AlignACE 3.0 10/20/99
AlignACE2 -i MP/MP_fusions009_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944246638
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	MG032	253	Mycoplasma pneumoniae, MG032 homolog, from M. genitalium
#1	MG032	300	Mycoplasma pneumoniae, MG032 homolog, from M. genitalium
#2	MG288	300	Mycoplasma pneumoniae, MG288 homolog, from M. genitalium
#3	MG288	30	Mycoplasma pneumoniae, MG288 homolog, from M. genitalium

Motif 1
AAAGAAATCACTACCCAAAATGGTAAACAA	2	142	0
TGGAAGGAAACTACCGCAAAGATACTTACA	0	95	1
ATCATTTAAATTACCCAAAAAACAAAAAGA	1	69	1
TGAGGAAACCTCGCCCCAAAGTTTAACCCA	1	206	0
GCCCCAAAGTTTAACCCAAAATTTTTATTT	1	194	0
GTTGGCAAAACCAACCAAAAGGATATTTAA	1	237	0
   GAGTTGACTGCCCAAATAAAATAAATG	1	7	1
GGCATTTCAATTGCCCCAAGTACCCGAACA	2	111	1
AAAGAAAGTGCCAACGAAAAAGAGGCTTCC	0	182	1
TCAAACTGCTTTAACGCAATGCTTTGAAGT	2	237	0
TAGTTTCCTTCCAACCTAATAAAGTTAGAT	0	78	0
          **********
MAP Score: 10.9864

Motif 2
CCCGTGCAGGGTTATACAAGGCACTGAAAGTTTCT	0	15	1
AACTTTATTAGGTTGGAAGGAAACTACCGCAAAGA	0	82	1
CAAGGCCTTCGGTTTAAAAGAAAGTGCCAACGAAA	0	166	1
CGAAAAAGAGGCTTCCAGGGTCATTACTCCGGGTT	0	196	1
TCCGGGTTATGGTTACCAAGGTATTCACTTAAAAC	0	223	1
GCGTCTTTTTGTTTTTTGGGTAATTTAAATGATGT	1	67	0
AGTTCTACCAGTTAAAAAAGACACTTTTAAACTCG	1	125	0
CCGTTTTTCCGGTGCACGAGGCATTTCAATTGCCC	2	92	1
CAACTGTTCGGGTACTTGGGGCAATTGAAATGCCT	2	110	0
ACCCTTAGGGGTTAATTGAGGAAAGAAATCACTAC	2	158	0
          ***    ****** *
MAP Score: 6.29384

Motif 3
TAGTTTCCTTCCAACCTAATAAAGTTAGATAGA	0	75	0
GGAAACTACCGCAAAGATACTTACAAAAGCTAA	0	100	1
AAAGAAAGTGCCAACGAAAAAGAGGCTTCCAGG	0	182	1
AGTTGACTGCCCAAATAAAATAAATGATTTTTT	1	11	1
TTAAATTACCCAAAAAACAAAAAGACGCCAAAA	1	74	1
AACTTTGTCTCAAAAATTAACAACAGTTAAACC	1	156	1
AGTTAAACCGGCAAAAATAAAAATTTTGGGTTA	1	180	1
GTTGGCAAAACCAACCAAAAGGATATTTAACTG	1	234	0
CGACAGTTTTGCAACAATACAAACTTCAAAGCA	2	215	1
AGTTTGATCTGAAACTAGAAAAACAACCGGACA	2	260	1
          ***** * ** **
MAP Score: 6.00777

Motif 4
    GAGTTGACTGCCCAAATAAAATAAAT	1	6	1
CTGTCATTTTATTACGCATACATCATTTAA	1	48	1
CATCATTTAAATTACCCAAAAAACAAAAAG	1	68	1
GCCAAAAATTAGTGTGCAAATTTTACGAGT	1	100	1
AGGATATTTAACTGAGGAAACCTCGCCCCA	1	218	0
AGGCATTTCAATTGCCCCAAGTACCCGAAC	2	110	1
GAAAGAAATCACTACCCAAAATGGTAAACA	2	143	0
TTAGGGGTTAATTGAGGAAAGAAATCACTA	2	159	0
  CTAGCAGAAGTAAGCAAATCGCTTGAGT	3	8	1
          **********
MAP Score: 5.84685

Motif 5
AAGGAAACTACCGCAAAGATACTTACAAAAGC	0	98	1
CCAAGGTATTCACTTAAAACAATCG       	0	238	1
GTTGACTGCCCAAATAAAATAAATGATTTTTT	1	12	1
ATTTAAATTACCCAAAAAACAAAAAGACGCCA	1	72	1
AACAAAAAGACGCCAAAAATTAGTGTGCAAAT	1	89	1
AGAACTTTGTCTCAAAAATTAACAACAGTTAA	1	154	1
ACAGTTAAACCGGCAAAAATAAAAATTTTGGG	1	178	1
GGAAACCTCGCCCCAAAGTTTAACCCAAAATT	1	201	0
ACGCGTGATACCGTTAAGTTAATTAATGACTT	2	34	1
TGATCTGAAACTAGAAAAACAACCGGACATTG	2	264	1
          * * ********
MAP Score: 4.59353

Motif 6
ACAGTTGTTTACCATTTTGGGTAGTGATTTCTTTCCTCA	2	138	1
TCCTCAATTAACCCCTAAGGGTTTAAATGTGACTGAGAA	2	171	1
AATGGTAAACAACTGTTCGGGTACTTGGGGCAATTGAAA	2	115	0
TCAGTTAAATATCCTTTTGGTTGGTTTTGCCAACAGTTT	1	233	1
TTCCAGGGTCATTACTCCGGGTTATGGTTACCAAGGTAT	0	208	1
TTTGCACACTAATTTTTGGCGTCTTTTTGTTTTTTGGGT	1	81	0
   TGACTCAAGCGATTTGCTTACTTCTGCTAG      	3	4	0
GGCAAAAATAAAAATTTTGGGTTAAACTTTGGGGCGAGG	1	189	1
CAAAATTTTTATTTTTGCCGGTTTAACTGTTGTTAATTT	1	169	0
          * *  *  ****  *  **
MAP Score: 4.17718

Motif 7
AACTTTATTAGGTTGGAAGGAAACTACCGCAAAGA	0	82	1
CAAGGCCTTCGGTTTAAAAGAAAGTGCCAACGAAA	0	166	1
AAATTTTACGAGTTTAAAAGTGTCTTTTTTAACTG	1	117	1
TATTTTTGCCGGTTTAACTGTTGTTAATTTTTGAG	1	164	0
AACCCCTAAGGGTTTAAATGTGACTGAGAATATTA	2	180	1
          ******** *    *
MAP Score: 0.806537