Origin IGS: ctcacaatcattaaagaattggaggtgcgatctctcttttttccgtacagtacgataattattcccttaaagctcccttgtctaaaggaggagggagagtcgccgga .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tccggcgactctccctcctcctttagacaagggagctttaagggaataattatcgtactgtacggaaaaaagagagatcgcacctccaattctttaatgattgtgag Mask Tandem Repeat Region ================================================ ctcacaatcattaaagaattggaggtgcgatctctcttttttccgtacagtacgataattattcccttaaagctcccttgtctaaaggaggagggagagtcgccgga Find is-nt database================================================ Query_seq: PG1229:PG1230|PG1229:PG1230:hypothetical protein:hypothetical protein:<-<-:1305943..1306049 107 ctcacaatcattaaagaattggaggtgcgatctctcttttttccgtacagtacgataattattcccttaaagctcccttgtctaaaggaggagggagagtcgccgga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG1229:PG1230|PG1229:PG1230:hypothetical protein:hypothetical protein:<-<-:1305943..1306049 107 ctcacaatcattaaagaattggaggtgcgatctctcttttttccgtacagtacgataattattcccttaaagctcccttgtctaaaggaggagggagagtcgccgga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG1229:PG1230|PG1229:PG1230:hypothetical protein:hypothetical protein:<-<-:1305943..1306049 107 ctcacaatcattaaagaattggaggtgcgatctctcttttttccgtacagtacgataattattcccttaaagctcccttgtctaaaggaggagggagagtcgccgga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ctcacaatcattaaagaattggaggtgcgatctctcttttttccgtacagtacgataattattcccttaaagctcccttgtctaaaggaggagggagagtcgccgga Predict ORF larger than 30AA ================================================ Protein_Len: 33 Strand: + Start: 7 End: 105 ...... M I K E L E V R S L F F P Y S T I I I P L K L P C L K E E G E S P .. Protein_Len: 30 Strand: + Start: 18 End: 107 ................. M G G A I S L F S V Q Y D N Y S L K A P L S K G G G R V A G ctcacaatcattaaagaattggaggtgcgatctctcttttttccgtacagtacgataattattcccttaaagctcccttgtctaaaggaggagggagagtcgccgga 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================================================ ctcacaatcattaaagaattggaggtgcgatctctcttttttccgtacagtacgataattattcccttaaagctcccttgtctaaaggaggagggagagtcgccgga Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PG1229:PG1230|PG1229:PG1230:hypothetical protein:hypothetical protein:<-<-:1305943..1306049 107 ctcacaatcattaaagaattggaggtgcgatctctcttttttccgtacagtacgataattattcccttaaagctcccttgtctaaaggaggagggagagtcgccgga Intra-Species Hit: Count: 1 Min: 1 Max: 107 Len: 107 Subject: NC_002950_PG1229_PG1230|hypothetical protein:hypothetical protein|NEGATIVE:NEGATIVE|[1305943,1306049]|107 HSP 1 e-value: 2.0E-54 bit: 212.0 Len: 107 Query Start:1 Query End:107 Subject Strand: POSITIVE Subject Start: 1 Subject End: 107 ctcacaatcattaaagaattggaggtgcgatctctcttttttccgtacagtacgataattattcccttaaagctcccttgtctaaaggaggagggagagtcgccgga ctcacaatcattaaagaattggaggtgcgatctctcttttttccgtacagtacgataattattcccttaaagctcccttgtctaaaggaggagggagagtcgccgga Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUCACAAUCAUUAAAGAAUUGGAGGUGCGAUCUCUCUUUUUUCCGUACAGUACGAUAAUUAUUCCCUUAAAGCUCCCUUGUCUAAAGGAGGAGGGAGAGUCGCCGGA (((.(((((......).)))))))..((((.(((((((((((((....((.((((......................))))))...))))))))))))))))).... (-28.05) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCCGGCGACUCUCCCUCCUCCUUUAGACAAGGGAGCUUUAAGGGAAUAAUUAUCGUACUGUACGGAAAAAAGAGAGAUCGCACCUCCAAUUCUUUAAUGAUUGUGAG ....((((((((((((.(((((((....))))))).....))))........(((((...))))).......)))).))))..