Locus 2397

Sequence ID	X_DroMel_CAF1
Location	6,421,559 – 6,421,650
Length	91
Max. P	0.992668

overview

Window 1

Location	6,421,559 – 6,421,650
Length	91
Sequences	6
Columns	112
Reading direction	forward
Mean pairwise identity	77.21
Mean single sequence MFE	-26.47
Consensus MFE	-14.42
Energy contribution	-14.95
Covariance contribution	0.53
Combinations/Pair	1.08
Mean z-score	-2.02
Structure conservation index	0.54
SVM decision value	0.81
SVM RNA-class probability	0.856351
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 6421559 91 + 22224390
-UUGGUCAACGUGUCGUAUGCGCACUUUGUAUAUUAUAUA------CUUGG--GCAUAUUACGCAUACGACAGGUAUGC------------AAUGACAUUGAUCAACUGCUG
-(((((((..(((((((((((.((....(((((...))))------).)).--))))))...((((((.....))))))------------...))))))))))))...... ( -29.30)
>DroSec_CAF1 38517 91 + 1
-UUGGUCAACGUGUCGUAUGCGCACUUUGUAUAUCGUAUA------CUUGG--GCAUAUUACGCAUACGACAGGUAUGC------------AAUGACAUUGAUCAACUGCUG
-(((((((..(((((((((((.((....(((((...))))------).)).--))))))...((((((.....))))))------------...))))))))))))...... ( -29.30)
>DroSim_CAF1 37580 91 + 1
-UUGGCCAACGUGUCGUAUGCGCACUUUGUAUAUUGUAUA------CUUGG--GCAUAUUACGCAUACGACAGGUAUGC------------AAUGACAUUGAUGAACUGCUG
-...((..((.((((((((((((.((..(((((...))))------)..))--)).......)))))))))).))..))------------..................... ( -24.61)
>DroEre_CAF1 38459 76 + 1
-UUGGUCAACAUGUCGUAUGCGCACUU---------------------UGG--GCAUAUUACGCAUACGACAGGUAUGC------------AAUGACAUUGAUCAACUGCUG
-(((((((..(((((((((((.(....---------------------.).--))))))...((((((.....))))))------------...))))))))))))...... ( -26.70)
>DroYak_CAF1 41239 91 + 1
-UUCGUCAACGCGUCGUAUGCGCACUUUGUAUAGUGUAUA------CUUGG--GCAUAUUACGCAUACGACAGGUAUGC------------AAUGACAUUGAUCAACUGCUG
-...((((....((.((((((.((....(((((...))))------).)).--)))))).))((((((.....))))))------------..))))............... ( -24.80)
>DroPer_CAF1 46708 110 + 1
GUGGGGCAACGUGUUGCAUACGU--UAUAUAUAUUAGAUAGAACCCCCAGAGCACACAUUACGCAUACGAGAGGUAUGCCCCCUGUUGUUUAGUUCAAUUAGUCAACUGCAG
.(((((.(((((((...))))))--)...(((.....)))....)))))..(((........((((((.....)))))).....((((.(((((...))))).))))))).. ( -24.10)
>consensus
_UUGGUCAACGUGUCGUAUGCGCACUUUGUAUAUUGUAUA______CUUGG__GCAUAUUACGCAUACGACAGGUAUGC____________AAUGACAUUGAUCAACUGCUG
........((.(((((((((((.......................................))))))))))).))..................................... (-14.42 = -14.95 +   0.53)

alignment

secondary structure

dotplot

Window 2

Location	6,421,559 – 6,421,650
Length	91
Sequences	6
Columns	112
Reading direction	reverse
Mean pairwise identity	77.21
Mean single sequence MFE	-27.26
Consensus MFE	-16.89
Energy contribution	-16.83
Covariance contribution	-0.05
Combinations/Pair	1.24
Mean z-score	-3.08
Structure conservation index	0.62
SVM decision value	2.34
SVM RNA-class probability	0.992668
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 6421559 91 - 22224390
CAGCAGUUGAUCAAUGUCAUU------------GCAUACCUGUCGUAUGCGUAAUAUGC--CCAAG------UAUAUAAUAUACAAAGUGCGCAUACGACACGUUGACCAA-
..(((((.(((....))))))------------))..((.(((((((((((((((((((--....)------)))))...........))))))))))))).)).......- ( -28.30)
>DroSec_CAF1 38517 91 - 1
CAGCAGUUGAUCAAUGUCAUU------------GCAUACCUGUCGUAUGCGUAAUAUGC--CCAAG------UAUACGAUAUACAAAGUGCGCAUACGACACGUUGACCAA-
..(((((.(((....))))))------------))..((.(((((((((((((.(((((--....)------))))............))))))))))))).)).......- ( -27.12)
>DroSim_CAF1 37580 91 - 1
CAGCAGUUCAUCAAUGUCAUU------------GCAUACCUGUCGUAUGCGUAAUAUGC--CCAAG------UAUACAAUAUACAAAGUGCGCAUACGACACGUUGGCCAA-
..(((((.((....))..)))------------))..((.(((((((((((((.(((((--....)------))))............))))))))))))).)).......- ( -24.92)
>DroEre_CAF1 38459 76 - 1
CAGCAGUUGAUCAAUGUCAUU------------GCAUACCUGUCGUAUGCGUAAUAUGC--CCA---------------------AAGUGCGCAUACGACAUGUUGACCAA-
..(((((.(((....))))))------------))..((.(((((((((((((...(..--...---------------------.).))))))))))))).)).......- ( -26.00)
>DroYak_CAF1 41239 91 - 1
CAGCAGUUGAUCAAUGUCAUU------------GCAUACCUGUCGUAUGCGUAAUAUGC--CCAAG------UAUACACUAUACAAAGUGCGCAUACGACGCGUUGACGAA-
..(((((.(((....))))))------------))..((.(((((((((((...(((((--....)------))))((((......))))))))))))))).)).......- ( -27.90)
>DroPer_CAF1 46708 110 - 1
CUGCAGUUGACUAAUUGAACUAAACAACAGGGGGCAUACCUCUCGUAUGCGUAAUGUGUGCUCUGGGGGUUCUAUCUAAUAUAUAUA--ACGUAUGCAACACGUUGCCCCAC
(((..(((..............)))..)))((((((.((.....((((((((.(((((((...((((.......)))).))))))).--)))))))).....)))))))).. ( -29.34)
>consensus
CAGCAGUUGAUCAAUGUCAUU____________GCAUACCUGUCGUAUGCGUAAUAUGC__CCAAG______UAUACAAUAUACAAAGUGCGCAUACGACACGUUGACCAA_
..................................((.((.(((((((((((((...................................))))))))))))).))))...... (-16.89 = -16.83 +  -0.05)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:33:33 2006