Origin IGS: tcttttctctcgcggacaggcatggaatccaaatattttggagcggaatgtcttgtgaatgaaaaaaatatcggaactttgcggccgttgcgattggtctttatcacctgaaaattatttgatagggctcgtcgcattctggtaaaatccaccttatcaaactcagtatgct .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 agcatactgagtttgataaggtggattttaccagaatgcgacgagccctatcaaataattttcaggtgataaagaccaatcgcaacggccgcaaagttccgatatttttttcattcacaagacattccgctccaaaatatttggattccatgcctgtccgcgagagaaaaga Mask Tandem Repeat Region ================================================ tcttttctctcgcggacaggcatggaatccaaatattttggagcggaatgtcttgtgaatgaaaaaaatatcggaactttgcggccgttgcgattggtctttatcacctgaaaattatttgatagggctcgtcgcattctggtaaaatccaccttatcaaactcagtatgct Find is-nt database================================================ Query_seq: PG0428:PG0429|PG0428:PG0429:hypothetical protein:pyruvate synthase:<-->:466068..466239 172 tcttttctctcgcggacaggcatggaatccaaatattttggagcggaatgtcttgtgaatgaaaaaaatatcggaactttgcggccgttgcgattggtctttatcacctgaaaattatttgatagggctcgtcgcattctggtaaaatccaccttatcaaactcagtatgct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG0428:PG0429|PG0428:PG0429:hypothetical protein:pyruvate synthase:<-->:466068..466239 172 tcttttctctcgcggacaggcatggaatccaaatattttggagcggaatgtcttgtgaatgaaaaaaatatcggaactttgcggccgttgcgattggtctttatcacctgaaaattatttgatagggctcgtcgcattctggtaaaatccaccttatcaaactcagtatgct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG0428:PG0429|PG0428:PG0429:hypothetical protein:pyruvate synthase:<-->:466068..466239 172 tcttttctctcgcggacaggcatggaatccaaatattttggagcggaatgtcttgtgaatgaaaaaaatatcggaactttgcggccgttgcgattggtctttatcacctgaaaattatttgatagggctcgtcgcattctggtaaaatccaccttatcaaactcagtatgct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tcttttctctcgcggacaggcatggaatccaaatattttggagcggaatgtcttgtgaatgaaaaaaatatcggaactttgcggccgttgcgattggtctttatcacctgaaaattatttgatagggctcgtcgcattctggtaaaatccaccttatcaaactcagtatgct Predict ORF larger than 30AA ================================================ Protein_Len: 50 Strand: - Start: 3 End: 152 .. K R E R V P M S D L Y K P A S H R T F S F F I P V K R G N R N T K I V Q F N N S L A R R M R T F D M .................... Protein_Len: 31 Strand: - Start: 2 End: 94 . K E R A S L C P I W I N Q L P I D Q S H F F Y R F K A A T A M .............................................................................. tcttttctctcgcggacaggcatggaatccaaatattttggagcggaatgtcttgtgaatgaaaaaaatatcggaactttgcggccgttgcgattggtctttatcacctgaaaattatttgatagggctcgtcgcattctggtaaaatccaccttatcaaactcagtatgct 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================================================ tcttttctctcgcggacaggcatggaatccaaatattttggagcggaatgtcttgtgaatgaaaaaaatatcggaactttgcggccgttgcgattggtctttatcacctgaaaattatttgatagggctcgtcgcattctggtaaaatccaccttatcaaactcagtatgct Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PG0428:PG0429|PG0428:PG0429:hypothetical protein:pyruvate synthase:<-->:466068..466239 172 tcttttctctcgcggacaggcatggaatccaaatattttggagcggaatgtcttgtgaatgaaaaaaatatcggaactttgcggccgttgcgattggtctttatcacctgaaaattatttgatagggctcgtcgcattctggtaaaatccaccttatcaaactcagtatgct Intra-Species Hit: Count: 1 Min: 1 Max: 172 Len: 172 Subject: NC_002950_PG0428_PG0429|hypothetical protein:pyruvate synthase|NEGATIVE:POSITIVE|[466068,466239]|172 HSP 1 e-value: 2.0E-80 bit: 299.0 Len: 172 Query Start:1 Query End:172 Subject Strand: POSITIVE Subject Start: 1 Subject End: 172 tcttttctctcgcggacaggcatggaatccaaatattttggagcggaatgtcttgtgaatgnnnnnnntatcggaactttgcggccgttgcgattggtctttatcacctgaaaattatttgatagggctcgtcgcattctggtaaaatccaccttatcaaactcagtatgct tcttttctctcgcggacaggcatggaatccaaatattttggagcggaatgtcttgtgaatgaaaaaaatatcggaactttgcggccgttgcgattggtctttatcacctgaaaattatttgatagggctcgtcgcattctggtaaaatccaccttatcaaactcagtatgct Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCUUUUCUCUCGCGGACAGGCAUGGAAUCCAAAUAUUUUGGAGCGGAAUGUCUUGUGAAUGAAAAAAAUAUCGGAACUUUGCGGCCGUUGCGAUUGGUCUUUAUCACCUGAAAAUUAUUUGAUAGGGCUCGUCGCAUUCUGGUAAAAUCCACCUUAUCAAACUCAGUAUGCU ..(((((..(((((((((..(......(((((.....)))))...)..)))).)))))..))))).......(((..(((...((((.((((((.((((((.((((..(((...)))..)))))))))).))))))...)))).))))))