AlignACE 3.0 10/20/99
AlignACE2 -i HP/HP_operons046_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944247319
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	HP0414	37	IS200 insertion sequence from SARA17
#1	HP0437	69	IS605 transposase (tnpA)
#2	HP0988	69	IS605 transposase (tnpA)
#3	HP0998	69	IS605 transposase (tnpA)
#4	HP1096	69	IS605 transposase (tnpA)

Motif 1
       AAATAACTCCTTATCTTTATCTTTTATTATTATACAA	1	3	1
ATCTTTATCTTTTATTATTATACAATGTTTTTATAAATAATGAA	1	22	1
CTATCCTTATTCATTATTTATAAAAACATTGTATAATAATAAAA	1	31	0
       AAATAACTCCTTATCTTTATCTTTTATTATTATACAA	2	3	1
ATCTTTATCTTTTATTATTATACAATGTTTTTATAAATAATGAA	2	22	1
CTATCCTTATTCATTATTTATAAAAACATTGTATAATAATAAAA	2	31	0
       AAATAACTCCTTATCTTTATCTTTTATTATTATACAA	3	3	1
ATCTTTATCTTTTATTATTATACAATGTTTTTATAAATAATGAA	3	22	1
CTATCCTTATTCATTATTTATAAAAACATTGTATAATAATAAAA	3	31	0
       AAATAACTCCTTATCTTTATCTTTTATTATTATACAA	4	3	1
ATCTTTATCTTTTATTATTATACAATGTTTTTATAAATAATGAA	4	22	1
CTATCCTTATTCATTATTTATAAAAACATTGTATAATAATAAAA	4	31	0
          *   *  ****       *  ***
MAP Score: 63.6002

Motif 2
GAAAGTATTTTAACCTCTTTTTGTTAAAATAGGTCT 	0	11	1
          AAATAACTCCTTATCTTTATCTTTTAT	1	0	1
CTCCTTATCTTTATCTTTTATTATTATACAATGTTTT	1	16	1
CTTTTATTATTATACAATGTTTTTATAAATAATGAAT	1	30	1
CCTCTATCCTTATTCATTATTTATAAAAACATTGTAT	1	41	0
          TCCTCTATCCTTATTCATTATTTATAA	1	52	0
          AAATAACTCCTTATCTTTATCTTTTAT	2	0	1
CTCCTTATCTTTATCTTTTATTATTATACAATGTTTT	2	16	1
TCATTATTTATAAAAACATTGTATAATAATAAAAGAT	2	28	0
CCTCTATCCTTATTCATTATTTATAAAAACATTGTAT	2	41	0
          TCCTCTATCCTTATTCATTATTTATAA	2	52	0
          AAATAACTCCTTATCTTTATCTTTTAT	3	0	1
CTCCTTATCTTTATCTTTTATTATTATACAATGTTTT	3	16	1
CCTCTATCCTTATTCATTATTTATAAAAACATTGTAT	3	41	0
          TCCTCTATCCTTATTCATTATTTATAA	3	52	0
          AAATAACTCCTTATCTTTATCTTTTAT	4	0	1
CTCCTTATCTTTATCTTTTATTATTATACAATGTTTT	4	16	1
TTTATTATTATACAATGTTTTTATAAATAATGAATAA	4	32	1
          TCCTCTATCCTTATTCATTATTTATAA	4	52	0
          *  *** *  ****  *
MAP Score: 50.4653

Motif 3
ATAATAATAAAAGATAAAGATAAGGAGTTATTT   	1	7	0
ATGTTTTTATAAATAATGAATAAGGATAGAGGA   	1	46	1
ATAATAATAAAAGATAAAGATAAGGAGTTATTT   	2	7	0
ATGTTTTTATAAATAATGAATAAGGATAGAGGA   	2	46	1
ATAATAATAAAAGATAAAGATAAGGAGTTATTT   	3	7	0
ATGTTTTTATAAATAATGAATAAGGATAGAGGA   	3	46	1
ATAATAATAAAAGATAAAGATAAGGAGTTATTT   	4	7	0
ATGTTTTTATAAATAATGAATAAGGATAGAGGA   	4	46	1
          **   *   *******
MAP Score: 40.7202

Motif 4
AGACCTATTTTAACAAAAAGAGGTTAAAATACT	0	14	0
AATAAAAGATAAAGATAAGGAGTTATTT     	1	5	0
CATTGTATAATAATAAAAGATAAAGATAAGGAG	1	16	0
ATGTTTTTATAAATAATGAATAAGGATAGAGGA	1	46	1
AAATAATGAATAAGGATAGAGGA          	1	56	1
TAATAAAAGATAAAGATAAGGAGTTATTT    	2	6	0
CATTGTATAATAATAAAAGATAAAGATAAGGAG	2	16	0
ATGTTTTTATAAATAATGAATAAGGATAGAGGA	2	46	1
AAATAATGAATAAGGATAGAGGA          	2	56	1
TAATAAAAGATAAAGATAAGGAGTTATTT    	3	6	0
CATTGTATAATAATAAAAGATAAAGATAAGGAG	3	16	0
ATGTTTTTATAAATAATGAATAAGGATAGAGGA	3	46	1
AAATAATGAATAAGGATAGAGGA          	3	56	1
TAATAAAAGATAAAGATAAGGAGTTATTT    	4	6	0
CATTGTATAATAATAAAAGATAAAGATAAGGAG	4	16	0
ATGTTTTTATAAATAATGAATAAGGATAGAGGA	4	46	1
AAATAATGAATAAGGATAGAGGA          	4	56	1
          *** ** *** **
MAP Score: 37.7206