AlignACE 3.0 10/20/99
AlignACE2 -i PA/PA_fusions005_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944248501
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	PAB0315	300	hypothetical protein
#1	mpg	70	PAB0317
#2	PAB0645	300	PAB0645
#3	PAB1665	46	hypothetical protein
#4	PAB0780	300	hypothetical protein
#5	graD-3	77	PAB0784
#6	PAB0816	300	hypothetical protein
#7	graD-1	112	PAB1053
#8	trpS	173	PAB1111
#9	PAB1112	21	hypothetical protein
#10	PAB1113	50	hypothetical protein

Motif 1
AACATTTAATATTCCCGCCCTTGTAAATTAT	1	36	1
GAAAAGAAGAACTTCCTTCGCTTCGCCCTCC	2	44	1
TTCCTTCGCTTCGCCCTCCTTTATCCCTAAT	2	56	1
TTTCCTATCAACTTCCTCCCAATAAGGTTCA	2	86	1
GATTGTCAACTTTTCCTCCTTGGAGGATACC	2	158	1
GAATTTCTTGTATTCCTCCCTAAGTGACATG	2	191	1
TTACTATTTAACTCCTTTCCTCTCAGAAATC	2	239	1
AACCTTCTCCTCTTCCTCCTCTGTGAAAACC	4	38	1
CTCTGTGAAAACCTCTTCCTCCTCTTCCTCC	4	56	1
CTCTTCCTCCTCTTCCTCCTCCAAGCTTGCT	4	68	1
TACTGGATTTTCCTCCGTCTCTGAGTATGTA	4	122	0
CTTCTCCTCATCTCCCATCTTCATCCCCCAC	4	212	1
TTCATCCCCCACTTCCCTCTTTTATTAATGG	4	231	1
    ATCCCGATTCCCGCCCCATCCTTAACT	6	6	1
TTATGTACTGTTTCCCTTCCTTCGTTAGTAC	6	65	1
ATCTAAATTCTTGCCCCCCCCCATTGCCACA	6	182	1
ATACCCTGATACCTCCATCCTGGTGGACGTT	7	90	1
      ACAGAATCCCCCCTAGATGGATCAA	8	158	0
       GCTTTTTCTTCCCTTTCAAAT   	9	3	1
TAATTTTATATATCCCTTCTCATTTTAATCA	10	21	1
          ****** ****
MAP Score: 21.2545

Motif 2
GTTTTCACAGAGGAGGAAGAGGAGAAGGTTAA	4	36	0
GAGGAGGAAGAGGAGGAAGAGGTTTTCACAGA	4	57	0
GGGATGAAGATGGGAGATGAGGAGAAGTTTGT	4	207	0
  ATTTGAAAGGGAAGAAAAAGC         	9	1	0
AAGAGGGAAGTGGGGGATGAAGATGGGAGATG	4	220	0
TGTGGCAATGGGGGGGGGCAAGAATTTAGATT	6	181	0
TTAGCAAGCTTGGAGGAGGAAGAGGAGGAAGA	4	69	0
AATTATCATCGGGAAAATAAGGTGCATTGATG	6	110	0
GGAAGATGCTGGCGAGATTAGGATTAGGAGGG	2	10	0
GATCCATCTAGGGGGGATTCTGT         	8	160	1
TTAAGGATGGGGCGGGAATCGGGAT       	6	3	0
TTAGGGATAAAGGAGGGCGAAGCGAAGGAAGT	2	54	0
ACATCATTTTAGGGAAAATAAGAGTAAAGGGC	0	197	0
TCAGAGACGGAGGAAAATCCAGTATCCTTGAT	4	129	1
ACACCTGCCAAGGTAAAATAGGTAAATTAAAC	6	213	1
          *******  ***
MAP Score: 16.4001

