Locus 5656

Sequence ID	3L_DroMel_CAF1
Location	15,533,169 – 15,533,266
Length	97
Max. P	0.786541

overview

Window 4

Location	15,533,169 – 15,533,266
Length	97
Sequences	5
Columns	105
Reading direction	forward
Mean pairwise identity	80.26
Mean single sequence MFE	-18.04
Consensus MFE	-10.32
Energy contribution	-10.16
Covariance contribution	-0.16
Combinations/Pair	1.06
Mean z-score	-2.07
Structure conservation index	0.57
SVM decision value	0.57
SVM RNA-class probability	0.786541
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15533169 97 + 23771897
UCGCUUCCCGUAUAUUCCCGAAUGUGUGUAGUAUGUACUACAUAUUAGUAUAUUUCGAUCCAAGUUUUGACCGAUUUAUACA------UAUA--UAAUUAUUAGC
..(((.....(((((........(((((((((....)))))))))..(((((..(((.((........)).)))..))))).------.)))--))......))) ( -20.00)
>DroSec_CAF1 3245 99 + 1
UCGCUUCCCGUAUA----CGAAUAUGUGUAGUAUGUACUACAUAUUAGUAUAUUUCGAUCCAAUUUUUGACCGUUUUAUACACACGUGUAUA--UAAUUAUUAGC
.........(((((----((...(((((((((....)))))))))..(((((...((.((........)).))...)))))...))))))).--........... ( -20.70)
>DroSim_CAF1 4411 101 + 1
UCGCUUCCCGUAUA----CGAAUAUGUGUAGUAUGUACUACAUAUUAGUAUAUUUCGAUCCAAUUUUUGACCGAUUUAUACACACGUAUAUAUUUAAUUAUUAGC
.........(((((----((...(((((((((....)))))))))..(((((..(((.((........)).)))..)))))...))))))).............. ( -23.80)
>DroEre_CAF1 6536 74 + 1
UCGCUUCCCGUAUA----CGAAUAUGUGUAGUAUGUAAUACAUAUUAAUAUAUUUCGAUCCCAU-UUUAACCGAUU--------------------------UGC
..............----(((((((((.(((((((.....)))))))))))).)))).......-...........--------------------------... ( -10.60)
>DroYak_CAF1 4832 90 + 1
ACGCUUCCCGUAAA----CGAAUAUGUGUAGUAUGUAAUACAUAUUAAUAUAUUUCGAUCCCAU-UUUAACCGAUUUGUACA--------UA--UAAUUAUUUGC
.........(((((----..(.(((((((((((((.....))))))).((((..(((.......-......)))..))))))--------))--)).)..))))) ( -15.12)
>consensus
UCGCUUCCCGUAUA____CGAAUAUGUGUAGUAUGUACUACAUAUUAGUAUAUUUCGAUCCAAUUUUUGACCGAUUUAUACA______UAUA__UAAUUAUUAGC
..................((((.((((((((((((.....))))))).)))))))))................................................ (-10.32 = -10.16 +  -0.16)

alignment

secondary structure

dotplot

Window 5

Location	15,533,169 – 15,533,266
Length	97
Sequences	5
Columns	105
Reading direction	reverse
Mean pairwise identity	80.26
Mean single sequence MFE	-18.50
Consensus MFE	-10.32
Energy contribution	-11.76
Covariance contribution	1.44
Combinations/Pair	1.11
Mean z-score	-1.95
Structure conservation index	0.56
SVM decision value	0.26
SVM RNA-class probability	0.656869
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15533169 97 - 23771897
GCUAAUAAUUA--UAUA------UGUAUAAAUCGGUCAAAACUUGGAUCGAAAUAUACUAAUAUGUAGUACAUACUACACACAUUCGGGAAUAUACGGGAAGCGA
(((....((((--((((------((((((..((((((........))))))..)))))..)))))))))..............((((........)))).))).. ( -20.30)
>DroSec_CAF1 3245 99 - 1
GCUAAUAAUUA--UAUACACGUGUGUAUAAAACGGUCAAAAAUUGGAUCGAAAUAUACUAAUAUGUAGUACAUACUACACAUAUUCG----UAUACGGGAAGCGA
(((.....(((--(((((....))))))))..(((((........)))))...(((((.(((((((.(((.....)))))))))).)----)))).....))).. ( -24.00)
>DroSim_CAF1 4411 101 - 1
GCUAAUAAUUAAAUAUAUACGUGUGUAUAAAUCGGUCAAAAAUUGGAUCGAAAUAUACUAAUAUGUAGUACAUACUACACAUAUUCG----UAUACGGGAAGCGA
(((..........((((((....))))))..((((((........))))))..(((((.(((((((.(((.....)))))))))).)----)))).....))).. ( -22.00)
>DroEre_CAF1 6536 74 - 1
GCA--------------------------AAUCGGUUAAA-AUGGGAUCGAAAUAUAUUAAUAUGUAUUACAUACUACACAUAUUCG----UAUACGGGAAGCGA
((.--------------------------..((((((...-....))))))..(((((.(((((((............))))))).)----))))......)).. ( -12.70)
>DroYak_CAF1 4832 90 - 1
GCAAAUAAUUA--UA--------UGUACAAAUCGGUUAAA-AUGGGAUCGAAAUAUAUUAAUAUGUAUUACAUACUACACAUAUUCG----UUUACGGGAAGCGU
((.........--((--------(((.....((((((...-....))))))(((((((....))))))).........)))))((((----....))))..)).. ( -13.50)
>consensus
GCUAAUAAUUA__UAUA______UGUAUAAAUCGGUCAAAAAUUGGAUCGAAAUAUACUAAUAUGUAGUACAUACUACACAUAUUCG____UAUACGGGAAGCGA
((......................(((((..((((((........))))))..))))).....((((((....))))))......................)).. (-10.32 = -11.76 +   1.44)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:55:50 2006