Origin IGS: tctattttatttttgaagtttgggaatcctttttttgtgatgtttttattcgctgtgtatataacaaaaaaagaagtaatcggttgtacggtcgatgaaaaagcttatctttcgaacgatttttcagaaagattcaaatcataaaaatgcactgtt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aacagtgcatttttatgatttgaatctttctgaaaaatcgttcgaaagataagctttttcatcgaccgtacaaccgattacttctttttttgttatatacacagcgaataaaaacatcacaaaaaaaggattcccaaacttcaaaaataaaataga Mask Tandem Repeat Region ================================================ tctattttatttttgaagtttgggaatcctttttttgtgatgtttttattcgctgtgtatataacaaaaaaagaagtaatcggttgtacggtcgatgaaaaagcttatctttcgaacgatttttcagaaagattcaaatcataaaaatgcactgtt Find is-nt database================================================ Query_seq: PG1321:PG1323|PG1321:PG1323:formate--tetrahydrofolate ligase:PhoH family protein:<-->:1401414..1401569 156 tctattttatttttgaagtttgggaatcctttttttgtgatgtttttattcgctgtgtatataacaaaaaaagaagtaatcggttgtacggtcgatgaaaaagcttatctttcgaacgatttttcagaaagattcaaatcataaaaatgcactgtt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG1321:PG1323|PG1321:PG1323:formate--tetrahydrofolate ligase:PhoH family protein:<-->:1401414..1401569 156 tctattttatttttgaagtttgggaatcctttttttgtgatgtttttattcgctgtgtatataacaaaaaaagaagtaatcggttgtacggtcgatgaaaaagcttatctttcgaacgatttttcagaaagattcaaatcataaaaatgcactgtt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG1321:PG1323|PG1321:PG1323:formate--tetrahydrofolate ligase:PhoH family protein:<-->:1401414..1401569 156 tctattttatttttgaagtttgggaatcctttttttgtgatgtttttattcgctgtgtatataacaaaaaaagaagtaatcggttgtacggtcgatgaaaaagcttatctttcgaacgatttttcagaaagattcaaatcataaaaatgcactgtt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tctattttatttttgaagtttgggaatcctttttttgtgatgtttttattcgctgtgtatataacaaaaaaagaagtaatcggttgtacggtcgatgaaaaagcttatctttcgaacgatttttcagaaagattcaaatcataaaaatgcactgtt Predict ORF larger than 30AA ================================================ Protein_Len: 46 Strand: + Start: 4 End: 141 ... M L F L K F G N P F F V M F L F A V Y I T K K E V I G C T V D E K A Y L S N D F S E R F K S ............... Protein_Len: 44 Strand: - Start: 5 End: 133 .... * K I K S T Q S D K K Q S T K I R Q T Y L L F L L L R N Y P R H F L K D K S R N K L F M ....................... tctattttatttttgaagtttgggaatcctttttttgtgatgtttttattcgctgtgtatataacaaaaaaagaagtaatcggttgtacggtcgatgaaaaagcttatctttcgaacgatttttcagaaagattcaaatcataaaaatgcactgtt 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================================================ tctattttatttttgaagtttgggaatcctttttttgtgatgtttttattcgctgtgtatataacaaaaaaagaagtaatcggttgtacggtcgatgaaaaagcttatctttcgaacgatttttcagaaagattcaaatcataaaaatgcactgtt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PG1321:PG1323|PG1321:PG1323:formate--tetrahydrofolate ligase:PhoH family protein:<-->:1401414..1401569 156 tctattttatttttgaagtttgggaatcctttttttgtgatgtttttattcgctgtgtatataacaaaaaaagaagtaatcggttgtacggtcgatgaaaaagcttatctttcgaacgatttttcagaaagattcaaatcataaaaatgcactgtt Intra-Species Hit: Count: 1 Min: 1 Max: 156 Len: 156 Subject: NC_002950_PG1321_PG1323|formate--tetrahydrofolate ligase:PhoH family protein|NEGATIVE:POSITIVE|[1401414,1401569]|156 HSP 1 e-value: 2.0E-58 bit: 226.0 Len: 156 Query Start:1 Query End:156 Subject Strand: POSITIVE Subject Start: 1 Subject End: 156 tctattttatttttgaagtttgggaatccnnnnnnngtgatgtttttattcgctgtgtatataacnnnnnnngaagtaatcggttgtacggtcgatgaaaaagcttatctttcgaacgatttttcagaaagattcaaatcataaaaatgcactgtt tctattttatttttgaagtttgggaatcctttttttgtgatgtttttattcgctgtgtatataacaaaaaaagaagtaatcggttgtacggtcgatgaaaaagcttatctttcgaacgatttttcagaaagattcaaatcataaaaatgcactgtt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCUAUUUUAUUUUUGAAGUUUGGGAAUCCUUUUUUUGUGAUGUUUUUAUUCGCUGUGUAUAUAACAAAAAAAGAAGUAAUCGGUUGUACGGUCGAUGAAAAAGCUUAUCUUUCGAACGAUUUUUCAGAAAGAUUCAAAUCAUAAAAAUGCACUGUU ....((((((.((((((.((((..((..((((((((((.((((...(((.....))).)))).)))))))))).........(((((.(((..(((((......)))))..))).)))))))..))))....))))))