AlignACE 3.0 10/20/99
AlignACE2 -i TP/TP_fusions003_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944238360
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	TP0314	22	T. pallidum predicted coding region TP0314
#1	TP0315	300	T. pallidum predicted coding region TP0315
#2	TP0617	95	T. pallidum predicted coding region TP0617
#3	TP0618	55	T. pallidum predicted coding region TP0618
#4	TP0620	57	tpr protein I (tprI)
#5	TP0621	59	tpr protein J (tprJ)

Motif 1
GAGGACTCCGCCATCTGTCCCAGCAAAAATTCAA	1	77	0
CTGAGCTCCACTATCAGTGGCAACCTTCGTCAGC	1	168	0
TCAGCAAGCACCCCCTGTTCCCACTGGGCGCTGA	1	198	0
        ACCACCTTCACCCCACAGATAAACGT	1	284	0
CACTCAAAACCCGCCGCTACCGACAGATACGTAT	2	10	0
CTGCGCTCATCTACGACAGCTACCATTACATCAC	2	46	1
CATTACATCACCATCCAGGCCCCCAATGAGGGTT	2	69	1
GGACCCGTTCCTCCCGGCGCCTCCC         	3	1	0
CTTCACTCCTCCCCGCAATTCTTCGACAGGACCC	3	29	0
CTCACCCCCCCCACCCGTCTAGCCGCGTGTGA  	4	8	0
CCTCTCACTTCTACCTCACCCCCCCCACCCGTCT	4	22	0
     TCACTCCCCCTCCTCTCACTTCTACCTCA	4	38	0
TGTCTAGTAGCCCCCTCACCCTTCTTTTCTAACA	5	10	0
CTCACCCCCCCCCCCGGCCCTGTCTAGTAGCCCC	5	30	0
         GCTACCTCACCCCCCCCCCCGGCCC	5	44	0
          ***** * ***  *
MAP Score: 28.1394

Motif 2
ACAGCGCGTTCGATGCCCTCAGGGTGGAGCAATACCGTGTA	1	23	1
CGGAGTCCTCGATTCTCGAGCGGGTGGGGCTTGCCCTCACG	1	101	1
GCTGACGAAGGTTGCCACTGATAGTGGAGCTCAGCGCCCAG	1	168	1
TAGTGGAGCTCAGCGCCCAGTGGGAACAGGGGGTGCTTGCT	1	189	1
TGGGTATTGCCGAGAGTATGTGGTCTGAGCGTTACTTTGGC	1	243	1
TACTTTGGCACGTTTATCTGTGGGGTGAAGGTGGT      	1	275	1
      ATACGTATCTGTCGGTAGCGGCGGGTTTTGAGTGC	2	4	1
GTGATGTAATGGTAGCTGTCGTAGATGAGCGCAGTGCACTC	2	39	0
         GGGAGGCGCCGGGAGGAACGGGTCCTGTCGAA	3	1	1
CGGGTCCTGTCGAAGAATTGCGGGGAGGAGTGAAGGT    	3	28	1
     TCACACGCGGCTAGACGGGTGGGGGGGGTGAGGTAG	4	5	1
TGGGGGGGGTGAGGTAGAAGTGAGAGGAGGGGGAGTGA   	4	29	1
         TGTTAGAAAAGAAGGGTGAGGGGGCTACTAGA	5	1	1
GGGTGAGGGGGCTACTAGACAGGGCCGGGGGGGGGGGTGAG	5	23	1
          *        * ***  *****
MAP Score: 20.6737

Motif 3
       AGGGGTCTGTCAGAACTATGCG          	0	3	1
GCTCCACCCTGAGGGCATCGAACGCGCTGTCAAACTTCT	1	14	0
TTGAATTTTTGCTGGGACAGATGGCGGAGTCCTCGATTC	1	77	1
GGCTTGCCCTCACGCTGCAGGACGGTACGCTCGTCTCTA	1	128	1
GCTGACGAAGGTTGCCACTGATAGTGGAGCTCAGCGCCC	1	168	1
AGCACCCCCTGTTCCCACTGGGCGCTGAGCTCCACTATC	1	187	0
ACAGATAAACGTGCCAAAGTAACGCTCAGACCACATACT	1	257	0
CTCAAAACCCGCCGCTACCGACAGATACGTAT       	2	3	0
AATGGTAGCTGTCGTAGATGAGCGCAGTGCACTCAAAAC	2	34	0
AACCCTCATTGGGGGCCTGGATGGTGATGTAATGGTAGC	2	64	0
         GGGAGGCGCCGGGAGGAACGGGTCCTGTCG	3	1	1
GGGTCCTGTCGAAGAATTGCGGGGAGGAGTGAAGGT   	3	29	1
  TCACACGCGGCTAGACGGGTGGGGGGGGTGAGGTAGA	4	8	1
TGGGGGGGGTGAGGTAGAAGTGAGAGGAGGGGGAGTGA 	4	29	1
         TGTTAGAAAAGAAGGGTGAGGGGGCTACTA	5	1	1
AAGGGTGAGGGGGCTACTAGACAGGGCCGGGGGGGGGGG	5	21	1
          *  *   * ** ** ** *
MAP Score: 18.8107

