AlignACE 3.0 10/20/99
AlignACE2 -i TP/TP_operons024_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944239761
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	TP0102	64	rep helicase, single-stranded DNA-dependent ATPase (rep)
#1	TP0105	166	DNA polymerase I (polA)
#2	TP0283	177	lipopolysaccharide core biosynthesis protein (kdtB)
#3	TP0634	118	DNA ligase (lig)
#4	TP1028	82	DNA helicase II (uvrD)
#5	TP1030	27	T. pallidum predicted coding region TP1030

Motif 1
TTGCACGCGTGGGAGGTGCGCCCCGGACGCTACA	3	77	1
CATGCCGTCAGTGCAGGGCGCCGCCCGGGCGCGG	4	14	1
CGTTCGCGCCGTGCGGTGCGCACGTTGTGTAGCT	2	19	1
       GAGGAGAAGCGTTCGCGCCGTGCGGTG	2	3	1
CACGCCCCCAGGGGACTGCGCCGCCGTTTTGGCA	3	20	1
GTGGCACTCGGTGCGGTGCGGCAGTTTTCGGTTG	4	47	1
CCGATTTTCCGCGAGGAGTTGACGGAGTGGGTGC	2	80	1
CCTGAACAACGTGAGGGGTTGCCGTGC       	2	160	1
TAGGAGCGGAAAGAAGGGTGCTGCACATAACCTT	1	105	1
TAGCTAGGAAGCGTAGAGAGCTCGCGTGAACACC	2	48	1
GCGTCGCGGCGGGGCGCGCTCAGGC         	5	1	0
CCTGTTTTTTGTGTAGTTCGCCGCATGTTCCTGA	2	131	1
GGCGCCGCCCGGGCGCGGTGGCACTCGGTGCGGT	4	30	1
CAGTTTTCGGTTGCAGGGCTGCGC          	4	68	1
GTCCCCTGGGGGCGTGAGTGCAGCGG        	3	2	0
CGACAAGACGAAGGAGCGTTGCACGCGTGGGAGG	3	59	1
TTTCCCGGAAAAGCAGATTGGCACAGCCTGTAAA	1	52	0
          * * ** **** **
MAP Score: 31.3046

Motif 2
AGCTACACAACGTGCGCACCGCACGGCGCGAACGCT	2	17	0
CAATGTGTAGCGTCCGGGGCGCACCTCCCACGCGTG	3	80	0
CAGTGCAGGGCGCCGCCCGGGCGCGGTGGCACTCGG	4	22	1
GCACCCACTCCGTCAACTCCTCGCGGAAAATCGGTG	2	78	0
CAACCGAAAACTGCCGCACCGCACCGAGTGCCACCG	4	45	0
CGGCAGTTTTCGGTTGCAGGGCTGCGC         	4	65	1
       GCACGGCAACCCCTCACGTTGTTCAGGAA	2	158	0
ACTCACGCCCCCAGGGGACTGCGCCGCCGTTTTGGC	3	17	1
GCACCTCCCACGCGTGCAACGCTCCTTCGTCTTGTC	3	60	0
          GCCTGAGCGCGCCCCGCCGCGACGCA	5	0	1
AGCTAGGAAGCGTAGAGAGCTCGCGTGAACACCGAT	2	49	1
CACCGCACGGCGCGAACGCTTCTCCTC         	2	1	0
AGTCCCCTGGGGGCGTGAGTGCAGCGG         	3	1	0
TGTGCAGCACCCTTCTTTCCGCTCCTAACGTGGCAT	1	96	0
    GGAACATGCCGTCAGTGCAGGGCGCCGCCCGG	4	6	1
ACGTGGCATACCCTTTGTCTTTCCCGGAAAAGCAGA	1	69	0
          **    * **** ***
MAP Score: 28.3299

Motif 3
TTTTTTCCGCCCTATTTTGCTACGCTTGTGCGTCT	0	39	1
GCACCGCACGGCGCGAACGCTTCTCCTC       	2	3	0
CCTAGCTACACAACGTGCGCACCGCACGGCGCGAA	2	21	0
CGGTGTTCACGCGAGCTCTCTACGCTTCCTAGCTA	2	48	0
CGCACCCACTCCGTCAACTCCTCGCGGAAAATCGG	2	80	0
TGAACAACGTGAGGGGTTGCCGTGC          	2	162	1
TCCCCTGGGGGCGTGAGTGCAGCGG          	3	0	0
CACTCACGCCCCCAGGGGACTGCGCCGCCGTTTTG	3	16	1
GGCGCACCTCCCACGCGTGCAACGCTCCTTCGTCT	3	64	0
ATGTGTAGCGTCCGGGGCGCACCTCCCACGCGTGC	3	79	0
  GGAACATGCCGTCAGTGCAGGGCGCCGCCCGGG	4	8	1
GCAGGGCGCCGCCCGGGCGCGGTGGCACTCGGTGC	4	26	1
GGCGCGGTGGCACTCGGTGCGGTGCGGCAGTTTTC	4	41	1
GCAGTTTTCGGTTGCAGGGCTGCGC          	4	67	1
          GCCTGAGCGCGCCCCGCCGCGACGC	5	0	1
          **  * ****  ***
MAP Score: 23.8523