..)))))).......... (-29.90) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AACAGUGCAUUUUUAUGAUUUGAAUCUUUCUGAAAAAUCGUUCGAAAGAUAAGCUUUUUCAUCGACCGUACAACCGAUUACUUCUUUUUUUGUUAUAUACACAGCGAAUAAAAACAUCACAAAAAAAGGAUUCCCAAACUUCAAAAAUAAAAUAGA ..........((((((..((((((......(((((((.(..((....))...).)))))))....................((((((((((((.........................)))))))))))).........)))))).)))))).... (-21.11) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 850 120 71 211 162 NC_002950:PG1321|5end_formate--tetrahydrofolate_ligase_1401323..1401553_NEGATIVE 287 68 28 139 95 NC_002950:PG0778|5end_hypothetical_protein_831869..832099_NEGATIVE 274 66 21 212 168 NC_002950:PG1890|5end_lipoprotein,_putative_1987565..1987795_POSITIVE 268 120 73 110 69 NC_002950:PG0771|5end_hypothetical_protein_824524..824754_POSITIVE 267 124 82 150 105 NC_002950:PG0439|5end_hypothetical_protein_477831..478061_POSITIVE 253 113 75 207 162 NC_002950:PG1847|5end_endoribonuclease_L-PSP,_putative_1946607..1946837_NEGATIVE 249 55 25 204 175 NC_002950:PG1636|5end_FtsK/SpoIIIE_family_protein_1718460..1718690_NEGATIVE 247 59 12 60 10 NC_002950:PG1435|5end_integrase_1520303..1520533_POSITIVE 245 120 80 80 45 NC_002950:PG0700|5end_hypothetical_protein_756595..756825_NEGATIVE 244 109 79 231 200 NC_002950:PG1072|5end_MutS_family_protein_1138976..1139206_POSITIVE 242 118 78 38 1 NC_002950:PG1365|5end_16S_rRNA-processing_protein_1446069..1446299_NEGATIVE 242 120 72 157 119 NC_002950:PG0172|5end_exonuclease_193493..193723_POSITIVE 241 119 82 138 105 NC_002950:PG2026|5end_phosphoglycerate_mutase_family_protein_2124932..2125162_POSITIVE 240 120 79 85 51 NC_002950:PG1247|5end_3-dehydroquinate_synthase_1324444..1324674_POSITIVE 237 114 73 66 15 NC_002950:PG1626|5end_hypothetical_protein_1708742..1708972_POSITIVE 237 114 79 69 42 NC_002950:PG0334|5end_glycosyl_transferase,_group_2_family_protein_369751..369981_NEGATIVE 236 126 82 187 137 NC_002950:PG0606|5end_hypothetical_protein_662558..662788_NEGATIVE 236 56 18 204 161 NC_002950:PG0474|5end_low-specificity_L-threonine_aldolase_516048..516278_NEGATIVE 235 126 81 54 1 NC_002950:PG0074|5end_peptide_chain_release_factor_1_89172..89402_NEGATIVE 233 117 71 191 136 NC_002950:PG1786|5end_hypothetical_protein_1874358..1874588_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 279 98 52 55 11 NC_002950:PG0193|3end_cationic_outer_membrane_protein_OmpH_230720..230870_POSITIVE 267 118 71 109 52 NC_002950:PG2092|3end_hypothetical_protein_2191651..2191801_NEGATIVE 257 58 17 63 15 NC_002950:PG1410|3end_hypothetical_protein_1493436..1493586_POSITIVE 249 127 83 84 47 NC_002950:PG0261|3end_ISPg3,_transposase_293862..294012_NEGATIVE 246 129 81 110 66 NC_002950:PG0046|3end_phosphatidate_cytidylyltransferase_56346..56496_NEGATIVE 240 120 79 70 36 NC_002950:PG1246|3end_alanyl-tRNA_synthetase_1324509..1324659_POSITIVE 239 105 73 48 11 NC_002950:PG2008|3end_TonB-dependent_receptor,_putative_2097824..2097974_POSITIVE 239 121 82 150 108 NC_002950:PG0438|3end_hypothetical_protein_477914..478064_POSITIVE 238 60 11 64 11 NC_002950:PG2029|3end_hypothetical_protein_2129202..2129352_POSITIVE 237 103 65 45 11 NC_002950:PG0662|3end_hypothetical_protein_710156..710306_POSITIVE 233 127 81 146 103 NC_002950:PG1578|3end_quinolinate_synthetase_1656472..1656622_POSITIVE 232 117 75 139 96 NC_002950:PG0336|3end_hypothetical_protein_370723..370873_NEGATIVE 230 58 18 91 50 NC_002950:PG0095|3end_DNA_mismatch_repair_protein_112088..112238_NEGATIVE 228 59 11 114 58 NC_002950:PG1274|3end_elongation_factor_P_1352489..1352639_POSITIVE 227 119 89 143 114 NC_002950:PG0463|3end_folylpolyglutamate_synthase_506317..506467_NEGATIVE 226 120 71 120 70 NC_002950:PG1961|3end_hypothetical_protein_2048886..2049036_NEGATIVE 225 127 81 60 32 NC_002950:PG1704|3end_thiol:disulfide_interchange_protein_dsbD,_putative_1790771..1790921_NEGATIVE 224 126 81 98 36 NC_002950:PG1173|3end_YkgG_family_protein_1253129..1253279_POSITIVE 222 118 71 143 101 NC_002950:PG1826|3end_hypothetical_protein_1919646..1919796_NEGATIVE 218 120 71 106 44 NC_002950:PG1583|3end_batB_protein_1661414..1661564_POSITIVE