Origin IGS: ataggatacagagcccgtaaaatacaaagtgaaaataggaaattcttacagtgagcgatgctcacaagagaatttatctttttcacacagtatttagggcgtgttcaactcctttcaaagaatgtagagtagttttttataaaataaaggatattttacgaaaattagtcccgtgttcaattactataagtaaccaaactatcctttctgtagttttaatgttttaaattacgttctttattttg .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 caaaataaagaacgtaatttaaaacattaaaactacagaaaggatagtttggttacttatagtaattgaacacgggactaattttcgtaaaatatcctttattttataaaaaactactctacattctttgaaaggagttgaacacgccctaaatactgtgtgaaaaagataaattctcttgtgagcatcgctcactgtaagaatttcctattttcactttgtattttacgggctctgtatcctat Mask Tandem Repeat Region ================================================ ataggatacagagcccgtaaaatacaaagtgaaaataggaaattcttacagtgagcgatgctcacaagagaatttatctttttcacacagtatttagggcgtgttcaactcctttcaaagaatgtagagtagttttttataaaataaaggatattttacgaaaattagtcccgtgttcaattactataagtaaccaaactatcctttctgtagttttaatgttttaaattacgttctttattttg Find is-nt database================================================ Query_seq: SSA_1226:SSA_1227|SSA_1226:SSA_1227:ParC, putative:Aminoglycoside adenylyltransferase, putative:<-<-:1251324..1251568 245 ataggatacagagcccgtaaaatacaaagtgaaaataggaaattcttacagtgagcgatgctcacaagagaatttatctttttcacacagtatttagggcgtgttcaactcctttcaaagaatgtagagtagttttttataaaataaaggatattttacgaaaattagtcccgtgttcaattactataagtaaccaaactatcctttctgtagttttaatgttttaaattacgttctttattttg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1226:SSA_1227|SSA_1226:SSA_1227:ParC, putative:Aminoglycoside adenylyltransferase, putative:<-<-:1251324..1251568 245 ataggatacagagcccgtaaaatacaaagtgaaaataggaaattcttacagtgagcgatgctcacaagagaatttatctttttcacacagtatttagggcgtgttcaactcctttcaaagaatgtagagtagttttttataaaataaaggatattttacgaaaattagtcccgtgttcaattactataagtaaccaaactatcctttctgtagttttaatgttttaaattacgttctttattttg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1226:SSA_1227|SSA_1226:SSA_1227:ParC, putative:Aminoglycoside adenylyltransferase, putative:<-<-:1251324..1251568 245 ataggatacagagcccgtaaaatacaaagtgaaaataggaaattcttacagtgagcgatgctcacaagagaatttatctttttcacacagtatttagggcgtgttcaactcctttcaaagaatgtagagtagttttttataaaataaaggatattttacgaaaattagtcccgtgttcaattactataagtaaccaaactatcctttctgtagttttaatgttttaaattacgttctttattttg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ataggatacagagcccgtaaaatacaaagtgaaaataggaaattcttacagtgagcgatgctcacaagagaatttatctttttcacacagtatttagggcgtgttcaactcctttcaaagaatgtagagtagttttttataaaataaaggatattttacgaaaattagtcccgtgttcaattactataagtaaccaaactatcctttctgtagttttaatgttttaaattacgttctttattttg Predict ORF larger than 30AA ================================================ Protein_Len: 60 Strand: + Start: 42 End: 224 ......................................... M L T V S D A H K R I Y L F H T V F R A C S T P F K E C R V V F Y K I K D I L R K L V P C S I T I S N Q T I L S V V L M ..................... ataggatacagagcccgtaaaatacaaagtgaaaataggaaattcttacagtgagcgatgctcacaagagaatttatctttttcacacagtatttagggcgtgttcaactcctttcaaagaatgtagagtagttttttataaaataaaggatattttacgaaaattagtcccgtgttcaattactataagtaaccaaactatcctttctgtagttttaatgttttaaattacgttctttattttg 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================================================ ataggatacagagcccgtaaaatacaaagtgaaaataggaaattcttacagtgagcgatgctcacaagagaatttatctttttcacacagtatttagggcgtgttcaactcctttcaaagaatgtagagtagttttttataaaataaaggatattttacgaaaattagtcccgtgttcaattactataagtaaccaaactatcctttctgtagttttaatgttttaaattacgttctttattttg Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_1226:SSA_1227|SSA_1226:SSA_1227:ParC, putative:Aminoglycoside