AlignACE 4.0 05/13/04
./AlignACE -i test.fa 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	1227623309
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	SEQ1; M: CTCAATCGTAGA at 52
#1	SEQ2; M: CTCAATCGTAGA at 172
#2	SEQ3; M: CTCAATCGTAGA at 112
#3	SEQ4; M: CTCAATCGTAGA at 173
#4	SEQ5; M: CTCAATCGTAGA at 185
#5	SEQ6; M: CTCAATCGTAGA at 105
#6	SEQ7; M: CTCAATCGTAGA at 177
#7	SEQ8; M: CTCAATCGTAGA at 172
#8	SEQ9; M: CTCAATCGTAGA at 93
#9	SEQ10; M: CTCAATCGTAGA at 3

Motif 1
TCTACGATTGAG	0	51	0
TCTACGATTGAG	1	171	0
TCTACGATTGAG	2	111	0
TCTACGATTGAG	3	172	0
TCTACGATTGAG	4	184	0
TCTACGATTGAG	5	104	0
TCTACGATTGAG	6	176	0
TCTACGATTGAG	7	171	0
TCTACGATTGAG	8	92	0
TCAAAGATAGAG	8	155	1
TCTACGATTGAG	9	2	0
** ***** ***
MAP Score: 57.9079

Motif 2
GCGAAGGAAGCAGCGCGTGTG	0	7	1
GGCACCGCCTCTACGATTGAG	0	51	0
CAGAGCTTAGCATTGAACGCG	0	93	0
CTAATGAAAGCAATGAGAGTG	0	154	1
CTTGTGCCCTCTAAGCGTCCG	1	73	1
GAGCACGACGCTTTGTACCTG	1	153	0
CGGCACTTAGCAGCGTATCGT	2	36	0
CTGGTTTCATCTACGATTGAG	2	111	0
GGGCCAATAGCGGCGCCGGAG	2	133	0
GTGGAGTTATCTTAGTGCGCG	2	158	0
GAGAGGTTATCTACGATTGAG	3	172	0
CTGCTCCCCGCATACAGCGCG	4	62	0
CAGAACCGAGGTCCGGTACGG	4	157	1
GTGCCCCAAGCTTACCCAGGG	5	40	1
CGCCTCTGATCTACGATTGAG	5	104	0
GTGCTCATAGGGACGTCGCGG	6	2	1
CTGCCCCCCGCATAGTAGGGG	6	45	1
GTAAAGAAATCGATGTGCCAG	6	72	0
CACCTGCAATTGCTGGCAGCG	6	128	0
GGCGGGCCATCCCTGTATGAA	8	65	0
CTCCAGGTCGCATGGAGAGAG	9	89	1
CCTCGGATCGCTTGGGAAGAG	9	134	0
* ** *  ***   *   * *
MAP Score: 19.6235

Motif 3
GTGCGCGAAGGAAGCAGCGCG	0	3	1
CAGAGCTTAGCATTGAACGCG	0	93	0
GTGCCCGATGACCACCCGTCG	0	117	0
GCCCTCTAAGCGTCCGCGGAT	1	78	1
GAGCACGACGCTTTGTACCTG	1	153	0
CGGCACTTAGCAGCGTATCGT	2	36	0
GGGCCAATAGCGGCGCCGGAG	2	133	0
GCGCACTAAGATAACTCCACG	2	159	1
CGGCCCGTTGTCCAGCAGACG	3	2	0
CTGCTCCCCGCATACAGCGCG	4	62	0
GTGCCCCAAGCTTACCCAGGG	5	40	1
GTGCTCATAGGGACGTCGCGG	6	2	1
CTGCCCCCCGCATAGTAGGGG	6	45	1
CGCCGCCATGCGACGCAGAGG	8	39	0
AACCTCTAAGCATACTCTACG	9	8	0
GACCTGGAGGCTTAGACTTGG	9	77	0
GCGCTCTTCCCAAGCGATCCG	9	131	1
GGGCCGTCAGCTCTCAAGTCT	9	153	1
* ** *   **   * *  **
MAP Score: 19.1804

