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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