Origin IGS: cttgttactcttttctcaatccagccaaaatgtgttataatagtactaatttattggaacacatgaaagttcttgaaattttcattggtttctagttaaggaagtaggaaaagt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 acttttcctacttccttaactagaaaccaatgaaaatttcaagaactttcatgtgttccaataaattagtactattataacacattttggctggattgagaaaagagtaacaag Mask Tandem Repeat Region ================================================ cttgttactcttttctcaatccagccaaaatgtgttataatagtactaatttattggaacacatgaaagttcttgaaattttcattggtttctagttaaggaagtaggaaaagt Find is-nt database================================================ Query_seq: SMT_395:SMT_396|SMT_395:SMT_396:hypothetical protein:putative nicotinate phosphoribosyltransferase:->->:325088..325201 114 cttgttactcttttctcaatccagccaaaatgtgttataatagtactaatttattggaacacatgaaagttcttgaaattttcattggtttctagttaaggaagtaggaaaagt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_395:SMT_396|SMT_395:SMT_396:hypothetical protein:putative nicotinate phosphoribosyltransferase:->->:325088..325201 114 cttgttactcttttctcaatccagccaaaatgtgttataatagtactaatttattggaacacatgaaagttcttgaaattttcattggtttctagttaaggaagtaggaaaagt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_395:SMT_396|SMT_395:SMT_396:hypothetical protein:putative nicotinate phosphoribosyltransferase:->->:325088..325201 114 cttgttactcttttctcaatccagccaaaatgtgttataatagtactaatttattggaacacatgaaagttcttgaaattttcattggtttctagttaaggaagtaggaaaagt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 cttgttactcttttctcaatccagccaaaatgtgttataatagtactaatttattggaacacatgaaagttcttgaaattttcattggtttctagttaaggaagtaggaaaagt Predict ORF larger than 30AA ================================================ cttgttactcttttctcaatccagccaaaatgtgttataatagtactaatttattggaacacatgaaagttcttgaaattttcattggtttctagttaaggaagtaggaaaagt Predict Promoter with matrix: RpoD-15 score > 80================================================ Predict Promoter with matrix: RpoD-16 score > 80================================================ Predict Promoter with matrix: RpoD-17 score > 80================================================ PromScan Matrix: RpoD-17 Strand: + Score: 87 Start: 12 End: 41 ...........TTTCTCAATCCAGCCAAAATGTGTTATAAT......................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ cttgttactcttttctcaatccagccaaaatgtgttataatagtactaatttattggaacacatgaaagttcttgaaattttcattggtttctagttaaggaagtaggaaaagt Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 41 HP_score: -2.5 Tail_Score: -2.78526 Start: 65 End: 83 Full_Region: TTTATTGGAACACAT GAAAGTT CTTGA AATTTTC ATTGGTTTCTAGTTA ................................................................GAAAGTTCTTGAAATTTTC............................... Find igs database================================================ Query_seq: SMT_395:SMT_396|SMT_395:SMT_396:hypothetical protein:putative nicotinate phosphoribosyltransferase:->->:325088..325201 114 cttgttactcttttctcaatccagccaaaatgtgttataatagtactaatttattggaacacatgaaagttcttgaaattttcattggtttctagttaaggaagtaggaaaagt Intra-Species Hit: Count: 1 Min: 1 Max: 114 Len: 114 Subject: smit_SMT_395_SMT_396|hypothetical protein:putative nicotinate phosphoribosyltransferase|POSITIVE:POSITIVE|[325088, 325201]|114 HSP 1 e-value: 1.0E-58 