AlignACE 3.0 10/20/99
AlignACE2 -i MJ/MJ_fusions005_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944239499
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	MJ0534	163	flavoprotein (fprA)
#1	MJ0732	78	flavoprotein (fprA)
#2	MJ0733	35	M. jannaschii predicted coding region MJ0733
#3	MJ0734	39	rubrerythrin (rr)
#4	MJ0735	89	rubredoxin 1 (rd1)
#5	MJ0736	75	alkyl hydroperoxide reductase
#6	MJ0737	39	rubredoxin-like non-heme iron protein
#7	MJ0738	25	conserved hypothetical protein
#8	MJ0739	71	M. jannaschii predicted coding region MJ0739
#9	MJ0740	171	rubredoxin 2 (rd2)
#10	MJ0741	104	desulfoferrodoxin, putative (rbo)
#11	MJ0742	128	conserved hypothetical protein
#12	MJ0743	48	heterodisulfide reductase, subunit B1 (hdrB1)
#13	MJ0744	218	heterodisulfide reductase, subunit C (hdrC)
#14	MJ0745	205	M. jannaschii predicted coding region MJ0745
#15	MJ0746	109	conserved hypothetical protein
#16	MJ0747	217	hemerythrin sipunculid
#17	MJ0748	212	flavoprotein (fpaA)
#18	MJ0749	105	conserved hypothetical protein
#19	MJ0750	81	ferredoxin-type protein (napH)
#20	MJ0751	83	conserved hypothetical protein
#21	MJ0752	200	M. jannaschii predicted coding region MJ0752
#22	MJ0754	286	M. jannaschii predicted coding region MJ0754
#23	MJ0755	241	N-acetylmuramoyl-L-alanine amidase
#24	MJ0756	124	M. jannaschii predicted coding region MJ0756
#25	MJ0760	197	conserved hypothetical protein
#26	MJ0762	23	C4-dicarboxylate transporter (mae1)
#27	MJ0764	197	M. jannaschii predicted coding region MJ0764
#28	MJ0765	270	[6Fe-6S] prismane-containing protein
#29	MJ0766	170	M. jannaschii predicted coding region MJ0766
#30	MJ0767	84	conserved hypothetical protein

Motif 1
TCAATTCCCATTTTATTATTTTACTTAAATAC	13	64	1
ACCATAAATATTTTATTTTTTTGTTA      	23	4	0
TAACTTTTGTTTTTATTGTTTTTAGTAAAACC	25	41	1
TTAATCCTTTTTTTACTTTTTTATTTTTTTAA	16	12	1
TTTCATCTCATTTTTTTATTTTTTATTGTAAA	22	13	1
TATTTTTTCATTTTTTTTATTTTATATATTAT	27	57	1
ATTTTTGTCATTTTTATGTTTTTATTTGAAAC	13	162	0
TTTTATTTAATTTTTATTTTTTAATTCTGTAT	14	24	1
         ATTTAATTAATTTAATCAATTAA	2	1	1
TATTTATTAATTTAATTTATTTCATACCCTTA	10	27	1
TTTTATTAGATTTATCTAATTTTTATCCTCCT	18	47	1
TATATTTATTTTTATATTATTTACCACTACTC	1	51	1
ATAGATAATCTTTTATTTATTAATTTAATTTA	10	14	1
CTTTTTAACTTTTTAATTATTACATTATAAAA	15	79	0
TTGGCAAAAATTTTAGTTATTAATTAAATATA	16	134	1
