Locus 4244

Sequence ID	X_DroMel_CAF1
Location	11,131,291 – 11,131,416
Length	125
Max. P	0.895405

overview

Window 2

Location	11,131,291 – 11,131,383
Length	92
Sequences	5
Columns	93
Reading direction	forward
Mean pairwise identity	89.84
Mean single sequence MFE	-27.94
Consensus MFE	-21.46
Energy contribution	-21.46
Covariance contribution	0.00
Combinations/Pair	1.08
Mean z-score	-1.85
Structure conservation index	0.77
SVM decision value	0.62
SVM RNA-class probability	0.802564
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 11131291 92 + 22224390
GCCUGUAAAUCCUCUAAGCCACAAUAUUUACUGUGAUGGCACAGUGGGCGAUGUGGGCAUACAACGGA-AAAGAAAAGGGGCGCCAGCAGUAG
..((((....(((((...(((((.(.(((((((((....))))))))).).)))))........(...-...)...))))).....))))... ( -23.50)
>DroSec_CAF1 46450 93 + 1
GCCUGUAAAUCCUAUAAGCCACAAUAUUUACUGUGAUGGCACAGUGGGCGAUGUGGGCAUGCAACGGGGCAAAAAAAGGGGCGCCAGCAGUAG
((.((((...((((((.(((........(((((((....))))))))))..))))))..))))..((.((..........)).)).))..... ( -25.70)
>DroSim_CAF1 14934 93 + 1
GCCUGUAAAUCCUCUAAGCCACAAUAUUUACUGUGAUGGCACAGUGGGUGAUGUGGGCAUGCAACGGGGCAAAAAAAGGGGCGCCAGCAGUGG
.(((((....(((((...(((((.(((((((((((....))))))))))).)))))...(((......))).....))))).....)))).). ( -31.40)
>DroEre_CAF1 46255 90 + 1
GCCUGUAAAUCCUCUAAGCCACAAUAUUUACUGUGAUGGCACAGUGGGCAAUGUGGGCAGACAACAGA---AAAACUGGGGCGGCAACAGAAG
((((........(((...(((((.(.(((((((((....))))))))).).)))))..)))...(((.---....)))))))(....)..... ( -25.60)
>DroYak_CAF1 49261 90 + 1
GCCUGUAAAUCCUCUAAGCCACAAUAUUUACUGUGAUGGCACAGUGGGUGUUGUGGGCAUACAACGGG---AAAAAAGGGGAGGCAACAGUAG
..((((...((((((...(((((((((((((((((....))))))))))))))))).....(....).---.....))))))....))))... ( -33.50)
>consensus
GCCUGUAAAUCCUCUAAGCCACAAUAUUUACUGUGAUGGCACAGUGGGCGAUGUGGGCAUACAACGGG__AAAAAAAGGGGCGCCAGCAGUAG
..((((....(((((...(((((.(.(((((((((....))))))))).).)))))(....)..............))))).....))))... (-21.46 = -21.46 +   0.00)

alignment

secondary structure

dotplot

Window 3

Location	11,131,305 – 11,131,416
Length	111
Sequences	5
Columns	112
Reading direction	forward
Mean pairwise identity	89.68
Mean single sequence MFE	-30.28
Consensus MFE	-21.44
Energy contribution	-22.22
Covariance contribution	0.78
Combinations/Pair	1.09
Mean z-score	-2.82
Structure conservation index	0.71
SVM decision value	0.99
SVM RNA-class probability	0.895405
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 11131305 111 + 22224390
UAAGCCACAAUAUUUACUGUGAUGGCACAGUGGGCGAUGUGGGCAUACAACGGA-AAAGAAAAGGGGCGCCAGCAGUAGUAAUACGAAAAUGGGGUGCGAAAAAACCAGAAA
....(((((.(.(((((((((....))))))))).).)))))............-.........(.((.(((...(((....))).....))).)).).............. ( -27.20)
>DroSec_CAF1 46464 112 + 1
UAAGCCACAAUAUUUACUGUGAUGGCACAGUGGGCGAUGUGGGCAUGCAACGGGGCAAAAAAAGGGGCGCCAGCAGUAGUUAUACGAAAAUGGGGUGCGAAAAAACCAGAAA
....(((((.(.(((((((((....))))))))).).)))))((((.(...((.((..........)).))....(((....))).......).)))).............. ( -29.10)
>DroSim_CAF1 14948 112 + 1
UAAGCCACAAUAUUUACUGUGAUGGCACAGUGGGUGAUGUGGGCAUGCAACGGGGCAAAAAAAGGGGCGCCAGCAGUGGUAAUACGAAAAUGGUGUGCGAAAAAACCAGAAA
....(((((.(((((((((((....))))))))))).)))))((((((...((.((..........)).))....(((....))).......)))))).............. ( -33.90)
>DroEre_CAF1 46269 108 + 1
UAAGCCACAAUAUUUACUGUGAUGGCACAGUGGGCAAUGUGGGCAGACAACAGA---AAAACUGGGGCGGCAACAGAAGUAAUACGAAAAUGGGGUGCGAAAA-ACCCAAAA
....(((((.(.(((((((((....))))))))).).)))))((.(.(..(((.---....)))..)).)).....................((((.......-)))).... ( -27.80)
>DroYak_CAF1 49275 108 + 1
UAAGCCACAAUAUUUACUGUGAUGGCACAGUGGGUGUUGUGGGCAUACAACGGG---AAAAAAGGGGAGGCAACAGUAGUAAUACGAAAAUGGGGUGCGAAAA-ACCUGAAA
....(((((((((((((((((....)))))))))))))))))((((.((.....---...........(....).(((....))).....))..)))).....-........ ( -33.40)
>consensus
UAAGCCACAAUAUUUACUGUGAUGGCACAGUGGGCGAUGUGGGCAUACAACGGG__AAAAAAAGGGGCGCCAGCAGUAGUAAUACGAAAAUGGGGUGCGAAAAAACCAGAAA
....(((((.(.(((((((((....))))))))).).)))))(((..(....................(....).(((....))).......)..))).............. (-21.44 = -22.22 +   0.78)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:20:05 2006