Motif 4
GCCCCAAGCTTACCCAGGGAC	5	42	1
GCCGTCTGCTGGACAACGGGC	3	0	1
GCCGACGGGTGGTCATCGGGC	0	115	1
GCCAATAGCGGCGCCGGAGTC	2	131	0
GCCCCCCGCATAGTAGGGGGA	6	47	1
GCCCGTACCGGACCTCGGTTC	4	159	0
GCCTCATGTACCGGAAGGGAC	3	24	1
GACACGCGCCTGGGAGGGTTC	2	11	1
GCCTTTGGCCTTGGATGAGAA	7	76	0
GGCCCTCGGATCGCTTGGGAA	9	137	0
GCATGTTGGGAATCCGCGGAC	1	89	0
GACACGCGCTGTATGCGGGGA	4	58	1
GCCAGGTACAAAGCGTCGTGC	1	151	1
GCGATCAGCTTGTGGGCGTGC	4	82	1
GACAAATCGGATACTGGGGCA	3	75	0
GCACTTAGCAGCGTATCGTTA	2	34	0
***    **    *  *** *
MAP Score: 18.0097

Motif 5
CGGCACAGAGCTT	0	106	0
ATCCGCGGACGCT	1	86	0
CGCCTGGGAGGGT	2	17	1
CGGAAGGGACGTT	3	35	1
ACACACAGACGGT	3	122	0
TGCCAGAGAGGTT	3	185	0
AGACTGAGACGTT	4	114	1
AATCGTAGAGGAT	4	187	1
CGTCTCGTAGGGT	5	61	0
CGTCGCGGAGGAT	6	15	1
CTTCTTAGACGCT	6	119	1
CGACGCAGAGGAT	8	37	0
ATGCTTAGAGGTT	9	16	1
AGACTTGGGCGAT	9	72	0
CGACCTGGAGGCT	9	86	0
** * ****** *
MAP Score: 16.8287

Motif 6
GTGCGCGAAGGAAGCAGCGCGTG	0	3	1
TTGAGCCGAGTAAAGGGCTGGTG	0	33	0
CAATGCTAAGCTCTGTGCCGACG	0	99	1
CAACTCTCTATGTAGTGCCCGAG	1	28	0
CGACGCTTTGTACCTGGCTTGCG	1	146	0
CGAGTCAATGACACGCGCCTGGG	2	2	1
CGATACGCTGCTAAGTGCCGTCC	2	37	1
CCGGGCCAATAGCGGCGCCGGAG	2	133	0
CCACGCTTCGACACGTGGTATAG	2	175	1
CCGAGCCTCATGTACCGGAAGGG	3	20	1
CTGCTCCCCGCATACAGCGCGTG	4	60	0
CCGAGGTCCGGTACGGGCAAGCC	4	162	1
GTGCTCATAGGGACGTCGCGGAG	6	2	1
CCCTACTATGCGGGGGGCAGGTC	6	42	0
GCCAGCAATTGCAGGTGGTCGTG	6	132	1
CTCTGCGTCGCATGGCGGCGTGG	8	40	1
GGAGGCTTAGACTTGGGCGATAC	9	70	0
GCATGGAGAGAGATCCGGAGGAG	9	98	1
* * **   *    * **  * *
MAP Score: 15.0441

Motif 7
GCGCGTGTGTGTAAC	0	19	1
GCACAGAGCTTAGCA	0	102	0
GGTGGTCATCGGGCA	0	122	1
GCGCGTGTCATTGAC	2	5	0
GGACGGCACTTAGCA	2	45	0
GCGCGTCCCGGGCCA	2	148	0
GCTCGGCCCGTTGTC	3	11	0
GCGCGTGTCCTTTAA	4	52	0
GCTGATCGCTGCTCC	4	76	0
GCCCGTACCGGACCT	4	165	0
GGACGTCGCGGAGGA	6	12	1
GCGGGGGGCAGGTCA	6	41	0
GGACGTACTGGCACA	6	65	1
GCAGGTGGTCGTGCA	6	142	1
GCGCATACCTTAACA	7	21	0
GCACGGGACTTCAAC	7	38	0
GCACGTAGCTGGTAA	7	116	0
GCTCGTCTATGGTCA	8	139	0
GCGCATGCTGGATCC	9	120	0
GGCCGTCAGCTCTCA	9	154	1
** **** * *  **
MAP Score: 13.3145

