Locus 6595

Sequence ID	3R_DroMel_CAF1
Location	17,356,891 – 17,356,983
Length	92
Max. P	0.823213

overview

Window 8

Location	17,356,891 – 17,356,983
Length	92
Sequences	6
Columns	104
Reading direction	forward
Mean pairwise identity	79.18
Mean single sequence MFE	-31.25
Consensus MFE	-17.82
Energy contribution	-18.12
Covariance contribution	0.31
Combinations/Pair	1.10
Mean z-score	-2.02
Structure conservation index	0.57
SVM decision value	0.59
SVM RNA-class probability	0.792277
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 17356891 92 + 27905053
GGGGGCUGGG-------CGGG--GC---GUGGCCUGUGGCCAUAGCUAUAGCACCACACGCCAAACAAUCGGAAACCGAAUGUCAUCUUCAAUUUCAAAUUCAA
((.(..((((-------(..(--((---((((((...)))))).)))...)).)))..).))..(((.((((...)))).)))..................... ( -29.20)
>DroPse_CAF1 11032 99 + 1
GGGGGAUGACCAGGAGGCGUG--GCCCAUUGGCCUGUGGCUGCUGC---UGCACCACACGCCAAACAAUCGGAAACCGAAUGUCAUCUUCAAUUUCAAAUUCAA
.(((((((((.....((((((--(((....)))).((((.(((...---.))))))))))))......((((...))))..))))))))).............. ( -40.30)
>DroGri_CAF1 9749 95 + 1
UGACACGAAU-CGGAGACUUG--GCCCAUUGGCCGGUGGCUA------UUGCACCACACGCCAAACAAUCGGAAACCGAAUGUCAUCUUCAAUUUCAAAUUCAA
......((((-..((((.(((--(....(((((..((((...------.....))))..)))))(((.((((...)))).))).....))))))))..)))).. ( -24.30)
>DroSim_CAF1 14661 92 + 1
GGGGGCGGGG-------CGGG--GC---GUGGCCUGUGGCCAUAGCUAUAGCACCACACGCCAAACAAUCGGAAACCGAAUGUCAUCUUCAAUUUCAAAUUCAA
...(((((((-------(..(--((---((((((...)))))).)))...)).))...))))..(((.((((...)))).)))..................... ( -28.80)
>DroAna_CAF1 2898 88 + 1
GGAGGCGUGG-------CCUGCCGA---GUGGCCUGCGGCCGA------UGAACCACACGCCAAACAAUCGGAAACCGAAUGUCAUCUUCAAUUUCAAAUUCAA
((((((((((-------(..(((..---..)))..))((....------....)).))))))..(((.((((...)))).)))................))).. ( -24.60)
>DroPer_CAF1 3823 99 + 1
GGGGGAUGACCAGGAGGCGUG--GCCCAUUGGCCUGUGGCUGCUGC---UGCACCACACGCCAAACAAUCGGAAACCGAAUGUCAUCUUCAAUUUCAAAUUCAA
.(((((((((.....((((((--(((....)))).((((.(((...---.))))))))))))......((((...))))..))))))))).............. ( -40.30)
>consensus
GGGGGCGGAG_______CGUG__GC___GUGGCCUGUGGCCAC_GC___UGCACCACACGCCAAACAAUCGGAAACCGAAUGUCAUCUUCAAUUUCAAAUUCAA
(((((........................((((.(((((..............))))).)))).(((.((((...)))).)))..))))).............. (-17.82 = -18.12 +   0.31)

alignment

secondary structure

dotplot

Window 9

Location	17,356,891 – 17,356,983
Length	92
Sequences	6
Columns	104
Reading direction	reverse
Mean pairwise identity	79.18
Mean single sequence MFE	-31.58
Consensus MFE	-24.25
Energy contribution	-24.28
Covariance contribution	0.03
Combinations/Pair	1.04
Mean z-score	-1.44
Structure conservation index	0.77
SVM decision value	0.69
SVM RNA-class probability	0.823213
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 17356891 92 - 27905053
UUGAAUUUGAAAUUGAAGAUGACAUUCGGUUUCCGAUUGUUUGGCGUGUGGUGCUAUAGCUAUGGCCACAGGCCAC---GC--CCCG-------CCCAGCCCCC
...((((.(((((((((.......))))))))).))))(((.((((.(.(((((....))..(((((...))))).---))--))))-------)).))).... ( -28.80)
>DroPse_CAF1 11032 99 - 1
UUGAAUUUGAAAUUGAAGAUGACAUUCGGUUUCCGAUUGUUUGGCGUGUGGUGCA---GCAGCAGCCACAGGCCAAUGGGC--CACGCCUCCUGGUCAUCCCCC
.................((((((..((((...))))......((((((((((((.---...))).)))).((((....)))--)))))).....)))))).... ( -36.20)
>DroGri_CAF1 9749 95 - 1
UUGAAUUUGAAAUUGAAGAUGACAUUCGGUUUCCGAUUGUUUGGCGUGUGGUGCAA------UAGCCACCGGCCAAUGGGC--CAAGUCUCCG-AUUCGUGUCA
.(((...((((.(((.((((((((.((((...)))).))))....(.(((((....------..))))))((((....)))--)..)))).))-)))))..))) ( -28.70)
>DroSim_CAF1 14661 92 - 1
UUGAAUUUGAAAUUGAAGAUGACAUUCGGUUUCCGAUUGUUUGGCGUGUGGUGCUAUAGCUAUGGCCACAGGCCAC---GC--CCCG-------CCCCGCCCCC
...((((.(((((((((.......))))))))).))))((.((((.((((((((....))....)))))).)))).---))--....-------.......... ( -27.80)
>DroAna_CAF1 2898 88 - 1
UUGAAUUUGAAAUUGAAGAUGACAUUCGGUUUCCGAUUGUUUGGCGUGUGGUUCA------UCGGCCGCAGGCCAC---UCGGCAGG-------CCACGCCUCC
...((((.(((((((((.......))))))))).))))(..((((.((((((...------...)))))).)))).---.)((.(((-------(...)))))) ( -31.80)
>DroPer_CAF1 3823 99 - 1
UUGAAUUUGAAAUUGAAGAUGACAUUCGGUUUCCGAUUGUUUGGCGUGUGGUGCA---GCAGCAGCCACAGGCCAAUGGGC--CACGCCUCCUGGUCAUCCCCC
.................((((((..((((...))))......((((((((((((.---...))).)))).((((....)))--)))))).....)))))).... ( -36.20)
>consensus
UUGAAUUUGAAAUUGAAGAUGACAUUCGGUUUCCGAUUGUUUGGCGUGUGGUGCA___GC_ACAGCCACAGGCCAA___GC__CACG_______CCCAGCCCCC
...((((.(((((((((.......))))))))).))))...((((.((((((............)))))).))))............................. (-24.25 = -24.28 +   0.03)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:25:27 2006