AlignACE 3.0 10/20/99
AlignACE2 -i CY/CY_fusions015_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944246615
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	trx	300	thioredoxin M
#1	trxA	151	thioredoxin
#2	hypothetical	65	hypothetical protein
#3	trxM	40	thioredoxin M
#4	hypothetical	110	hypothetical protein

Motif 1
CAATGAGTTATTTTTGTCCTACGACGATTT	0	24	1
GTCCTACGACGATTTTCCCTGGTTTAAAAA	0	39	1
ATTGAAAATATGTTTTACCAGAGCGTTTTT	0	64	0
TCTGGACGTAGATTTGACCTTGGACATCAT	0	132	1
CATCCTGAACGTTTTCCCCTAGTTTGTACT	0	166	1
CCCTTGGTTTTGCTAGCCCAGACGACGGGC	0	244	0
GATCAGTTGGGATCAGTCCTCCCTTTGGGG	0	274	1
TAACGCCCAAGGTCTTTCCA          	1	0	0
TCACAAGGTAGGTTTGCCCTAACGCCCAAG	1	19	0
CCCGACTCTCTATCATCCCACGAAATTAAC	1	52	0
GAGTCGGGTTGGCATTCCCTAGTCCTTCCA	1	74	1
ATCAAAAGAGTTCTTGACCATTACC     	1	136	1
        GGTATTTTCCCTCGCAAAGATA	3	28	0
GCTCCGTATTTATTTGTCCATTTAGTTCTG	4	53	1
        GGGGCCTCTCCTCGGCTTAATA	4	98	0
          **********
MAP Score: 11.3067

Motif 2
GTCCTACGACGATTTTCCCTGGTTTAAAAACGCTCTGGT	0	39	1
TCTGGACGTAGATTTGACCTTGGACATCATCAAACATCC	0	132	1
CATCCTGAACGTTTTCCCCTAGTTTGTACTGAATCTTAA	0	166	1
TGAATCTTAATTAATTACCTGGCTTGTTAAAGGCCACTT	0	195	1
CTGATCCCAACTGATCCCCTTGGTTTTGCTAGCCCAGAC	0	251	0
         TGGAAAGACCTTGGGCGTTAGGGCAAACCT	1	1	1
TTGGGCGTTAGGGCAAACCTACCTTGTGATGGGTTAATT	1	20	1
GAGTCGGGTTGGCATTCCCTAGTCCTTCCATTGCCCAAC	1	74	1
CTTTGGATGAGCTAAAACCTAGCTCCGTATTTATTTGTC	4	32	1
          *   * **** *  * * *
MAP Score: 7.21042

Motif 3
TTTTTGTCCTACGACGATTTTCCCTGGTTTAAA	0	34	1
CCGATCTGGACGTAGATTTGACCTTGGACATCA	0	128	1
CGGGCGATCGCCGTGAAGTGGCCTTTAACAAGC	0	216	0
CGGCGATCGCCCGTCGTCTGGGCTAGCAAAACC	0	236	1
CAACTGATCCCCTTGGTTTTGCTAGCCCAGACG	0	250	0
CGACCCCAAAGGGAGGACTGATCCCAACTGATC	0	274	0
GCCCTAACGCCCAAGGTCTTTCCA         	1	1	0
CCCATCACAAGGTAGGTTTGCCCTAACGCCCAA	1	20	0
TAGAGAGTCGGGTTGGCATTCCCTAGTCCTTCC	1	70	1
ATTCCCTAGTCCTTCCATTGCCCAACTGAATAG	1	87	1
TAAATACGGAGCTAGGTTTTAGCTCATCCAAAG	4	32	0
CAATATTAAGCCGAGGAGAGGCCCC        	4	95	1
          ******  ** **
MAP Score: 6.86754

Motif 4
CTACGACGATTTTCCCTGGTTTAAAAACGCTCTGGTAA	0	42	1
ATATTTTCAATGTCATTGAGCCAACCGCCAATCATTTT	0	83	1
TTCAGGATGTTTGATGATGTCCAAGGTCAAATCTACGT	0	137	0
TAGTTTGTACTGAATCTTAATTAATTACCTGGCTTGTT	0	185	1
CATCACAAGGTAGGTTTGCCCTAACGCCCAAGGTCTTT	1	13	0
CAAACCTACCTTGTGATGGGTTAATTTCGTGGGATGAT	1	33	1
      TTGTTAGAACTGGATTAATATCTTTGCGAGGG	3	4	1
GAATAGAAACTTTGGATGAGCTAAAACCTAGCTCCGTA	4	23	1
CTCGGCTTAATATTGGTTAACTAATGACAGAACTAAAT	4	72	0
          * *   *** ****   *
MAP Score: 3.97556

Motif 5
GACAAAAATAACTCATTGTCCCCAGACAACA	0	11	0
GACAATGAGTTATTTTTGTCCTACGACGATT	0	22	1
ATATTTTCAATGTCATTGAGCCAACCGCCAA	0	83	1
CGCCAATCATTTTTATTGGCCCGATCTGGAC	0	108	1
GACGTAGATTTGACCTTGGACATCATCAAAC	0	136	1
TTACCTGGCTTGTTAAAGGCCACTTCACGGC	0	209	1
TCCCCTTGGTTTTGCTAGCCCAGACGACGGG	0	245	0
     TGGAAAGACCTTGGGCGTTAGGGCAA	1	5	1
CGGGTTGGCATTCCCTAGTCCTTCCATTGCC	1	78	1
TCCCTAGTCCTTCCATTGCCCAACTGAATAG	1	89	1
TAATCAAAAGAGTTCTTGACCATTACC    	1	134	1
TAGCTCCGTATTTATTTGTCCATTTAGTTCT	4	51	1
          ******** **
MAP Score: 1.20412

Motif 6
GAGTTATTTTTGTCCTACGACGATTTTCCCT	0	28	1
GACGTAGATTTGACCTTGGACATCATCAAAC	0	136	1
     TGGAAAGACCTTGGGCGTTAGGGCAA	1	5	1
GCGTTAGGGCAAACCTACCTTGTGATGGGTT	1	24	1
GGCATTCCCTAGTCCTTCCATTGCCCAACTG	1	84	1
CTAAGAATAGAAACTTTGGATGAGCTAAAAC	4	19	1
GGATGAGCTAAAACCTAGCTCCGTATTTATT	4	36	1
          ********* *
MAP Score: 0.441301