CTTTGTGCTATTTTTGTCATTATTTATCTTAG	9	149	0
TTTACTGTTATTTTTGTTATTACTTTTTAATA	23	176	0
TACTAATCTGTTTTTATATTTATCCTATCTAT	1	11	1
AGGAAATATCTTTTTCTCATTATTTCTTTTTC	13	34	1
     ATTAATTTTTATTTTTATTTTTGCACT	28	5	1
TGAATGTATCTTTTTTTGTTTAATGCTACTGC	29	125	0
TATTTGTAGTTATTAGTTATTTTATTATCAGT	17	181	0
ACGATTATCGTATTTGTGATTTTTTATATGCA	9	58	0
TCATATATTATATTTTTGATTTTAGATAGTAT	11	42	0
TCTTTACTTTTATTTTTATTTTTGGTTTTTAT	12	13	0
TTATGCGAAATTTAAGTGATTAATGATATATA	9	106	1
TTTAAGTAAATTTTATTTATATTGTGAAATAG	17	61	1
TTGGTAGTATTTTTAGTAATATCTTCACTGGT	22	108	1
AACCTTTAATTTTTAATTTTATCTTTTATTTT	27	31	1
ATATAAATTGTTTTAATTTTATTTTTCAAATA	17	24	0
ATTATTAATTTATAATTTTTTTATACAATCCT	25	155	1
TTAAGTTCTTTATAAGTTATTTTTTGAGTGGT	11	87	0
AAGTAATCTTTATAAATGTTTTAGTTTGATTA	0	32	0
TTCTAAATCTTTTTAATTAATTGTAATTGTTT	4	53	1
AGTTATTAGTTTTTAGTTTATTATTTTTTACT	9	26	0
ATCATCGCTATTTTTTTCATATTTATCACCTT	22	75	0
GTTTTATTGGTTTTTATTTTATATTTGCTTTT	5	13	0
TATCTTCTAATTTTTCTTATATATATATTACT	16	82	0
TCTCCCCTCCTTTTTATTTTATCTTTTGTTTA	5	50	0
GTGAGTCGTTTATATCTCATTTGAATCAACAA	22	262	0
GTAAAATTTATATATTTGTTTTCTTACACTAC	24	51	1
TTATTGTAATTATATATAATTTCTTAAAAAGG	30	21	0
TTACGGTATATATTATTAATTATACGAATTTC	16	170	0
TAAAAACTTCTATTTTTTATTAACAATTATAC	18	10	1
CCTCAAATATTATTTTTGTTTAAAAGGAATAT	23	212	0
CTTTTGTTTATTTAAGTTTTATTGGTTTTTAT	5	28	0
         CTTTAATTATATTTGTAGTTATT	17	199	0
ATCACTTTATATTTACTAATTTTTTAATTTGT	14	110	1
AATCGAAAGGTTTATATATTATGAGTGTTAAT	25	94	1
TATTTTGGATTTTATATTATAT          	27	0	0
ACCAACAAATTTTTAATTATAATTTATAATTT	29	21	0
TACTTAAAGATTTATATAAATTGTTTTAATTT	17	37	0
TTTTATATATTATAATTAATTATAAGATTGTA	27	76	1
          ATTTTTTATTTTCATGGTTGTG	24	0	1
GTTTATTATTTTTTACTTTATAAAAATGGGAT	9	11	0
         TTTTTTATCATAAATTATAAATT	29	1	1
ATCGATATTTTATTACTCATATCTTCTAATTT	16	101	0
TATTATCAGTTATTTATTTTATTGTGTAAGTA	17	159	0
TTATAATATTATTATATGTTTTATCACTTTAT	14	88	1
ACTTTCAAAATTTAAATATATAATTAT     	25	5	0
ATCGTGATTGTTTATTTTATAATGTAATAATT	15	65	1
TTTGGGTTCTTATAATTAATATTTTT      	0	147	1
AGATAGTTGATATAATTATTATGATAAATCCT	28	100	0
AAATAAAAATTTTTAATTAAAT          	14	0	0
TTAGTTGTTATTTTACTTAAATTAACATTGGA	0	62	1
TTTTTCATTGTATAAATATATTTTTGACCTTC	28	172	0
AATATATTTGTATATGTAAATTAATAGTATTA	16	45	1
ATTTAAAGAATATTTTTTATAAATGCAACTGA	27	152	0
CACCAAAAAGTTTAATTAAAATAATTTTATTA	6	12	0
          ***** * ****
MAP Score: 65.3336