Locus 5199

Sequence ID	3R_DroMel_CAF1
Location	13,619,717 – 13,619,819
Length	102
Max. P	0.991693

overview

Window 5

Location	13,619,717 – 13,619,819
Length	102
Sequences	6
Columns	119
Reading direction	forward
Mean pairwise identity	77.64
Mean single sequence MFE	-34.50
Consensus MFE	-20.64
Energy contribution	-22.46
Covariance contribution	1.82
Combinations/Pair	1.11
Mean z-score	-3.11
Structure conservation index	0.60
SVM decision value	2.28
SVM RNA-class probability	0.991693
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 13619717 102 + 27905053
GCGGAAUGAGCCACAAUUCGGCACGAAAGAUCGUUCCAAUUGGAACAUGAGACCGCG---ACGAGUGCACCUCCAUGCAUUCGCAUU------------CGCACUCGUAUUCA--UACU
..((((((((((.......))).(....).))))))).....(((.(((((...(((---(((((((((......))))))))...)------------))).))))).))).--.... ( -36.70)
>DroSec_CAF1 68684 102 + 1
GCGGAAUGAGCCACAAUUCGGCACGAAAGAUCGUUCCAAUUGGAACAUGAGACCGCG---ACGAGUGCACCUCCAUGCAUUCGCAUU------------CGCACUCGUAUUCA--UACU
..((((((((((.......))).(....).))))))).....(((.(((((...(((---(((((((((......))))))))...)------------))).))))).))).--.... ( -36.70)
>DroSim_CAF1 62308 102 + 1
GCGGAAUGAGCCACAAUUCGGCACGAAAGAUCGUUCCAAUUGGAACAUGAGACCGCG---ACGAGUGCACCUCCAUGCAUUCGCAUU------------CGCACUCGUAUUCA--UACU
..((((((((((.......))).(....).))))))).....(((.(((((...(((---(((((((((......))))))))...)------------))).))))).))).--.... ( -36.70)
>DroEre_CAF1 59961 113 + 1
GCGGAAUGAGCCACAAUUCGGCACGAAAGAUCGUUCCAAUUGGAACAUGAGACCGCG---ACGAGUGCACCUCCAUGCAUUCGCAUUCGCAU-CGCACUCGCAUUCGUAUUCA--UACU
..((((((((((.......))).(....).))))))).....(((.(((((...(((---(((((((((......))))))))...))))..-.((....)).))))).))).--.... ( -37.20)
>DroYak_CAF1 61782 113 + 1
-CGGAAUGAGCCACAAUUCGGCACGAAAGAUCGUUCCAAUUGGAACAUGAGACCGCG---AAGAGUGCACCUCCAUGCAUUCGCAAUCGCAUUUGCACUCGCACUCGUAUUCA--UACU
-.((((((((((.......))).(....).))))))).....(((.(((((...(((---(.(((((((......)))))))((((......))))..)))).))))).))).--.... ( -39.80)
>DroPer_CAF1 69877 88 + 1
AUGGUAUGAGGAAUGAUUGCGC-------UUCGUUAUAAAUGGAACGUGAGUCUACACAUUCGUAUUCACAUUCCUGCAUUCAUA------------------------UUCAUGUAUU
((((.((((((((((.(..((.-------(((((.....))))).))..)(..(((......)))..).))))))).))))))).------------------------.......... ( -19.90)
>consensus
GCGGAAUGAGCCACAAUUCGGCACGAAAGAUCGUUCCAAUUGGAACAUGAGACCGCG___ACGAGUGCACCUCCAUGCAUUCGCAUU____________CGCACUCGUAUUCA__UACU
..((((((((((.......))).(....).))))))).....(((.(((((...........(((((((......)))))))((................)).))))).)))....... (-20.64 = -22.46 +   1.82)

alignment

secondary structure

dotplot

Window 6

Location	13,619,717 – 13,619,819
Length	102
Sequences	6
Columns	119
Reading direction	reverse
Mean pairwise identity	77.64
Mean single sequence MFE	-34.15
Consensus MFE	-18.24
Energy contribution	-20.80
Covariance contribution	2.56
Combinations/Pair	1.18
Mean z-score	-1.87
Structure conservation index	0.53
SVM decision value	0.34
SVM RNA-class probability	0.697237
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 13619717 102 - 27905053
AGUA--UGAAUACGAGUGCG------------AAUGCGAAUGCAUGGAGGUGCACUCGU---CGCGGUCUCAUGUUCCAAUUGGAACGAUCUUUCGUGCCGAAUUGUGGCUCAUUCCGC
....--.....(((((((((------------.((((....)))).....)))))))))---.((((......((..(((((((.((((....)))).)).)))))..)).....)))) ( -36.00)
>DroSec_CAF1 68684 102 - 1
AGUA--UGAAUACGAGUGCG------------AAUGCGAAUGCAUGGAGGUGCACUCGU---CGCGGUCUCAUGUUCCAAUUGGAACGAUCUUUCGUGCCGAAUUGUGGCUCAUUCCGC
....--.....(((((((((------------.((((....)))).....)))))))))---.((((......((..(((((((.((((....)))).)).)))))..)).....)))) ( -36.00)
>DroSim_CAF1 62308 102 - 1
AGUA--UGAAUACGAGUGCG------------AAUGCGAAUGCAUGGAGGUGCACUCGU---CGCGGUCUCAUGUUCCAAUUGGAACGAUCUUUCGUGCCGAAUUGUGGCUCAUUCCGC
....--.....(((((((((------------.((((....)))).....)))))))))---.((((......((..(((((((.((((....)))).)).)))))..)).....)))) ( -36.00)
>DroEre_CAF1 59961 113 - 1
AGUA--UGAAUACGAAUGCGAGUGCG-AUGCGAAUGCGAAUGCAUGGAGGUGCACUCGU---CGCGGUCUCAUGUUCCAAUUGGAACGAUCUUUCGUGCCGAAUUGUGGCUCAUUCCGC
.(((--....)))....(((((((((-...(..((((....)))).)...)))))))))---.((((......((..(((((((.((((....)))).)).)))))..)).....)))) ( -37.50)
>DroYak_CAF1 61782 113 - 1
AGUA--UGAAUACGAGUGCGAGUGCAAAUGCGAUUGCGAAUGCAUGGAGGUGCACUCUU---CGCGGUCUCAUGUUCCAAUUGGAACGAUCUUUCGUGCCGAAUUGUGGCUCAUUCCG-
.(.(--(((.(((((...((.(..(..(((.((((((((((((((....)))))...))---))))))).)))(((((....)))))........)..)))..)))))..)))).)..- ( -37.40)
>DroPer_CAF1 69877 88 - 1
AAUACAUGAA------------------------UAUGAAUGCAGGAAUGUGAAUACGAAUGUGUAGACUCACGUUCCAUUUAUAACGAA-------GCGCAAUCAUUCCUCAUACCAU
.....((((.------------------------.((((.(((.(((((((((.((((....))))...))))))))).(((.....)))-------..))).))))...))))..... ( -22.00)
>consensus
AGUA__UGAAUACGAGUGCG____________AAUGCGAAUGCAUGGAGGUGCACUCGU___CGCGGUCUCAUGUUCCAAUUGGAACGAUCUUUCGUGCCGAAUUGUGGCUCAUUCCGC
...........(((((((((.............((((....)))).....)))))))))....((((.....((((((....)))))).......(.((((.....)))).)...)))) (-18.24 = -20.80 +   2.56)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:48:53 2006