Origin IGS: acaagaggttaggaagaaaaagaaaggagaggagactgtcggcatgtacagatctcctctcctttgtttatttgttggaggctttacgtccacaggatggcgcagtatatgtctgcccgttt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aaacgggcagacatatactgcgccatcctgtggacgtaaagcctccaacaaataaacaaaggagaggagatctgtacatgccgacagtctcctctcctttctttttcttcctaacctcttgt Mask Tandem Repeat Region ================================================ acaagaggttaggaagaaaaagaaaggagaggagactgtcggcatgtacagatctcctctcctttgtttatttgttggaggctttacgtccacaggatggcgcagtatatgtctgcccgttt Find is-nt database================================================ Query_seq: PG0322:PG0323|PG0322:PG0323:serine/threonine transporter:hypothetical protein:-><-:357027..357148 122 acaagaggttaggaagaaaaagaaaggagaggagactgtcggcatgtacagatctcctctcctttgtttatttgttggaggctttacgtccacaggatggcgcagtatatgtctgcccgttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG0322:PG0323|PG0322:PG0323:serine/threonine transporter:hypothetical protein:-><-:357027..357148 122 acaagaggttaggaagaaaaagaaaggagaggagactgtcggcatgtacagatctcctctcctttgtttatttgttggaggctttacgtccacaggatggcgcagtatatgtctgcccgttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG0322:PG0323|PG0322:PG0323:serine/threonine transporter:hypothetical protein:-><-:357027..357148 122 acaagaggttaggaagaaaaagaaaggagaggagactgtcggcatgtacagatctcctctcctttgtttatttgttggaggctttacgtccacaggatggcgcagtatatgtctgcccgttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 acaagaggttaggaagaaaaagaaaggagaggagactgtcggcatgtacagatctcctctcctttgtttatttgttggaggctttacgtccacaggatggcgcagtatatgtctgcccgttt Predict ORF larger than 30AA ================================================ Protein_Len: 36 Strand: - Start: 1 End: 108 C S T L F F F F P S S V T P M Y L D G R R Q K N T P P K V D V P H R L M .............. acaagaggttaggaagaaaaagaaaggagaggagactgtcggcatgtacagatctcctctcctttgtttatttgttggaggctttacgtccacaggatggcgcagtatatgtctgcccgttt 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================================================ acaagaggttaggaagaaaaagaaaggagaggagactgtcggcatgtacagatctcctctcctttgtttatttgttggaggctttacgtccacaggatggcgcagtatatgtctgcccgttt Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 100 HP_score: -11.0 Tail_Score: -5.1356 Start: 22 End: 66 Full_Region: cctccaacaaataaa caaaggagaggagatctgt acatgccg acagtctcctctcctttc tttttcttcctaacc .....................caaaggagaggagatctgtacatgccgacagtctcctctcctttc........................................................ TransTerm Strand: - Conf: 100 HP_score: -11.8 Tail_Score: -5.06961 Start: 26 End: 62 Full_Region: caacaaataaacaaa ggagaggagatctgt acatgccg acagtctcctctcc tttctttttcttcct .........................ggagaggagatctgtacatgccgacagtctcctctcc............................................................ Find igs database================================================ Query_seq: PG0322:PG0323|PG0322:PG0323:serine/threonine transporter:hypothetical protein:-><-:357027..357148 122 acaagaggttaggaagaaaaagaaaggagaggagactgtcggcatgtacagatctcctctcctttgtttatttgttggaggctttacgtccacaggatggcgcagtatatgtctgcccgttt Intra-Species Hit: Count: 1 Min: 1 Max: 122 Len: 122 Subject: NC_002950_PG0322_PG0323|serine/threonine transporter:hypothetical protein|POSITIVE:NEGATIVE|[357027,357148]|122 HSP 1 e-value: 2.0E-63 bit: 242.0 Len: 122 Query Start:1 Query End:122 Subject Strand: POSITIVE Subject Start: 1 Subject End: 122 acaagaggttaggaagaaaaagaaaggagaggagactgtcggcatgtacagatctcctctcctttgtttatttgttggaggctttacgtccacaggatggcgcagtatatgtctgcccgttt acaagaggttaggaagaaaaagaaaggagaggagactgtcggcatgtacagatctcctctcctttgtttatttgttggaggctttacgtccacaggatggcgcagtatatgtctgcccgttt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACAAGAGGUUAGGAAGAAAAAGAAAGGAGAGGAGACUGUCGGCAUGUACAGAUCUCCUCUCCUUUGUUUAUUUGUUGGAGGCUUUACGUCCACAGGAUGGCGCAGUAUAUGUCUGCCCGUUU ..............(((.(((.(((((((((((((((((........)))).))))))))))))).))).)))..((((.(.....).))))..((((((.((((.......)))))))))) (-43.40) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAACGGGCAGACAUAUACUGCGCCAUCCUGUGGACGUAAAGCCUCCAACAAAUAAACAAAGGAGAGGAGAUCUGUACAUGCCGACAGUCUCCUCUCCUUUCUUUUUCUUCCUAACCUCUUGU ....