Locus 1188

Sequence ID	2R_DroMel_CAF1
Location	4,713,871 – 4,714,021
Length	150
Max. P	0.989954

overview

Window 6

Location	4,713,871 – 4,713,988
Length	117
Sequences	3
Columns	120
Reading direction	forward
Mean pairwise identity	76.45
Mean single sequence MFE	-20.70
Consensus MFE	-17.00
Energy contribution	-16.57
Covariance contribution	-0.43
Combinations/Pair	1.24
Mean z-score	-1.11
Structure conservation index	0.82
SVM decision value	0.43
SVM RNA-class probability	0.733181
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4713871 117 + 20766785
AUUUUAAAAUCAGUUCUUCAAUU---AAGCCGUAUCUUAGAGAUUCAUUAUCUUGUGUCUUAGAGAUUUAUCAGCUGUAUCUUUAAUCAGAUUAAUCAGUUGUAUCUUAGAGAUUCAUCG
.......................---.............(((((.....)))))(.(((((.(((((....((((((.((((......))))....)))))).))))).))))).).... ( -20.10)
>DroSec_CAF1 7380 104 + 1
------------GUUCU-CAUUUAAGAAGCUGUAUCUUAGAGAUUCAUUAUCUUGUAUCUUAGAGAUUCACCAGCGUUAUCCUAG---AGAUUCUUUAGCUGUAUCUUCGAGAUUUAUCA
------------..(((-(....((((.((((.(((((.(((((.((......)).))))).)))))....))))......((((---((...)))))).....)))).))))....... ( -22.00)
>DroSim_CAF1 6693 104 + 1
------------GUUCU-UAUUUCAGAAGCUGUAUCUCAGAGAUUCAUUAUCUUGUAUCUUAAAGAUUCACCAGCUGUAUCCUAG---AGAUUCUUUAGCUGUAUUUUCGAGAUUCAUCG
------------.((((-......))))(.((.(((((.(((((.((......)).)))))...((.....((((((.(((....---.)))....)))))).....))))))).)).). ( -20.00)
>consensus
____________GUUCU_CAUUU_AGAAGCUGUAUCUUAGAGAUUCAUUAUCUUGUAUCUUAGAGAUUCACCAGCUGUAUCCUAG___AGAUUCUUUAGCUGUAUCUUCGAGAUUCAUCG
............................(.((.(((((.(((((.((......)).))))).(((((....((((((.(((........)))....)))))).))))).))))).)).). (-17.00 = -16.57 +  -0.43)

alignment

secondary structure

dotplot

Window 7

Location	4,713,908 – 4,714,021
Length	113
Sequences	3
Columns	113
Reading direction	forward
Mean pairwise identity	82.74
Mean single sequence MFE	-22.97
Consensus MFE	-22.46
Energy contribution	-22.03
Covariance contribution	-0.43
Combinations/Pair	1.23
Mean z-score	-1.54
Structure conservation index	0.98
SVM decision value	2.19
SVM RNA-class probability	0.989954
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4713908 113 + 20766785
AGAUUCAUUAUCUUGUGUCUUAGAGAUUUAUCAGCUGUAUCUUUAAUCAGAUUAAUCAGUUGUAUCUUAGAGAUUCAUCGGAAUAGUGCAGUCAAUUCAUGAUUAAAUUUGCA
.((((((((((((((.(((((.(((((....((((((.((((......))))....)))))).))))).))))).))..)).)))))).)))).................... ( -26.20)
>DroSec_CAF1 7407 110 + 1
AGAUUCAUUAUCUUGUAUCUUAGAGAUUCACCAGCGUUAUCCUAG---AGAUUCUUUAGCUGUAUCUUCGAGAUUUAUCAGAAUAGUGCAGUCAAAUUAUUAUUAAAGAUUUA
.((((((((((..((.((((..(((((....((((...(((....---.)))......)))).)))))..))))....))..)))))).)))).................... ( -23.40)
>DroSim_CAF1 6720 110 + 1
AGAUUCAUUAUCUUGUAUCUUAAAGAUUCACCAGCUGUAUCCUAG---AGAUUCUUUAGCUGUAUUUUCGAGAUUCAUCGGAAUAAUGCAGACAAUUUAUGAUUAAAGAUUCA
.((.((...(((((........)))))(((..((.(((...((((---((...))))))((((((((((((......)))))..)))))))))).))..))).....)).)). ( -19.30)
>consensus
AGAUUCAUUAUCUUGUAUCUUAGAGAUUCACCAGCUGUAUCCUAG___AGAUUCUUUAGCUGUAUCUUCGAGAUUCAUCGGAAUAGUGCAGUCAAUUUAUGAUUAAAGAUUCA
.((((((((((..((.((((..(((((....((((((.(((........)))....)))))).)))))..))))....))..)))))).)))).................... (-22.46 = -22.03 +  -0.43)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:58:37 2006