AlignACE 3.0 10/20/99
AlignACE2 -i CY/CY_fusions021_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944246814
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	hypothetical	300	hypothetical protein
#1	patA	83	PatA protein
#2	Na/H	291	Na/H antiporter
#3	potassium	123	potassium channel
#4	NaH-antiporter	300	NaH-antiporter protein
#5	hypothetical	297	hypothetical protein
#6	ATP-dependent	299	ATP-dependent Clp protease proteolytic subunit
#7	tig	300	trigger factor

Motif 1
GTTTTCTCCTCCCCCGGAGTCATCCCTATCGAATCC	0	264	1
AGGAGTCGATGGCCGCAATTTTGCCAGCCTAAAGC 	1	9	0
ATGGTCTGCAGGGGTAGGGTCACCCCTCTGAAATAA	3	48	1
ATAGGATCATCCCGCTCAATCGCCCCACTAAAATCC	4	52	1
TTGAGGTGTGGCAGTTAAATCTCCCCCTTGTTTGAG	4	91	0
TGCAAATCTCGGCGGCAATTTAGCCCTACTTTCAAT	5	125	0
CGTCCGTATAGGCAGTTTATCAACCCTAATTTAGAA	5	221	0
CTGCCTATACGGACGGTGTTTTTCCATTCTTGGGCT	5	242	1
AGGGAGGGCAGGAGGTTAATCTGCCCTGTCAATTTA	6	89	0
CCCTGTCCTAGGGCGTTAGTCCCCCAAGGCTCAAGT	6	121	1
AGAAAAAGGCGGACAGGGATCAAGCCGGCGTCCAAG	6	241	0
ATCTTTTCCCGCCGGGGGGTCCCCCAGGCCGGTTTG	7	33	0
CCCCCCGGCGGGAAAAGATTCTCGCCCTAGGAAAAA	7	50	1
TTGGGTTGACCGCCACAGGTCTTCCCCGAGCCATTG	7	113	1
GGGGCAGTGGGCACTAAGTTCACCCCTGGAGGGCTG	7	245	0
TGCCCACTGCCCCCATTGTTTCACCATCGAGATTTC	7	268	1
          ****   * **  ***
MAP Score: 18.8974

Motif 2
TATCAATCCATTGCCCCGCGCCCTTGAATTTG	0	163	1
CCGCCGGGGGGTCCCCCAGGCCGGTTTGAGAG	7	29	0
CGCCACAGGTCTTCCCCGAGCCATTGCGTTGC	7	123	1
TGGGAATTTAGTGTCCTTCGCCACAATTTTCT	5	193	1
TAGGGCGTTAGTCCCCCAAGGCTCAAGTAAAT	6	129	1
CTATTGACCATTGCCCCTGGTCTACAGTGAAA	4	174	1
GGTGAACTTAGTGCCCACTGCCCCCATTGTTT	7	257	1
AAGGGAAACATTTCCCTCGGTCTAAGTGAACC	7	163	1
TTTCCCTACCTTTCCCCGTACCTAACCC    	6	281	1
AAAAGTTTTTTTTCCCCACTCCTTGGACGCCG	6	220	1
GGGTGCCATTTTTTCCTAGGGCGAGAATCTTT	7	63	0
CCTGCCCTCCCTGTCCTAGGGCGTTAGTCCCC	6	113	1
TGTATTTTCAGAGTCCTACGCCACTAAAAATT	4	233	1
TTTCAGAGGGGTGACCCTACCCCTGCAGACCA	3	49	0
GAACTGCTCCTTTCCCTATGCAGACTGGATCT	2	149	1
TCTTAAGGTTTTCTCCTCCCCCGGAGTCATCC	0	257	1
GCCCTGTCAATTTACCTATTCCGGAGATTTCT	6	71	0
          *******  ***
MAP Score: 16.2906