Motif 8
GAACCGAGGTCCGGTACGGGC	4	159	1
GCCCCCCGCATAGTAGGGGGA	6	47	1
GTCCCTGGGTAAGCTTGGGGC	5	42	0
ACTCCACGCTTCGACACGTGG	2	172	1
ATCCTCTGCGTCGCATGGCGG	8	37	1
GTTCAATGCTAAGCTCTGTGC	0	96	1
GCTCATAGGGACGTCGCGGAG	6	4	1
GTCCCGGGCCAATAGCGGCGC	2	138	0
GCACTTAGCAGCGTATCGTTA	2	34	0
GGCCCTCGGATCGCTTGGGAA	9	137	0
CTGCTGGACAACGGGCCGAGC	3	5	1
GGGCACTACATAGAGAGTTGC	1	31	1
AGCCTCCAGGTCGCATGGAGA	9	86	1
AATCGTAGATCAGAGGCGAGA	5	107	1
GAACTCCACTAAGACTTGAGA	9	164	0
GAGCAGCGATCAGCTTGTGGG	4	77	1
GCCAGGTACAAAGCGTCGTGC	1	151	1
AGTCAATGACACGCGCCTGGG	2	4	1
GGTCATGGAATCTTATGTAGC	4	5	1
GTAGATAACAGAGGTCGGGGG	1	178	1
*  *   **  **   ** **
MAP Score: 11.6098

Motif 9
CCGAGTAAAGGGCTG	0	36	0
GTGGTCATCGGGCAC	0	123	1
GATAACAGAGGTCGG	1	181	1
CGGCGCCGGAGTCTG	2	129	0
GCGCGTCCCGGGCCA	2	148	0
CTGGACAACGGGCCG	3	8	1
CGGATACTGGGGCAG	3	74	0
GGGAGCAGCGATCAG	4	75	1
CAGAACCGAGGTCCG	4	157	1
GGGTCCCTGGGTAAG	5	50	0
GTGCTCATAGGGACG	6	2	1
GAGATCCGGAGGAGG	9	107	1
GCGATCCGAGGGCCG	9	144	1
GAGTTCACATGGCTG	9	179	1
* *  ** ***** *
MAP Score: 11.2943

Motif 10
TAGAGGCGGTG	0	59	1
GCTAAGCTCTG	0	103	1
TGGAAGCAGTG	1	121	1
GCGAGGCTGTG	1	138	0
ACGACGCTTTG	1	159	0
GGGACGCGCAC	2	154	1
TCGAAGCGTGG	2	175	0
TGTATGCGGGG	4	67	1
GGTAAGCTTGG	5	45	0
TGTACGCTGGG	5	148	1
ACTATGCGGGG	6	50	0
GGTATGCGCTG	7	27	1
GGTACCCGGAG	7	157	1
GCGACGCAGAG	8	40	0
TGGCGGCGTGG	8	52	1
TCTAGGCGGGC	8	79	0
AGTATGCTTAG	9	13	1
TGGAGGCTTAG	9	83	0
**** ******
MAP Score: 9.7924

Motif 11
GCACAGAGCTTAGCATTGAAC	0	96	0
GTCCGCGGATTCCCAACATGC	1	89	1
ATACACAGCCTCGCAAGCCAG	1	135	1
GGCCCGGGACGCGCACTAAGA	2	149	1
GCCCGTTGTCCAGCAGACGGC	3	0	0
GAGCAGCGATCAGCTTGTGGG	4	77	1
GAACCGAGGTCCGGTACGGGC	4	159	1
GTCCCTGGGTAAGCTTGGGGC	5	42	0
GACCTGCCCCCCGCATAGTAG	6	42	1
AACCAGCGCATACCTTAACAG	7	20	0
ATCCTCTGCGTCGCATGGCGG	8	37	1
GACCATAGACGAGCATCAAAG	8	140	1
GGCCCTCGGATCGCTTGGGAA	9	137	0
* **   *   ****    **
MAP Score: 9.01393

Motif 12
GCCGTCCGTC	2	53	1
GGCGTGCGCG	0	0	1
GGCGCGTGTC	2	11	0
AGCGCGTGTG	0	18	1
GCGGTGCGTG	8	108	0
AGCGCGTGTC	4	58	0
AGCGTCCGCG	1	86	1
ACCGTCTGTG	3	122	1
GCCATGCGAC	8	46	0
ACCACCCGTC	0	118	0
GGCGCCGGAG	2	133	0
ACCACGTGTC	2	184	0
GGCTTGCGAG	1	144	0
GCGATCCGAG	9	144	1
AGTGCGCGTC	2	156	0
AGTGCCCGAG	1	28	0
**********
MAP Score: 7.51121

