AlignACE 3.0 10/20/99
AlignACE2 -i PA/PA_fusions004_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944248449
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	PAB0088	300	hypothetical protein
#1	PAB0089	39	hypothetical protein
#2	ndaD	206	PAB0090
#3	dppA-1	27	PAB0091
#4	PAB0247	53	hypothetical protein
#5	trkH	49	PAB0248
#6	PAB0432	133	hypothetical protein
#7	PAB1929	67	PAB1929
#8	PAB1872	130	PAB1872
#9	PAB1871	232	PAB1871
#10	PAB1867	78	PAB1867
#11	PAB1865	36	hypothetical protein
#12	PAB1864	60	PAB1864
#13	PAB1703	21	PAB1703
#14	PAB1702	300	PAB1702
#15	PAB2428	49	PAB2428
#16	PAB1533	300	hypothetical protein

Motif 1
TCATTGAAACTTTTTCATTTGGACAAATGT	2	43	1
GTTCAGTTTATTTTACATTTTTTCTACAGG	9	136	1
    TTTTGATTTTTCTTTTCATCATTTTG	0	6	1
CAATCACCCCTTTTTCTTTTCAAGTTATTT	16	206	1
        ACTTTTACTTTTTTGTAAAAAT	2	2	1
CTTTCTCAAGTTTTTAATTTAACTGTTTTG	7	31	0
GCACTATAATTTTTAAATTTATTAAAGATC	2	109	0
ATTTTGTAATTTTTTTATTTGGGAAAGTAT	0	30	1
ATGATCTAACTTTTTCATTATTATACCCCA	9	70	1
CTCTTAAATCTATTTCTTTTTAGTATGTAC	11	15	1
ATGCCAAGTCTTTTATTTTTAAAATTGGCG	2	76	1
ATTGCTAATATATTAAATTTTCACACTAAT	2	152	0
GATGTTATATTATTTTATTTCTGAGGGATT	0	68	1
AAAAAGTTTTTATTATATTTTAACATAGAA	14	16	1
GGGCTGAGGTTTTTAAATTAAAGTAGACCT	15	10	1
AGACTTGGCATTATACATTTGTCCAAATGA	2	57	0
AACACCAAAATTTTTATTTAGGCGTTTAGT	8	61	1
GTAAAAGAAACTTTACATTTATAAGGTTTT	6	97	0
          **********
MAP Score: 18.0136

Motif 2
CTATTTATACTTTCCCAAATAAAAAAATTACAAAATGA	0	28	0
CATTATACATTTGTCCAAATGAAAAAGTTTCAATGAAA	2	41	0
CGTCAGATCTTTAATAAATTTAAAAATTATAGTGCCTG	2	104	1
AATTTCAGGGTTTAAAAACTTTCAAATTAAGGGGGGTT	4	14	0
          TTCAACACCTGTTAAAATTAGATTTAAG	6	0	1
        AGTTCTTCACCTCCAAAAATGGTGCGC   	3	7	0
AACAGTTAAATTAAAAACTTGAGAAAGTAATCTGGTGG	7	34	1
AATGAGACAGTTGCACAAGCAGGAAATTTGATCCAGAG	16	48	0
TCTTGAGTTCTTAAGAAAGCTTAAAAATCAACCTTCGA	12	12	1
TTTAACTGTTTTGCACAAGGATTAAATTCAAGCA    	7	6	0
CAATAATATGTTATGCAATTGGTATAATATTGACGAAC	0	211	1
CTGACGCCAATTTTAAAAATAAAAGACTTGGCATTATA	2	72	0
TATTAATTAATTGCTAATATATTAAATTTTCACACTAA	2	153	0
GAAAGTATTTTTACAAAAAAGTAAAAGT          	2	0	0
GCAAGAAAAATTGGGAAAATGGTAAAGAAGGGTAGAAA	8	15	0
ATATATAGGGTTTGGCACGTAAATAACTTGAAAAGAAA	16	218	0
        CCTGCATCACCTGGGAAATTGTCCAAAGGA	9	212	0
          **   *** *   *** *
MAP Score: 16.07

