#AFTER BAUM-WELCH, FINAL MODEL 
Alphabet: ACGT
################################################
State BEGIN  
	E:   0.25  0.25  0.25  0.25
	T:   BG 0.9995    B1 0.0004    END 1e-04  
State BG  
	E:   0.25  0.25  0.25  0.25
	T:   BG 0.9995    B1 0.0004    END 1e-04  
State B1  
	E:   0.29206  0.101948  0.58113  0.0248624
	T:   B2 1  
State B2  
	E:   0.214357  0.0294873  0.731603  0.0245528
	T:   B3 1  
State B3  
	E:   0.530061  0.000491463  0.430018  0.0394304
	T:   B4 1  
State B4  
	E:   0.000497874  0.975296  0.0236938  0.000512775
	T:   B5 1  
State B5  
	E:   0.849241  0.0251269  0.0505407  0.0750911
	T:   B6 1  
State B6  
	E:   0.186192  0.0245128  0.0686175  0.720678
	T:   B7 1  
State B7  
	E:   0.000489623  0.00125761  0.997726  0.000526346
	T:   B8 1  
State B8  
	E:   0.113864  0.274767  0.0015993  0.60977
	T:   B9 1  
State B9  
	E:   0.0245812  0.862425  0.000527625  0.112466
	T:   B10 1  
State B10  
	E:   0.183  0.343821  0.0761561  0.397023
	T:   SP 0.2    B11 0.8  
State SP  
	E:   0.25  0.25  0.25  0.25
	T:   SP 0.1    B11 0.9  
State B11  
	E:   0.395066  0.0710984  0.424031  0.109805
	T:   B12 1  
State B12  
	E:   0.118912  0.000544213  0.85523  0.0253136
	T:   B13 1  
State B13  
	E:   0.676661  0.000885743  0.321697  0.000756051
	T:   B14 1  
State B14  
	E:   0.000502508  0.998403  0.000603199  0.000491504
	T:   B15 1  
State B15  
	E:   0.854091  0.000748933  0.0253598  0.1198
	T:   B16 1  
State B16  
	E:   0.14049  0.0492683  0.0735262  0.736716
	T:   B17 1  
State B17  
	E:   0.000650054  0.000573553  0.997811  0.000965028
	T:   B18 1  
State B18  
	E:   0.133545  0.430546  0.00260625  0.433303
	T:   B19 1  
State B19  
	E:   0.0242522  0.756146  0.0274555  0.192146
	T:   B20 1  
State B20  
	E:   0.136459  0.483288  0.0949622  0.285291
	T:   BG 0.9998    B1 1e-04    END 1e-04  
State END  
	E:   0.25  0.25  0.25  0.25
	T:   END 0
################################################
#
NULLMODEL:  0.25  0.25  0.25  0.25 
#
fix_tr: 
#
fix_em:  BEGIN  BG  SP  END 
#
#
#avoid states being in more than one tie group!
#
#avoid blank lines, especially a trailing blank line
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