Motif 4
TGAGGGCATCGAACGCGCTGTCAAACTTCTCC	1	12	0
TGAGGGCAAGCCCCACCCGCTCGAGAATCGAG	1	108	0
TGGGGCTTGCCCTCACGCTGCAGGACGGTACG	1	125	1
GCAAGCACCCCCTGTTCCCACTGGGCGCTGAG	1	197	0
GGGGGTGCTTGCTGACGCTCCTTACATGGGTA	1	217	1
AACGCTCAGACCACATACTCTCGGCAATACCC	1	244	0
GCACTCAAAACCCGCCGCTACCGACAGATACG	2	13	0
CATCACCATCCAGGCCCCCAATGAGGGTTCG 	2	74	1
CCCGTTCCTCCCGGCGCCTCCC          	3	0	0
AATTCTTCGACAGGACCCGTTCCTCCCGGCGC	3	15	0
      ACCTTCACTCCTCCCCGCAATTCTTC	3	39	0
          TCACACGCGGCTAGACGGGTGG	4	0	1
ACCTCACCCCCCCCACCCGTCTAGCCGCGTGT	4	12	0
CACTCCCCCTCCTCTCACTTCTACCTCACCCC	4	34	0
CTAGTAGCCCCCTCACCCTTCTTTTCTAACA 	5	9	0
CACCCCCCCCCCCGGCCCTGTCTAGTAGCCCC	5	30	0
      GCTACCTCACCCCCCCCCCCGGCCCT	5	43	0
          ** * *******
MAP Score: 14.2865

Motif 5
TCAGCGCCCAGTGGGAACAGGGGGTGCTTGCTGACG	1	198	1
AACCCTCATTGGGGGCCTGGATGGTGATGTAATGGT	2	67	0
GGAGGCGCCGGGAGGAACGGGTCCTGTCGAAGAATT	3	11	1
TCGAAGAATTGCGGGGAGGAGTGAAGGT        	3	37	1
ACGCGGCTAGACGGGTGGGGGGGGTGAGGTAGAAGT	4	14	1
GGTGAGGTAGAAGTGAGAGGAGGGGGAGTGA     	4	36	1
TGTTAGAAAAGAAGGGTGAGGGGGCTACTAGACAGG	5	10	1
AGACAGGGCCGGGGGGGGGGGTGAGGTAGC      	5	39	1
          * ***  **** *  *
MAP Score: 10.9616

Motif 6
AATTTTTGCTGGGACAGATGGCGGAGTCCTCGAT	1	80	1
TAGTGGAGCTCAGCGCCCAGTGGGAACAGGGGGT	1	189	1
AGTGGGAACAGGGGGTGCTTGCTGACGCTCCTTA	1	207	1
GGGTATTGCCGAGAGTATGTGGTCTGAGCGTTAC	1	244	1
CGTTTATCTGTGGGGTGAAGGTGGT         	1	285	1
ATACGTATCTGTCGGTAGCGGCGGGTTTTGAGTG	2	10	1
AACCCTCATTGGGGGCCTGGATGGTGATGTAATG	2	69	0
GGGAGGCGCCGGGAGGAACGGGTCCTGTCGAAGA	3	10	1
GTCGAAGAATTGCGGGGAGGAGTGAAGGT     	3	36	1
CACACGCGGCTAGACGGGTGGGGGGGGTGAGGTA	4	11	1
TGAGGTAGAAGTGAGAGGAGGGGGAGTGA     	4	38	1
TGTTAGAAAAGAAGGGTGAGGGGGCTACTAGACA	5	10	1
GGGGCTACTAGACAGGGCCGGGGGGGGGGGTGAG	5	30	1
          *****    *****
MAP Score: 9.02921