Motif 3
  TTTTGATTTTTCTTTTCATCATTTTGTAATTTTT	0	8	1
TACTTTCCAATTTCATTGAAACTTTTTCATTTGGAC	2	31	1
TGCCAAGTCTTTTATTTTTAAAATTGGCGTCAGATC	2	77	1
GGAACCCCCCTTAATTTGAAAGTTTTTAAACCCTGA	4	12	1
CCTGTTAAAATTAGATTTAAGCTTATTAAAGTTTCT	6	17	1
       TGCTTGAATTTAATCCTTGTGCAAAACAG	7	3	1
TTCTCAAGTTTTTAATTTAACTGTTTTGCACAAGGA	7	23	0
ACACCAAAATTTTTATTTAGGCGTTTAGTATACCCT	8	62	1
TCTCGTGACATTTTTTCTAATTATTGAACCTTAATT	9	99	0
GACGTTCAGTTTATTTTACATTTTTTCTACAGGTTG	9	133	1
CTAGGTTATATTCCTTTGGACAATTTCCCAGGTGAT	9	201	1
CTTAAATCTATTTCTTTTTAGTATGTACC       	11	17	1
GTTTCGAAGGTTGATTTTTAAGCTTTCTTAAGAACT	12	17	0
AAAGTTTTTATTATATTTTAACATAGAATTTTATGA	14	18	1
ATCACCCCTTTTTCTTTTCAAGTTATTTACGTGCCA	16	208	1
          **  **** *   ***
MAP Score: 11.3527

Motif 4
GCATTTTCTTTCTGGTTAACAAGGAGGTACAGC	0	156	1
TAATTAATAATCAGGGAATGAGGTGACTTAAGT	2	182	1
CACCATTTTTGGAGGTGAAGAACT         	3	13	1
          GTAGGGCAAAAATCTTTTATCTG	5	0	1
GAACCTCGAAGTAGGGGACGAGGCTT       	5	33	1
AAATGGTAAAGAAGGGTAGAAAGGAGG      	8	4	0
TCGAAACGCCGATGGGGAGGAAGC         	12	46	1
AACTACCCATGGAGGTGATAATGTATGGCAAAG	14	53	1
AAGGAGATCCTCAGAGTACAAGGGAACCAAAGA	14	103	1
GGGAAATGATGAAGCTAAGGAGGAATTAATATG	14	191	1
TGCGAAAAAAGAAGAGAAACAGGGAATACATCA	14	240	1
AGCTCAAACCGCAGGACAGCAAGCAAATGAGAC	16	78	0
ATTAAGTACTTGAGGGGATCAGCTCAAACCGCA	16	98	0
TTGAAGATGAGAAGGGCACAAGGAGCTATAGAA	16	176	0
          * **** * ****
MAP Score: 9.57467

Motif 5
GTTAAAATATAATAAAAACTTTTTTGAAAC  	14	8	0
CGCCATCCGGAAAAGAAACTTTAATAAGCTTA	6	34	0
TTCTTTACGTAAAAGAAACTTTACATTTATAA	6	103	0
AATTTCAGGGTTTAAAAACTTTCAAATTAAGG	4	20	0
AAACAGTTAAATTAAAAACTTGAGAAAGTAAT	7	33	1
ATTTGTCCAAATGAAAAAGTTTCAATGAAATT	2	39	0
AATGAACTTAACCAAAAACCTTATAAATGTAA	6	83	1
TCTTTTACGTAAAGAAAACTTTAC        	6	119	1
GAAATAGACATCGAAAAACTTATTAGCACGAT	9	168	1
GGGTATAATAATGAAAAAGTTAGATCATTGAT	9	66	0
TAAACGCCTAAATAAAAATTTTGGTGTTTAAT	8	57	0
AATTTTAAAAATAAAAGACTTGGCATTATACA	2	70	0
TACTTTTTTGTAAAAATACTTTCCAATTTCAT	2	15	1
ACTTTCCCAAATAAAAAAATTACAAAATGATG	0	26	0
          *  *********
MAP Score: 7.43504