adenylyltransferase, putative:<-<-:1251324..1251568 245 ataggatacagagcccgtaaaatacaaagtgaaaataggaaattcttacagtgagcgatgctcacaagagaatttatctttttcacacagtatttagggcgtgttcaactcctttcaaagaatgtagagtagttttttataaaataaaggatattttacgaaaattagtcccgtgttcaattactataagtaaccaaactatcctttctgtagttttaatgttttaaattacgttctttattttg Intra-Species Hit: Count: 1 Min: 1 Max: 245 Len: 245 Subject: NC_009009_SSA_1226_SSA_1227|ParC, putative:Aminoglycoside adenylyltransferase, putative|NEGATIVE:NEGATIVE|[1251324,1251568]|245 HSP 1 e-value: 1.0E-136 bit: 486.0 Len: 245 Query Start:1 Query End:245 Subject Strand: POSITIVE Subject Start: 1 Subject End: 245 ataggatacagagcccgtaaaatacaaagtgaaaataggaaattcttacagtgagcgatgctcacaagagaatttatctttttcacacagtatttagggcgtgttcaactcctttcaaagaatgtagagtagttttttataaaataaaggatattttacgaaaattagtcccgtgttcaattactataagtaaccaaactatcctttctgtagttttaatgttttaaattacgttctttattttg ataggatacagagcccgtaaaatacaaagtgaaaataggaaattcttacagtgagcgatgctcacaagagaatttatctttttcacacagtatttagggcgtgttcaactcctttcaaagaatgtagagtagttttttataaaataaaggatattttacgaaaattagtcccgtgttcaattactataagtaaccaaactatcctttctgtagttttaatgttttaaattacgttctttattttg Inter-species Hit: Count: 7 Min: 5 Max: 231 Len: 227 Subject: NC_003098_spr0756_spr0757|DNA topoisomerase IV subunit B:DNA topoisomerase IV subunit A|POSITIVE:POSITIVE|[751831,752240]|410 HSP 1 e-value: 7.0E-56 bit: 218.0 Len: 194 Query Start:12 Query End:205 Subject Strand: NEGATIVE Subject Start: 218 Subject End: 410 ...........agcccgtaaaatacaaagtgaaaataggaaattcttacagtgagcgatgctcacaagagaatttatctttttcacacagtatttagggcgtgttcaactcctttcaaagaatgtagagtagttttttataaaataaaggatattttacgaaaattagtcccgtgttcaattactataagtaaccaaactatcct........................................ ...........agcccataaaataccaagtgaaaatagaaaattcttgaagtaagcaaa-ctcacaagagaatttatctttttcacacagtatctagggcgtgttcaactcctttcaaagaatgtagagtaggtttttatgcagtaaaagatattttacgggaattcgtcccgtgttcagttacgataagtaaccaaactatcct........................................ Subject: NC_008533_SPD_0747_SPD_0748|hypothetical protein:DNA topoisomerase IV, A subunit|POSITIVE:POSITIVE|[759608,759771]|164 HSP 1 e-value: 2.0E-43 bit: 176.0 Len: 165 Query Start:12 Query End:176 Subject Strand: NEGATIVE Subject Start: 1 Subject End: 164 ...........agcccgtaaaatacaaagtgaaaataggaaattcttacagtgagcgatgctcacaagagaatttatctttttcacacagtatttagggcgtgttcaactcctttcaaagaatgtagagtagttttttataaaataaaggatattttacgaaaattagtcccgtgt..................................................................... ...........agcccataaaataccaagtgaaaatagaaaattcttgaagtaagcaaa-ctcacaagagaatttatctttttcacacagtatctagggcgtgttcaactcctttcaaagaatgtagagtaggtttttatgcagtaaaagatattttacgggaattcgtcccgtgt..................................................................... Subject: NC_003028_SP_0854_SP_0855|hypothetical protein:DNA topoisomerase IV subunit A|POSITIVE:POSITIVE|[800527,800699]|173 HSP 1 e-value: 9.0E-43 bit: 174.0 Len: 156 Query Start:5 Query End:160 Subject Strand: NEGATIVE Subject Start: 17 Subject End: 171 ....gatacagagcccgtaaaatacaaagtgaaaataggaaattcttacagtgagcgatgctcacaagagaatttatctttttcacacagtatttagggcgtgttcaactcctttcaaagaatgtagagtagttttttataaaataaaggatattttacg..................................................................................... ....gatacaaagcccataaaataccaagtgaaaatagaaaattcttgaagtaagcaaa-ctcacaagagaatttatctttttcacacagtatctagggcgtgttcaactcctttcaaagaatgtagagtaggtttttatgcagtaaaagatattttacg..................................................................................... Subject: smit_SMT_544_SMT_545|aminoglycoside 6-adenylyltransferase:hypothetical