Motif 3
GGGCTCTAAGCCTCTCCTTAACCTTCTCCTCTTCCTCCTC	4	19	1
CTGTGAAAACCTCTTCCTCCTCTTCCTCCTCCAAGCTTGC	4	58	1
CGATTCCCGCCCCATCCTTAACTTCTATATATGAAATTGC	6	14	1
TATCCTTGATCCTGTTCTCTATCTTCTCGTAAAGCGTTTT	4	151	1
CTTTTTAGGCCCTTTACTCTTATTTTCCCTAAAATGATGT	0	189	1
CTATTTAACTCCTTTCCTCTCAGAAATCTTATAAAGGGAA	2	242	1
ATTTTATATATCCCTTCTCATTTTAATCATTCTGGCA   	10	23	1
CCCTCCTAATCCTAATCTCGCCAGCATCTTCCAGGAAAAG	2	10	1
        TCCCCATTCTCTTCTTTTATAACCATAACATT	1	2	1
CCATCTTCATCCCCCACTTCCCTCTTTTATTAATGGCTTT	4	226	1
TTGTTACAAACTTCTCCTCATCTCCCATCTTCATCCCCCA	4	202	1
AGAAGAACTTCCTTCGCTTCGCCCTCCTTTATCCCTAATT	2	48	1
TGTACTGTTTCCCTTCCTTCGTTAGTACGAGGATAAAATT	6	68	1
TTATCTTATCTCCATGCTCGGTGGTCGTTTTTGGGACTTC	8	95	1
ATTTAATATTCCCGCCCTTGTAAATTATTTGGGATTCGAC	1	39	1
GTAAATTAAACTTAATCTTTTCGCAAACGTAGCATCGTTT	6	234	1
TTGTCAACTTTTCCTCCTTGGAGGATACCTTGAATTTCTT	2	160	1
TACAAAATTTCCCTTACTAAAACTTGGTGTAGTAA     	5	52	1
          *** * ***  *     * *
MAP Score: 14.4331

Motif 4
TTAACCTTCTCCTCTTCCTCCTCTGTGAAAAC	4	36	1
TCTGTGAAAACCTCTTCCTCCTCTTCCTCCTC	4	57	1
AATTTCCTATCAACTTCCTCCCAATAAGGTTC	2	84	1
CCTCATCTCCCATCTTCATCCCCCACTTCCCT	4	217	1
ATCCCGATTCCCGCCCCATCCTTAACTTCTAT	6	10	1
GCGATTGTCAACTTTTCCTCCTTGGAGGATAC	2	156	1
         CCCTCCTAATCCTAATCTCGCCA	2	1	1
      TCCCCATTCTCTTCTTTTATAACCAT	1	4	1
AGAACTTCCTTCGCTTCGCCCTCCTTTATCCC	2	51	1
CTTCATCCCCCACTTCCCTCTTTTATTAATGG	4	230	1
TATACCCTGATACCTCCATCCTGGTGGACGTT	7	89	1
GCTTTTTAGGCCCTTTACTCTTATTTTCCCTA	0	188	1
GTTACAAACTTCTCCTCATCTCCCATCTTCAT	4	204	1
TTAACGAGGTACTTTTAATCCTTCCAC     	3	29	1
ACTATTTAACTCCTTTCCTCTCAGAAATCTTA	2	241	1
TGTACTGTTTCCCTTCCTTCGTTAGTACGAGG	6	68	1
         GCTTTTTCTTCCCTTTCAAAT  	9	1	1
CAAGGGCTCTAAGCCTCTCCTTAACCTTCTCC	4	16	1
TAGGTAAATTAAACTTAATCTTTTCGCAAACG	6	231	1
          ** **** ****
MAP Score: 13.7457