Motif 3
TATCAATCCATTGCCCCGCGCCCTTGAATTTGTT	0	163	1
TGGCAAAATTGCGGCCATCGACTCCTTTGTTCAT	1	19	1
AAAGTGGATGTTGACCTACTTCCCTGGTTGATCA	2	180	0
ACAACTTCTATTGACCATTGCCCCTGGTCTACAG	4	167	1
TGTATTTTCAGAGTCCTACGCCACTAAAAATTGG	4	233	1
TGGGAATTTAGTGTCCTTCGCCACAATTTTCTAA	5	193	1
TTCTTGGGCTTTGCCGATCGCCGTTTAGTCCGTT	5	268	1
TGAGCCTTGGGGGACTAACGCCCTAGGACAGGGA	6	120	0
GGGAAGACCTGTGGCGGTCAACCCAATTGATCAT	7	105	0
GTTTCCCTTCTAGCCCCGCAACGCAATGGCTCGG	7	138	0
ATCGGTCTGTGGGCCCTTCTACCCGTGTTATGCT	7	196	0
GGTGAACTTAGTGCCCACTGCCCCCATTGTTTCA	7	257	1
          * * **  ******
MAP Score: 14.6242

Motif 4
CGCTGATTATCAATCCATTGCCCCGCGCCCTTGAATTTG	0	156	1
TTTAGGCTGGCAAAATTGCGGCCATCGACTCCTTTGTTC	1	12	1
ACAAGGGGGAGATTTAACTGCCACACCTCAATTTTTCAA	4	96	1
ATTGAAAGTAGGGCTAAATTGCCGCCGAGATTTGCATTT	5	125	1
GGCGAATTGGGAATTTAGTGTCCTTCGCCACAATTTTCT	5	186	1
  AGTTAAACGGACTAAACGGCGATCGGCAAAGCCCAAG	5	270	0
ACACCCCAAGGGTAATTTGGGCCAACGGG          	6	0	0
TTACCCTTGGGGTGTCAGAGGCATACCGGGCCTCCGCAA	6	24	1
TGAGCCTTGGGGGACTAACGCCCTAGGACAGGGAGGGCA	6	115	0
TCTCGCCCTAGGAAAAAATGGCACCCGGCTTATATTATG	7	69	1
ATGATCAATTGGGTTGACCGCCACAGGTCTTCCCCGAGC	7	105	1
GGGCTAGAAGGGAAACATTTCCCTCGGTCTAAGTGAACC	7	156	1
GCATAACACGGGTAGAAGGGCCCACAGACCGATTTCTGC	7	197	1
CTCCAGGGGTGAACTTAGTGCCCACTGCCCCCATTGTTT	7	250	1
          **    *  ****  ** *
MAP Score: 14.0981

Motif 5
GTATATCTCCAAATTGTGGACCAATGGTGTCAA	0	26	1
TGATTAACTTAAGTTGAGGCTAACTAACTAACC	0	77	0
TAGGCTGGCAAAATTGCGGCCATCGACTCCTTT	1	14	1
AGGCTACACGAAATTAGGGATAATTACTATGAC	2	94	1
TTTTCCAAGCAAATTTTGGGAAATCAAAACCTA	2	251	1
TAAGTCAATTAAAGATAGGATCATCCCGCTCAA	4	38	1
ACGCCACTAAAAATTGGGGAGCTTTTGCCTTAT	4	250	1
TTAGTAATTGAAAGTAGGGCTAAATTGCCGCCG	5	119	1
ACTCCAGACAAAATTATGAAAAAATGCAAATCT	5	152	0
CTAATTTAGAAAATTGTGGCGAAGGACACTAAA	5	199	0
ACAATTTTCTAAATTAGGGTTGATAAACTGCCT	5	215	1
GGCCTCCGCAAACTAGAGGAGAAATCTCCGGAA	6	52	1
ACCTAAAGCAAAGTAAAGGAAAAGTTTTTTTTC	6	201	1
GCCGGCGTCCAAGGAGTGGGGAAAAAAAACTTT	6	221	0
GGTACGGGGAAAGGTAGGGAAAATTAAGAAAAA	6	270	0
          ****** **  **
MAP Score: 12.6441

