AlignACE 3.0 10/20/99
AlignACE2 -i CY/CY_fusions018_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944246702
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	glcE	230	glycolate oxidase subunit  GlcE
#1	glcF	67	glycolate oxidase subunit, (Fe-S)protein
#2	hypothetical	146	hypothetical protein
#3	sdhB	293	succinate dehydrogenase iron- sulphur protein subunit
#4	sdhB	166	succinate dehydrogenase iron-sulfur protein

Motif 1
AGACTCCTTTACCACCGTCCTTCCGTTGAACAGG	0	41	0
CTCCCTTACCCCTAGACAAATTCTAGCAACTACC	0	73	1
GAATATGGGACCCTCAGTCTTGCCTTAATTTGTT	0	131	1
CAAATAGCAACCCCCAAAATCTCCAATTACAACG	0	197	0
GTCCATAAATCCCCCGCTAGCACC          	2	0	0
ATTCGCTGCCCCCTGGGCATTAACCCATGGAAAG	3	58	1
CACTAAGCCTGCCACTAAAATTCCCAAGGCGATC	3	131	0
TTGTCGAGAACCCCCTAGAATTGTGCCTATTTTC	3	193	0
TATTGCTTTTCCCAGGGTATTTCCT         	3	278	1
CCCCATTAGTCCCAGCAAATTAGCC         	4	1	0
AGGGGGACATCCTCCTACAATTCCCCATTGATCT	4	45	1
TATTCCTGGTCCCGGCAAAATTCCATAGATCAAT	4	71	0
AAAATTATTGCCCCCGGCCCTTCCGTAATAGGAA	4	105	1
GCCTTTTTTGCCCTGTTGATTTCCTCATACC   	4	145	1
          *** * * * ****
MAP Score: 19.7008

Motif 2
       TGTCCCCTATGATCACACTTTTTTCT	1	51	0
CAAATAGCAACCCCCAAAATCTCCAATTACAAC	0	198	0
ATAGGTCGATCCCCTAAGCTTACTGCCGGGGTC	2	112	0
TAGATTAAGACCCCGTTGCTGGCTTTTTTTGTC	3	222	0
TAAATTTTATCCCCATTAGTCCCAGCAAATTAG	4	12	0
AAGGCGATCGCCCCTAAAATCCAATCTAAATTA	3	107	0
TCCTACAATTCCCCATTGATCTATGGAATTTTG	4	57	1
TGTCGAGAACCCCCTAGAATTGTGCCTATTTTC	3	193	0
GCCTTTTTTGCCCTGTTGATTTCCTCATACC  	4	145	1
GGAGGATGTCCCCCTTAAATTTTATCCCCATTA	4	27	0
AAATTATTGCCCCCGGCCCTTCCGTAATAGGAA	4	106	1
ACTAAGCCTGCCACTAAAATTCCCAAGGCGATC	3	131	0
GAATATGGGACCCTCAGTCTTGCCTTAATTTGT	0	131	1
GACTCCTTTACCACCGTCCTTCCGTTGAACAGG	0	41	0
ATTCGCTGCCCCCTGGGCATTAACCCATGGAAA	3	58	1
GTCCATAAATCCCCCGCTAGCACC         	2	1	0
          **** * **** *
MAP Score: 18.7778

Motif 3
ACAGGTCAAACTTTTTATCCCGTCCCTGAGAGG	0	13	0
TAAGGGAGACTCCTTTACCACCGTCCTTCCGTT	0	48	0
TAAAGGAGTCTCCCTTACCCCTAGACAAATTCT	0	64	1
AATGTTAGCATTGCTGACCCCGGCAGTAAGCTT	2	97	1
TCCAAATCATTCGCTGCCCCCTGGGCATTAACC	3	50	1
AGAATTGTGCCTATTTTCCCAAGTCTTTGACAC	3	178	0
TCCGCCCATATTGCTTTTCCCAGGGTATTTCCT	3	270	1
AATTTTATCCCCATTAGTCCCAGCAAATTAGCC	4	10	0
ATAATTTTTATTCCTGGTCCCGGCAAAATTCCA	4	80	0
GGAATAAAAATTATTGCCCCCGGCCCTTCCGTA	4	99	1
AAGGTCGAGCCTTTTTTGCCCTGTTGATTTCCT	4	137	1
          ** *** **** *
MAP Score: 12.8473

Motif 4
ACCTCTCAGGGACGGGATAAAAAGTTTGAC	0	12	1
TCAACGGAAGGACGGTGGTAAAGGAGTCTC	0	46	1
TAGAATTTGTCTAGGGGTAAGGGAGACTCC	0	68	0
CGTCAAAATCGACGTTGTAATTGGAGATTT	0	185	1
TAAGCTTACTGCCGGGGTCAGCAATGCTAA	2	101	0
TATGCTCTAGGACTGGGTGAAAAGTAGTCA	3	10	1
CGAATGATTTGGATGGGTAACCATGACTAC	3	33	0
GGGTTAATGCCCAGGGGGCAGCGAATGATT	3	54	0
TCCATACTTTCCATGGGTTAATGCCCAGGG	3	68	0
AGGGGCGATCGCCTTGGGAATTTTAGTGGC	3	125	1
TGGTGTCAAAGACTTGGGAAAATAGGCACA	3	176	1
  AGGAAATACCCTGGGAAAAGCAATATGG	3	275	0
TTCCATAGATCAATGGGGAATTGTAGGAGG	4	55	0
TTACGGAAGGGCCGGGGGCAATAATTTTTA	4	103	0
          **********
MAP Score: 11.9694

