AlignACE 3.0 10/20/99
AlignACE2 -i HP/HP_sum_all048_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944250730
 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
AAAAACATTGTATAATAATAAAAGATAAAGATAAGGAGTTATTT	1	10	0
ATTCATTATTTATAAAAACATTGTATAATAATAAAAGATAAAGA	1	23	0
CTTTTATTATTATACAATGTTTTTATAAATAATGAATAAGGATA	1	30	1
AAAAACATTGTATAATAATAAAAGATAAAGATAAGGAGTTATTT	2	10	0
ATTCATTATTTATAAAAACATTGTATAATAATAAAAGATAAAGA	2	23	0
CTTTTATTATTATACAATGTTTTTATAAATAATGAATAAGGATA	2	30	1
AAAAACATTGTATAATAATAAAAGATAAAGATAAGGAGTTATTT	3	10	0
ATTCATTATTTATAAAAACATTGTATAATAATAAAAGATAAAGA	3	23	0
CTTTTATTATTATACAATGTTTTTATAAATAATGAATAAGGATA	3	30	1
AAAAACATTGTATAATAATAAAAGATAAAGATAAGGAGTTATTT	4	10	0
ATTCATTATTTATAAAAACATTGTATAATAATAAAAGATAAAGA	4	23	0
CTTTTATTATTATACAATGTTTTTATAAATAATGAATAAGGATA	4	30	1
          *  *  *      *****  *  *
MAP Score: 50.2162

Motif 2
TTATCTTTATCTTTTATTATTATACAATGTTTTTATAAATA	1	20	1
         TCCTCTATCCTTATTCATTATTTATAAAAACA	1	47	0
TTATCTTTATCTTTTATTATTATACAATGTTTTTATAAATA	2	20	1
         TCCTCTATCCTTATTCATTATTTATAAAAACA	2	47	0
TTATCTTTATCTTTTATTATTATACAATGTTTTTATAAATA	3	20	1
         TCCTCTATCCTTATTCATTATTTATAAAAACA	3	47	0
TTATCTTTATCTTTTATTATTATACAATGTTTTTATAAATA	4	20	1
         TCCTCTATCCTTATTCATTATTTATAAAAACA	4	47	0
          *     *  **** *  * **
MAP Score: 38.419

Motif 3
AGTATTTTAACCTCTTTTTGTTAAAATAGGTCT	0	14	1
   AAATAACTCCTTATCTTTATCTTTTATTAT	1	7	1
CTTATCTTTATCTTTTATTATTATACAATGTTT	1	19	1
TATTATACAATGTTTTTATAAATAATGAATAAG	1	37	1
CTATCCTTATTCATTATTTATAAAAACATTGTA	1	42	0
         TCCTCTATCCTTATTCATTATTTA	1	55	0
   AAATAACTCCTTATCTTTATCTTTTATTAT	2	7	1
CTTATCTTTATCTTTTATTATTATACAATGTTT	2	19	1
TATTATACAATGTTTTTATAAATAATGAATAAG	2	37	1
   TCCTCTATCCTTATTCATTATTTATAAAAA	2	49	0
   AAATAACTCCTTATCTTTATCTTTTATTAT	3	7	1
CTTATCTTTATCTTTTATTATTATACAATGTTT	3	19	1
TATTATACAATGTTTTTATAAATAATGAATAAG	3	37	1
CTATCCTTATTCATTATTTATAAAAACATTGTA	3	42	0
   AAATAACTCCTTATCTTTATCTTTTATTAT	4	7	1
TATTATACAATGTTTTTATAAATAATGAATAAG	4	37	1
CTATCCTTATTCATTATTTATAAAAACATTGTA	4	42	0
          ** **** * ***
MAP Score: 34.9189

Motif 4
ACAAAAAGAGGTTAAAATACTTTCT        	0	2	0
ATAATAATAAAAGATAAAGATAAGGAGTTATTT	1	10	0
ATAAAAACATTGTATAATAATAAAAGATAAAGA	1	23	0
ATTCATTATTTATAAAAACATTGTATAATAATA	1	34	0
AATGTTTTTATAAATAATGAATAAGGATAGAGG	1	45	1
ATAATAATAAAAGATAAAGATAAGGAGTTATTT	2	10	0
AAAACATTGTATAATAATAAAAGATAAAGATAA	2	20	0
ATTCATTATTTATAAAAACATTGTATAATAATA	2	34	0
ATAATAATAAAAGATAAAGATAAGGAGTTATTT	3	10	0
AAAACATTGTATAATAATAAAAGATAAAGATAA	3	20	0
ATTCATTATTTATAAAAACATTGTATAATAATA	3	34	0
ATAAAAACATTGTATAATAATAAAAGATAAAGA	4	23	0
ATTCATTATTTATAAAAACATTGTATAATAATA	4	34	0
          *  ***** ****
MAP Score: 15.0619