Motif 6
CTCCAAATTGTGGACCAATGGTGTCAAATGTTACGGATAGTTAAG	0	32	1
 GCTTTAGGCTGGCAAAATTGCGGCCATCGACTCCTTTGTTCATA	1	9	1
ATTGTCCTTTTGGCGGGATATTGTGTTTTCCAAGCAAATTTTGGG	2	226	1
AATTTGGATATGGTCTGCAGGGGTAGGGTCACCCCTCTGAAATAA	3	39	1
GGGATTTTAGTGGGGCGATTGAGCGGGATGATCCTATCTTTAATT	4	44	0
TGAAAAATTGAGGTGTGGCAGTTAAATCTCCCCCTTGTTTGAGTA	4	89	0
GTGAATGGTTTGGATTGTATTTTCAGAGTCCTACGCCACTAAAAA	4	218	1
CACTAAAAATTGGGGAGCTTTTGCCTTATCCTGCTTAGAGATGAC	4	254	1
TAGTTAGTAATTGAAAGTAGGGCTAAATTGCCGCCGAGATTTGCA	5	116	1
AAATTACCCTTGGGGTGTCAGAGGCATACCGGGCCTCCGCAAACT	6	21	1
CCCTAGGACAGGGAGGGCAGGAGGTTAATCTGCCCTGTCAATTTA	6	89	0
TCCCCACTCCTTGGACGCCGGCTTGATCCCTGTCCGCCTTTTTCT	6	232	1
TATGATCAATTGGGTTGACCGCCACAGGTCTTCCCCGAGCCATTG	7	104	1
CCTGGAGGGCTGGGAAGGACTGCAGAAATCGGTCTGTGGGCCCTT	7	212	0
          ***   *   * *     **   **
MAP Score: 11.2519

Motif 7
TCGCAATGATGTATCTCCCCGTCAGCGCTG	0	131	1
TCCTCCCCCGGAGTCATCCCTATCGAATCC	0	270	1
          AGATCTTCCAGGATTCGATA	0	290	0
TAACGCGTTAGGAGCCCCCC          	3	0	0
TGCAGGGGTAGGGTCACCCCTCTGAAATAA	3	54	1
ATTAAAGATAGGATCATCCCGCTCAATCGC	4	45	1
TGTGGCAGTTAAATCTCCCCCTTGTTTGAG	4	91	0
GGATAAGGCAAAAGCTCCCCAATTTTTAGT	4	255	0
TCCCGCCGGGGGGTCCCCCAGGCCGGTTTG	7	33	0
TGACCGCCACAGGTCTTCCCCGAGCCATTG	7	119	1
GTGGGCACTAAGTTCACCCCTGGAGGGCTG	7	245	0
          **********
MAP Score: 10.8246

Motif 8
ATTGAAAGTAGGGCTAAATTGCCGCCGAGATTTGCA	5	125	1
TATTTCAGAGGGGTGACCCTACCCCTGCAGACCATA	3	47	0
CTCTCAAACCGGCCTGGGGGACCCCCCGGCGGGAAA	7	29	1
GGGGCTAGAAGGGAAACATTTCCCTCGGTCTAAGTG	7	155	1
CCAGTCTAACGCGTTAGGAGCCCCCC          	3	0	0
TAAATTGACAGGGCAGATTAACCTCCTGCCCTCCCT	6	89	1
TCAAACAAGGGGGAGATTTAACTGCCACACCTCAAT	4	92	1
AGCATAACACGGGTAGAAGGGCCCACAGACCGATTT	7	196	1
TTCTAAATTAGGGTTGATAAACTGCCTATACGGACG	5	221	1
CTTGAGCCTTGGGGGACTAACGCCCTAGGACAGGGA	6	120	0
GGGTGTCAGAGGCATACCGGGCCTCCGCAAACTAGA	6	33	1
AGCCCTCCAGGGGTGAACTTAGTGCCCACTGCCCCC	7	246	1
ACCCCCCGGCGGGAAAAGATTCTCGCCCTAGGAAAA	7	49	1
    CCCGTTGGCCCAAATTACCCTTGGGGTGTCAG	6	6	1
ACTAAAAATTGGGGAGCTTTTGCCTTATCCTGCTTA	4	255	1
CCAAGGAGTGGGGAAAAAAAACTTTTCCTTTACTTT	6	210	0
          ***  *   * *****
MAP Score: 10.8051

