Locus 4838

Sequence ID	3R_DroMel_CAF1
Location	12,655,468 – 12,655,568
Length	100
Max. P	0.991146

overview

Window 7

Location	12,655,468 – 12,655,568
Length	100
Sequences	6
Columns	108
Reading direction	forward
Mean pairwise identity	79.12
Mean single sequence MFE	-30.12
Consensus MFE	-18.05
Energy contribution	-18.97
Covariance contribution	0.92
Combinations/Pair	1.04
Mean z-score	-4.10
Structure conservation index	0.60
SVM decision value	2.25
SVM RNA-class probability	0.991146
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12655468 100 + 27905053
UAUAAUAAAACGAAAUUUUUAAAAGAGUAUAAAAAUUUCGUGUAAUUGGUAAUUCUUGCUGCCAGCGCGGGCAGCGGCGUCGACAGAAACGGCGGCAG--------AG
..((((...((((((((((((........))))))))))))...)))).....(((.((((((......))))))(.(((((.......))))).)))--------). ( -31.20)
>DroVir_CAF1 24347 88 + 1
UAUAAUAAAACGAAAUUUUUAAAAGAGUAUAAAAAUUUCGUGUAAUUGGUAAUUUUUGCUGCCGGCGCUGGCAGCGACGCAAA------------CAG--------CG
..((((...((((((((((((........))))))))))))...)))).......(((((((((....)))))))))(((...------------..)--------)) ( -27.10)
>DroPse_CAF1 29302 88 + 1
UAUAAUAAAACGAAAUUUUUAAAAGAGUAUAAAAAUUUCGUGUAAUUGGUAAUUCUUGCUGCCGGCGUUGAC------------AGA-GCGGCAGCAG-------CAG
..((((...((((((((((((........))))))))))))...))))........((((((.(.((((...------------..)-))).).))))-------)). ( -26.70)
>DroWil_CAF1 47598 100 + 1
UAUAAUAAAACGAAAUUUUUAAAAGAGUAUAAAAAUUUCGUGUAAUUGGUAAUUCUUGCUGCCAGCAAUGGCAGUGCAGUCGACGGCGACUGAGACAC--------AG
...........((((((((((........))))))))))((((..............(((((((....))))))).((((((....))))))..))))--------.. ( -32.50)
>DroYak_CAF1 24020 108 + 1
UAUAAUAAAACGAAAUUUUUAAAAGAGUAUAAAAAUUUCGUGUAAUUGGUAAUUCUUGCUGCCAGCGCGGGCAGCGGCGUCGACUGAAACGGCGGCAGAGUGGAAGAG
..((((...((((((((((((........))))))))))))...))))...(((((.((((((......))))))(.(((((.......))))).))))))....... ( -33.20)
>DroMoj_CAF1 34515 88 + 1
UAUAAUAAAACGAAAUUUUUAAAAGAGUAUAAAAAUUUCGUGUAAUUGGUAAUUUUUGCUGCCAGCGCUGGCAGAGGCGCGAG------------CAG--------CG
..((((...((((((((((((........))))))))))))...)))).........(((((..(((((......)))))..)------------)))--------). ( -30.00)
>consensus
UAUAAUAAAACGAAAUUUUUAAAAGAGUAUAAAAAUUUCGUGUAAUUGGUAAUUCUUGCUGCCAGCGCUGGCAGCGGCGUCGA__GA_ACGGCGGCAG________AG
..((((...((((((((((((........))))))))))))...))))........(((((((......)))))))................................ (-18.05 = -18.97 +   0.92)

alignment

secondary structure

dotplot

Window 8

Location	12,655,468 – 12,655,568
Length	100
Sequences	6
Columns	108
Reading direction	reverse
Mean pairwise identity	79.12
Mean single sequence MFE	-25.98
Consensus MFE	-16.17
Energy contribution	-16.37
Covariance contribution	0.19
Combinations/Pair	1.06
Mean z-score	-4.46
Structure conservation index	0.62
SVM decision value	2.18
SVM RNA-class probability	0.989858
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12655468 100 - 27905053
CU--------CUGCCGCCGUUUCUGUCGACGCCGCUGCCCGCGCUGGCAGCAAGAAUUACCAAUUACACGAAAUUUUUAUACUCUUUUAAAAAUUUCGUUUUAUUAUA
.(--------((...(.((((......)))).)((((((......)))))).)))............((((((((((((........))))))))))))......... ( -24.90)
>DroVir_CAF1 24347 88 - 1
CG--------CUG------------UUUGCGUCGCUGCCAGCGCCGGCAGCAAAAAUUACCAAUUACACGAAAUUUUUAUACUCUUUUAAAAAUUUCGUUUUAUUAUA
((--------(..------------...)))..((((((......))))))................((((((((((((........))))))))))))......... ( -25.40)
>DroPse_CAF1 29302 88 - 1
CUG-------CUGCUGCCGC-UCU------------GUCAACGCCGGCAGCAAGAAUUACCAAUUACACGAAAUUUUUAUACUCUUUUAAAAAUUUCGUUUUAUUAUA
...-------.(((((((((-...------------......).))))))))...............((((((((((((........))))))))))))......... ( -24.00)
>DroWil_CAF1 47598 100 - 1
CU--------GUGUCUCAGUCGCCGUCGACUGCACUGCCAUUGCUGGCAGCAAGAAUUACCAAUUACACGAAAUUUUUAUACUCUUUUAAAAAUUUCGUUUUAUUAUA
..--------((((..((((((....))))))..((((((....))))))...............))))((((((((((........))))))))))........... ( -26.30)
>DroYak_CAF1 24020 108 - 1
CUCUUCCACUCUGCCGCCGUUUCAGUCGACGCCGCUGCCCGCGCUGGCAGCAAGAAUUACCAAUUACACGAAAUUUUUAUACUCUUUUAAAAAUUUCGUUUUAUUAUA
.((((.....((((((.(((..(((.((....)))))...))).)))))).))))............((((((((((((........))))))))))))......... ( -26.50)
>DroMoj_CAF1 34515 88 - 1
CG--------CUG------------CUCGCGCCUCUGCCAGCGCUGGCAGCAAAAAUUACCAAUUACACGAAAUUUUUAUACUCUUUUAAAAAUUUCGUUUUAUUAUA
.(--------(((------------((.((((........)))).))))))................((((((((((((........))))))))))))......... ( -28.80)
>consensus
CU________CUGCCGCCGU_UC__UCGACGCCGCUGCCAGCGCUGGCAGCAAGAAUUACCAAUUACACGAAAUUUUUAUACUCUUUUAAAAAUUUCGUUUUAUUAUA
..................................(((((......))))).................((((((((((((........))))))))))))......... (-16.17 = -16.37 +   0.19)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:40:05 2006