AlignACE 3.0 10/20/99
AlignACE2 -i CP/CP_operons025_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944238259
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	rs21	178	S21 Ribosomal Protein
#1	dnaJ	35	Heat Shock Protein J
#2	proS	299	Prolyl tRNA Synthetase
#3	hrcA	91	HTH Transcriptional Repressor
#4	dnaK	29	Heat Shock Protein-70
#5	CPn0849	285	SWI/SNF family helicase_2

Motif 1
AGTGGTACAATCGAGGCTCTTCTAAAAGACATAG	0	84	1
ATTAAAATAATACATAATCCTGACCCCAATTGTT	2	100	1
TAATTTTTTCTATAGACTCTTGACGATCAATCAC	2	254	1
ATTCGAGTGCTAAATTCTCTTGACCTTCTCGGGT	3	55	1
GGTCGTGAGTTCAAGCCTCATCACCCGCTTTTCC	5	38	0
TAGTCGTTGCTAAAAACTCTTCAAAAATCTAAAC	5	128	0
TCTATGATACTAAAGACTCTAGTCGTTGCTAAAA	5	147	0
TTTAGTATCATAGAAATTCGTGTCTCTTCCCCCT	5	167	1
AAAAATTTTATCAAAGCCCTTCTCAGGGGGAAGA	5	191	0
GTAAGCAGATTATATTATCCACTCTTATTCCAGA	5	255	1
          ** *  *** ****
MAP Score: 9.96295

Motif 2
AACAATGTAAAAAATATTTAGAAAATACAAA    	0	6	0
ATAGTTGAATCGATTCGGAAGCAACAATGTAAAAA	0	28	0
CAAAAATAAAAGATTAATAAGTATACACTTAATTA	2	23	1
TGAGATTATTAAATTTCTAAATAAAAACAAAAATA	2	63	1
TTGATCGTCAAGAGTCTATAGAAAAAATTACAGGC	2	249	0
TAACCCCTAGAGATTAGGTACCAAAC         	4	13	1
CCTTTTTATTAGACTTGAAAGGAAAAGCGGGTGAT	5	18	1
AGATTTTTGAAGAGTTTTTAGCAACGACTAGAGTC	5	132	1
AGCAACGACTAGAGTCTTTAGTATCATAGAAATTC	5	151	1
CTCTGGAATAAGAGTGGATAATATAATCTGCTTAC	5	255	0
          *** *   *** ***
MAP Score: 7.79976

Motif 3
TTCGGAAGCAACAATGTAAAAAATATTTAGAAAATACAAA   	0	7	0
AATCGATTCAACTATCCCTTGAAGCCTAATAGAAGTAGTGGTA	0	48	1
AAGTAGTGGTACAATCGAGGCTCTTCTAAAAGACATAGTAAGA	0	80	1
ACATAGTAAGAAGATTATTATTGTGTTTATAGAAGGCCAGAGA	0	112	1
       AGTACTACAATTACAAAAATAAAAGATTAATAAGTA	2	3	1
AAATAAAAACAAAAATATAATTAAAATAATACATAATCCTGAC	2	81	1
TCATAGCTAAACTAAATCTACTAGCTTAAAAGACTCTCGATAT	2	194	1
TAACTTTTTTACGAGGAGGGCAGCGATCAAAGAG         	3	1	0
  TATAGGAAAAGAACCCGAGAAGGTCAAGAGAATTTAGCACT	3	60	0
TTTAGCAACGACTAGAGTCTTTAGTATCATAGAAATTCGTGTC	5	148	1
          ** *       **   * * ***
MAP Score: 7.65235

Motif 4
CGGAAGCAACAATGTAAAAAATATTTAGAAAAT	0	15	0
GGCCTTCTATAAACACAATAATAATCTTCTTAC	0	117	0
  AGTACTACAATTACAAAAATAAAAGATTAAT	2	8	1
AAAATAAAAGATTAATAAGTATACACTTAATTA	2	25	1
TTTTGTTTTTATTTAGAAATTTAATAATCTCAA	2	62	0
ATTTCTAAATAAAAACAAAAATATAATTAAAAT	2	75	1
ACAAAAATATAATTAAAATAATACATAATCCTG	2	89	1
TCAAGAGTCTATAGAAAAAATTACAGGCTATTG	2	244	0
CTACACCCGCAAAGAAAAGAATAGTTTAGATTT	5	105	1
          *** * ** ****
MAP Score: 7.6034

Motif 5
TATGTCTTTTAGAAGAGCCTCGATTGTACCACTA	0	83	0
TTGTGTTTATAGAAGGCCAGAGATTTGTTATTTA	0	132	1
TAACTTAACAATTGGGGTCAGGATTATGTATTAT	2	106	0
        AGAGTGGGGCTGTTATCTTCAGTGAT	2	283	0
CTTTTTTACGAGGAGGGCAGCGATCAAAGAG   	3	7	0
CGCAAAGAAAAGAATAGTTTAGATTTTTGAAGAG	5	112	1
CTTCCCCCTGAGAAGGGCTTTGATAAAATTTTTC	5	192	1
          ** *****   ***
MAP Score: 7.01674

Motif 6
TTTGATCGCTGCCCTCCTCGTAAAAAAGTT	3	13	1
AAATTCTCTTGACCTTCTCGGGTTCTTTTC	3	66	1
TTGAACTCACGACCTTCACGTTGGCAACGT	5	58	1
TTTTATCAAAGCCCTTCTCAGGGGGAAGAG	5	190	0
          **********
MAP Score: 5.45358