Motif 9
TGATTATCAATCCATTGCCCCGCGCCCTTGA	0	159	1
TCTTAAGGTTTTCTCCTCCCCCGGAGTCATC	0	257	1
ATCATCCCGCTCAATCGCCCCACTAAAATCC	4	57	1
GTGTGGCAGTTAAATCTCCCCCTTGTTTGAG	4	91	0
ACTTCTATTGACCATTGCCCCTGGTCTACAG	4	170	1
ATTTTCAGAGTCCTACGCCACTAAAAATTGG	4	236	1
GAATTTAGTGTCCTTCGCCACAATTTTCTAA	5	196	1
          CCCGTTGGCCCAAATTACCCT	6	0	1
GGGCAGATTAACCTCCTGCCCTCCCTGTCCT	6	99	1
TTTTCCCCACTCCTTGGACGCCGGCTTGATC	6	229	1
GCCGGCTTGATCCCTGTCCGCCTTTTTCTTA	6	248	1
TAATTTTCCCTACCTTTCCCCGTACCTAACC	6	277	1
GGTCTGTGGGCCCTTCTACCCGTGTTATGCT	7	196	0
GAACTTAGTGCCCACTGCCCCCATTGTTTCA	7	260	1
          *** *******
MAP Score: 9.38004

Motif 10
GGTTAGTTAGTTAGCCTCAACTTAAGTTAATCA	0	77	1
AATGATGTATCTCCCCGTCAGCGCTGATTATCA	0	135	1
ATCAATCCATTGCCCCGCGCCCTTGAATTTGTT	0	164	1
TCTTAAGGTTTTCTCCTCCCCCGGAGTCATCCC	0	257	1
AAAAGGGAACTGCTCCTTTCCCTATGCAGACTG	2	143	1
      GGGGGGCTCCTAACGCGTTAGACTGGC	3	4	1
TTCAGAGGGGTGACCCTACCCCTGCAGACCATA	3	47	0
TGAAATAATTGTCTCCTGATCTTAAATCGACTG	3	76	1
GGCAGTTAAATCTCCCCCTTGTTTGAGTAGGGA	4	85	0
TATTGACCATTGCCCCTGGTCTACAGTGAAAAT	4	175	1
TTGGGGAGCTTTTGCCTTATCCTGCTTAGAGAT	4	263	1
TTCCGGAGATTTCTCCTCTAGTTTGCGGAGGCC	6	52	0
GCCCTGTCAATTTACCTATTCCGGAGATTTCTC	6	70	0
TAACCTCCTGCCCTCCCTGTCCTAGGGCGTTAG	6	107	1
TAGGGCGTTAGTCCCCCAAGGCTCAAGTAAATC	6	129	1
GAAAAAAAACTTTTCCTTTACTTTGCTTTAGGT	6	201	0
AAAAGTTTTTTTTCCCCACTCCTTGGACGCCGG	6	220	1
GACGCCGGCTTGATCCCTGTCCGCCTTTTTCTT	6	245	1
TTTTTCTTAATTTTCCCTACCTTTCCCCGTACC	6	270	1
CCGCCGGGGGGTCCCCCAGGCCGGTTTGAGAGA	7	28	0
GGGTGCCATTTTTTCCTAGGGCGAGAATCTTTT	7	62	0
TTTCTGCAGTCCTTCCCAGCCCTCCAGGGGTGA	7	229	1
TAGTGCCCACTGCCCCCATTGTTTCACCATCGA	7	265	1
          *******   ***
MAP Score: 8.93446

