Origin IGS: ttctttttattgctgtccggtaaaaaaatgaatattcttcaaaacgtactgtaatgaagggatttacgtgagatattcgtatgccagaagcaatagcatattgagtc .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 gactcaatatgctattgcttctggcatacgaatatctcacgtaaatcccttcattacagtacgttttgaagaatattcatttttttaccggacagcaataaaaagaa Mask Tandem Repeat Region ================================================ ttctttttattgctgtccggtaaaaaaatgaatattcttcaaaacgtactgtaatgaagggatttacgtgagatattcgtatgccagaagcaatagcatattgagtc Find is-nt database================================================ Query_seq: PG0722:PG0723|PG0722:PG0723:hypothetical protein:hypothetical protein:<-->:774982..775088 107 ttctttttattgctgtccggtaaaaaaatgaatattcttcaaaacgtactgtaatgaagggatttacgtgagatattcgtatgccagaagcaatagcatattgagtc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG0722:PG0723|PG0722:PG0723:hypothetical protein:hypothetical protein:<-->:774982..775088 107 ttctttttattgctgtccggtaaaaaaatgaatattcttcaaaacgtactgtaatgaagggatttacgtgagatattcgtatgccagaagcaatagcatattgagtc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG0722:PG0723|PG0722:PG0723:hypothetical protein:hypothetical protein:<-->:774982..775088 107 ttctttttattgctgtccggtaaaaaaatgaatattcttcaaaacgtactgtaatgaagggatttacgtgagatattcgtatgccagaagcaatagcatattgagtc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ttctttttattgctgtccggtaaaaaaatgaatattcttcaaaacgtactgtaatgaagggatttacgtgagatattcgtatgccagaagcaatagcatattgagtc Predict ORF larger than 30AA ================================================ Protein_Len: 31 Strand: - Start: 2 End: 94 . R K I A T R Y F F S Y E E F R V T I F P N V H S I R I G S A M ............. ttctttttattgctgtccggtaaaaaaatgaatattcttcaaaacgtactgtaatgaagggatttacgtgagatattcgtatgccagaagcaatagcatattgagtc Predict Promoter with matrix: RpoD-15 score > 80================================================ Predict Promoter with matrix: RpoD-16 score > 80================================================ Predict Promoter with matrix: RpoD-17 score > 80================================================ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ ttctttttattgctgtccggtaaaaaaatgaatattcttcaaaacgtactgtaatgaagggatttacgtgagatattcgtatgccagaagcaatagcatattgagtc Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PG0722:PG0723|PG0722:PG0723:hypothetical protein:hypothetical protein:<-->:774982..775088 107 ttctttttattgctgtccggtaaaaaaatgaatattcttcaaaacgtactgtaatgaagggatttacgtgagatattcgtatgccagaagcaatagcatattgagtc Intra-Species Hit: Count: 1 Min: 1 Max: 107 Len: 107 Subject: NC_002950_PG0722_PG0723|hypothetical protein:hypothetical protein|NEGATIVE:POSITIVE|[774982,775088]|107 HSP 1 e-value: 6.0E-42 bit: 170.0 Len: 107 Query Start:1 Query End:107 Subject Strand: POSITIVE Subject Start: 1 Subject End: 107 ttctttttattgctgtccggtnnnnnnntgaatattcttcaaaacgtactgtaatgaagggatttacgtgagatattcgtatgccagaagcaatagcatattgagtc ttctttttattgctgtccggtaaaaaaatgaatattcttcaaaacgtactgtaatgaagggatttacgtgagatattcgtatgccagaagcaatagcatattgagtc Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUCUUUUUAUUGCUGUCCGGUAAAAAAAUGAAUAUUCUUCAAAACGUACUGUAAUGAAGGGAUUUACGUGAGAUAUUCGUAUGCCAGAAGCAAUAGCAUAUUGAGUC ......((((((((.((.((((.....(((((((.((((((..((.....))..))))))......(....).))))))).)))).))))))))))........... (-21.60) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GACUCAAUAUGCUAUUGCUUCUGGCAUACGAAUAUCUCACGUAAAUCCCUUCAUUACAGUACGUUUUGAAGAAUAUUCAUUUUUUUACCGGACAGCAAUAAAAAGAA ............((((((((((((..((((.........)))).....(((((..((.....))..)))))................))))).)))))))