AlignACE 3.0 10/20/99
AlignACE2 -i TP/TP_operons026_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944239847
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	TP0116	150	excinuclease ABC, subunit B (uvrB)
#1	TP0344	152	transcription-repair coupling factor (trcF)
#2	TP0514	113	excinuclease ABC, subunit A (uvrA)
#3	TP0687	55	DNA recombinase (recG)
#4	TP0689	35	GTP-binding protein
#5	TP0691	27	conserved hypothetical protein
#6	TP0692	260	recA protein (recA)

Motif 1
CTCATAATCCGCGGGTCGCCGGTTCAAGTCCA	6	160	1
CAAATAGTATGGGCCCAGCTGGACTTGAACCG	6	179	0
TCAAAGGGAAAGGCACAGCATGTACTACAGAT	0	89	1
  CTATTTCCACGCGCTGGCGGCCACTGA   	5	7	0
GCAGGTGGTAGCGCGTCTCTTGCGCCTTGCGC	6	214	1
ATCGGGGTATGGGGATAGGATGAGAGGGTGTT	6	27	1
GAAAGGGAGAACGTGTCGCAGGACGTTCGC  	2	93	1
CAGCAGGAGAGGGCAAGGGAGGAGAACAGGAA	1	29	0
ACGTATGCTCGCACACTGCCTGAA        	3	41	1
TGAGCGAGAAGGATGCAGCAGGAGAGGGCAAG	1	44	0
AGTCTGTAAAGGAGATGGCCGGAGG       	4	20	1
CATAAAAATTGCGCATAGTCTGCCCTCTTATG	2	46	1
CATACTATTTGTGTGCAGGTGGTAGCGCGTCT	6	200	1
TATTCACCATGGGTGTGGTTTGTCAACCAGAG	0	40	1
GGGTACGAGCGTGCATTTCTTGAGCGCGTGTT	1	122	0
ACTGAGCTATAGGCCCTTCCGGCGGGACTTGT	6	112	0
TGAAGAATTGACGCGTGTGTTGTTTCGTGCTA	6	81	1
TCTTATGGATGGGGATCGCGTAGAAAGGGAGA	2	71	1
GGGGTTTTTCATGGGAGGCTTGTG        	6	246	1
TGAATAGAGTGGACCCCGCTTAAGAGGAGGCA	0	14	0
GCGCGTGTTGACACACGGCCGAGTGTAACGGA	1	99	0
          ****** ** **
MAP Score: 19.5795

Motif 2
TGAATAGAGTGGACCCCGCTTAAGAGGAGGCACGT	0	11	0
CAAAATCAAAGGGAAAGGCACAGCATGTACTACAG	0	84	1
GAGGAGAACAGGAAGGAGCACCGGTAGTAGTTG  	1	8	0
CAGCAGGAGAGGGCAAGGGAGGAGAACAGGAAGGA	1	26	0
TGAGCGAGAAGGATGCAGCAGGAGAGGGCAAGGGA	1	41	0
TTCTCGCTCAGGGACTAGCACAAGGCACAGTGCTC	1	66	1
         TGCGGTCTGCCGCGAAGGGAGTGGAA	2	1	1
GAGTGGAATTGCATAAAGCATAAAAATTGCGCATA	2	28	1
TCTTATGGATGGGGATCGCGTAGAAAGGGAGAACG	2	71	1
GCGTAGAAAGGGAGAACGTGTCGCAGGACGTTCGC	2	88	1
AGTCTGTAAAGGAGATGGCCGGAGG          	4	20	1
ATCGGGGTATGGGGATAGGATGAGAGGGTGTTCCC	6	27	1
TAGGATGAGAGGGTGTTCCCCGGGGTTTGTACAGC	6	42	1
CCCTTCCGGCGGGACTTGTAGCACGAAACAACACA	6	96	0
TAGCTCAGTTGGTTAGAGCAGCGGACTCATAATCC	6	135	1
CAAATAGTATGGGCCCAGCTGGACTTGAACCGGCG	6	176	0
CTATTTGTGTGCAGGTGGTAGCGCGTCTCTTGCGC	6	204	1
GAAAAACCCCGCGCAAGGCGCAAGAGACGCGCTAC	6	221	0
GCCTTGCGCGGGGTTTTTCATGGGAGGCTTGTG  	6	237	1
          ***    ** *****
MAP Score: 17.3181