Motif 11
GATTATCAATCCATTGCCCCGCGCCCTTGA	0	160	1
TTAAGGTTTTCTCCTCCCCCGGAGTCATCC	0	259	1
AAGGGAACTGCTCCTTTCCCTATGCAGACT	2	145	1
GGATGTTGACCTACTTCCCTGGTTGATCAG	2	179	0
AGAGGGGTGACCCTACCCCTGCAGACCATA	3	47	0
CTTCTATTGACCATTGCCCCTGGTCTACAG	4	171	1
AATTGGGGAGCTTTTGCCTTATCCTGCTTA	4	261	1
GCAGATTAACCTCCTGCCCTCCCTGTCCTA	6	101	1
AGTTTTTTTTCCCCACTCCTTGGACGCCGG	6	223	1
GCCGGCTTGATCCCTGTCCGCCTTTTTCTT	6	248	1
AATTTTCCCTACCTTTCCCCGTACCTAACC	6	278	1
TAGGGCGAGAATCTTTTCCCGCCGGGGGGT	7	49	0
AATGTTTCCCTTCTAGCCCCGCAACGCAAT	7	145	0
CTGCAGTCCTTCCCAGCCCTCCAGGGGTGA	7	232	1
AACTTAGTGCCCACTGCCCCCATTGTTTCA	7	261	1
          **********
MAP Score: 6.20894

Motif 12
GGTTAGTTAGTTAGCCTCAACTTAAGTTAATCAAAATTGACAAA	0	77	1
TCTTAAGGTTTTCTCCTCCCCCGGAGTCATCCCTATCGAATCCT	0	257	1
AAAGGAGCAGTTCCCTTTTACGTCAGTTACTACAGGTCATAGTA	2	118	0
TCAGTCTTTTTAGTTCTAAACTTAAGTCAATTAAAGATAGGATC	4	16	1
TATTGACCATTGCCCCTGGTCTACAGTGAAAATATCTATCTCAG	4	175	1
AGGGCGTTAGTCCCCCAAGGCTCAAGTAAATCTAGGTAAGATGA	6	130	1
CAAAGTTGAGTTAACCTAAAGCAAAGTAAAGGAAAAGTTTTTTT	6	188	1
AAGGGAAACATTTCCCTCGGTCTAAGTGAACCTAGCATAACACG	7	163	1
          *   ***   *   *** *    *
MAP Score: 5.1632

Motif 13
ATTCAAGGGCGCGGGGCAATGGATTGATAATCAGCGCTGACGGGGAG	0	145	0
    GCTTTAGGCTGGCAAAATTGCGGCCATCGACTCCTTTGTTCAT	1	6	1
TAACTGACGTAAAAGGGAACTGCTCCTTTCCCTATGCAGACTGGATC	2	133	1
CCATATCCAAATTTGGCCAGTCTAACGCGTTAGGAGCCCCCC     	3	5	0
CAATTATTTCAGAGGGGTGACCCTACCCCTGCAGACCATATCCAAAT	3	40	0
GTCAATTAAAGATAGGATCATCCCGCTCAATCGCCCCACTAAAATCC	4	41	1
CCCTACTCAAACAAGGGGGAGATTTAACTGCCACACCTCAATTTTTC	4	86	1
CGCCACTAAAAATTGGGGAGCTTTTGCCTTATCCTGCTTAGAGATGA	4	251	1
GGAGTTGGCGAATTGGGAATTTAGTGTCCTTCGCCACAATTTTCTAA	5	180	1
CAAAGCCCAAGAATGGAAAAACACCGTCCGTATAGGCAGTTTATCAA	5	234	0
CCCAAATTACCCTTGGGGTGTCAGAGGCATACCGGGCCTCCGCAAAC	6	18	1
AGGTAAATTGACAGGGCAGATTAACCTCCTGCCCTCCCTGTCCTAGG	6	86	1
GAAAAAGGCGGACAGGGATCAAGCCGGCGTCCAAGGAGTGGGGAAAA	6	229	0
CTTTTCCCGCCGGGGGGTCCCCCAGGCCGGTTTGAGAGAATGGGACT	7	20	0
TATTATGATCAATTGGGTTGACCGCCACAGGTCTTCCCCGAGCCATT	7	101	1
TTCACTTAGACCGAGGGAAATGTTTCCCTTCTAGCCCCGCAACGCAA	7	146	0
AGAAATCGGTCTGTGGGCCCTTCTACCCGTGTTATGCTAGGTTCACT	7	187	0
CAATGGGGGCAGTGGGCACTAAGTTCACCCCTGGAGGGCTGGGAAGG	7	239	0
          *  ****        * *   *   **
MAP Score: 4.1222