Motif 5
    TGACCTCTCAGGGACGGGATAAAAAGTTTGACCTG	0	6	1
AAAGGAGTCTCCCTTACCCCTAGACAAATTCTAGCAACT	0	65	1
GACTGAGGGTCCCATATTCTTGGACAATAGCATAATGCT	0	111	0
GAATATGGGACCCTCAGTCTTGCCTTAATTTGTTTTAAA	0	131	1
TTTAAATTAACCACAAAACTGCGTCAAAATCGACGTTGT	0	164	1
      TATGCTCTAGGACTGGGTGAAAAGTAGTCATGG	3	4	1
CCAAATCATTCGCTGCCCCCTGGGCATTAACCCATGGAA	3	51	1
TGAGCAACATCACTAAGCCTGCCACTAAAATTCCCAAGG	3	136	0
GCTCAATGGTGTCAAAGACTTGGGAAAATAGGCACAATT	3	170	1
GACAAAAAAAGCCAGCAACGGGGTCTTAATCTAAACTGT	3	222	1
         AGGAAATACCCTGGGAAAAGCAATATGGGC	3	273	0
        GGCTAATTTGCTGGGACTAATGGGGATAAAA	4	2	1
ATGGAATTTTGCCGGGACCAGGAATAAAAATTATTGCCC	4	79	1
TTCCTATTACGGAAGGGCCGGGGGCAATAATTTTTATTC	4	100	0
  GGTATGAGGAAATCAACAGGGCAAAAAAGGCTCGACC	4	139	0
          * *     * ***  ****
MAP Score: 11.6477

Motif 6
ACCCCTAGACAAATTCTAGCAACTACCGTCAAGCATTATGC	0	80	1
TAATTTAAAACAAATTAAGGCAAGACTGAGGGTCCCATATT	0	132	0
AATTAACCACAAAACTGCGTCAAAATCGACGTTGTAATTGG	0	168	1
TTCAGACTAGAAAAAAGTGTGATCATAGGGGACA       	1	43	1
CCTAAAACTTAAAGAAATGTAAAAACCGCGACATTTTTCTT	2	56	1
TAACCCATGGAAAGTATGGAAAATACGGCTAATTTAGATTG	3	78	1
CAATGGTGTCAAAGACTTGGGAAAATAGGCACAATTCTAGG	3	173	1
GGGTTCTCGACAAAAAAAGCCAGCAACGGGGTCTTAATCTA	3	214	1
      GGCTAATTTGCTGGGACTAATGGGGATAAAATTTA	4	4	1
GGTCCCGGCAAAATTCCATAGATCAATGGGGAATTGTAGGA	4	57	0
          ***     * **  *  * **
MAP Score: 9.89397

Motif 7
TGAACAGGTCAAACTTTTTATCCCGTCCCTGAGA	0	15	0
GGGGTAAGGGAGACTCCTTTACCACCGTCCTTCC	0	51	0
AATTAAGGCAAGACTGAGGGTCCCATATTCTTGG	0	127	0
ACTTTTGACTAGAATTTTTAACTACCTAAAACTT	2	32	1
TCTTAATGTTAGCATTGCTGACCCCGGCAGTAAG	2	93	1
GGTGAAAAGTAGTCATGGTTACCCATCCAAATCA	3	25	1
AATCTAAATTAGCCGTATTTTCCATACTTTCCAT	3	84	0
TATTTTCCCAAGTCTTTGACACCATTGAGCAACA	3	166	0
GGGGAATTGTAGGAGGATGTCCCCCTTAAATTTT	4	37	0
ACCAGGAATAAAAATTATTGCCCCCGGCCCTTCC	4	95	1
AGGAAGGTCGAGCCTTTTTTGCCCTGTTGATTTC	4	134	1
          ** *** **  ***
MAP Score: 5.07924

Motif 8
CTTCCGTTGAACAGGTCAAACTTTTTATCCCGTCCCTGAGAG	0	14	0
        TGATAAAGACAAATAGCAACCCCCAAAATCTCCA	0	206	0
CATTTTTCTTAATGTTAGCATTGCTGACCCCGGCAGTAAGCT	2	87	1
TGGATGGGTAACCATGACTACTTTTCACCCAGTCCTAGAGCA	3	12	0
ATGGTTACCCATCCAAATCATTCGCTGCCCCCTGGGCATTAA	3	39	1
TGCCGGGACCAGGAATAAAAATTATTGCCCCCGGCCCTTCCG	4	88	1
CGTAATAGGAAGGTCGAGCCTTTTTTGCCCTGTTGATTTCCT	4	128	1
          *     *  * *  * **** *
MAP Score: 1.79167

Motif 9
ACAGGTCAAACTTTTTATCCCGTCCCTGAGAGGT	0	12	0
ATAGCAACCCCCAAAATCTCCAATTACAACGTCG	0	194	0
AGTCAAAAGTCCATAAATCCCCCGCTAGCACC  	2	8	0
ACCATGACTACTTTTCACCCAGTCCTAGAGCATA	3	10	0
GCCGTATTTTCCATACTTTCCATGGGTTAATGCC	3	73	0
GGCGATCGCCCCTAAAATCCAATCTAAATTAGCC	3	104	0
AAGCCTGCCACTAAAATTCCCAAGGCGATCGCCC	3	127	0
TAGAATTGTGCCTATTTTCCCAAGTCTTTGACAC	3	178	0
AATTTTATCCCCATTAGTCCCAGCAAATTAGCC 	4	9	0
AGGAATAAAAATTATTGCCCCCGGCCCTTCCGTA	4	98	1
GAAGGTCGAGCCTTTTTTGCCCTGTTGATTTCCT	4	136	1
          *****  ****  *
MAP Score: 1.76233