Motif 5
TCTAAGGGGTTTCCTCTTGGCGTCGTTGGTAG	0	28	1
      TTTTGCCGTCGTGTTGATGAGAAACC	0	284	0
AAGAAGAACTTCCTTCGCTTCGCCCTCCTTTA	2	47	1
TTCCTTTAAAATCCTCTTGGCGATTGTCAACT	2	137	1
TGTCAACTTTTCCTCCTTGGAGGATACCTTGA	2	161	1
CTTCTCCTCTTCCTCCTCTGTGAAAACCTCTT	4	41	1
TGGATTTTCCTCCGTCTCTGAGTATGTAACTT	4	118	0
ATCCCCCACTTCCCTCTTTTATTAATGGCTTT	4	234	1
          GCCTTCCTGTTTATTAGAATTT	4	288	0
ATATGAAATTGCCTTCTTGTTGATTATGTACT	6	42	1
ATGTACTGTTTCCCTTCCTTCGTTAGTACGAG	6	67	1
ATAATAAAAGTCCTTTCTGGAGAAATTATCAT	6	133	0
CCCTGATACCTCCATCCTGGTGGACGTTT   	7	93	1
ATGCTCGGTGGTCGTTTTTGGGACTTCTGATA	8	108	1
CTTTAATTGATCCATCTAGGGGGGATTCTGT 	8	152	1
          *** ****** *
MAP Score: 10.716

Motif 6
TTAAAAGGGATCATGCTCTAAGGGGTTTCCTCTTGGCGTCGT	0	12	1
CAGCATCTTCCAGGAAAAGAAGAACTTCCTTCGCTTCGCCCT	2	31	1
TCCTTTATCCCTAATTTCCTATCAACTTCCTCCCAATAAGGT	2	72	1
GTTCACTTTCCGAAAGCTTGATTAGTTCCTTTAAAATCCTCT	2	112	1
AAAATCCTCTTGGCGATTGTCAACTTTTCCTCCTTGGAGGAT	2	144	1
CTTCGACTAATTACTATTTAACTCCTTTCCTCTCAGAAATCT	2	229	1
GTCCACCTGATTTTATTCTAAAGTTTTCCCTTTATAAGATTT	2	265	0
    GGTAGCCAAGGGCTCTAAGCCTCTCCTTAACCTTCTCC	4	6	1
TCCTCTTCCTCCTCTGTGAAAACCTCTTCCTCCTCTTCCTCC	4	45	1
CTTCCTCCTCCAAGCTTGCTAAGACCTCCCTCAAAACATAAG	4	79	1
TTTGGAATCTCAATTGTTACAAACTTCTCCTCATCTCCCATC	4	189	1
TACAGTTAAGCTTTTATTACAAAATTTCCCTTACTAAAACTT	5	35	1
TGCCTTCTTGTTGATTATGTACTGTTTCCCTTCCTTCGTTAG	6	51	1
AAATAAGGTGCATTGATGAAAATTTTATCCTCGTACTAACGA	6	86	0
TATCAGGGTATATCCTTTATATTTTTTCGCTCGGTTAAGTTA	7	59	0
  CCTTTAGACCTTAATTTTATATATCCCTTCTCATTTTAAT	10	8	1
          *     *   *    *******
MAP Score: 9.91655

Motif 7
    TCCCCATTCTCTTCTTTTATAACCAT	1	6	1
ACATTTAATATTCCCGCCCTTGTAAATTAT	1	37	1
       CCCTCCTAATCCTAATCTCGCCA	2	3	1
AAGGAAGTTCTTCTTTTCCTGGAAGATGCT	2	32	0
TTCCTTCGCTTCGCCCTCCTTTATCCCTAA	2	56	1
CTCTTGGCGATTGTCAACTTTTCCTCCTTG	2	150	1
         ATCGTCCACCTGATTTTATTC	2	289	0
CTCCTTAACCTTCTCCTCTTCCTCCTCTGT	4	32	1
AACCTCTTCCTCCTCTTCCTCCTCCAAGCT	4	65	1
TGTTACAAACTTCTCCTCATCTCCCATCTT	4	203	1
CCCATCTTCATCCCCCACTTCCCTCTTTTA	4	225	1
ATATATGAAATTGCCTTCTTGTTGATTATG	6	40	1
TATGTACTGTTTCCCTTCCTTCGTTAGTAC	6	66	1
     GCTTTTTCTTCCCTTTCAAAT    	9	5	1
          **********
MAP Score: 6.37436