protein predicted by Glimmer/Critica|POSITIVE:POSITIVE|[461251,461388]|138 HSP 1 e-value: 2.0E-34 bit: 147.0 Len: 138 Query Start:94 Query End:231 Subject Strand: NEGATIVE Subject Start: 2 Subject End: 138 .............................................................................................ttagggcgtgttcaactcctttcaaagaatgtagagtagttttttataaaataaaggatattttacgaaaattagtcccgtgttcaattactataagtaaccaaactatcctttctgtagttttaatgttttaaatta.............. .............................................................................................ttagggcgtgttcaactcctttcaaagaatgtagagtaggtttttatgcagtaaaagatattttacgggaattagtcccatgttcagttaccttaaggaaccaaacaatcctttctgtag-tttaatcttttaaatta.............. Subject: NC_008532_STER_0633_STER_0634|DNA topoisomerase IV subunit B:DNA topoisomerase IV subunit A|POSITIVE:POSITIVE|[576342,577013]|672 HSP 1 e-value: 4.0E-20 bit: 99.6 Len: 62 Query Start:80 Query End:141 Subject Strand: NEGATIVE Subject Start: 385 Subject End: 446 ...............................................................................ttttcacacagtatttagggcgtgttcaactcctttcaaagaatgtagagtagttttttata........................................................................................................ ...............................................................................ttttcacacagtatttagggcgtgttcaactcctttcaaagaatgttgagtggttttctata........................................................................................................ HSP 2 e-value: 2.0E-6 bit: 54.0 Len: 51 Query Start:162 Query End:212 Subject Strand: NEGATIVE Subject Start: 483 Subject End: 533 .................................................................................................................................................................aaattagtcccgtgttcaattactataagtaaccaaactatcctttctgta................................. .................................................................................................................................................................aaattagtcccgtgttcagttacattcagtaaccaaacgaccctttctgta................................. Subject: NC_006449_str0588_str0589|DNA topoisomerase IV subunit B:DNA topoisomerase IV subunit A|POSITIVE:POSITIVE|[553699,554271]|573 HSP 1 e-value: 4.0E-20 bit: 99.6 Len: 62 Query Start:80 Query End:141 Subject Strand: NEGATIVE Subject Start: 385 Subject End: 446 ...............................................................................ttttcacacagtatttagggcgtgttcaactcctttcaaagaatgtagagtagttttttata........................................................................................................ ...............................................................................ttttcacacagtatttagggcgtgttcaactcctttcaaagaatgttgagtggttttctata........................................................................................................ HSP 2 e-value: 9.0E-9 bit: 61.9 Len: 51 Query Start:162 Query End:212 Subject Strand: NEGATIVE Subject Start: 483 Subject End: 533 .................................................................................................................................................................aaattagtcccgtgttcaattactataagtaaccaaactatcctttctgta................................. .................................................................................................................................................................aaattagtcccgtgttcagttacattcagtaaccaaacgatcctttctgta................................. Subject: NC_006448_stu0588_stu0589|DNA topoisomerase IV subunit B:DNA topoisomerase IV subunit A|POSITIVE:POSITIVE|[558515,559087]|573 HSP 1 e-value: 4.0E-20 bit: 99.6 Len: 62 Query Start:80 Query End:141 Subject Strand: NEGATIVE Subject Start: 385 Subject End: 446 ...............................................................................ttttcacacagtatttagggcgtgttcaactcctttcaaagaatgtagagtagttttttata........................................................................................................ ...............................................................................ttttcacacagtatttagggcgtgttcaactcctttcaaagaatgttgagtggttttctata........................................................................................................ HSP 2 e-value: 2.0E-6 bit: 54.0 Len: 51 Query Start:162 Query End:212 Subject Strand: NEGATIVE Subject Start: 483 Subject End: 533 .................................................................................................................................................................aaattagtcccgtgttcaattactataagtaaccaaactatcctttctgta................................. .................................................................................................................................................................aaattagtcccgtgttcagttacattcagtaaccaaacgaccctttctgta................................. Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAUACAGAGCCCGUAAAAUACAAAGUGAAAAUAGGAAAUUCUUACAGUGAGCGAUGCUCACAAGAGAAUUUAUCUUUUUCACACAGUAUUUAGGGCGUGUUCAACUCCUUUCAAAGAAUGUAGAGUAGUUUUUUAUAAAAUAAAGGAUAUUUUACGAAAAUUAGUCCCGUGUUCAAUUACUAUAAGUAACCAAACUAUCCUUUCUGUAGUUUUAAUGUUUUAAAUUA ..((((((((((...((((((...(((((((.(((((((((((...((((((...))))))..)))))))).))))))))))...)))))).))))...................(((..(.((.((((((((..(((((((.....))))))).)))))))).))..)..)))..((((.....)))).............))))))................... (-52.70) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAUUUAAAACAUUAAAACUACAGAAAGGAUAGUUUGGUUACUUAUAGUAAUUGAACACGGGACUAAUUUUCGUAAAAUAUCCUUUAUUUUAUAAAAAACUACUCUACAUUCUUUGAAAGGAGUUGAACACGCCCUAAAUACUGUGUGAAAAAGAUAAAUUCUCUUGUGAGCAUCGCUCACUGUAAGAAUUUCCUAUUUUCACUUUGUAUUUUACGGGCUCUGUAUC ...................((((((((((((((((..(((((.....)))))..)))(((..(.....)..)))....)))))))).............(.(((((.((.....))...))))).).....((((.((((((...(((((((....(((((((...((((((...))))))....)))))))....)))))))...))))))...)))).))))).. (-57.00) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 874 100 51 195 146 NC_009009:SSA_1226|5end_ParC,_putative_1251233..1251463_NEGATIVE 482 80 31 102 53 NC_009009:SSA_1258|5end_Purine_nucleoside_phosphorylase,_family_1,_putative_1284652..1284882_NEGATIVE 416 103 62 197 155 NC_009009:SSA_0241|5end_Ribosomal_protein_L11_methyltransferase,_putative_234021..234251_POSITIVE 414 100 51 213 163 NC_009009:SSA_1313|5end_hypothetical_protein_1330548..1330778_NEGATIVE 349 59 11 154 106 NC_009009:SSA_2005|5end_Chaperone_protein_dnaJ,_putative_2006384..2006614_NEGATIVE 276 79 31 191 144 NC_009009:SSA_1175|5end_Acetoin_dehydrogenase_complex,_E2_component,_dihydrolipoamide_acetyltransferase,_putative_1203976..1204206_NEGATIVE 258 133 92 135 85 NC_009009:SSA_2088|5end_Carbohydrate_isomerase,_AraD/FucA_family,_putative_2093476..2093706_NEGATIVE 255 210 165 133 86 NC_009009:SSA_2175|5end_hypothetical_protein_2174042..2174272_NEGATIVE 250 77 39 95 51 NC_009009:SSA_0477|5end_Cobalamin_biosynthesis_protein_CbiM_(ABC-type_cobalt_transporter),_putative_479223..479453_POSITIVE 249 88 