Были установлены следующие параметры для MEME:
- распределение количества встреч каждого мотива:"Zero or one per sequence"
- максимальная и минимальная длина мотива: по 16 (ищем мотивы строго заданной длины)
- число различных мотивов: 1
В поле name of file - файл с последовательностями, LOGO:
Матрица PSSM:
| A | C | G | T | Pattern | |
| 1 | 149 | -1023 | 10 | -1023 | R |
| 2 | -68 | 110 | -48 | -68 | C |
| 3 | -1023 | -148 | 198 | -1023 | G |
| 4 | -1023 | 198 | -148 | -1023 | C |
| 5 | 190 | -1023 | -1023 | -1023 | A |
| 6 | 190 | -1023 | -1023 | -1023 | A |
| 7 | 90 | -148 | -148 | 32 | W |
| 8 | -1023 | 210 | -1023 | -1023 | C |
| 9 | -1023 | -1023 | 210 | -1023 | G |
| 10 | -168 | -1023 | -48 | 149 | T |
| 11 | -1023 | -1023 | -1023 | 190 | T |
| 12 | -1023 | -1023 | -1023 | 190 | T |
| 13 | -68 | -1023 | -148 | 149 | T |
| 14 | -168 | 198 | -1023 | -1023 | C |
| 15 | -168 | 110 | 52 | -168 | S |
| 16 | -10 | -48 | -1023 | 113 | T |
Таблица найденных мотивов:
| имя последовательности | Цепь (+/-) | координата первого нуклеотида | P-VALUE |
| purE | + | 163 | 6.28e-09 |
| purL | + | 158 | 7.77e-09 |
| cypA | + | 178 | 9.61e-09 |
| codB | - | 167 | 1.13e-08 |
| purR | + | 189 | 2.47e-08 |
| purC | - | 183 | 5.59e-08 |
| carA | + | 13 | 6.06e-08 |
| purA | - | 128 | 9.50e-08 |
| purM | - | 170 | 1.93e-07 |
| folD | - | 271 | 2.56e-07 |
| guaB | + | 181 | 5.69e-07 |
| glnB | + | 167 | 6.65e-07 |
Исходные последовательности (найденные мотивы подчеркнуты):
>codB tacggacctgaaccgtaggtcggataaggcgctcgcgtcgcatccgacaccatgctcagatgcctgatgcgacgctgacgcgtcttatca ggcctacccactgtttttacaccgataatttttcccccacctttttgcactcattcatataaaaaatatatttccccacgaaaacgattg ctttttatcttcagatgaatagaatgcggcggattttttgggtttcaaacagcaaaaagggggaatttcgtgtcgcaagataacaacttt agccaggggccagtcccgcagtcggcgcgg >purE tcgcccggcggtgcatgaacttatcgccaatcagcaacctgcttttcgcgtggtactgggtgcctggcatacggaaggttcaatggtgaaa gtcacggcggatgacgttgagctgattcattttccgttttaaaaaacccgcaactttgctgatttcacagccacgcaaccgttttcct tgctctctttccgtgctattctctgtgccctctaaagccgagagttgtgcaccacaggagttttaagacgcatgtcttcccgcaata atccggcgcgtgtcgccatcgtgatggggtccaa >pyrC gaaccaggcattacgcaattactttaaccagcaacctgcttacgtcctgcgcgaagatggcagccagggcgaagcaatggcgaaaaaactg gcgaaaggcattgaagtgaagccaggcgaaattgtcattccatttactgattaatcacgagggcgcattcgcgccctttatttttcgtgca aaggaaaacgtttccgcttatcctttgtgtccggcaaaaacatcccttcagccggagcatagagattaatgactgcaccatcccaggtatt aaagatccgccgcccagacgactggca >purR ttacacactgtgatgaaaaaatctcccgtcatttataatgataagtgtttttaccacttccccttttcgtcaagatcggccaaaattccacg cttacactatttgcgtactggccattgaccccttcctgacgctccgtgtcgtttttccggcgtaccgcaacacttttgttgtgcgtaaggtg tgtaaaggcaaacgtttaccttgcgattttgcaggagctgaagttagggtctggagtgaaatggaatggcaacaataaaagatgtagcgaaa cgagcaaacgtttccactacaact >cvpA tgcctgatgcgacgctggcgcgtcttatcaggcctacgcaggggtagaaccgtaggtcggataaggcgtttacgccgcatccgacacgcatt gcccgatgccgcaaaggcataaaaagtcgatggcgttgaatattttttcagcgccatttttattgatgcgcgggaaggaaatccctacgcaa acgttttctttttctgttagaatgcgccccgaacaggatgacagggcgtaaaatcgtgggacacatatggtctggattgattacgccataat