Motif 6
TTTCTTTCTGGTTAACAAGGAGGTACAGCTGGGC	0	160	1
TACATTTGTCCAAATGAAAAAGTTTCAATGAAAT	2	40	0
TTCTTCACCTCCAAAAATGGTGCGC         	3	1	0
TAAAAACTTTCAAATTAAGGGGGGTTCCTC    	4	6	0
ATTGATTATCCAAAATAAGCAGTTTGCGAACTAT	9	38	0
ATTTTATGAACTACCCATGGAGGTGATAATGTAT	14	45	1
GAGTACAAGGGAACCAAAGAAGATGTCCCATTTG	14	116	1
TACTACGAGGGAAATGATGAAGCTAAGGAGGAAT	14	183	1
AGAATATGTGCGAAAAAAGAAGAGAAACAGGGAA	14	232	1
TATGTTGGATCCACTCAAGAAGTTCCATTTAA  	14	278	1
AATAACTACTGCAATTATGATGAGAGCCGCTGCA	16	128	1
GAGAGCCGCTGCAATCATGAAGAGGTATTCTATA	16	149	1
TAAATAACTTGAAAAGAAAAAGGGGTGATTGAAG	16	203	0
          * **  ****** *
MAP Score: 2.44355

Motif 7
TGGTTAACAAGGAGGTACAGCTGGGCGGCAAA	0	168	1
GGTACAGCTGGGCGGCAAAGATAAGCGCCGCA	0	181	1
TTTTCCGGATGGCGGTTAAGTTAAAGCGATTA	6	52	1
TAATGTGCAAGGAGGGACAGAT          	8	118	1
GCAATACTACGAGGGAAATGATGAAGCTAAGG	14	179	1
TAAGTACTTGAGGGGATCAGCTCAAACCGCAG	16	97	0
CTACAAATTTGAGGGCAAAGGTATATATAGGG	16	246	0
          ***** **** *
MAP Score: 2.4353

Motif 8
AAGTATAAATAGGTGATGTTATATTATTTT	0	54	1
CCATTTTTGGAGGTGAAGAACT        	3	15	1
TAATTTTAACAGGTGTTGAA          	6	0	0
GCACGATACTAGGTTATATTCCTTTGGACA	9	193	1
ACAATTTCCCAGGTGATGCAGG        	9	220	1
  TTATCTTTAGGTGATATTGAG       	13	8	1
CTACCCATGGAGGTGATAATGTATGGCAAA	14	55	1
          **********
MAP Score: 2.26508

Motif 9
TTCTGGTTAACAAGGAGGTACAGCTGGGCGGCA	0	165	1
GGAGGTACAGCTGGGCGGCAAAGATAAGCGCCG	0	178	1
GCGCACCATTTTTGGAGGTGAAGAACT      	3	10	1
GAACCTCGAAGTAGGGGACGAGGCTT       	5	33	1
TTCTTTTCCGGATGGCGGTTAAGTTAAAGCGAT	6	49	1
AAATGGTAAAGAAGGGTAGAAAGGAGG      	8	4	0
CAATAATGTGCAAGGAGGGACAGAT        	8	115	1
GGACAATTTCCCAGGTGATGCAGG         	9	218	1
TCGAAACGCCGATGGGGAGGAAGC         	12	46	1
AACTACCCATGGAGGTGATAATGTATGGCAAAG	14	53	1
GCAATACTACGAGGGAAATGATGAAGCTAAGGA	14	179	1
CCTCAAATTTGTAGGTAGTTAGGACAGCAATGT	16	264	1
          *  ** *******
MAP Score: 1.03319

Motif 10
  TTTTGATTTTTCTTTTCATCATTTTGTAATTT	0	8	1
GTAAAAATACTTTCCAATTTCATTGAAACTTTTT	2	24	1
CTTATTAAAGTTTCTTTTCCGGATGGCGGTTAAG	6	38	1
ATGATCTAACTTTTTCATTATTATACCCCAATTA	9	70	1
CTTAAATCTATTTCTTTTTAGTATGTACC     	11	17	1
CCAAAGAAGATGTCCCATTTGTATGTGCTGCTTG	14	129	1
ATGTGCTGCTTGTCTGATCTGCATATCAGCAATA	14	151	1
GTATTCCCTGTTTCTCTTCTTTTTTCGCACATAT	14	235	0
CTTGTGCAACTGTCTCATTTGCTTGCTGTCCTGC	16	67	1
ATCACCCCTTTTTCTTTTCAAGTTATTTACGTGC	16	208	1
          ***** ***   **
MAP Score: 0.89908