Locus 8238

Sequence ID	X_DroMel_CAF1
Location	20,457,018 – 20,457,181
Length	163
Max. P	0.777337

overview

Window 2

Location	20,457,018 – 20,457,123
Length	105
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	86.95
Mean single sequence MFE	-37.20
Consensus MFE	-31.02
Energy contribution	-31.22
Covariance contribution	0.19
Combinations/Pair	1.04
Mean z-score	-1.74
Structure conservation index	0.83
SVM decision value	0.16
SVM RNA-class probability	0.612488
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 20457018 105 + 22224390
-------CC--A----UCCAACCC-UUGGAACAUGGCAUCAUUACACGGCCGCGUCGCACGCAAAAUUGUGCGAAAUUUGGUGAGCCGCGUGUGGCA-AGUCGUGUGGCGGAUUCAAUUC
-------..--.----((((....-.))))...(((.(((.(((((((((...(((((((((.(((((......)))))((....))))))))))).-.)))))))))..)))))).... ( -35.30)
>DroVir_CAF1 50904 104 + 1
-------UC--A----UC--GCUC-AUGGCACAUGGCAUCAUUACACGGCCGCUUCGCACGCAAAAUUGUGCGAAAUUUGGUGAGCCGCGUGUGGCAUAGUCGUGUGGCAAAUUCAAUUC
-------..--.----..--....-.((.((((((((.((((.((.(((((((((((((((......))))))).....)))).)))).))))))....)))))))).)).......... ( -37.10)
>DroGri_CAF1 48240 106 + 1
-------CCACG----CC--GCUA-AGGGCACAUGGCAUCAUUACACGGCCGCUUCGCACGCAAAAUUGUGCGAAAUUUGGUGAGCCGCGUGUGGCAUAGUCGUGUGGCAAAUUCAAUUC
-------(((((----(.--((((-..(.((((((...........(((((((((((((((......))))))).....)))).)))))))))).).)))).))))))............ ( -38.90)
>DroWil_CAF1 51832 117 + 1
UGCUUUUCC--AUGGGUCCUUCUCCAUGGCACAUGGCAUCAUUACAUGGCCACGUCGCACGCAAAAUUGUGCGAAAUUUGGUGAGCCGCGUGUGGCA-AGUCGUGUGGCGUAUUCAAUUC
.((....((--(((((......)))))))((((((((..(((...)))((((((.(((.((((......))))......((....))))))))))).-.))))))))))........... ( -42.90)
>DroYak_CAF1 29028 106 + 1
-------CC--A----UCCAACCCCUAGGAACAUGGCAUCAUUACACGGCCGCGUCGCACGCAAAAUUGUGCGAAAUUUGGUGAGCCGCGUGUGGCA-AGUCGUGUGGCGGAUUCAAUUC
-------..--.----(((........)))...(((.(((.(((((((((...(((((((((.(((((......)))))((....))))))))))).-.)))))))))..)))))).... ( -34.40)
>DroMoj_CAF1 67636 104 + 1
-------CC--A----UC--GCUU-AUGGCACAUGGCAUCAUUACACAGCCGCCUCGCACGCAAAAUUGUGCGAAAUUUGGUGAGCCGCGUGUGGCAUAGUCGUGUGGCAAAUUCAAUUC
-------..--.----..--....-.((.((((((((....((((((.(((((((((((((......))))))).....)))).))...))))))....)))))))).)).......... ( -34.60)
>consensus
_______CC__A____UC__GCUC_AUGGCACAUGGCAUCAUUACACGGCCGCGUCGCACGCAAAAUUGUGCGAAAUUUGGUGAGCCGCGUGUGGCA_AGUCGUGUGGCAAAUUCAAUUC
...........................(.((((((((...........((((..(((((((......)))))))....))))..((((....))))...)))))))).)........... (-31.02 = -31.22 +   0.19)

alignment

secondary structure

dotplot

Window 3

Location	20,457,084 – 20,457,181
Length	97
Sequences	3
Columns	103
Reading direction	forward
Mean pairwise identity	94.79
Mean single sequence MFE	-33.05
Consensus MFE	-31.53
Energy contribution	-31.64
Covariance contribution	0.11
Combinations/Pair	1.04
Mean z-score	-1.79
Structure conservation index	0.95
SVM decision value	0.55
SVM RNA-class probability	0.777337
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 20457084 97 + 22224390
GUGAGCCGCGUGUGGCAAGUCGUGUGGCGGAUUCAAUUCGCAAACUUUUCAGCCCCCCAAACGAGCACACA------CACACACGCACGAGAUACGGCUCGAA
.(((((((((((((....((.(((((((((((...))))))..........(((........).)).))))------)))...)))))).....))))))).. ( -32.10)
>DroSec_CAF1 30763 103 + 1
GUGAGCCGCGUGUGGCAAGUCGUGUGGCGGAUUCAAUUCGCAAACUUUUCAGCCCCCCAAACGAGCACACACACACACACACACGCCCGAGAUACGGCUCGAA
.(((((((((((((....((.(((((((((((...))))))..........(((........).))...)))))))...)))))))..(.....))))))).. ( -33.50)
>DroSim_CAF1 35691 101 + 1
GUGAGCCGCGUGUGGCAAGUCGUGUGGCGGAUUCAAUUCGCAAACUUUUCAGCCCCCCAAACGAGUACACACAC--ACACACACGCACGAGAUACGGCUCGAA
.(((((((((((((....((.(((((((((((...))))))..((((...............)))).)))))))--...)))))))..(.....))))))).. ( -33.56)
>consensus
GUGAGCCGCGUGUGGCAAGUCGUGUGGCGGAUUCAAUUCGCAAACUUUUCAGCCCCCCAAACGAGCACACACAC__ACACACACGCACGAGAUACGGCUCGAA
.(((((((((((((.......(((((((((((...))))))..........(((........).)).))))).......)))))))..(.....))))))).. (-31.53 = -31.64 +   0.11)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:59:06 2006