AlignACE 3.0 10/20/99
AlignACE2 -i AG/AG_fusions016_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944241498
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	AF0680	145	glutamine ABC transporter, ATP-binding protein (glnQ)
#1	AF1019	30	conserved hypothetical protein
#2	AF1020	57	A. fulgidus predicted coding region AF1020
#3	AF1466	300	conserved hypothetical protein
#4	AF1467	70	signal-transducing histidine kinase
#5	AF1468	231	A. fulgidus predicted coding region AF1468
#6	AF1814	83	A. fulgidus predicted coding region AF1814
#7	AF1815	36	acetylornithine aminotransferase (argD-2)
#8	AF1817	139	transcriptional regulatory protein, TetR family

Motif 1
TATACTAACTGTTGCCTCTCTTTAAAATTCA	0	53	1
GGGGGCGATGTTTCCAGCTATCCGCACGCTC	3	130	1
GTGCATCTTTTGTCCATCTGCAC        	4	2	0
GAAAAGAAAATGTGCATCTTTTGTCCATCTG	4	13	0
GCACATTTTCTTTTCCTCTTTCTTAAATGCC	4	29	1
TCCTTTATTGTTTTCATCTATAATGAACTTA	5	137	1
GTGCATTTTTGGTCCATTTTTCCAGATTAAG	5	164	0
GAAAGAAAGATGTGCATTTTTGGTCCATTTT	5	175	0
        GCTTTTCAGTTGTAAAGAAACAA	6	70	0
TAATGATTTATTTCTATTTTTTGC       	7	22	1
TCCCTTTATGGTTTCATCTCTGGCCTTTAAG	8	11	0
AAAAAGCAGGTTTCCCTTTATGGTTTCATCT	8	23	0
GGAAACCTGCTTTTTATCTCCGCTATTATAC	8	39	1
          ********* *
MAP Score: 10.6581

Motif 2
GTACGCACGAGAAAAAAGATTTTATATAACA	0	107	1
AATAGTTGAACGACAAAAATTCAAAT     	2	41	1
TGCTGCGATAGACCCGATATTCAACGTGACT	3	84	1
 GTGCAGATGGACAAAAGATGCACATTTTCT	4	9	1
AGAATTGTTTGAACCAAAATGCT        	5	2	0
TAACCGCACAGACCAGAATTGTTTGAACCAA	5	16	0
GAGCTTCTCTGACGAGAATTTCCAAGTTGCT	5	56	1
TCTGAGAAAAGGAGCAACTTGGAAATTCTCG	5	68	0
TGGAAAAATGGACCAAAAATGCACATCTTTC	5	171	1
    GGCCACCACCAAAATTGGTGGAAAAGT	6	6	1
CAGTTGTAAAGAAACAAATTTAGCTGACGGA	6	56	0
         AGGAAAAATATTTAATGATTTA	7	1	1
   CCTTAAAGGCCAGAGATGAAACCATAAA	8	7	1
GGATATCACACGACCGATTTTAATGAAAAAT	8	90	1
          ******* ***
MAP Score: 6.82882

Motif 3
TAGTTGAACGACAAAAATTCAAAT      	2	43	1
GTGCAGATGGACAAAAGATGCACATTTTCT	4	10	1
AATTGTTTGAACCAAAATGCT         	5	1	0
AACCGCACAGACCAGAATTGTTTGAACCAA	5	16	0
ATAGATGAAAACAATAAAGGATTTTATCTG	5	128	0
GGAAAAATGGACCAAAAATGCACATCTTTC	5	172	1
   GGCCACCACCAAAATTGGTGGAAAAGT	6	7	1
CAGAGATGAAACCATAAAGGGAAACCTGCT	8	20	1
          **********
MAP Score: 6.52852

Motif 4
CTCGTGTAATCTACAATTGATTGTAGCTCCTT	3	19	0
AACATCGCCCCCCTCGTTGATTATTGGAGTCA	3	110	0
ATGCAACTTCCTTAGGTTGGTTAGGGATACTT	3	189	1
GCCCTTGAACCCTTTGTTGGTTG         	4	57	1
ACCGCACAGACCAGAATTGTTTGAACCAAAAT	5	13	0
CAGATAAAATCCTTTATTGTTTTCATCTATAA	5	128	1
  GGCCACCACCAAAATTGGTGGAAAAGTAGG	6	8	1
CCTCCGTCAGCTAAATTTGTTTCTTTACAACT	6	54	1
AGCAGGTTTCCCTTTATGGTTTCATCTCTGGC	8	18	0
          ***  *******
MAP Score: 3.7688

Motif 5
ACCCCTCAAAGCGTGGTGCTGCGATAGACC	3	68	1
AATAATCAACGAGGGGGGCGATGTTTCCAG	3	117	1
CGGGCCACGAGCGTGCGGATAGCTGGAAAC	3	139	0
CTCGTGGCCCGCAGGGGGATGTTGTAAGAA	3	158	1
TCCTTAGGTTGGTTAGGGATACTTGAGTTT	3	197	1
ATCGACATAAGAGTACGGATAAAGGTTTAG	3	246	1
TGGTCTGTGCGGTTACGGCTTCAAGAGCTT	5	32	1
ATTGGTGGAAAAGTAGGGCTATATAAATAT	6	23	1
AACAAATTTAGCTGACGGAGGAATATTTAT	6	45	0
          **********
MAP Score: 1.10765

Motif 6
  GTGCAGATGGACAAAAGATGCACATTTTCTTTTC	4	8	1
TAAGAAAGAGGAAAAGAAAATGTGCATCTTTTGTCC	4	18	0
CTGGAAAAATGGACCAAAAATGCACATCTTTCTTTC	5	170	1
TAACCTGGGAGAAAGAAAGATGTGCATTTTTGGTCC	5	180	0
          * *   ** **** **
MAP Score: 0.74309

Motif 7
AGTACGCACGAGAAAAAAGATTTTATATAACA	0	106	1
CTCAACTTGAGGATATAAAGTTTAATAGTTGA	2	18	1
ATAAGAGTACGGATAAAGGTTTAGGAGTCATC	3	252	1
  GTGCAGATGGACAAAAGATGCACATTTTCT	4	8	1
TTAAGAAAGAGGAAAAGAAAATGTGCATCTTT	4	23	0
GTCGGAAGTCTGAGAAAAGGAGCAACTTGGAA	5	75	0
AACTTAATCTGGAAAAATGGACCAAAAATGCA	5	162	1
ATATAACCTGGGAGAAAGAAAGATGTGCATTT	5	187	0
TTTAGCTGACGGAGGAATATTTATATAGCCCT	6	37	0
         AGGAAAAATATTTAATGATTTAT	7	1	1
GTATAATAGCGGAGATAAAAAGCAGGTTTCCC	8	38	0
          *** ***** **
MAP Score: 0.497376