Motif 14
TATCAATCCATTGCCCCGCGCCCTTGAATTTG	0	163	1
ATCTTAAGGTTTTCTCCTCCCCCGGAGTCATC	0	256	1
CTATTGACCATTGCCCCTGGTCTACAGTGAAA	4	174	1
TTCTTGGGCTTTGCCGATCGCCGTTTAGTCCG	5	268	1
GATTAACCTCCTGCCCTCCCTGTCCTAGGGCG	6	104	1
AAAAGTTTTTTTTCCCCACTCCTTGGACGCCG	6	220	1
TTTTCTTAATTTTCCCTACCTTTCCCCGTACC	6	271	1
GCGAGAATCTTTTCCCGCCGGGGGGTCCCCCA	7	43	0
GGTGCCATTTTTTCCTAGGGCGAGAATCTTTT	7	62	0
CGCCACAGGTCTTCCCCGAGCCATTGCGTTGC	7	123	1
AAATGTTTCCCTTCTAGCCCCGCAACGCAATG	7	144	0
AAGGGAAACATTTCCCTCGGTCTAAGTGAACC	7	163	1
TTCTGCAGTCCTTCCCAGCCCTCCAGGGGTGA	7	230	1
          ******  ****
MAP Score: 2.23276

Motif 15
CAATGATGTATCTCCCCGTCAGCGCTGATTATC	0	134	1
GCTGATTATCAATCCATTGCCCCGCGCCCTTGA	0	157	1
CTTAAGGTTTTCTCCTCCCCCGGAGTCATCCCT	0	258	1
TGAACAAAGGAGTCGATGGCCGCAATTTTGCCA	1	19	0
GTATTTTCAGAGTCCTACGCCACTAAAAATTGG	4	234	1
GGGAATTTAGTGTCCTTCGCCACAATTTTCTAA	5	194	1
TCTTGGGCTTTGCCGATCGCCGTTTAGTCCGTT	5	269	1
TCAGAGGCATACCGGGCCTCCGCAAACTAGAGG	6	38	1
CTAGGGCGTTAGTCCCCCAAGGCTCAAGTAAAT	6	128	1
AGGTAAGATGAGACCATGTCGGCAACAAAGTTG	6	163	1
TTTTTTCCCCACTCCTTGGACGCCGGCTTGATC	6	227	1
ACGCCGGCTTGATCCCTGTCCGCCTTTTTCTTA	6	246	1
CGCCGGGGGGTCCCCCAGGCCGGTTTGAGAGAA	7	27	0
TCAATTGGGTTGACCGCCACAGGTCTTCCCCGA	7	109	1
TTTCCCTTCTAGCCCCGCAACGCAATGGCTCGG	7	138	0
TCGGTCTGTGGGCCCTTCTACCCGTGTTATGCT	7	196	0
CGATTTCTGCAGTCCTTCCCAGCCCTCCAGGGG	7	226	1
          *****  * ****
MAP Score: 0.129691