUUUGCCUCAUUGCUUUUUAUUAUAAUUUCAAUU-UUGUGUAUCUAUGAGAUACGCGCAACGUGAAUUGGCAUUUUCCAUUUGGCAAUU---------------------UGCA
...((...(((((....................((((...-.((((((((.....)))))))).....)))).(((......)))...)))))..---------------------.)). ( -20.50)
>DroEre_CAF1 14787 97 - 1
ACCGUUU-UUGCCUCAUUGCUUUUUAUUAUAAUUUCAAUU-UUGUGUAUCUAUGAGAUACGCGCAACGUGAAUUGGCAUUUUCCAUUUGGCAAUU---------------------UGCA
...((..-(((((....................((((...-.((((((((.....)))))))).....)))).(((......)))...)))))..---------------------.)). ( -20.20)
>DroWil_CAF1 14757 118 - 1
-GC-CUAUGAGCCUCAGGGGGCAGUCUUAUAAUUUCAAUUUUUGUGUAUCUAUGAGAUACGCGCUAGGUGAAUUGGCAUUUUGCAUUUUGCAAUUCGCCAAUCGUAAUUUGCAAUUUGCA
-((-(.....((((....))))...........((((.((..((((((((.....))))))))..)).))))..)))....((((..((((((.(..(.....)..).))))))..)))) ( -34.90)
>DroYak_CAF1 14892 98 - 1
ACCGUUUUUUGCCUCAUUGCUUUUUAUUAUAAUUUCAAUU-UUGUGUAUCUAUGAGAUACGCGCAACGUGAAUUGGCAUUUUCCAUUUGGCAAUU---------------------UGCA
...((...(((((....................((((...-.((((((((.....)))))))).....)))).(((......)))...)))))..---------------------.)). ( -20.50)
>consensus
ACCGUUUUUUGCCUCAUUGCUUUUUAUUAUAAUUUCAAUU_UUGUGUAUCUAUGAGAUACGCGCAACGUGAAUUGGCAUUUUCCAUUUGGCAAUU_____________________UGCA
........(((((....................((((.....((((((((.....)))))))).....)))).(((......)))...)))))........................... (-15.34 = -16.14 +   0.80)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:27:54 2006