bit: 226.0 Len: 114 Query Start:1 Query End:114 Subject Strand: POSITIVE Subject Start: 1 Subject End: 114 cttgttactcttttctcaatccagccaaaatgtgttataatagtactaatttattggaacacatgaaagttcttgaaattttcattggtttctagttaaggaagtaggaaaagt cttgttactcttttctcaatccagccaaaatgtgttataatagtactaatttattggaacacatgaaagttcttgaaattttcattggtttctagttaaggaagtaggaaaagt Inter-species Hit: Count: 3 Min: 1 Max: 114 Len: 114 Subject: NC_008533_SPD_1251_SPD_1252|nicotinate phosphoribosyltransferase, putative:hypothetical protein|NEGATIVE:NEGATIVE|[1281224,1281338]|115 HSP 1 e-value: 2.0E-42 bit: 172.0 Len: 114 Query Start:1 Query End:114 Subject Strand: NEGATIVE Subject Start: 1 Subject End: 115 cttgttactcttttctcaatccagccaaaatgtgttataatagtactaatttattggaacacatgaaagttcttg-aaattttcattggtttctagttaaggaagtaggaaaagt cttgttactcttttctcaatccagctaaaatgtgatataatagtactaatttattggaatacatgaaagttcttgaaaattttcatgggtttctagctaaggaagtaggaaaagt Subject: NC_003098_spr1277_spr1278|nicotinate phosphoribosyltransferase:hypothetical protein|NEGATIVE:NEGATIVE|[1273693,1273807]|115 HSP 1 e-value: 2.0E-42 bit: 172.0 Len: 114 Query Start:1 Query End:114 Subject Strand: NEGATIVE Subject Start: 1 Subject End: 115 cttgttactcttttctcaatccagccaaaatgtgttataatagtactaatttattggaacacatgaaagttcttg-aaattttcattggtttctagttaaggaagtaggaaaagt cttgttactcttttctcaatccagctaaaatgtgatataatagtactaatttattggaatacatgaaagttcttgaaaattttcatgggtttctagctaaggaagtaggaaaagt Subject: NC_003028_SP_1421_SP_1422|nicotinate phosphoribosyltransferase:hypothetical protein|NEGATIVE:NEGATIVE|[1343091,1343205]|115 HSP 1 e-value: 2.0E-42 bit: 172.0 Len: 114 Query Start:1 Query End:114 Subject Strand: NEGATIVE Subject Start: 1 Subject End: 115 cttgttactcttttctcaatccagccaaaatgtgttataatagtactaatttattggaacacatgaaagttcttg-aaattttcattggtttctagttaaggaagtaggaaaagt cttgttactcttttctcaatccagctaaaatgtgatataatagtactaatttattggaatacatgaaagttcttgaaaattttcatgggtttctagctaaggaagtaggaaaagt Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUUGUUACUCUUUUCUCAAUCCAGCCAAAAUGUGUUAUAAUAGUACUAAUUUAUUGGAACACAUGAAAGUUCUUGAAAUUUUCAUUGGUUUCUAGUUAAGGAAGUAGGAAAAGU .........(((((((...(((((((((.(((((((.((((((.......)))))).)))))))(((((((.....))))))).)))))).........)))....))))))). (-23.30) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACUUUUCCUACUUCCUUAACUAGAAACCAAUGAAAAUUUCAAGAACUUUCAUGUGUUCCAAUAAAUUAGUACUAUUAUAACACAUUUUGGCUGGAUUGAGAAAAGAGUAACAAG .(((((((....(((....((((((....((((((.(((...))).))))))(((((..((((.........))))..))))).))))))..)))..).))))))......... (-16.50) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 301 49 8 164 130 smit:SMT_1411|5end_ATP-dependent_nuclease_subunit_B_1395478..1395708_NEGATIVE 238 44 1 46 2 smit:SMT_1348|5end_exoribonuclease_II_1327502..1327732_NEGATIVE 235 38 8 73 35 smit:SMT_1250|5end_hypothetical_protein_1211345..1211575_NEGATIVE 217 50 10 219 180 smit:SMT_1720|5end_hypothetical_protein_1706959..1707189_POSITIVE 210 110 62 206 155 smit:SMT_486|5end_hypothetical_protein_422305..422535_NEGATIVE 209 110 70 131 94 smit:SMT_904|5end_hypothetical_protein_852698..852928_NEGATIVE 207 28 2 229 207 smit:SMT_378|5end_hypothetical_protein_predicted_by_Glimmer/Critica_315884..316114_POSITIVE 206 97 