((((((((.......))))).))) (-27.00) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 908 100 51 191 142 NC_002950:PG1229|5end_hypothetical_protein_1305852..1306082_NEGATIVE 327 56 17 198 147 NC_002950:PG0151|5end_signal_recognition_particle-docking_protein_FtsY_174494..174724_NEGATIVE 310 57 18 207 170 NC_002950:PG0657|5end_Maf-like_protein_707782..708012_NEGATIVE 306 65 24 223 187 NC_002950:PG1021|5end_hypothetical_protein_1083592..1083822_NEGATIVE 281 94 53 173 129 NC_002950:PG0805|5end_prolipoprotein_diacylglyceryl_transferase_862650..862880_NEGATIVE 280 58 16 199 145 NC_002950:PG1479|5end_conjugative_transposon_protein_TraJ_1555234..1555464_NEGATIVE 274 61 21 66 13 NC_002950:PG0718|5end_hypothetical_protein_771573..771803_NEGATIVE 272 99 62 192 153 NC_002950:PG1618|5end_hypothetical_protein_1697903..1698133_POSITIVE 271 52 21 52 10 NC_002950:PG0790|5end_GTP-binding_protein_Obg_842583..842813_NEGATIVE 267 98 71 160 129 NC_002950:PG0011|5end_glycosyl_hydrolase,_family_3_11494..11724_POSITIVE 265 95 72 153 133 NC_002950:PG1672|5end_hypothetical_protein_1757637..1757867_POSITIVE 265 95 72 153 133 NC_002950:PG0100|5end_hypothetical_protein_119219..119449_NEGATIVE 263 56 20 51 4 NC_002950:PG1854|5end_5-formyltetrahydrofolate_cyclo-ligase_family_protein_1953882..1954112_NEGATIVE 262 47 2 61 18 NC_002950:PG0839|5end_hypothetical_protein_897213..897443_POSITIVE 261 48 2 189 140 NC_002950:PG1508|5end_hypothetical_protein_1586060..1586290_POSITIVE 261 95 53 206 155 NC_002950:PG1219|5end_hypothetical_protein_1296671..1296901_POSITIVE 260 96 64 50 12 NC_002950:PG1859|5end_glycerate_kinase_family_protein_1958334..1958564_NEGATIVE 258 68 21 169 109 NC_002950:PG1015|5end_hypothetical_protein_1076020..1076250_NEGATIVE 254 66 21 89 31 NC_002950:PG2202|5end_Holliday_junction_resolvase-like_protein_2309933..2310163_NEGATIVE 251 92 61 156 130 NC_002950:PG2094|5end_hypothetical_protein_2197868..2198098_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 315 100 58 59 8 NC_002950:PG0045|3end_heat_shock_protein_90_56193..56343_POSITIVE 281 94 53 136 92 NC_002950:PG0806|3end_oxidoreductase,_Gfo/Idh/MocA_family_862687..862837_NEGATIVE 279 52 16 50 6 NC_002950:PG0844|3end_hypothetical_protein_905461..905611_POSITIVE 277 67 21 123 81 NC_002950:PG1614|3end_succinate_dehydrogenase_1693800..1693950_NEGATIVE 274 96 62 108 64 NC_002950:PG0815|3end_hypothetical_protein_876447..876597_POSITIVE 263 56 20 91 44 NC_002950:PG1855|3end_carboxyl-terminal_protease_1953842..1953992_NEGATIVE 262 99 53 58 12 NC_002950:PG0052|3end_sensor_histidine_kinase_64686..64836_POSITIVE 258 50 14 72 33 NC_002950:PG1797|3end_DNA-binding_response_regulator/sensor_histidine_kinase_1892978..1893128_POSITIVE 257 97 64 57 32 NC_002950:PG0143|3end_hydrolase,_carbon-nitrogen_family_165747..165897_NEGATIVE 250 44 1 149 115 NC_002950:PG0152|3end_carboxynorspermidine_decarboxylase_174521..174671_NEGATIVE 249 100 71 84 50 NC_002950:PG0541|3end_hypothetical_protein_595136..595286_POSITIVE 246 54 13 69 26 NC_002950:PG1741|3end_aspartate_ammonia-lyase_1825856..1826006_NEGATIVE 246 100 59 84 51 NC_002950:PG1089|3end_DNA-binding_response_regulator_RprY_1155523..1155673_NEGATIVE 246 97 61 75 41 NC_002950:PG1070|3end_L-lysine_2,3-aminomutase_1137959..1138109_POSITIVE 243 69 22 42 1 NC_002950:PG1537|3end_hypothetical_protein_1617603..1617753_POSITIVE 243 100 60 90 39 NC_002950:PG0173|3end_transcriptional_regulator,_putative_194388..194538_NEGATIVE 241 42 1 44 6 NC_002950:PG0471|3end_hypothetical_protein_513432..513582_POSITIVE 238 99 74 74 49 NC_002950:PG2199|3end_ABC_transporter,_ATP-binding_protein,_putative_2304786..2304936_NEGATIVE 238 100 64 43 9 NC_002950:PG2072|3end_UvrD/REP_helicase_domain_protein_2170757..2170907_POSITIVE 238 98 71 78 50 NC_002950:PG2029|3end_hypothetical_protein_2129202..2129352_POSITIVE