Locus 1339

Sequence ID	2R_DroMel_CAF1
Location	5,163,243 – 5,163,363
Length	120
Max. P	0.982239

overview

Window 7

Location	5,163,243 – 5,163,334
Length	91
Sequences	6
Columns	118
Reading direction	forward
Mean pairwise identity	75.63
Mean single sequence MFE	-30.48
Consensus MFE	-18.63
Energy contribution	-18.97
Covariance contribution	0.33
Combinations/Pair	1.00
Mean z-score	-2.29
Structure conservation index	0.61
SVM decision value	1.91
SVM RNA-class probability	0.982239
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 5163243 91 + 20766785
----------GAAGGAC---------UCU----GCGCGGCUUGUUAAUUUCAAGUGGCAUGUUAACUUUCUGACAUUAAGUUGGCAUUUCAUGUCAACUAUGC-AGCCG---UUGUUG
----------.((.(((---------.((----((((.(((((.......))))).))((((((......))))))..(((((((((...)))))))))..))-))..)---)).)). ( -28.60)
>DroVir_CAF1 52191 95 + 1
----------GU--UCG---------CUUUGGUUAGGGGCUUGUUAAUUUCAAGUGGCAUGUUAACUUUCUGACAUUAAGUUGGCAUUUCAUGUCAACUAUGCCAGCGC--ACACUCA
----------((--.((---------((..........(((((.......)))))(((((((((......))))....(((((((((...)))))))))))))))))).--))..... ( -27.30)
>DroPse_CAF1 39069 110 + 1
GUGUGUGUGUGGAGGACUGCACCGUGUGU----GAGCGGCUUGUUAAUUUCAAGUGGCAUGUUAACUUUCUGACAUUAAGUUGGCAUUUCAUGUCAACUAUGC-AGCCC---UUGUUA
...........((((.(((((...(((((----((((.(((((.......))))).))((((((((((.........)))))))))).))))).))....)))-)).))---)).... ( -33.00)
>DroWil_CAF1 50128 91 + 1
----------UAAGUGU---------GUG----GCGCGGCUUGUUAAUUUCAAGUGGCAUGUUAACUUUCUGACAUUAAGUUGGCAUUUCAUGUCAACUAUGC-AGCCA---UUGUUG
----------.......---------(((----((((.(((((.......))))).))((((((......))))))..(((((((((...)))))))))....-.))))---)..... ( -28.00)
>DroMoj_CAF1 53897 98 + 1
----------GCGCCAG---------CCUGGG-CUGGGGCUUGUUAAUUUCAAGUGGCAUGUUAACUUUCUGACAUUAAGUUGGCAUUUCAUGUCAACUAUGCCAGCACACACACUCA
----------((.((((---------(....)-)))).(((((.......)))))(((((((((......))))....(((((((((...)))))))))))))).))........... ( -33.00)
>DroPer_CAF1 38860 110 + 1
GUGUGUGUGUGGAGGACUGCACCGUGUGU----GAGCGGCUUGUUAAUUUCAAGUGGCAUGUUAACUUUCUGACAUUAAGUUGGCAUUUCAUGUCAACUAUGC-AGCCC---UUGUUA
...........((((.(((((...(((((----((((.(((((.......))))).))((((((((((.........)))))))))).))))).))....)))-)).))---)).... ( -33.00)
>consensus
__________GAAGGAC_________UCU____GAGCGGCUUGUUAAUUUCAAGUGGCAUGUUAACUUUCUGACAUUAAGUUGGCAUUUCAUGUCAACUAUGC_AGCCC___UUGUUA
...................................((.(((((.......))))).))((((((......))))))..(((((((((...)))))))))................... (-18.63 = -18.97 +   0.33)

alignment

secondary structure

dotplot

Window 8

Location	5,163,258 – 5,163,363
Length	105
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	77.72
Mean single sequence MFE	-25.17
Consensus MFE	-19.22
Energy contribution	-19.38
Covariance contribution	0.17
Combinations/Pair	1.00
Mean z-score	-1.82
Structure conservation index	0.76
SVM decision value	1.36
SVM RNA-class probability	0.946350
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 5163258 105 + 20766785
GCUUGUUAAUUUCAAGUGGCAUGUUAACUUUCUGACAUUAAGUUGGCAUUUCAUGUCAACUAUGC-AGCCG---UUGUUGAGUGCC----------ACCC-GGAAUCCCCAAAUCCCCGA
..(((...(((((..(((((((.(((((...(((.(((..(((((((((...)))))))))))))-))...---..))))))))))----------))..-)))))...)))........ ( -29.60)
>DroPse_CAF1 39103 96 + 1
GCUUGUUAAUUUCAAGUGGCAUGUUAACUUUCUGACAUUAAGUUGGCAUUUCAUGUCAACUAUGC-AGCCC---UUGUUAAGUGUC----------CUCUGUGUCUGCCC----------
(((((.......)))))(((((.(((((...(((.(((..(((((((((...)))))))))))))-))...---..))))))))))----------..............---------- ( -22.70)
>DroWil_CAF1 50143 106 + 1
GCUUGUUAAUUUCAAGUGGCAUGUUAACUUUCUGACAUUAAGUUGGCAUUUCAUGUCAACUAUGC-AGCCA---UUGUUGAGAGUG----------UCCUGUAUAUCCUUUGAGUGCGUA
(((((.......)))))(((((.(((((...(((.(((..(((((((((...)))))))))))))-))...---..)))))..)))----------))..((((.((....))))))... ( -24.70)
>DroMoj_CAF1 53915 116 + 1
GCUUGUUAAUUUCAAGUGGCAUGUUAACUUUCUGACAUUAAGUUGGCAUUUCAUGUCAACUAUGCCAGCACACACACUCAAGCAUAGUCUUGCCCCACCC-CCAUCCUCCG---CCCCCU
(((((...........((((((((((......))))....(((((((((...)))))))))))))))...........))))).................-..........---...... ( -24.75)
>DroAna_CAF1 60836 106 + 1
GCUUGUUAAUUUCAAGUGGCAUGUUAACUUUCUGACAUUAAGUUGGCAUUUCAUGUCAACUAUGC-AGCCG---UUGUUGAGUGCC----------ACCUUCGUCUCCCGUCCUUGCCUA
...............(((((((.(((((...(((.(((..(((((((((...)))))))))))))-))...---..))))))))))----------))...................... ( -26.60)
>DroPer_CAF1 38894 96 + 1
GCUUGUUAAUUUCAAGUGGCAUGUUAACUUUCUGACAUUAAGUUGGCAUUUCAUGUCAACUAUGC-AGCCC---UUGUUAAGUGUC----------CUCUGUGUCUCCCC----------
(((((.......)))))(((((.(((((...(((.(((..(((((((((...)))))))))))))-))...---..))))))))))----------..............---------- ( -22.70)
>consensus
GCUUGUUAAUUUCAAGUGGCAUGUUAACUUUCUGACAUUAAGUUGGCAUUUCAUGUCAACUAUGC_AGCCC___UUGUUAAGUGUC__________ACCUGUGUCUCCCC______CC_A
(((((.......)))))(((((((((......))))))..(((((((((...)))))))))......))).................................................. (-19.22 = -19.38 +   0.17)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:02:35 2006