...................... (-42.10) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGCAUACUGAGUUUGAUAAGGUGGAUUUUACCAGAAUGCGACGAGCCCUAUCAAAUAAUUUUCAGGUGAUAAAGACCAAUCGCAACGGCCGCAAAGUUCCGAUAUUUUUUUCAUUCACAAGACAUUCCGCUCCAAAAUAUUUGGAUUCCAUGCCUGUCCGCGAGAGAAAAGA .((...((((((((((((.((((.((((.....)))).).....))).)))))))).....))))(((((........))))).......)).............(((((((.(((.(..((((....(((((((.....)))))......)).)))).).))).))))))) (-29.70) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 943 50 1 141 92 NC_002950:PG0428|5end_hypothetical_protein_465977..466207_NEGATIVE 350 47 8 67 28 NC_002950:PG2219|5end_potassium_uptake_protein_TrkH_2332947..2333177_POSITIVE 348 50 2 145 103 NC_002950:PG0068|5end_hypothetical_protein_81748..81978_POSITIVE 338 48 1 79 30 NC_002950:PG0287|5end_hypothetical_protein_320457..320687_POSITIVE 333 134 91 153 106 NC_002950:PG1312|5end_capA_protein,_putative_1390286..1390516_POSITIVE 330 110 68 131 90 NC_002950:PG0158|5end_competence_protein_F-related_protein_180175..180405_POSITIVE 329 97 51 139 79 NC_002950:PG1617|5end_hypothetical_protein_1697755..1697985_NEGATIVE 329 108 61 170 123 NC_002950:PG0157|5end_regulatory_protein_RecX_179706..179936_POSITIVE 323 88 41 119 76 NC_002950:PG2104|5end_hypothetical_protein_2213619..2213849_NEGATIVE 322 128 81 134 83 NC_002950:PG2019|5end_hypothetical_protein_2111662..2111892_NEGATIVE 322 59 11 123 76 NC_002950:PG0297|5end_hypothetical_protein_335518..335748_NEGATIVE 315 129 81 175 129 NC_002950:PG1695|5end_hypothetical_protein_1779440..1779670_POSITIVE 315 106 71 230 186 NC_002950:PG0523|5end_inositol-5-monophosphate_dehydrogenase_568394..568624_NEGATIVE 313 110 82 218 190 NC_002950:PG1139|5end_hypothetical_protein_1222064..1222294_NEGATIVE 308 114 82 44 3 NC_002950:PG0789|5end_hypothetical_protein_841418..841648_NEGATIVE 305 98 70 155 121 NC_002950:PG2205|5end_2-dehydropantoate_2-reductase_2316121..2316351_POSITIVE 305 47 4 224 185 NC_002950:PG0971|5end_McrBC_restriction_endonuclease_system,_McrB_subunit,_putative_1030946..1031176_POSITIVE 305 47 4 226 187 NC_002950:PG0020|5end_transcriptional_regulator,_MarR_family_23382..23612_POSITIVE 299 120 71 93 46 NC_002950:PG2043|5end_conserved_hypothetical_protein_TIGR00486_2142218..2142448_POSITIVE 297 47 1 141 98 NC_002950:PG0858|5end_hypothetical_protein_917540..917770_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 350 47 8 40 1 NC_002950:PG2218|3end_potassium_uptake_protein_TrkA_2333000..2333150_POSITIVE 334 90 41 145 96 NC_002950:PG0571|3end_aspartate-semialdehyde_dehydrogenase_627492..627642_POSITIVE 333 134 91 142 95 NC_002950:PG1311|3end_hypothetical_protein_1390355..1390505_POSITIVE 330 110 68 147 106 NC_002950:PG0157|3end_regulatory_protein_RecX_180271..180421_POSITIVE 316 127 82 121 79 NC_002950:PG1140|3end_glycosyl_transferase,_group_2_family_protein_1222175..1222325_NEGATIVE 310 58 18 53 12 NC_002950:PG2194|3end_ISPg4,_transposase_2300962..2301112_NEGATIVE 310 58 18 53 12 NC_002950:PG1673|3end_ISPg4,_transposase_1759625..1759775_POSITIVE 310 58 18 53 12 NC_002950:PG1658|3end_ISPg4,_transposase_1741747..1741897_NEGATIVE 310 58 18 53 12 NC_002950:PG1261|3end_ISPg4,_transposase_1339608..1339758_POSITIVE 310 58 18 53 12 NC_002950:PG0970|3end_ISPg4,_transposase_1030843..1030993_POSITIVE 310 58 18 53 12 NC_002950:PG0487|3end_ISPg4,_transposase_526276..526426_NEGATIVE 310 58 18 53 12 NC_002950:PG0225|3end_ISPg4,_transposase_258485..258635_NEGATIVE 310 58 18 53 12 NC_002950:PG0177|3end_ISPg4,_transposase_200324..200474_POSITIVE 310 58 18 53 12 NC_002950:PG0050|3end_ISPg4,_transposase_62153..62303_POSITIVE 310 58 18 53 12 NC_002950:PG0019|3end_ISPg4_transposase_23277..23427_POSITIVE 309 114 72 63 18 NC_002950:PG0790|3end_GTP-binding_protein_Obg_841399..841549_NEGATIVE 308 126 81 102 53 NC_002950:PG1421|3end_ferredoxin,_4Fe-4S_1506874..1507024_NEGATIVE 306 99 72 139 107 NC_002950:PG0746|3end_sensor_histidine_kinase_792536..792686_NEGATIVE 305 98 70 141 107 NC_002950:PG2204|3end_hypothetical_protein_2316187..2316337_POSITIVE 297 47 1 144 101 NC_002950:PG0857|3end_transcriptional_regulator,_putative_917623..917773_POSITIVE