AlignACE 3.0 10/20/99
AlignACE2 -i MT/MT_fusions008_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944249851
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	echA13	224	echA13
#1	fadE26	214	fadE26
#2	Rv3545c	111	hypothetical protein Rv3545c
#3	fadE30_fadD3	47	fadE30: fadE30, fadD3: fadD3

Motif 1
ATCCGACCGGTACAACCAGGAAGGGTTGAC	0	11	0
CAGCGCGCCGGGCATCCGACCGGTACAACC	0	24	0
TTGGCTAAGGGACGGGTAACCTCGCACAGG	0	174	1
ACTGGACGTGAACGGCTGACCTGTGCGAGG	0	193	0
TGGAACTAGCAGCGACCGGGGGGATGGTCA	1	26	0
AAGGCCCTGCTACATCCGAGGAAACGGTCG	1	60	1
CTCTGAATCCAGCGACCGTTTCCTCGGATG	1	72	0
TAGAACGTGTTACAACCGGGAAGACGGCCG	1	104	1
CAACCGGGAAGACGGCCGGGTTGCCGTTGG	1	116	1
ACTAGCTGTCGACAACCAACGCCAACGGCA	1	137	0
GTTGGTTGTCGACAGCTAGTGGACGGCTGC	1	147	1
ACTGGCCGTCAGCAGCCGTCCACTAGCTGT	1	158	0
GACGGCTGCTGACGGCCAGTGATAAAGACG	1	168	1
TTCAATCGGAGGCAGCTGAG          	1	204	1
TCATTACTATGACAAGCAAGGTTGCTTCAA	2	31	1
          **********
MAP Score: 13.0537

Motif 2
CCTTCCTGGTTGTACCGGTCGGATGCCCGGCGCGCTGC	0	17	1
GGACATGTTGGCTAAGGGACGGGTAACCTCGCACAGGT	0	167	1
GCTCCTTACTGGACGTGAACGGCTGACCTGTGCGAGGT	0	192	0
GGAACTAGCAGCGACCGGGGGGATGGTCAGGGTAAGGA	1	17	0
TTACAACCGGGAAGACGGCCGGGTTGCCGTTGGCGTTG	1	113	1
GTTGTCGACAGCTAGTGGACGGCTGCTGACGGCCAGTG	1	151	1
AACAAAGCAAGTGCTTGGTAGGTTAGCCTACAGGGC  	3	21	1
          *     ** *** * ***
MAP Score: 11.7187

Motif 3
CCGCAGCGCGCCGGGCATCCGACCGGTACAACCAGG	0	21	0
CTATGGACATGTTGGCTAAGGGACGGGTAACCTCGC	0	163	1
GACGTGAACGGCTGACCTGTGCGAGGTTACCCGTCC	0	183	0
CCTCCTTACCCTGACCATCCCCCCGGTCGCTGCTAG	1	15	1
TCGGATGTAGCAGGGCCTTATGGTGGAACTAGCAGC	1	43	0
TCTGAATCCAGCGACCGTTTCCTCGGATGTAGCAGG	1	65	0
CAACGGCAACCCGGCCGTCTTCCCGGTTGTAACACG	1	109	0
AGACGGCCGGGTTGCCGTTGGCGTTGGTTGTCGACA	1	125	1
GTTGGTTGTCGACAGCTAGTGGACGGCTGCTGACGG	1	147	1
TGATAAAGACGCGATCATTCAATCGGAGGCAGCTGA	1	187	1
      GGGGCCAGGCTAGAACACGTTTCATTACTA	2	4	1
GCCAGTAAAACATGCCTTCACCGCAGACAAAAGGCA	2	61	0
CTGTCCTAGTGAGGACCTTCTGCCAGTAAAACATGC	2	82	0
ACGCTCCTAACAAAGCAAGTGCTTGGTAGGTTAGCC	3	13	1
          ** *** *   * ***
MAP Score: 10.5835

Motif 4
CCTGGTTGTACCGGTCGGATGCCCGGCGCGCTGCGG	0	21	1
CTATGGACATGTTGGCTAAGGGACGGGTAACCTCGC	0	163	1
CTAGCAGCGACCGGGGGGATGGTCAGGGTAAGGAGG	1	15	0
CCTGCTACATCCGAGGAAACGGTCGCTGGATTCAGA	1	65	1
CGTGTTACAACCGGGAAGACGGCCGGGTTGCCGTTG	1	109	1
GTTGTCGACAGCTAGTGGACGGCTGCTGACGGCCAG	1	151	1
CTGCTGACGGCCAGTGATAAAGACGCGATCATTCAA	1	173	1
          ** **   * ** ***
MAP Score: 6.40852

