AlignACE 3.0 10/20/99
AlignACE2 -i PA/PA_fusions006_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944248520
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	PAB2334	39	PAB2334
#1	PAB2333	162	PAB2333
#2	PAB0102	106	PAB0102
#3	malE	100	PAB0119
#4	malC	21	PAB0120
#5	msmK	40	PAB0123
#6	PAB1872	130	PAB1872
#7	PAB1696	26	PAB1696
#8	PAB1694	191	hypothetical protein
#9	PAB1195	22	PAB1195
#10	PAB1194	186	PAB1194

Motif 1
       TTTCTTCCTCCTTTTATTATT  	4	3	1
   TTACTCCCTCCCTCCTAAAATAAATAA	5	23	0
      ATCTGTCCCTCCTTGCACATTATT	6	116	0
CATATCCCTCCTCCTTTCTTTATCTTCCAT	8	85	1
    TTAAGCATCCCTCCATAAACAAAAAA	0	23	0
TCTTTTCTTAATTCTTCCTTAGTTTTTATA	10	22	1
GACTCCTTAGCACCTTTCTTGCTCATATCC	8	62	1
TAACAATAAATTTCCTCCAT          	8	0	0
 CCTCCTTTCTACCCTTCTTTACCATTTTC	6	9	1
    TCTCTGAACCTTTCTTTTCTTAATTC	10	6	1
  ACACTCATCTCCTCCATTATTGATTCAA	3	82	0
     TTTAATTCCTCTCTTTTTTGTTTAT	0	5	1
CTCCTTTCTTTATCTTCCATTAGAAACATC	8	95	1
    TTATCACACCTCCCAATGATAGTCAT	10	170	0
ATTAAAAAGGTATCCTCATTGACTTAATTT	1	33	1
TTATGACTTAATTCTTTATTTGCTTTTCGA	1	121	0
          **********
MAP Score: 13.965

Motif 2
CTCCATAAACAAAAAAGAGAGGAATTAAA        	0	2	0
AAAAATCGAAAAGCAAATAAAGAATTAAGTCATAAAA	1	116	1
GCTTCATCTAAACGATAAGTGGAAACGCTTAACAGAA	2	47	1
CTTCCCATTGAATCAATAATGGAGGAGATGAGTGT  	3	75	1
       AATAATAAAAGGAGGAAGAAA         	4	1	0
CTCCTAAAATAAATAAATTTAGAAGAGAA        	5	2	0
GGAAAATGGTAAAGAAGGGTAGAAAGGAGG       	6	3	0
TAATTATAGCAAGAAAAATTGGGAAAATGGTAAAGAA	6	24	0
AATGGAAGATAAAGAAAGGAGGAGGGATATGAGCAAG	8	79	0
ACTAAGGAAGAATTAAGAAAAGAAAGGTTCAGAGA  	10	8	0
CTTCAAGGTATAAAAACTAAGGAAGAATTAAGAAAAG	10	23	0
          **  **   *****  *
MAP Score: 12.9538

Motif 3
TCCATAAACAAAAAAGAGAGGAATTAAA         	0	1	0
TCTCTTTTTTGTTTATGGAGGGATGCTTAA       	0	19	1
TAAGTCATAAAAAATCGGTGGTGATTTGAAT      	1	141	1
TCAAAATGAAAAGCTCGTAGGTGGTTAA         	2	1	0
     CGCTAGACATCGGATGTGTTAACTTAAAAAAG	2	84	0
CCATTGAATCAATAATGGAGGAGATGAGTGT      	3	79	1
      AATAATAAAAGGAGGAAGAAA          	4	0	0
AAATTTATTTATTTTAGGAGGGAGGGAGTAA      	5	19	1
GAAAATGGTAAAGAAGGGTAGAAAGGAGG        	6	2	0
CTCCTTGCACATTATTGGATCAAATCATCGTCTAAGG	6	95	0
ATCCAATAATGTGCAAGGAGGGACAGAT         	6	112	1
GAGGAAATTTATTGTTAGAGGTAAATAGCTTCTCAGT	8	13	1
GGATATGAGCAAGAAAGGTGCTAAGGAGTCCGGATTA	8	55	0
ATGGAAGATAAAGAAAGGAGGAGGGATATGAGCAAGA	8	78	0
AAGGTATAAAAACTAAGGAAGAATTAAGAAAAGAAAG	10	19	0
          **  * ***** *   *
MAP Score: 12.2949

Motif 4
        TTTAATTCCTCTCTTTTTTGTTTATGGA	0	2	1
AATTCTTTATTTGCTTTTCGATTTTTGCTATTATGA	1	106	0
CCAATTATATTACCTTCCCATTGAATCAATAATGGA	3	62	1
     ACACTCATCTCCTCCATTATTGATTCAATGG	3	79	0
         TTTCTTCCTCCTTTTATTATT      	4	1	1
         TTCTCTTCTAAATTTATTTATTTTAGG	5	1	1
          TTACTCCCTCCCTCCTAAAATAAATA	5	24	0
        CCTCCTTTCTACCCTTCTTTACCATTTT	6	2	1
CCTTCTTTACCATTTTCCCAATTTTTCTTGCTATAA	6	22	1
TAGAGGTAAATAGCTTCTCAGTTTCTATAATCCGGA	8	28	1
CCGGACTCCTTAGCACCTTTCTTGCTCATATCCCTC	8	59	1
CTTGCTCATATCCCTCCTCCTTTCTTTATCTTCCAT	8	79	1
TCTGAACCTTTCTTTTCTTAATTCTTCCTTAGTTTT	10	12	1
          *  ******  **  *
MAP Score: 11.1853

Motif 5
   TTTAATTCCTCTCTTTTTTGTTTATGGAGGGAT	0	7	1
TAAAAAGGTATCCTCATTGACTTAATTTAGACTTGT	1	35	1
AGACTTGTTAATGTTCTAATTTCGATATAAGGTTTC	1	63	1
CACCACCGATTTTTTATGACTTAATTCTTTATTTGC	1	128	0
TTCATTTTGACCTTTAAAAGCTTCATCTAAACGATA	2	28	1
CTCATCTCCTCCATTATTGATTCAATGGGAAGGTAA	3	71	0
        TTTCTTCCTCCTTTTATTATT       	4	2	1
        TTCTCTTCTAAATTTATTTATTTTAGGA	5	2	1
       CCTCCTTTCTACCCTTCTTTACCATTTTC	6	3	1
CTCCTTAGCACCTTTCTTGCTCATATCCCTCCTCCT	8	64	1
TTGCTCATATCCCTCCTCCTTTCTTTATCTTCCATT	8	80	1
ATCTTATAGCCTTTTATGATTTTCATCAAAAGGTCA	8	125	1
  TCTCTGAACCTTTCTTTTCTTAATTCTTCCTTAG	10	8	1
          ** ****   **  **
MAP Score: 5.2995