cgcggtgattgctttttcctctct >purM ttttcgttgactttagtcaaaatgataacggtttgagataaagttattttatattcagatggttatgaaagaagattattccatccgaaaac taacctttaccctggcacaagtcttctttcgccgcgcgcctggggaaaagacgtgcaaaaaggttgtgtaaagcagtctcgcaaacgtttgc tttccctgttagaattgcgccgaattttatttttctaccgcaagtaacgcgtggggacccaagcagtgaccgataaaacctctcttagctac aaagatgccggtgttgatattgac >guaB acctgtcccatctcatgctcaagcagcagacgaaccgtttgattcaggcgactaacggtaaaaattgcaggggattgagaaggtaacatgtg agcgagatcaaattctaaatcagcaggttattcagtcgatagtaacccgcccttcggggatagcaagcattttttgcaaaaaggggtagatg caatcggttacgctctgtataatgccgcggcaatatttattaaccactctggtcgagatattgcccatgctacgtatcgctaaagaagctct gacgtttgacgacgttctcctcgt >glnB gggtgaaaatacggcgctgccaacctttgttgaggcacgtaatcagtttgaactcaactatttgcgtaagctgctgcaaatcaccaaaggca acgtcacccacgcggcgagaatggcggggcgcaaccggacagaattttataaactgctttcccgacacgagctggatgcaaacgatttcaag gaatgaattggcgttatgtgttacgtttagcagatcaaaagacaggcgaccttttcaaggaatagcatgaaaaagattgatgcgattataaa acccttcaagctggacgatgtccg >purL attctctgtgtcgtgcgcgtcccagcttgaaaaaacgtaataatagtgaaaggtttactcataaatgagcggcattttgcgtaaacctgcgc cagatggcaacttattacagccattggcggcacgcgttgctaattcacgatggtgattttatttccacgcaaacggtttcgtcagcgcatca gattctttataatgacgcccgtttcccccccttgggtacaccgaaagcttagaagacgagagacttatgatggaaattctgcgtggttcgcc tgcactgtcggcattccgaatcaa >purA tagggccgatgctttacccgaaggcatggaagaagatgatctctgcgatgaccaatttgcccgataatattttacgtcgttttggcggtgga cttgtggttgcgggcgttgtggtctactacatgttgaggaaaacgattggctgaacaaaaaacagactgatcgaggtcatttttgagtgcaa aaagtgctgtaactctgaaaaagcgatggtagaatccatttttaagcaaacggtgattttgaaaaatgggtaacaacgtcgtcgtactgggc acccaatggggtgacgaaggtaaa >folD aaattctttttatattgtcaggtatttcttaaattatcttaatccttagacaaggaaataaatcagttccagatttacaacgccatcatgga cgaaaaatgaagctttcagtctcagcgacggtgcgcctcaccttcgcaagaggtcgcttcacgcgataaatctgaaacgaaacctgacagcg cgccccgcttctgacaaaataggcgcatccccttcgatctacgtaacagatggaatcctctctctgatggcagcaaagattattgacggtaa aacgattgcgcagcaggtgcgctc >rpiA ttgaatggcgtggcgttattgcctcaatttgcctgtaaacaggggcttgcgaacggtgaactggtgcgcctgtttgcaccgtggagcggcatac ccagaccgttgtatgctttatttgcggggcgaaaggggatgcctgccattgcgcgatattttatggatgagttaaccacgcggcttgccaacgg ggtctgaatcgctttttttgtatataatgcgtgtgaaatttcataccacaggcgaaacgatcatgacgcaggatgaattgaaaaaagcagtagg atgggcggcacttcagta >carA caatcttcttgctgcgcaagcgttttccagaacaggttagatgatctttttgtcgcttaatgcctgtaaaacatgcatgagccacaaaataa tataaaaaatcccgccattaagttgacttttagcgcccatatctccagaatgccgccgtttgccagaaattcgtcggtaagcagatttgcat tgatttacgtcatcattgtgaattaatatgcaaataaagtgagtgaatattctctggagggtgttttgattaagtcagcgctattggttctg gaagacggaacccagtttcacggt
Программа MEME ошиблась в выборе только 2х сайтов узнавания: purR и purA.
Для purR это:
>purR ggcgtaccgcaacacttttgttgtgcgtaaggtgtgtaaaggcaaacgtttaccttgcgattttgcaggagctgaagttagggtc
Для purA:
>purA aggtcatttttgagtgcaaaaagtgctgtaactctgaaaaagcgatggtagaatccatttttaagcaaacggtgattttgaaaaa
Всего предсказано: 12
Правильно предсказано: 8
Чувствительность = правильно предсказанных / всего правильных = 8/10 = 0.8
Специфичность = правильно предсказанных / всего предсказанных = 8/12= 0.667