Origin IGS: gtatcgttagtttctcattgatgaagccataaacttttagctatcctttcagttttagaatatttgagaatcctgtataatataataaagtaataagttagatagttaagaattctaaatcgtgctaattcagctagctttagaaaatatgagaagtgaaaggtgctatc .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 gatagcacctttcacttctcatattttctaaagctagctgaattagcacgatttagaattcttaactatctaacttattactttattatattatacaggattctcaaatattctaaaactgaaaggatagctaaaagtttatggcttcatcaatgagaaactaacgatac Mask Tandem Repeat Region ================================================ gtatcgttagtttctcattgatgaagccataaacttttagctatcctttcagttttagaatatttgagaatcctgtataatataataaagtaataagttagatagttaagaattctaaatcgtgctaattcagctagctttagaaaatatgagaagtgaaaggtgctatc Find is-nt database================================================ Query_seq: SSA_0749:SSA_0750|SSA_0749:SSA_0750:Competence protein, putative:hypothetical protein:->->:731759..731928 170 gtatcgttagtttctcattgatgaagccataaacttttagctatcctttcagttttagaatatttgagaatcctgtataatataataaagtaataagttagatagttaagaattctaaatcgtgctaattcagctagctttagaaaatatgagaagtgaaaggtgctatc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0749:SSA_0750|SSA_0749:SSA_0750:Competence protein, putative:hypothetical protein:->->:731759..731928 170 gtatcgttagtttctcattgatgaagccataaacttttagctatcctttcagttttagaatatttgagaatcctgtataatataataaagtaataagttagatagttaagaattctaaatcgtgctaattcagctagctttagaaaatatgagaagtgaaaggtgctatc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0749:SSA_0750|SSA_0749:SSA_0750:Competence protein, putative:hypothetical protein:->->:731759..731928 170 gtatcgttagtttctcattgatgaagccataaacttttagctatcctttcagttttagaatatttgagaatcctgtataatataataaagtaataagttagatagttaagaattctaaatcgtgctaattcagctagctttagaaaatatgagaagtgaaaggtgctatc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gtatcgttagtttctcattgatgaagccataaacttttagctatcctttcagttttagaatatttgagaatcctgtataatataataaagtaataagttagatagttaagaattctaaatcgtgctaattcagctagctttagaaaatatgagaagtgaaaggtgctatc Predict ORF larger than 30AA ================================================ Protein_Len: 32 Strand: - Start: 18 End: 113 ................. Q H L W L S K A I R E T K S Y K L I R Y L I I F Y Y T L Y N L M ......................................................... gtatcgttagtttctcattgatgaagccataaacttttagctatcctttcagttttagaatatttgagaatcctgtataatataataaagtaataagttagatagttaagaattctaaatcgtgctaattcagctagctttagaaaatatgagaagtgaaaggtgctatc 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: 83 Start: 52 End: 81 ...................................................GTTTTAGAATATTTGAGAATCCTGTATAAT......................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ gtatcgttagtttctcattgatgaagccataaacttttagctatcctttcagttttagaatatttgagaatcctgtataatataataaagtaataagttagatagttaagaattctaaatcgtgctaattcagctagctttagaaaatatgagaagtgaaaggtgctatc Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_0749:SSA_0750|SSA_0749:SSA_0750:Competence protein, putative:hypothetical protein:->->:731759..731928 170 gtatcgttagtttctcattgatgaagccataaacttttagctatcctttcagttttagaatatttgagaatcctgtataatataataaagtaataagttagatagttaagaattctaaatcgtgctaattcagctagctttagaaaatatgagaagtgaaaggtgctatc