Motif 4
GAACTACGTTCTTTACAGGCTGTGCCAATCTGCTT	1	41	1
ACGTTAGGAGCGGAAAGAAGGGTGCTGCACATAAC	1	101	1
  GAGGAGAAGCGTTCGCGCCGTGCGGTGCGCACG	2	8	1
TTTCCGCGAGGAGTTGACGGAGTGGGTGCGAATAT	2	85	1
TGAACAACGTGAGGGGTTGCCGTGC          	2	162	1
TGCACTCACGCCCCCAGGGGACTGCGCCGCCGTTT	3	14	1
TTCCGACAAGACGAAGGAGCGTTGCACGCGTGGGA	3	56	1
AGCGTTGCACGCGTGGGAGGTGCGCCCCGGACGCT	3	73	1
  GGAACATGCCGTCAGTGCAGGGCGCCGCCCGGG	4	8	1
GCAGGGCGCCGCCCGGGCGCGGTGGCACTCGGTGC	4	26	1
GGCGCGGTGGCACTCGGTGCGGTGCGGCAGTTTTC	4	41	1
GCAGTTTTCGGTTGCAGGGCTGCGC          	4	67	1
        GCCTGAGCGCGCCCCGCCGCGACGCAG	5	2	1
          * *  ** ** ****
MAP Score: 18.4451

Motif 5
CGTGCGCACCGCACGGCGCGAACGCTTCTCCTC   	2	7	0
CTTCCTAGCTACACAACGTGCGCACCGCACGGCGCG	2	23	0
TAGCTAGGAAGCGTAGAGAGCTCGCGTGAACACCGA	2	48	1
GTCCCCTGGGGGCGTGAGTGCAGCGG          	3	0	0
CACGCCCCCAGGGGACTGCGCCGCCGTTTTGGCATC	3	20	1
AGACGAAGGAGCGTTGCACGCGTGGGAGGTGCGCCC	3	64	1
GCAATGTGTAGCGTCCGGGGCGCACCTCCCACGCGT	3	81	0
   GGAACATGCCGTCAGTGCAGGGCGCCGCCCGGG	4	7	1
AGTGCAGGGCGCCGCCCGGGCGCGGTGGCACTCGGT	4	23	1
GGGCGCGGTGGCACTCGGTGCGGTGCGGCAGTTTTC	4	40	1
GGCAGTTTTCGGTTGCAGGGCTGCGC          	4	66	1
         GCCTGAGCGCGCCCCGCCGCGACGCAG	5	1	1
          ** * * * ** * **
MAP Score: 17.8299

Motif 6
AAGGTTATGTGCAGCACCCTTCTTTCCGCTCCTA	1	105	0
CACCGCACGGCGCGAACGCTTCTCCTC       	2	3	0
AGCTACACAACGTGCGCACCGCACGGCGCGAACG	2	19	0
GGTGTTCACGCGAGCTCTCTACGCTTCCTAGCTA	2	48	0
TGTGTAGTTCGCCGCATGTTCCTGAACAACGTGA	2	140	1
TCCTGAACAACGTGAGGGGTTGCCGTGC      	2	159	1
        CCGCTGCACTCACGCCCCCAGGGGAC	3	2	1
CCAAAACGGCGGCGCAGTCCCCTGGGGGCGTGAG	3	18	0
ACAAGACGAAGGAGCGTTGCACGCGTGGGAGGTG	3	61	1
TGTAGCGTCCGGGGCGCACCTCCCACGCGTGCAA	3	77	0
  AGCACAAGGCCGCAATGTGTAGCGTCCGGGGC	3	96	0
CCGCGCCCGGGCGGCGCCCTGCACTGACGGCATG	4	14	0
GGGCGCCGCCCGGGCGCGGTGGCACTCGGTGCGG	4	29	1
ACCGAAAACTGCCGCACCGCACCGAGTGCCACCG	4	45	0
GCAGTTTTCGGTTGCAGGGCTGCGC         	4	67	1
GCGTCGCGGCGGGGCGCGCTCAGGC         	5	1	0
          ** **** ** * *
MAP Score: 12.1119