Motif 5
CCGGGCATCCGACCGGTACAACCAGGAAGGGTTGACG     	0	5	0
TGTGTACAACGAAGTATCTTGGTAGTACTGTGATATACGCAA	0	66	0
CCATAGCCAATACGCACATGAGAGTGATCGATATAGACAAAT	0	127	0
ATTGGCTATGGACATGTTGGCTAAGGGACGGGTAACCTCGCA	0	158	1
TACTGGACGTGAACGGCTGACCTGTGCGAGGTTACCCGTCCC	0	182	0
CGACCGGGGGGATGGTCAGGGTAAGGAGGGTGCC        	1	2	0
AAGGCCCTGCTACATCCGAGGAAACGGTCGCTGGATTCAGAG	1	60	1
CAACCGGGAAGACGGCCGGGTTGCCGTTGGCGTTGGTTGTCG	1	116	1
GACGGCTGCTGACGGCCAGTGATAAAGACGCGATCATTCAAT	1	168	1
TTTACTGGCAGAAGGTCCTCACTAGGACAGCTA         	2	88	1
        CGGACGCTCCTAACAAAGCAAGTGCTTGGTAGGT	3	2	1
          ***** *      * *   * *
MAP Score: 3.85787

Motif 6
TCCTGGTTGTACCGGTCGGATGCCCGGCGCGCTG	0	20	1
GGATGCCCGGCGCGCTGCGGTGGCGCCCTTTGCG	0	37	1
CGTATTGGCTATGGACATGTTGGCTAAGGGACGG	0	155	1
ATGTTGGCTAAGGGACGGGTAACCTCGCACAGGT	0	171	1
ACTAGCAGCGACCGGGGGGATGGTCAGGGTAAGG	1	18	0
GTTCCACCATAAGGCCCTGCTACATCCGAGGAAA	1	50	1
AACCGGGAAGACGGCCGGGTTGCCGTTGGCGTTG	1	117	1
GTCGACAGCTAGTGGACGGCTGCTGACGGCCAGT	1	154	1
ATTACTATGACAAGCAAGGTTGCTTCAATGCCTT	2	33	1
ATGCCTTTTGTCTGCGGTGAAGGCATGTTTTACT	2	60	1
TAACAAAGCAAGTGCTTGGTAGGTTAGCCTACAG	3	20	1
          ** **  ** ****
MAP Score: 2.64549

Motif 7
CGTCAACCCTTCCTGGTTGTACCGGTCGGATGCCCGGCG	0	10	1
CGCAAAGGGCGCCACCGCAGCGCGCCGGGCATCCGACCG	0	32	0
ATCTTGGTAGTACTGTGATATACGCAAAGGGCGCCACCG	0	54	0
TTGGCTAAGGGACGGGTAACCTCGCACAGGTCAGCCGTT	0	174	1
CCTCGCACAGGTCAGCCGTTCACGTCCAGTAAGGAGCGG	0	193	1
AACTAGCAGCGACCGGGGGGATGGTCAGGGTAAGGAGGG	1	14	0
CAACCGGGAAGACGGCCGGGTTGCCGTTGGCGTTGGTTG	1	116	1
ACAGCTAGTGGACGGCTGCTGACGGCCAGTGATAAAGAC	1	158	1
AATGCCTTTTGTCTGCGGTGAAGGCATGTTTTACTGGCA	2	59	1
          * * ***     ***  **
MAP Score: 0.929248

Motif 8
AAGGGCGCCACCGCAGCGCGCCGGGCATCCGACCGGTACAACCAG	0	22	0
TGCAAAGAAGCACTTGTGTACAACGAAGTATCTTGGTAGTACTGT	0	77	0
TGGACGTGAACGGCTGACCTGTGCGAGGTTACCCGTCCCTTAGCC	0	176	0
     GGCACCCTCCTTACCCTGACCATCCCCCCGGTCGCTGCTA	1	5	1
CTGAATCCAGCGACCGTTTCCTCGGATGTAGCAGGGCCTTATGGT	1	55	0
AACGGCAACCCGGCCGTCTTCCCGGTTGTAACACGTTCTAGTCTC	1	99	0
TGGCCGTCAGCAGCCGTCCACTAGCTGTCGACAACCAACGCCAAC	1	141	0
TGCCTTTTGTCTGCGGTGAAGGCATGTTTTACTGGCAGAAGGTCC	2	61	1
          *  * *  * *   *  **  *  *
MAP Score: 0.690633

Motif 9
       CGTCAACCCTTCCTGGTTGTACCGGTCGGAT	0	3	1
GCGTATATCACAGTACTACCAAGATACTTCGTTGTACA	0	68	1
ACCATCCCCCCGGTCGCTGCTAGTTCCACCATAAGGCC	1	28	1
ACATCCGAGGAAACGGTCGCTGGATTCAGAGACTAGAA	1	71	1
GCCGTCTTCCCGGTTGTAACACGTTCTAGTCTCTGAAT	1	94	0
    GGGGCCAGGCTAGAACACGTTTCATTACTATGAC	2	6	1
CTTTTGTCTGCGGTGAAGGCATGTTTTACTGGCAGAAG	2	64	1
          ****     *  *** **
MAP Score: 0.495413