Motif 3
GCCTCCTCTTAAGCGGGGTCCACTCTATTCAC	0	15	1
GGGAGGAGAACAGGAAGGAGCACCGGTAGTAG	1	13	0
AGGAGAGGGCAAGGGAGGAGAACAGGAAGGAG	1	25	0
CCTGAGCGAGAAGGATGCAGCAGGAGAGGGCA	1	46	0
CCTTCTCGCTCAGGGACTAGCACAAGGCACAG	1	64	1
GAGTGTAACGGAGCACTGTGCCTTGTGCTAGT	1	79	0
CATTTCTTGAGCGCGTGTTGACACACGGCCGA	1	109	0
CAAGAAATGCACGCTCGTACCCAGGAGCCT  	1	132	1
GTCTGCCGCGAAGGGAGTGGAATTGCATAAAG	2	14	1
TATGGATGGGGATCGCGTAGAAAGGGAGAACG	2	74	1
TAGAAAGGGAGAACGTGTCGCAGGACGTTCGC	2	91	1
CAGTGGCCGCCAGCGCGTGGAAATAG      	5	11	1
GATAGGATGAGAGGGTGTTCCCCGGGGTTTGT	6	40	1
GGGGTTTGTACAGCGTTTTGAAGAATTGACGC	6	63	1
GACTCATAATCCGCGGGTCGCCGGTTCAAGTC	6	158	1
GGTTCAAGTCCAGCTGGGCCCATACTATTTGT	6	180	1
TATTTGTGTGCAGGTGGTAGCGCGTCTCTTGC	6	205	1
GAAAAACCCCGCGCAAGGCGCAAGAGACGCGC	6	224	0
          ***** ** ***
MAP Score: 16.3826

Motif 4
     AACGTGCCTCCTCTTAAGCGGGGTCCACTCTATTC	0	5	1
ACCTCTGGTTGACAAACCACACCCATGGTGAATAGAGTGG	0	34	0
GAGGTTCTAAGAGAGCAAAATCAAAGGGAAAGGCACAGCA	0	69	1
GAAGGATGCAGCAGGAGAGGGCAAGGGAGGAGAACAGGAA	1	29	0
ACACGGCCGAGTGTAACGGAGCACTGTGCCTTGTGCTAGT	1	79	0
CTCAAGAAATGCACGCTCGTACCCAGGAGCCT        	1	130	1
         TGCGGTCTGCCGCGAAGGGAGTGGAATTGCA	2	1	1
GCGTAGAAAGGGAGAACGTGTCGCAGGACGTTCGC     	2	88	1
       TCAGTGGCCGCCAGCGCGTGGAAATAG      	5	3	1
TCTTCAAAACGCTGTACAAACCCCGGGGAACACCCTCTCA	6	47	0
GTTGTTTCGTGCTACAAGTCCCGCCGGAAGGGCCTATAGC	6	99	1
TAGAGCAGCGGACTCATAATCCGCGGGTCGCCGGTTCAAG	6	148	1
GCGGGTCGCCGGTTCAAGTCCAGCTGGGCCCATACTATTT	6	170	1
AGCCTCCCATGAAAAACCCCGCGCAAGGCGCAAGAGACGC	6	226	0
          *    * *   *** *** *
MAP Score: 13.4696

Motif 5
CAAAATCAAAGGGAAAGGCACAGCATGTACTACAGA	0	84	1
CTGCCGCGAAGGGAGTGGAATTGCATAAAGCATAAA	2	16	1
GGTGTTCCCCGGGGTTTGTACAGCGTTTTGAAGAAT	6	53	1
TGCCCTCTTATGGATGGGGATCGCGTAGAAAGGGAG	2	66	1
CTATTTGTGTGCAGGTGGTAGCGCGTCTCTTGCGCC	6	204	1
CTTGCGCCTTGCGCGGGGTTTTTCATGGGAGGCTTG	6	232	1
CGTAGATCGGGGTATGGGGATAGGATGAGAGGGTGT	6	22	1
TATTCACCATGGGTGTGGTTTGTCAACCAGAGGTTC	0	40	1
  AGGCTCCTGGGTACGAGCGTGCATTTCTTGAGCG	1	128	0
GGATGCAGCAGGAGAGGGCAAGGGAGGAGAACAGGA	1	30	0
          ***   ** *  ****
MAP Score: 7.92672

Motif 6
      AACGTGCCTCCTCTTAAGCGGGGTCCACTCTAT	0	4	1
AGAGGTTCTAAGAGAGCAAAATCAAAGGGAAAGGCACAG	0	68	1
CCTCTCCTGCTGCATCCTTCTCGCTCAGGGACTAGCACA	1	49	1
GCTCAAGAAATGCACGCTCGTACCCAGGAGCCT      	1	129	1
          TGCGGTCTGCCGCGAAGGGAGTGGAATTG	2	0	1
GCGCATAGTCTGCCCTCTTATGGATGGGGATCGCGTAGA	2	56	1
TCAGGCAGTGTGCGAGCATACGTAATGGTAACGCAAGAA	3	25	0
GGGGATAGGATGAGAGGGTGTTCCCCGGGGTTTGTACAG	6	37	1
TGGTTAGAGCAGCGGACTCATAATCCGCGGGTCGCCGGT	6	144	1
CGCTACCACCTGCACACAAATAGTATGGGCCCAGCTGGA	6	188	0
TCTTGCGCCTTGCGCGGGGTTTTTCATGGGAGGCTTGTG	6	231	1
          ****  *   *   * ***
MAP Score: 6.69636