Motif 13
GCCGACGGGTGGTCATCGGG	0	115	1
GCACGACGCTTTGTACCTGG	1	152	0
CCTGGGAGGGTTCAATAACG	2	19	1
GCGCGTCCCGGGCCAATAGC	2	143	0
GCCGTCTGCTGGACAACGGG	3	0	1
GTCCCTTCCGGTACATGAGG	3	25	0
GCTGCTCCCCGCATACAGCG	4	64	0
GCCCCAAGCTTACCCAGGGA	5	42	1
ACCGGCTGACGCTAATACGG	5	84	0
GCGGGGGGCAGGTCATTACA	6	36	0
GCTGGCAGCGTCTAAGAAGG	6	118	0
GCAGGTGGTCGTGCAATACG	6	142	1
GCTGGTTGAAGTCCCGTGCG	7	34	1
GCACGTAGCTGGTAAATAGG	7	111	0
GCGGCGTGGATTTCATACAG	8	54	1
CCTGGAGGCTTAGACTTGGG	9	76	0
** **  ** *   *   **
MAP Score: 5.63667

Motif 14
GCCGACGGGTGGTCATCGGG	0	115	1
ATCCGCGGACGCTTAGAGGG	1	79	0
ACGCTTTGTACCTGGCTTGC	1	147	0
ACGGACGGCACTTAGCAGCG	2	42	0
GCCGTCTGCTGGACAACGGG	3	0	1
ACACACAGACGGTTGAAAGG	3	115	0
GCCGATAGTGCTTAAGTTCG	3	147	1
CTTGCCCGTACCGGACCTCG	4	163	0
ACCGGCTGACGCTAATACGG	5	84	0
GCCCCCCGCATAGTAGGGGG	6	47	1
GCTGGCAGCGTCTAAGAAGG	6	118	0
GCAGGTGGTCGTGCAATACG	6	142	1
ACGCACGGGACTTCAACCAG	7	35	0
GCACGTAGCTGGTAAATAGG	7	111	0
ATCCTCTGCGTCGCATGGCG	8	37	1
** * * *  * * *   **
MAP Score: 3.89842

Motif 15
GAGGCTGTGTAT	1	135	0
GAGGTCGGGGGT	1	188	1
GACGGACGGCAC	2	51	0
TTGGCCCGGGAC	2	147	1
GAGGCTCGGCCC	3	17	0
CACGCGCTGTAT	4	60	1
TAGGCCAGGTAT	4	127	0
GAGGTCCGGTAC	4	164	1
TACGCTGGGGAT	5	150	1
GTCGCGGAGGAT	6	16	1
TACGCACGGGAC	7	44	0
TACTCCGGGTAC	7	158	0
GACGCAGAGGAT	8	37	0
TAGGCGGGCCAT	8	76	0
***** *** **
MAP Score: 3.33444

Motif 16
CGGCTCAATCGTAGAGGC	0	48	1
CGACGGGTGGTCATCGGG	0	117	1
CGCTTAGAGGGCACAAGC	1	72	0
TGACACGCGCCTGGGAGG	2	10	1
CGATACGCTGCTAAGTGC	2	37	1
CGTCCCGGGCCAATAGCG	2	142	0
CCACGCTTCGACACGTGG	2	175	1
CGTCTGCTGGACAACGGG	3	2	1
ACACAGACGGTTGAAAGG	3	115	0
TGCTCCCCGCATACAGCG	4	64	0
TGAGGCTTGCCCGTACCG	4	170	0
TGCCCCAAGCTTACCCAG	5	41	1
CGGCTGACGCTAATACGG	5	84	0
CGCGACGTCCCTATGAGC	6	4	0
TGCCCCCCGCATAGTAGG	6	46	1
CGTTGCCTTCTTAGACGC	6	113	1
TGACTCAATCGTAGACCC	6	173	1
AGTCCCGTGCGTATGTGG	7	43	1
AGGCTCGCACGTAGCTGG	7	119	0
CCACGCCGCCATGCGACG	8	45	0
AGCCTCCAGGTCGCATGG	9	86	1
** * *  ** **   **
MAP Score: 1.0395