55 63 13 smit:SMT_397|5end_NAD(+)_synthetase_326519..326749_POSITIVE 199 108 68 113 68 smit:SMT_1535|5end_exodeoxyribonuclease_V_alpha_chain_1518067..1518297_POSITIVE 199 75 31 115 71 smit:SMT_842|5end_hypothetical_protein_789262..789492_NEGATIVE 199 105 62 131 89 smit:SMT_755|5end_shikimate_5-dehydrogenase_659917..660147_NEGATIVE 197 109 71 227 192 smit:SMT_403|5end_two-component_sensor_kinase_YesM_331580..331810_POSITIVE 196 52 18 231 192 smit:SMT_1392|5end_dihydroxyacetone_kinase_1368531..1368761_POSITIVE 193 94 57 179 143 smit:SMT_1569|5end_dihydroxy-acid_dehydratase_1561285..1561515_POSITIVE 190 27 8 124 99 smit:SMT_1451|5end_K02057_simple_sugar_transport_system_permease_protein_1434683..1434913_NEGATIVE 190 36 1 51 6 smit:SMT_1118|5end_hypothetical_protein_1055150..1055380_NEGATIVE 186 93 53 206 171 smit:SMT_364|5end_ribosome-binding_factor_A_300923..301153_POSITIVE 185 110 62 137 89 smit:SMT_1745|5end_UDP-glucose_4-epimerase_1725541..1725771_NEGATIVE 183 94 56 44 3 smit:SMT_1727|5end_uridine_kinase_1712483..1712713_POSITIVE 183 51 21 33 3 smit:SMT_467|5end_UDP-N-acetylglucosamine--N-acetylmuramyl-_(pentapeptide)_pyrophosphoryl-undecaprenol_N-acetylglucosamine_transferase_404329..404559_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 252 108 67 132 96 smit:SMT_618|3end_methionine_aminopeptidase_527637..527787_POSITIVE 235 38 8 89 51 smit:SMT_1251|3end_hypothetical_protein_1211329..1211479_NEGATIVE 209 110 70 63 26 smit:SMT_905|3end_hypothetical_protein_predicted_by_Glimmer/Critica_852766..852916_NEGATIVE 207 28 2 113 91 smit:SMT_377|3end_hypothetical_protein_315848..315998_POSITIVE 205 108 69 121 69 smit:SMT_1625|3end_DNA_polymerase_IV_1615066..1615216_POSITIVE 199 75 31 113 69 smit:SMT_843|3end_hypothetical_protein_789264..789414_NEGATIVE 199 105 62 141 99 smit:SMT_756|3end_3-dehydroquinate_dehydratase_659907..660057_NEGATIVE 197 105 64 110 62 smit:SMT_2022|3end_hypothetical_protein_1938993..1939143_POSITIVE 196 110 84 43 16 smit:SMT_831|3end_transcriptional_activator,_putative_774355..774505_POSITIVE 190 27 8 131 106 smit:SMT_1452|3end_ABC-type_uncharacterized_transport_system,_ATPase_component_1434676..1434826_NEGATIVE 185 52 11 81 43 smit:SMT_297|3end_ABC_transporter_substrate-binding_protein_-_oligopeptide_transport_240606..240756_POSITIVE 184 107 67 78 31 smit:SMT_2087|3end_cadmium_efflux_system_accessory_protein_1984108..1984258_POSITIVE 184 107 67 78 31 smit:SMT_1234|3end_cadmium_efflux_system_accessory_protein_1195350..1195500_POSITIVE 182 25 1 77 48 smit:SMT_1739|3end_hypothetical_protein_1721633..1721783_POSITIVE 181 108 79 34 7 smit:SMT_1753|3end_tryptophan_synthase_beta_chain_1731652..1731802_POSITIVE 181 46 8 33 4 smit:SMT_826|3end_hypothetical_protein_749591..749741_NEGATIVE 181 35 7 61 35 smit:SMT_348|3end_K07707_two-component_system,_AgrA_family,_response_regulator_AgrA_287282..287432_POSITIVE 177 110 66 147 100 smit:SMT_1445|3end_hypothetical_protein_1427948..1428098_NEGATIVE 177 109 67 139 77 smit:SMT_115|3end_hypothetical_protein_66482..66632_POSITIVE 176 108 68 149 107 smit:SMT_590|3end_tetratricopeptide_repeat_family_protein_508046..508196_POSITIVE