AlignACE 3.0 10/20/99
AlignACE2 -i CY/CY_fusions011_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944246464
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	prfC	114	peptide-chain-release factor 3
#1	hypothetical	47	hypothetical protein
#2	icfA	58	carbonic anhydrase
#3	icfA	90	carbonic anhydrase
#4	low	284	low affinity sulfate transporter
#5	low	161	low affinity sulfate transporter

Motif 1
CCGCTGTTAACTTGAGACAATGTTTGCAGCTA	0	39	1
TCGGTCTAAAACTTAGTCTTTTACAAGATTTT	1	22	0
GGGCTGTATTCCTTTGTCTTTG          	3	0	0
GGAATACAGCCCTAGGAATATGAGACGATAGT	3	20	1
CGATAGTCCACCTTGTCATTTTCCCACTTAGT	3	45	1
ACTTAGTGCCCCCAGGGAATTTTTCTGACT  	3	70	1
CCCAGCCCCCATTGAGCAAATTTTTCTCTA  	4	8	0
GTGAGATCAATTTTGGCCAATGATTAAACTAA	4	102	0
CGGGAGTCCTCTTTTGACATTTGGTATAGATT	4	148	1
CTGGTTTTTACTTCAGGCAATGATACAGATAG	4	184	0
TAAAAACCAGCCCTAGAATATTCTCTATGGAA	4	206	1
TAGTCATAGTCTTTAGTCTATTTAAAATAGAT	4	238	0
CTAACCCATTTTTGGGGATATTGAATA     	4	267	1
AGATTCATAACCCTGGTCTATGCTGACGATTA	5	108	1
GATTAGCAATCTTGATGCAATTCCCCTTCCTT	5	135	1
TGATGCAATTCCCCTTCCTTTTCC        	5	147	1
          *** ** *****
MAP Score: 6.07006

Motif 2
ATTTGCTCAATGGGGGCTGGGGAAGATTTATG	4	19	1
AATTTAGTAATGGGGGACGTGGACGGGGGTAG	5	35	1
ATCTGTCCAATGGTGGGTTGGGTTTTGCC   	0	7	0
CCGGAAATGCTGATGGTTGTGGGTTCCAGATT	5	81	1
CTAAATCTTTTTAGGGATAGGGATTGATCGGT	4	74	0
TAACCCATTTTTGGGGATATTGAATA      	4	268	1
GTGCAAACGATGGAGGTCATTAAAACCTTTCC	2	36	1
TAGACCAGGGTTATGAATCTGGAACCCACAAC	5	96	0
          ****** * ***
MAP Score: 5.96109

Motif 3
  GCGATGGGAAAAAATAAGCGGGCATTAG	0	96	0
AAATCTTGTAAAAGACTAAGTTTTAGACCG	1	23	1
CAATCCAAAGAATAACAAAGAAGTA     	2	5	0
         CAAAGACAAAGGAATACAGCC	3	1	1
TAAGTGGGAAAATGACAAGGTGGACTATCG	3	45	0
TAAATAGACTAAAGACTATGACTAACCCAT	4	246	1
          **********
MAP Score: 5.18604

Motif 4
CAAAACCCAACCCACCATTGGACAGATCCG	0	12	1
GGCTCTAGCTGCAAACATTGTCTCAAGTTA	0	46	0
TAGAAAGAGTGGGCCCATTGCTAATGCCCG	0	76	1
CCCACTTAGTGCCCCCAGGGAATTTTTCTG	3	67	1
ATCTTCCCCAGCCCCCATTGAGCAAATTTT	4	16	0
TTAATCATTGGCCAAAATTGATCTCACCGC	4	107	1
CCCGTCCACGTCCCCCATTACTAAATTCGA	5	32	0
          **********
MAP Score: 3.99378

Motif 5
TAGCTGCAAACATTGTCTCAAGTTAACAGCGGAT	0	37	0
TCCACCTTGTCATTTTCCCACTTAGTGCCCCCAG	3	51	1
CCCCAGCCCCCATTGAGCAAATTTTTCTCTA   	4	7	0
TTAGTTTAATCATTGGCCAAAATTGATCTCACCG	4	102	1
CTATCTGTATCATTGCCTGAAGTAAAAACCAGCC	4	184	1
         CCATTATCCAATTCTCGATTAATCG	5	1	1
TAATCGTCAGCATAGACCAGGGTTATGAATCTGG	5	106	0
          ***** ** *  **
MAP Score: 2.76184

Motif 6
ACTTGAGACAATGTTTGCAGCTAGAGCCTAGAAAGA	0	48	1
TGTGCAAACGATGGAGGTCATTAAAACCTTTCC   	2	35	1
AATTTGCTCAATGGGGGCTGGGGAAGATTTATGGTT	4	18	1
GGGAAGATTTATGGTTGCCAAGCTCGACAGCAGAGC	4	38	1
GAATTTAGTAATGGGGGACGTGGACGGGGGTAGAAC	5	34	1
GGAAATGCTGATGGTTGTGGGTTCCAGATTCATAAC	5	83	1
          **** **  * *  **
MAP Score: 0.17131

Motif 7
GCGGATCTGTCCAATGGTGGGTTGGGTTTT	0	13	0
GGGCCCATTGCTAATGCCCGCTTATTTTTT	0	86	1
GTCTCATATTCCTAGGGCTGTATTCCTTTG	3	16	0
AAAAATTTGCTCAATGGGGGCTGGGGAAGA	4	15	1
CTGGGGAAGATTTATGGTTGCCAAGCTCGA	4	35	1
TAGAGAATATTCTAGGGCTGGTTTTTACTT	4	203	0
ATCGAATTTAGTAATGGGGGACGTGGACGG	5	31	1
TCCGGAAATGCTGATGGTTGTGGGTTCCAG	5	80	1
          **********
MAP Score: 0.149357