....... (-21.30) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 864 100 51 191 142 NC_002950:PG0722|5end_hypothetical_protein_774891..775121_NEGATIVE 327 38 8 142 113 NC_002950:PG0572|5end_hypothetical_protein_627571..627801_NEGATIVE 289 88 42 227 176 NC_002950:PG0884|5end_hypothetical_protein_946479..946709_POSITIVE 251 86 59 172 151 NC_002950:PG1742|5end_hypothetical_protein_1827250..1827480_POSITIVE 243 98 54 132 90 NC_002950:PG1884|5end_alpha-L-fucosidase_precursor,_putative_1980992..1981222_NEGATIVE 232 89 45 189 152 NC_002950:PG2152|5end_DNA-binding_protein,_histone-like_family_2259750..2259980_POSITIVE 223 90 48 38 1 NC_002950:PG2215|5end_mannose-1-phosphate_guanylyltransferase_2327695..2327925_NEGATIVE 222 97 55 182 129 NC_002950:PG1888|5end_hypothetical_protein_1985596..1985826_POSITIVE 221 86 45 168 139 NC_002950:PG1589|5end_dihydropteroate_synthase_1667438..1667668_NEGATIVE 220 86 53 207 177 NC_002950:PG0794|5end_penicillin-binding_protein_1A,_putative_846411..846641_POSITIVE 216 84 43 105 64 NC_002950:PG0324|5end_histidine_ammonia-lyase_359082..359312_NEGATIVE 216 99 51 222 175 NC_002950:PG0042|5end_serine_hydroxymethyltransferase_49629..49859_POSITIVE 214 94 57 79 41 NC_002950:PG1786|5end_hypothetical_protein_1874358..1874588_POSITIVE 214 97 51 174 139 NC_002950:PG0444|5end_oligopeptide_transporter,_OPT_family_483256..483486_POSITIVE 211 88 43 227 178 NC_002950:PG0951|5end_phosphoribosylaminoimidazole_carboxylase,_PurE_protein_1010242..1010472_POSITIVE 210 79 48 227 191 NC_002950:PG2052|5end_dihydrodipicolinate_synthase_2149636..2149866_POSITIVE 210 25 6 200 181 NC_002950:PG1770|5end_hypothetical_protein_1857284..1857514_POSITIVE 210 90 44 109 62 NC_002950:PG1395|5end_cell_shape-determining_protein_MreC,_putative_1477669..1477899_NEGATIVE 210 98 51 207 163 NC_002950:PG1202|5end_hypothetical_protein_1283014..1283244_NEGATIVE 210 97 51 207 155 NC_002950:PG0374|5end_hypothetical_protein_405564..405794_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 267 99 51 111 62 NC_002950:PG1574|3end_hypothetical_protein_1652461..1652611_NEGATIVE 266 41 8 89 64 NC_002950:PG0542|3end_hypothetical_protein_595377..595527_NEGATIVE 264 99 58 66 23 NC_002950:PG0371|3end_hypothetical_protein_404224..404374_POSITIVE 244 24 7 64 47 NC_002950:PG1268|3end_hypothetical_protein_1347549..1347699_POSITIVE 243 98 54 59 17 NC_002950:PG1885|3end_polyphosphate_kinase_1981065..1981215_NEGATIVE 230 98 58 119 85 NC_002950:PG0795|3end_hypothetical_protein_849603..849753_POSITIVE 227 85 46 79 38 NC_002950:PG1296|3end_hypothetical_protein_1375329..1375479_POSITIVE 223 99 53 71 20 NC_002950:PG0155|3end_riboflavin_biosynthesis_protein_RibD_177861..178011_NEGATIVE 220 86 53 51 21 NC_002950:PG0793|3end_fructose-1,6-bisphosphatase_846335..846485_POSITIVE 217 98 56 44 2 NC_002950:PG2089|3end_hypothetical_protein_2189904..2190054_POSITIVE 216 97 57 40 1 NC_002950:PG1300|3end_hypothetical_protein_1378530..1378680_NEGATIVE 216 84 43 102 61 NC_002950:PG0325|3end_hypothetical_protein_359085..359235_NEGATIVE 212 89 45 62 12 NC_002950:PG0522|3end_tRNA_delta(2)-isopentenylpyrophosphate_transferase_565993..566143_NEGATIVE 210 90 44 71 24 NC_002950:PG1396|3end_cell_shape-determining_protein_MreB_1477707..1477857_NEGATIVE 209 96 54 57 8 NC_002950:PG0459|3end_ISPg5,_transposase_Orf1_501517..501667_NEGATIVE 207 78 36 140 94 NC_002950:PG1992|3end_glucose-inhibited_division_protein_A_2083367..2083517_POSITIVE 204 88 41 101 52 NC_002950:PG1467|3end_methlytransferase,_UbiE/COQ5_family_1543901..1544051_POSITIVE 204 39 10 74 37 NC_002950:PG1462|3end_hypothetical_protein_1541167..1541317_POSITIVE 202 97 59 56 9 NC_002950:PG1898|3end_transporter,_putative_1996727..1996877_NEGATIVE 202 96 58 62 17 NC_002950:PG0347|3end_UDP-glucose_4-epimerase_382382..382532_POSITIVE