((((((.......)))).))....((((((.(.....).))).))).......(((((((((((((.((((........)))))))))))))))))...................... (-37.90) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 407 119 71 162 121 NC_002950:PG0684|5end_ABC_transporter,_permease_protein,_putative_737648..737878_POSITIVE 372 68 21 114 55 NC_002950:PG1806|5end_v-type_ATPase,_subunit_I_1900200..1900430_POSITIVE 361 103 63 200 158 NC_002950:PG1946|5end_ABC_3_transporter_family_protein_2032133..2032363_POSITIVE 360 119 79 185 136 NC_002950:PG0352|5end_sialidase,_putative_387187..387417_POSITIVE 358 63 26 223 180 NC_002950:PG0006|5end_MATE_efflux_family_protein_6332..6562_NEGATIVE 357 50 2 95 39 NC_002950:PG2104|5end_hypothetical_protein_2213619..2213849_NEGATIVE 355 66 35 207 182 NC_002950:PG1163|5end_cobyrinic_acid_a,c-diamide_synthase_1243381..1243611_NEGATIVE 355 120 87 218 171 NC_002950:PG0060|5end_hypothetical_protein_71916..72146_POSITIVE 353 120 71 153 101 NC_002950:PG0705|5end_glutamate_racemase_759529..759759_POSITIVE 349 97 57 185 139 NC_002950:PG1683|5end_hypothetical_protein_1769644..1769874_POSITIVE 340 59 15 86 51 NC_002950:PG1083|5end_hypothetical_protein_1151834..1152064_NEGATIVE 334 115 77 79 28 NC_002950:PG1008|5end_hypothetical_protein_1067644..1067874_NEGATIVE 333 120 71 154 107 NC_002950:PG0329|5end_formiminotransferase-cyclodeaminase-related_protein_364429..364659_NEGATIVE 330 120 73 86 37 NC_002950:PG1964|5end_bacterial_sugar_transferase_2052910..2053140_POSITIVE 330 103 63 102 62 NC_002950:PG0132|5end_hypothetical_protein_152879..153109_POSITIVE 328 69 26 221 168 NC_002950:PG0333|5end_hypothetical_protein_367823..368053_POSITIVE 327 68 21 81 34 NC_002950:PG1706|5end_hypothetical_protein_1794211..1794441_NEGATIVE 327 115 72 231 187 NC_002950:PG0064|5end_heavy_metal_efflux_pump,_CzcA_family_80193..80423_NEGATIVE 323 107 62 107 46 NC_002950:PG0606|5end_hypothetical_protein_662558..662788_NEGATIVE 322 120 77 179 141 NC_002950:PG1542|5end_collagenase_1620788..1621018_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 503 65 23 68 26 NC_002950:PG0322|3end_serine/threonine_transporter_356966..357116_POSITIVE 407 119 71 135 94 NC_002950:PG0683|3end_ABC_transporter,_permease_protein,_putative_737701..737851_POSITIVE 388 100 51 131 78 NC_002950:PG1959|3end_ribosomal_protein_L33_2048217..2048367_NEGATIVE 372 68 21 117 58 NC_002950:PG1805|3end_V-type_ATP_synthase_subunit_D_1900283..1900433_POSITIVE 362 117 76 131 66 NC_002950:PG0814|3end_hypothetical_protein_875904..876054_NEGATIVE 353 120 71 91 39 NC_002950:PG0704|3end_phosphoglycerate_mutase_family_protein_759547..759697_POSITIVE 345 67 21 68 22 NC_002950:PG1226|3end_peptidyl-prolyl_cis-trans_isomerase,_cyclophilin-type_1304048..1304198_POSITIVE 340 59 15 38 3 NC_002950:PG1084|3end_thioredoxin_family_protein_1151882..1152032_NEGATIVE 334 115 77 82 31 NC_002950:PG1009|3end_hypothetical_protein_1067641..1067791_NEGATIVE 333 120 71 105 58 NC_002950:PG0330|3end_DNA-binding_protein,_histone-like_family_364478..364628_NEGATIVE 332 69 25 75 28 NC_002950:PG0409|3end_hypothetical_protein_442350..442500_POSITIVE 330 120 73 89 40 NC_002950:PG1963|3end_Sua5/YciO/YrdC/YwlC_family_protein_2052993..2053143_POSITIVE 328 118 77 90 47 NC_002950:PG2102|3end_immunoreactive_61_kDa_antigen_PG91_2211424..2211574_NEGATIVE 327 68 21 60 13 NC_002950:PG1707|3end_hypothetical_protein_1794232..1794382_NEGATIVE 318 103 61 83 31 NC_002950:PG1972|3end_hemagglutinin_protein_HagB_2061203..2061353_POSITIVE 313 69 21 86 27 NC_002950:PG1543|3end_thioesterase_family_protein_1622587..1622737_POSITIVE 311 120 72 56 6 NC_002950:PG0979|3end_hypothetical_protein_1040990..1041140_POSITIVE 310 80 31 84 32 NC_002950:PG2033|3end_glutamate_synthase,_small_subunit_2133415..2133565_NEGATIVE 308 120 73 134 77 NC_002950:PG1994|3end_D-tyrosyl-tRNA_deacylase_2085659..2085809_POSITIVE 307 118 71 47 5 NC_002950:PG1734|3end_transporter,_putative_1821620..1821770_NEGATIVE