Intra-Species Hit: Count: 1 Min: 1 Max: 170 Len: 170 Subject: NC_009009_SSA_0749_SSA_0750|Competence protein, putative:hypothetical protein|POSITIVE:POSITIVE|[731759,731928]|170 HSP 1 e-value: 7.0E-92 bit: 337.0 Len: 170 Query Start:1 Query End:170 Subject Strand: POSITIVE Subject Start: 1 Subject End: 170 gtatcgttagtttctcattgatgaagccataaacttttagctatcctttcagttttagaatatttgagaatcctgtataatataataaagtaataagttagatagttaagaattctaaatcgtgctaattcagctagctttagaaaatatgagaagtgaaaggtgctatc gtatcgttagtttctcattgatgaagccataaacttttagctatcctttcagttttagaatatttgagaatcctgtataatataataaagtaataagttagatagttaagaattctaaatcgtgctaattcagctagctttagaaaatatgagaagtgaaaggtgctatc Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GUAUCGUUAGUUUCUCAUUGAUGAAGCCAUAAACUUUUAGCUAUCCUUUCAGUUUUAGAAUAUUUGAGAAUCCUGUAUAAUAUAAUAAAGUAAUAAGUUAGAUAGUUAAGAAUUCUAAAUCGUGCUAAUUCAGCUAGCUUUAGAAAAUAUGAGAAGUGAAAGGUGCUAUC (((((.((..((((((((...((((((.......((((((((((((((....(((((..(((((..((....))....)))))..)))))....)))...)))))))))))............(((.....)))..))))))......))))))))..)).))))).... (-33.10) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAUAGCACCUUUCACUUCUCAUAUUUUCUAAAGCUAGCUGAAUUAGCACGAUUUAGAAUUCUUAACUAUCUAACUUAUUACUUUAUUAUAUUAUACAGGAUUCUCAAAUAUUCUAAAACUGAAAGGAUAGCUAAAAGUUUAUGGCUUCAUCAAUGAGAAACUAACGAUAC ...............(((((((........(((((((((...(((((....((((((((........((((..........................))))........)))))))).((....))...))))).)))...)))))).....)))))))........... (-23.78) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 278 46 1 191 144 NC_009009:SSA_2315|5end_Conserved_uncharacterized_protein_2316945..2317175_NEGATIVE 249 73 33 49 6 NC_009009:SSA_1842|5end_Two-component_response_transcriptional_regulator_(CheY-like_receiver_and_HTH_DNA-binding_domains),_putative_1836494..1836724_NEGATIVE 245 167 122 125 76 NC_009009:SSA_1493|5end_hypothetical_protein_1499480..1499710_NEGATIVE 243 79 32 166 116 NC_009009:SSA_2255|5end_Transcriptional_regulator,_XRE_family,_putative_2250144..2250374_POSITIVE 237 48 3 144 105 NC_009009:SSA_1721|5end_DNA_polymerase_III,_delta'_subunit,_putative_1708028..1708258_NEGATIVE 233 141 109 80 41 NC_009009:SSA_2017|5end_Hypothetical_protein_(possibly_membrane-associated)_2017331..2017561_NEGATIVE 232 50 9 105 63 NC_009009:SSA_0749|5end_Competence_protein,_putative_730668..730898_POSITIVE 230 170 131 92 47 NC_009009:SSA_0988|5end_TfoX_N-terminal_domain_family_protein,_putative_990662..990892_POSITIVE 229 82 41 205 165 NC_009009:SSA_1924|5end_Transcriptional_regulator,_TetR/AcrR_family,_putative_1913248..1913478_NEGATIVE 228 170 124 104 63 NC_009009:SSA_1605|5end_Major_facilitator_superfamily_multi-drug_resistance_efflux_pump_pmrA,_putative_1611732..1611962_NEGATIVE 228 139 99 59 21 NC_009009:SSA_1175|5end_Acetoin_dehydrogenase_complex,_E2_component,_dihydrolipoamide_acetyltransferase,_putative_1203976..1204206_NEGATIVE 224 76 34 107 55 