Motif 7
TGAGGGCAAGCCCCACCCGCTCGAGAATCGAGGAC	1	105	0
CGAGCGGGTGGGGCTTGCCCTCACGCTGCAGGACG	1	117	1
CACGCTGCAGGACGGTACGCTCGTCTCTACGCTGA	1	138	1
AGCAAGCACCCCCTGTTCCCACTGGGCGCTGAGCT	1	195	0
CAGGGGGTGCTTGCTGACGCTCCTTACATGGGTAT	1	215	1
         ACCACCTTCACCCCACAGATAAACGT	1	284	0
GGGTTTTGAGTGCACTGCGCTCATCTACGACAGCT	2	32	1
TTCGACAGGACCCGTTCCTCCCGGCGCCTCCC   	3	7	0
TTCTACCTCACCCCCCCCACCCGTCTAGCCGCGTG	4	13	0
     TCACTCCCCCTCCTCTCACTTCTACCTCAC	4	37	0
CTGTCTAGTAGCCCCCTCACCCTTCTTTTCTAACA	5	10	0
ACCTCACCCCCCCCCCCGGCCCTGTCTAGTAGCCC	5	31	0
          **** * * ***  *
MAP Score: 7.80969

Motif 8
GGTATTGCTCCACCCTGAGGGCATCGAACGCGCTG	1	24	0
GCAAGCCCCACCCGCTCGAGAATCGAGGACTCCGC	1	100	0
GTGGGGCTTGCCCTCACGCTGCAGGACGGTACGCT	1	124	1
TGCAGGACGGTACGCTCGTCTCTACGCTGACGAAG	1	143	1
ACCCCCTGTTCCCACTGGGCGCTGAGCTCCACTAT	1	188	0
TCAGACCACATACTCTCGGCAATACCCATGTAAGG	1	236	0
        ACCACCTTCACCCCACAGATAAACGTG	1	283	0
GCACTCAAAACCCGCCGCTACCGACAGATACGTAT	2	10	0
GGGTTTTGAGTGCACTGCGCTCATCTACGACAGCT	2	32	1
ACCATTACATCACCATCCAGGCCCCCAATGAGGGT	2	67	1
CAGGACCCGTTCCTCCCGGCGCCTCCC        	3	2	0
  ACCTTCACTCCTCCCCGCAATTCTTCGACAGGA	3	32	0
         TCACACGCGGCTAGACGGGTGGGGGG	4	1	1
CACTTCTACCTCACCCCCCCCACCCGTCTAGCCGC	4	16	0
TCACTCCCCCTCCTCTCACTTCTACCTCACCCCCC	4	32	0
CACCCCCCCCCCCGGCCCTGTCTAGTAGCCCCCTC	5	27	0
         GCTACCTCACCCCCCCCCCCGGCCCT	5	43	0
          *** **** * *  *
MAP Score: 5.97234

Motif 9
CTGAGGGCATCGAACGCGCTGTCAAACTTC	1	15	0
GAATCGAGGACTCCGCCATCTGTCCCAGCA	1	86	0
AGGGCAAGCCCCACCCGCTCGAGAATCGAG	1	108	0
GTGGGGCTTGCCCTCACGCTGCAGGACGGT	1	124	1
TAGAGACGAGCGTACCGTCCTGCAGCGTGA	1	137	0
TCCCACTGGGCGCTGAGCTCCACTATCAGT	1	184	0
TCAGCAAGCACCCCCTGTTCCCACTGGGCG	1	202	0
TGCTTGCTGACGCTCCTTACATGGGTATTG	1	222	1
CAAAGTAACGCTCAGACCACATACTCTCGG	1	252	0
      ACCACCTTCACCCCACAGATAAAC	1	286	0
ACTCAAAACCCGCCGCTACCGACAGATACG	2	13	0
GTTTTGAGTGCACTGCGCTCATCTACGACA	2	34	1
ACATCACCATCCAGGCCCCCAATGAGGGTT	2	73	1
          CGAACCCTCATTGGGGGCCT	2	85	0
CCGTTCCTCCCGGCGCCTCCC         	3	1	0
TCGACAGGACCCGTTCCTCCCGGCGCCTCC	3	11	0
 ACCTTCACTCCTCCCCGCAATTCTTCGAC	3	36	0
CCTCACCCCCCCCACCCGTCTAGCCGCGTG	4	13	0
TCTCACTTCTACCTCACCCCCCCCACCCGT	4	24	0
   TCACTCCCCCTCCTCTCACTTCTACCT	4	40	0
TCTAGTAGCCCCCTCACCCTTCTTTTCTAA	5	12	0
CCCCCCCCCCCGGCCCTGTCTAGTAGCCCC	5	30	0
 GCTACCTCACCCCCCCCCCCGGCCCTGTC	5	40	0
          **********
MAP Score: 1.20085