AlignACE 3.0 10/20/99
AlignACE2 -i PH/PH_operons027_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944256413
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	PH0114	40	316aa long hypothetical molybdenum cofactor biosynthesis protein
#1	PH0115	298	296aa long hypothetical protein
#2	PH0184	54	149aa long hypothetical molybdopterinconverting factor, subunit
#3	PH0827	135	552aa long hypothetical nitrite reductase
#4	PH1615	61	420aa long hypothetical protein
#5	PH1811	84	159aa long hypothetical molybdenum cofactor biosynthesis protein

Motif 1
AATAACATTTTGGGGTTGCAGAGTTGAAGGA	1	104	0
AGAGGCGATATGGGGAGGCCTCGGGGTTGGT	1	171	1
CGGGGTTGGTTGGGGTAAAAGCCAAGAAAAG	1	192	1
CTATAAGAGATGGGGATTACGTT        	1	285	1
CTTAAATATGTTGGGATGAGGG         	2	42	1
TAAATAGTATTGGGGAGGAGGTATTATCGAG	3	20	0
ACTGTACTCTTGGGGATTCTT          	5	73	1
          ********* *
MAP Score: 9.36566

Motif 2
TTAGCGCATGACTTATATTTTTAACAATATCT	0	15	1
AAATAGCATCCCTTGACCCCTTTGCAATTTCT	1	21	1
CCCACCGAGACTTTGAAAATTTGATTCCAGAA	1	49	0
AATCTCTGATCCTTCTCAACTTCTCCTTCAAC	1	81	1
CTCAACTTCTCCTTCAACTCTGCAACCCCAAA	1	95	1
GGCAATATTAATTTAACTTCTTTTGCTTAAAT	1	132	0
CGGAGAAAATCCTTCAACTTTTAAAATCTCAA	1	228	1
TATTTAAGTTCCTTGAAATTTAAGATTAGCGG	2	18	0
ATTTCAAGGAACTTAAATATGTTGGGATGAGG	2	31	1
CCCCAATACTATTTAAATTTTTCGGATATATT	3	36	1
AAGGTTAAGACCTAAAAAGCTTTGTCTCTACA	4	29	1
AAAGTTTAGAACTTAAAAACTTTCAAGTAAAT	5	20	1
TCAAGTAAATACTAAAAGTCTTTAATCCTTTA	5	42	1
          *******  ***
MAP Score: 8.00581

Motif 3
CATCCCTTGACCCCTTTGCAATTTCTGGAATCA	1	27	1
GGAATCTCTGATCCTTCTCAACTTCTCCTTCAA	1	79	1
TTCTCAACTTCTCCTTCAACTCTGCAACCCCAA	1	93	1
CCCGAGGCCTCCCCATATCGCCTCTTCAAAAGG	1	163	0
AGGATTTTCTCCGCTTCACTTTTCTTGGCTTTT	1	208	0
AGCGGAGAAAATCCTTCAACTTTTAAAATCTCA	1	226	1
  AACGTAATCCCCATCTCTTATAGGCCTTCTC	1	277	0
         TCTCCTTCCCGCTAATCTTAAATT	2	1	1
         CCCTCATCCCAACATATTTAAGTT	2	40	0
TCGATAATACCTCCTCCCCAATACTATTTAAAT	3	21	1
AAAGTCTTTAATCCTTTACTGTACTCTTGGGGA	5	56	1
          ******* *  **
MAP Score: 7.45722

Motif 4
GATATTGTTAAAAATATAAGTCATGCGCTAACAAA	0	11	0
GAAATTGCAAAGGGGTCAAGGGATGCTATTTCAAA	1	17	0
TTGCAGAGTTGAAGGAGAAGTTGAGAAGGATCAGA	1	85	0
CGCCTCTTCAAAAGGGCAATATTAATTTAACTTCT	1	143	0
GGGGTTGGTTGGGGTAAAAGCCAAGAAAAGTGAAG	1	193	1
AAAAGCCAAGAAAAGTGAAGCGGAGAAAATCCTTC	1	208	1
AAAACCTGTTAGATGGAAAGAGAAGGCCTATAAGA	1	258	1
TAAGTTCCTTGAAATTTAAGATTAGCGGGAAGGAG	2	11	0
AAGTTTATCACAAGGAACAGAACAAGCTAAACAGG	3	104	1
CCTTACTGAAGAAGGTTAAGACCTAAAAAGCTTTG	4	18	1
      GGTTAAAAGAAAAGTTTAGAACTTAAAAA	5	4	1
AAGAATCCCCAAGAGTACAGTAAAGGATTAAAGAC	5	59	0
          *****  ***   **
MAP Score: 5.87719

Motif 5
ATTTTCAAAGTCTCGGTGGGAATCTCTGATCC	1	61	1
AGAGTTGAAGGAGAAGTTGAGAAGGATCAGAG	1	84	0
TTTTGGGGTTGCAGAGTTGAAGGAGAAGTTGA	1	96	0
GAGGCCTCGGGGTTGGTTGGGGTAAAAGCCAA	1	185	1
GCCAAGAAAAGTGAAGCGGAGAAAATCCTTCA	1	212	1
TTTGAGATTTTAAAAGTTGAAGGATTTTCTCC	1	229	0
TCTCAAAACCTGTTAGATGGAAAGAGAAGGCC	1	254	1
AGAAGGCCTATAAGAGATGGGGATTACGTT  	1	278	1
TGAAATTTAAGATTAGCGGGAAGGAGA     	2	5	0
ACTTAAATATGTTGGGATGAGGG         	2	41	1
TTAAATAGTATTGGGGAGGAGGTATTATCGAG	3	20	0
GTGATAAACTTTATGGTTGAGATATGTCAGAT	3	83	0
          * * ********
MAP Score: 4.79303

Motif 6
TAGCGCATGACTTATATTTTTAACAATATC	0	16	1
AATTTCTGGAATCAAATTTTCAAAGTCTCG	1	46	1
TCTGATCCTTCTCAACTTCTCCTTCAACTC	1	85	1
CAACTTCTCCTTCAACTCTGCAACCCCAAA	1	97	1
GCAATATTAATTTAACTTCTTTTGCTTAAA	1	133	0
ATTTTCTCCGCTTCACTTTTCTTGGCTTTT	1	208	0
GAGAAAATCCTTCAACTTTTAAAATCTCAA	1	230	1
CTTTTAAAATCTCAAAACCTGTTAGATGGA	1	245	1
 AACGTAATCCCCATCTCTTATAGGCCTTC	1	279	0
CCCAATACTATTTAAATTTTTCGGATATAT	3	37	1
AAAGCTTTGTCTCTACATCTGGGCGAG   	4	44	1
AAGTTCTAAACTTTTCTTTTAACC      	5	4	0
AGTTTAGAACTTAAAAACTTTCAAGTAAAT	5	22	1
TACTAAAAGTCTTTAATCCTTTACTGTACT	5	51	1
TAATCCTTTACTGTACTCTTGGGGATTCTT	5	64	1
          **********
MAP Score: 0.554652

Motif 7
GAGGCGATATGGGGAGGCCTCGGGGTTGGT	1	172	1
TAGATGGAAAGAGAAGGCCTATAAGAGATG	1	267	1
AGGTATTATCGAGGTGACCTGAG       	3	3	0
TAGTATTGGGGAGGAGGTATTATCGAGGTG	3	17	0
CTGTACTCTTGGGGATTCTT          	5	74	1
          **********
MAP Score: 0.498865