AlignACE 3.0 10/20/99
AlignACE2 -i HI/HI_sum_all043_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944243746
 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	1	1
ATTTCACCAATAATTGGGCAAATGTAATTCACCCCTACGA    	0	6	0
ATTGGTGAAATATCGGGGCTAATATAATTAGCCCCTACAAAATC	0	39	1
    AGATTTTGTAGGGGCTAATTATATTAGCCCCGATATTTCA	0	44	0
AGATTTTACTTGTAGGGGCAAATCACATTTGCCCTTGAACATTC	1	29	1
TCAACGAATGTTCAAGGGCAAATGTGATTTGCCCCTACAAGTAA	1	34	0
TTCGTTGATATATAGGGGCAAATGTAACTTGCCCCTACACCC  	1	70	1
       GGGTGTAGGGGCAAGTTACATTTGCCCCTATATATCA	1	75	0
CTTTAACGGATTTAGGTGCGTTGTTGCACTTGGTCGATCCAACT	2	16	1
CGAATTAGTGTAAAAGGGCGTGTACGATACGCCTCTTACTTGAT	3	27	1
ATATTTTTATTTTGTGGGCTAAAGCCCACCCTACGG        	4	2	0
TTTTTTTCTTTCAAGGGGCTTACAAAAAATTCTGACAAAATATT	5	62	1
          *   ***** *     *    * *
MAP Score: 31.9075

Motif 2
     TCGTAGGGGTGAATTACATTTGCCCAATTATTGGT	0	5	1
GTGAAATATCGGGGCTAATATAATTAGCCCCTACAAAATC	0	43	1
TTTACTTGTAGGGGCAAATCACATTTGCCCTTGAACATTC	1	33	1
TTGATATATAGGGGCAAATGTAACTTGCCCCTACACCC  	1	74	1
GTTGTTGCACTTGGTCGATCCAACTTTACCGATTGGTGGA	2	35	1
ACTTTACCGATTGGTGGATTTAACCATTCCAATGGCTTGG	2	57	1
TATCAAGTAAGAGGCGTATCGTACACGCCCTTTTACACTA	3	32	0
TATTTTTATTTTGTGGGCTAAAGCCCACCCTACGG     	4	5	0
GTTCCTTGTAGGGTGGGCTTTAGCCCACCATTGATATTTT	4	39	0
          * **   **   **   ***
MAP Score: 16.2226

Motif 3
        TCGTAGGGGTGAATTACATTTGCCCAATT	0	2	1
   AGATTTTGTAGGGGCTAATTATATTAGCCCCGAT	0	50	0
          GTGCGGTTATTTTTTATTGAGATTTTA	1	0	1
GATTTTACTTGTAGGGGCAAATCACATTTGCCCTTGA	1	30	1
      GGGTGTAGGGGCAAGTTACATTTGCCCCTAT	1	81	0
AACGGATTTAGGTGCGTTGTTGCACTTGGTCGATCCA	2	20	1
TGTTGCACTTGGTCGATCCAACTTTACCGATTGGTGG	2	37	1
TTTACCGATTGGTGGATTTAACCATTCCAATGGCTTG	2	59	1
    CCGTAGGGTGGGCTTTAGCCCACAAAATAAAAA	4	6	1
AAATATCAATGGTGGGCTAAAGCCCACCCTACAAGGA	4	40	1
TAATTTGTAAGTGCGGTTTCTATATAAGGAGGATTTT	5	28	1
TTCTATATAAGGAGGATTTTTTTTCTTTCAAGGGGCT	5	45	1
          ** *** *    * ***
MAP Score: 12.2347

Motif 4
     GTGCGGTTATTTTTTATTGAGATTTTA	1	5	1
ATTTTTTATTGAGATTTTACTTGTAGGGGCAA	1	18	1
CAGCTACAATGATTTCTTATTTATCAAGTAAG	3	61	0
GCCCACCATTGATATTTTTATTTTGTGGGCTA	4	25	0
ATATAAGGAGGATTTTTTTTCTTTCAAGGGGC	5	49	1
ATTCTGACAAAATATTTTTCCTATTTTAGATT	5	90	1
TCCTATTTTAGATTTTTTACGTAAAATTCGCT	5	108	1
          *********  *
MAP Score: 4.67379

Motif 5
          AGATTTTGTAGGGGCTAATTATATT	0	59	0
TTATTGAGATTTTACTTGTAGGGGCAAATCACATT	1	23	1
TATATATCAACGAATGTTCAAGGGCAAATGTGATT	1	49	0
TGAACATTCGTTGATATATAGGGGCAAATGTAACT	1	64	1
CATAGACGAATTAGTGTAAAAGGGCGTGTACGATA	3	21	1
GATTTCTTATTTATCAAGTAAGAGGCGTATCGTAC	3	48	0
AGCTGTAGTTTTTCTTTCGAAGAGAAGAAAGTGGA	3	88	1
GAGAAGAAAGTGGATTTATAGAGGAAAG       	3	109	1
GGGCTAAAGCCCACCCTACAAGGAACAAAGAT   	4	53	1
GCACTTACAAATTATTAAGAAGGAAATTAATC   	5	7	0
GTAAGTGCGGTTTCTATATAAGGAGGATTTTTTTT	5	34	1
GGAGGATTTTTTTTCTTTCAAGGGGCTTACAAAAA	5	55	1
          **  * *  ******
MAP Score: 2.1653