NC_009009:SSA_2010|5end_ABC-type_multidrug_transport_system,_permease_component,_putative_2012024..2012254_NEGATIVE 224 156 112 73 34 NC_009009:SSA_0426|5end_hypothetical_protein_424386..424616_NEGATIVE 222 71 36 42 2 NC_009009:SSA_1450|5end_hypothetical_protein_1452710..1452940_NEGATIVE 221 166 124 163 123 NC_009009:SSA_1907|5end_hypothetical_protein_1900446..1900676_POSITIVE 220 168 121 113 52 NC_009009:SSA_1856|5end_hypothetical_protein_1852208..1852438_NEGATIVE 218 168 131 204 155 NC_009009:SSA_0730|5end_Arsenical_resistance_operon_transcription_repressor_(ArsR),_putative_714818..715048_POSITIVE 215 58 20 170 134 NC_009009:SSA_2278|5end_Ukp_protein,_putative_2281669..2281899_NEGATIVE 215 142 101 45 12 NC_009009:SSA_1432|5end_HflX_GTPase,_putative_1439901..1440131_NEGATIVE 214 50 4 191 143 NC_009009:SSA_0067|5end_Acyltransferase_(yrhL-like_subfamily_of_SGNH-hydrolases),_putative_68005..68235_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 249 73 33 71 28 NC_009009:SSA_1843|3end_Histidine_kinase,_putative_1836472..1836622_NEGATIVE 245 167 122 91 42 NC_009009:SSA_1494|3end_Conserved_uncharacterized_protein_1499514..1499664_NEGATIVE 237 48 3 147 108 NC_009009:SSA_1722|3end_Thymidylate_kinase,_putative_1708025..1708175_NEGATIVE 235 168 121 151 103 NC_009009:SSA_0156|3end_ATPase_with_chaperone_activity,_ATP-binding_subunit,_putative_153322..153472_POSITIVE 234 49 5 92 41 NC_009009:SSA_0706|3end_RNA_helicase,_putative_692909..693059_POSITIVE 233 144 109 77 35 NC_009009:SSA_0911|3end_hypothetical_protein_922898..923048_POSITIVE 229 166 121 57 3 NC_009009:SSA_0336|3end_Isopentenyl-diphosphate_delta-isomerase,_putative_330879..331029_POSITIVE 228 67 23 63 17 NC_009009:SSA_2101|3end_Amino_acid_ABC_transporter,_periplasmic_amino_acid-binding_protein,_putative_2104509..2104659_NEGATIVE 227 170 123 147 96 NC_009009:SSA_1498|3end_50S_ribosomal_protein_L20,_putative_1503753..1503903_NEGATIVE 225 56 18 140 100 NC_009009:SSA_0936|3end_FAD_synthase,_putative_946151..946301_POSITIVE 224 76 34 114 62 NC_009009:SSA_2011|3end_ABC-type_multidrug_transport_system,_ATPase_component,_putative_2012017..2012167_NEGATIVE 217 75 33 45 6 NC_009009:SSA_0480|3end_Cobalt_ABC_transporter,_ATP-binding_protein,_putative_482057..482207_POSITIVE 210 170 121 147 100 NC_009009:SSA_0380|3end_Enzyme_of_poly-gamma-glutamate_biosynthesis_(capsule_formation),_putative_372378..372528_POSITIVE 208 44 1 129 87 NC_009009:SSA_1932|3end_Biotin_carboxylase,_putative_1919507..1919657_NEGATIVE 207 68 26 146 101 NC_009009:SSA_0584|3end_hypothetical_protein_576689..576839_POSITIVE 206 170 121 144 87 NC_009009:SSA_0838|3end_GtfB,_putative_826829..826979_POSITIVE 206 50 4 51 15 NC_009009:SSA_0576|3end_Conserved_GTPase,_putative_571225..571375_POSITIVE 206 53 17 126 90 NC_009009:SSA_0083|3end_hypothetical_protein_85840..85990_POSITIVE 205 140 93 55 10 NC_009009:SSA_0836|3end_SecA-like_protein,_putative_823969..824119_POSITIVE 205 145 102 63 20 NC_009009:SSA_0795|3end_hypothetical_protein_777065..777215_POSITIVE