Motif 7
TATTCACCATGGGTGTGGTTTGTCAACCAGAG	0	40	1
TCAAAGGGAAAGGCACAGCATGTACTACAGAT	0	89	1
CAGCAGGAGAGGGCAAGGGAGGAGAACAGGAA	1	29	0
TAGTCCCTGAGCGAGAAGGATGCAGCAGGAGA	1	51	0
TGCATTTCTTGAGCGCGTGTTGACACACGGCC	1	111	0
 TGCGGTCTGCCGCGAAGGGAGTGGAATTGCA	2	9	1
CATAAAAATTGCGCATAGTCTGCCCTCTTATG	2	46	1
GAAAGGGAGAACGTGTCGCAGGACGTTCGC  	2	93	1
       TTTCGGTGAATGATGTTCTTGCGTT	3	3	1
  TCAGTGGCCGCCAGCGCGTGGAAATAG   	5	8	1
TTATTTCGTAGATCGGGGTATGGGGATAGGAT	6	16	1
AGAGGGTGTTCCCCGGGGTTTGTACAGCGTTT	6	49	1
TGAAGAATTGACGCGTGTGTTGTTTCGTGCTA	6	81	1
TAGGCCCTTCCGGCGGGACTTGTAGCACGAAA	6	103	0
AACCGGCGACCCGCGGATTATGAGTCCGCTGC	6	152	0
CAAATAGTATGGGCCCAGCTGGACTTGAACCG	6	179	0
GCAGGTGGTAGCGCGTCTCTTGCGCCTTGCGC	6	214	1
ATGAAAAACCCCGCGCAAGGCGCAAGAGACGC	6	226	0
GGTTTTTCATGGGAGGCTTGTG          	6	248	1
          ***** *** **
MAP Score: 6.29222

Motif 8
          AACGTGCCTCCTCTTAAGCGGGG	0	0	1
CTCCTCTTAAGCGGGGTCCACTCTATTCACCAT	0	17	1
TGTAGTACATGCTGTGCCTTTCCCTTTGATTTT	0	85	0
 CAACTACTACCGGTGCTCCTTCCTGTTCTCCT	1	9	1
CTGTTCTCCTCCCTTGCCCTCTCCTGCTGCATC	1	32	1
TACACTCGGCCGTGTGTCAACACGCGCTCAAGA	1	104	1
TATTTCCACGCGCTGGCGGCCACTGA       	5	3	0
AGGGTGTTCCCCGGGGTTTGTACAGCGTTTTGA	6	51	1
AGAATTGACGCGTGTGTTGTTTCGTGCTACAAG	6	84	1
ACTCATAATCCGCGGGTCGCCGGTTCAAGTCCA	6	159	1
TTCAAGTCCAGCTGGGCCCATACTATTTGTGTG	6	182	1
TATTTGTGTGCAGGTGGTAGCGCGTCTCTTGCG	6	205	1
TTGCGCCTTGCGCGGGGTTTTTCATGGGAGGCT	6	233	1
          ********  * *
MAP Score: 5.73126

Motif 9
GGTTGACAAACCACACCCATGGTGAATAGA	0	38	0
CCGTGTGTCAACACGCGCTCAAGAAATGCA	1	113	1
TTATGCAATTCCACTCCCTTCGCGGCAGAC	2	14	0
        GCGAACGTCCTGCGACACGTTC	2	101	0
GTATGCTCGCACACTGCCTGAA        	3	43	1
    CTATTTCCACGCGCTGGCGGCCACTG	5	11	0
CATCCTATCCCCATACCCCGATCTACGAAA	6	19	0
AAACCCCGGGGAACACCCTCTCATCCTATC	6	40	0
AAAACGCTGTACAAACCCCGGGGAACACCC	6	52	0
GTCAATTCTTCAAAACGCTGTACAAACCCC	6	63	0
GCACGAAACAACACACGCGTCAATTCTTCA	6	81	0
GTTTCGTGCTACAAGTCCCGCCGGAAGGGC	6	102	1
GCCTCCCATGAAAAACCCCGCGCAAGGCGC	6	235	0
          **********
MAP Score: 4.46896

Motif 10
       CAACTACTACCGGTGCTCCTTCCTGTTCTCCTCC	1	3	1
TGTTCTCCTCCCTTGCCCTCTCCTGCTGCATCCTTCTCGCT	1	33	1
AATTTTTATGCTTTATGCAATTCCACTCCCTTCGCGGCAGA	2	15	0
TCCTGCGACACGTTCTCCCTTTCTACGCGATCCCCATCCAT	2	75	0
    TTCAGGCAGTGTGCGAGCATACGTAATGGTAACGCAA	3	28	0
CATCCTATCCCCATACCCCGATCTACGAAATAAACACAA  	6	8	0
          *  *  **    ** **  **
MAP Score: 0.213415