AlignACE 3.0 10/20/99
AlignACE2 -i HI/HI_sum_all043_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944243737
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	HI0535	74	urease accessory protein (ureH)
#1	HI0536	102	urease accessory protein (ureG)
#2	HI0537	107	urease accessory protein (ureF)
#3	HI0538	127	urease accessory protein (ureE)
#4	HI0540	75	urease, beta subunit (ureB)
#5	HI0541	162	urease, gamma subunit (ureA)

Motif 1
     TCGTAGGGGTGAATTACATTTGCCCAATTATTGGT	0	5	1
CACCAATAATTGGGCAAATGTAATTCACCCCTACGA    	0	6	0
GTGAAATATCGGGGCTAATATAATTAGCCCCTACAAAATC	0	43	1
AGATTTTGTAGGGGCTAATTATATTAGCCCCGATATTTCA	0	44	0
TTTACTTGTAGGGGCAAATCACATTTGCCCTTGAACATTC	1	33	1
CGAATGTTCAAGGGCAAATGTGATTTGCCCCTACAAGTAA	1	34	0
TTGATATATAGGGGCAAATGTAACTTGCCCCTACACCC  	1	74	1
   GGGTGTAGGGGCAAGTTACATTTGCCCCTATATATCA	1	75	0
   ACGTTGCTGGACGAAGGTTTCCAAGCCATTGGAATGG	2	80	0
TATCAAGTAAGAGGCGTATCGTACACGCCCTTTTACACTA	3	32	0
TTTTATTTTGTGGGCTAAAGCCCACCCTACGG        	4	2	0
ATATCAATGGTGGGCTAAAGCCCACCCTACAAGGAACAAA	4	42	1
TTTCTTTCAAGGGGCTTACAAAAAATTCTGACAAAATATT	5	66	1
          ***** **         ***
MAP Score: 43.1591

Motif 2
ATTTCACCAATAATTGGGCAAATGTAATTCAC	0	18	0
ATTGGTGAAATATCGGGGCTAATATAATTAGC	0	39	1
    AGATTTTGTAGGGGCTAATTATATTAGC	0	56	0
AGATTTTACTTGTAGGGGCAAATCACATTTGC	1	29	1
TCAACGAATGTTCAAGGGCAAATGTGATTTGC	1	46	0
TTCGTTGATATATAGGGGCAAATGTAACTTGC	1	70	1
       GGGTGTAGGGGCAAGTTACATTTGC	1	87	0
AAAGTGGATTTATAGAGGAAAG          	3	115	1
ATATTTTTATTTTGTGGGCTAAAGCCCACCCT	4	14	0
TTTTTTTCTTTCAAGGGGCTTACAAAAAATTC	5	62	1
          * * ********
MAP Score: 24.2706

Motif 3
ATAATTAGCCCCTACAAAATCT         	0	62	1
GTGATTTGCCCCTACAAGTAAAATCTCAATA	1	24	0
TGGGCTTTAGCCCACAAAATAAAAATATCAA	4	18	1
TAAAGCCCACCCTACAAGGAACAAAGAT   	4	57	1
AGAAACCGCACTTACAAATTATTAAGAAGGA	5	18	0
TTTCAAGGGGCTTACAAAAAATTCTGACAAA	5	70	1
ACAAAAAATTCTGACAAAATATTTTTCCTAT	5	83	1
          ******** **
MAP Score: 9.80996

Motif 4
TAATTAGCCCCTACAAAATCT         	0	63	1
TAAAATCTCAATAAAAAATAACCGCAC   	1	7	0
TACTTGATAAATAAGAAATCATTGTAGCTG	3	63	1
GGGCTTTAGCCCACAAAATAAAAATATCAA	4	19	1
CCCTTGAAAGAAAAAAAATCCTCCTTATAT	5	49	0
CAAGGGGCTTACAAAAAATTCTGACAAAAT	5	73	1
AAAAATTCTGACAAAATATTTTTCCTATTT	5	86	1
CGAATTTTACGTAAAAAATCTAAAATAGGA	5	108	0
TGACTTTCGTATAATAAATTAAGGAATGAA	5	139	1
          **********
MAP Score: 2.97461