Motif 8
ATTTTAGGGAAAATAAGAGTAAAGGGCCTAAAAAGC	0	188	0
TTATGGTTATAAAAGAAGAGAATGGGGA        	1	2	0
GTCGAATCCCAAATAATTTACAAGGGCGGGAATATT	1	43	0
GATGCTGGCGAGATTAGGATTAGGAGGG        	2	2	0
AATTAGGGATAAAGGAGGGCGAAGCGAAGGAAGTTC	2	52	0
ACAATCGCCAAGAGGATTTTAAAGGAACTAATCAAG	2	128	0
CTTTAGAATAAAATCAGGTGGACGAT          	2	284	1
AGGAGGAAGAGGAGAAGGTTAAGGAGAGGCTTAGAG	4	22	0
GCTTGGAGGAGGAAGAGGAGGAAGAGGTTTTCACAG	4	58	0
GAGAAGATAGAGAACAGGATCAAGGATACTGGATTT	4	143	0
AGTGGGGGATGAAGATGGGAGATGAGGAGAAGTTTG	4	208	0
AGCCATTAATAAAAGAGGGAAGTGGGGGATGAAGAT	4	228	0
TCGTACTAACGAAGGAAGGGAAACAGTACATAATCA	6	62	0
ATCATCGGGAAAATAAGGTGCATTGATGAAAATTTT	6	102	0
CTGCCAAGGTAAAATAGGTAAATTAAACTTAATCTT	6	217	1
TTAACCGAGCGAAAAAATATAAAGGATATACCCTGA	7	63	1
TGGATCAATTAAAGTAGTCCTAAGGATATCAGAAGT	8	130	0
          ***  ***   * ***
MAP Score: 4.05234

Motif 9
     AGTTAAAAGGGATCATGCTCTAAGGG	0	5	1
GACTTTGAATAAAGGAGCCCAAATAAACTCT	0	58	0
CGGCCTGAGTCAAGGAATTATACTCACTTAT	0	155	0
AAATAAGAGTAAAGGGCCTAAAAAGCAACGG	0	183	0
CTTGATACAAAAAAGATTTATAACCTCAAGG	0	254	1
TTTATAACCTCAAGGGTTTCTCATCAACACG	0	270	1
AGAGGATTTTAAAGGAACTAATCAAGCTTTC	2	123	0
TTCTGAGAGGAAAGGAGTTAAATAGTAATTA	2	236	0
    GGTAGCCAAGGGCTCTAAGCCTCTCCT	4	6	1
ATTTCTCCAGAAAGGACTTTTATTATGCCGA	6	139	1
CTTTAAAACTAAAAGACTTATCTTATCTCCA	8	78	1
          ****** ****
MAP Score: 2.90408

Motif 10
AGGCCCTTTACTCTTATTTTCCCTAAAATGATGT	0	195	1
AGCGAAGGAAGTTCTTCTTTTCCTGGAAGATGCT	2	32	0
TTCGCTTCGCCCTCCTTTATCCCTAATTTCCTAT	2	60	1
TCTTGGCGATTGTCAACTTTTCCTCCTTGGAGGA	2	151	1
ATACCTTGAATTTCTTGTATTCCTCCCTAAGTGA	2	184	1
TGATTTTATTCTAAAGTTTTCCCTTTATAAGATT	2	266	0
GGGCTCTAAGCCTCTCCTTAACCTTCTCCTCTTC	4	19	1
AAGCTTTTATTACAAAATTTCCCTTACTAAAACT	5	42	1
TTGTTGATTATGTACTGTTTCCCTTCCTTCGTTA	6	58	1
AAGTTTAATTTACCTATTTTACCTTGGCAGGTGT	6	213	0
GTATATCCTTTATATTTTTTCGCTCGGTTAAGTT	7	60	0
GTTTTTGGGACTTCTGATATCCTTAGGACTACTT	8	121	1
TAGACCTTAATTTTATATATCCCTTCTCATTTTA	10	14	1
          * **   *******
MAP Score: 0.819731