41 230 178 NC_009009:SSA_0468|5end_Precorrin-6y_C5,15-methyltransferase-like,_putative_471706..471936_POSITIVE 244 131 96 126 89 NC_009009:SSA_0273|5end_hypothetical_protein_267071..267301_POSITIVE 232 109 64 80 35 NC_009009:SSA_1778|5end_Segregation_and_condensation_protein_B,_putative_1765711..1765941_NEGATIVE 231 127 91 115 84 NC_009009:SSA_0875|5end_Rod_shape_determining_protein_(cell-cycle_protein),_putative_868928..869158_POSITIVE 229 118 71 110 73 NC_009009:SSA_1281|5end_Uracil-DNA_glycosylase,_putative_1302192..1302422_NEGATIVE 228 97 54 97 54 NC_009009:SSA_1266|5end_crcB-like_protein_1,_putative_1291000..1291230_NEGATIVE 228 113 77 109 71 NC_009009:SSA_0929|5end_ABC-type_multidrug_transporter,_ATPase_and_permease_components,_putative_938438..938668_POSITIVE 227 127 84 48 1 NC_009009:SSA_1050|5end_ABC_transporter_membrane-spanning_permease-spermidine/putrescine_transport,_putative_1064888..1065118_POSITIVE 226 116 82 73 34 NC_009009:SSA_0973|5end_hypothetical_protein_980296..980526_POSITIVE 224 129 103 121 97 NC_009009:SSA_0346|5end_hypothetical_protein_339448..339678_POSITIVE 223 107 69 154 115 NC_009009:SSA_1952|5end_ABC-type_Fe-S_cluster_assembly_transporter,_permease_component,_putative_1949624..1949854_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 416 103 62 56 14 NC_009009:SSA_0240|3end_Acetyltransferase,_GNAT_family,_putative_233960..234110_POSITIVE 258 133 92 135 85 NC_009009:SSA_2089|3end_L-xylulose-5-phosphate_3-epimerase,_putative_2093476..2093626_NEGATIVE 250 77 39 73 29 NC_009009:SSA_0476|3end_Precorrin-2_C20-methyltransferase,_putative_479281..479431_POSITIVE 245 140 95 58 11 NC_009009:SSA_0827|3end_Conserved_uncharacterized_cytosolic_protein,_putative_806952..807102_POSITIVE 232 109 64 87 42 NC_009009:SSA_1779|3end_Segregation_and_condensation_protein_A,_putative_1765704..1765854_NEGATIVE 231 127 91 102 71 NC_009009:SSA_0874|3end_hypothetical_protein_868995..869145_POSITIVE 229 118 71 56 19 NC_009009:SSA_1282|3end_Dipeptidase_V,_putative_1302246..1302396_NEGATIVE 228 97 54 124 81 NC_009009:SSA_1267|3end_crcB-like_protein_2,_putative_1290973..1291123_NEGATIVE 228 113 77 116 78 NC_009009:SSA_0928|3end_ABC-type_multidrug_transporter,_ATPase_and_permease_components,_putative_938525..938675_POSITIVE 227 127 84 51 4 NC_009009:SSA_1049|3end_ABC_transporter_membrane-spanning_permease-spermidine/putrescine_transport,_putative_1064971..1065121_POSITIVE 226 116 82 61 22 NC_009009:SSA_0972|3end_hypothetical_protein_980364..980514_POSITIVE 225 134 94 137 104 NC_009009:SSA_2262|3end_Arginyl-tRNA_synthetase,_putative_2260685..2260835_POSITIVE 223 107 69 136 97 NC_009009:SSA_1953|3end_NifU_family_protein,_putative_1949642..1949792_NEGATIVE 222 113 74 60 22 NC_009009:SSA_0025|3end_DNA_repair_protein_recO,_putative_30547..30697_POSITIVE 218 110 69 57 9 NC_009009:SSA_1079|3end_hypothetical_protein_1097448..1097598_POSITIVE 216 97 55 111 60 NC_009009:SSA_1678|3end_ABC-type_multidrug_transport_system,_permease_component,_putative_1671336..1671486_NEGATIVE 215 133 101 105 64 NC_009009:SSA_1445|3end_Imidazole_glycerol-phosphate_dehydratase,_putative_1447302..1447452_NEGATIVE 215 60 11 66 30 NC_009009:SSA_0999|3end_Biotin--[acetyl-CoA-carboxylase]_ligase,_putative_998781..998931_NEGATIVE 213 108 61 139 77 NC_009009:SSA_2198|3end_hypothetical_protein_2197842..2197992_NEGATIVE 213 97 51 104 54 NC_009009:SSA_0268|3end_Phosphotransferase_system_(PTS)_cellobiose-specific_component_IIB,_putative_262621..262771_POSITIVE