Origin IGS: gattattccttttaagtgtaatgaaattattataacacataccaaactaagaatttgcttttatgttataaaatacaaagaatccgctaaaaagaaaagttgaaataagatt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aatcttatttcaacttttctttttagcggattctttgtattttataacataaaagcaaattcttagtttggtatgtgttataataatttcattacacttaaaaggaataatc Mask Tandem Repeat Region ================================================ gattattccttttaagtgtaatgaaattattataacacataccaaactaagaatttgcttttatgttataaaatacaaagaatccgctaaaaagaaaagttgaaataagatt Find is-nt database================================================ Query_seq: SSA_1718:SSA_1719|SSA_1718:SSA_1719:Site-specific DNA-methyltransferase, putative:Conserved uncharacterized protein:<-<-:1705902..1706013 112 gattattccttttaagtgtaatgaaattattataacacataccaaactaagaatttgcttttatgttataaaatacaaagaatccgctaaaaagaaaagttgaaataagatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1718:SSA_1719|SSA_1718:SSA_1719:Site-specific DNA-methyltransferase, putative:Conserved uncharacterized protein:<-<-:1705902..1706013 112 gattattccttttaagtgtaatgaaattattataacacataccaaactaagaatttgcttttatgttataaaatacaaagaatccgctaaaaagaaaagttgaaataagatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1718:SSA_1719|SSA_1718:SSA_1719:Site-specific DNA-methyltransferase, putative:Conserved uncharacterized protein:<-<-:1705902..1706013 112 gattattccttttaagtgtaatgaaattattataacacataccaaactaagaatttgcttttatgttataaaatacaaagaatccgctaaaaagaaaagttgaaataagatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gattattccttttaagtgtaatgaaattattataacacataccaaactaagaatttgcttttatgttataaaatacaaagaatccgctaaaaagaaaagttgaaataagatt Predict ORF larger than 30AA ================================================ Protein_Len: 33 Strand: + Start: 2 End: 100 . M I P F K C N E I I I T H T K L R I C F Y V I K Y K E S A K K K S ............ gattattccttttaagtgtaatgaaattattataacacataccaaactaagaatttgcttttatgttataaaatacaaagaatccgctaaaaagaaaagttgaaataagatt 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================================================ gattattccttttaagtgtaatgaaattattataacacataccaaactaagaatttgcttttatgttataaaatacaaagaatccgctaaaaagaaaagttgaaataagatt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_1718:SSA_1719|SSA_1718:SSA_1719:Site-specific DNA-methyltransferase, putative:Conserved uncharacterized protein:<-<-:1705902..1706013 112 gattattccttttaagtgtaatgaaattattataacacataccaaactaagaatttgcttttatgttataaaatacaaagaatccgctaaaaagaaaagttgaaataagatt Intra-Species Hit: Count: 1 Min: 1 Max: 112 Len: 112 Subject: NC_009009_SSA_1718_SSA_1719|Site-specific DNA-methyltransferase, putative:Conserved uncharacterized protein|NEGATIVE:NEGATIVE|[1705902,1706013]|112 HSP 1 e-value: 2.0E-57 bit: 222.0 Len: 112 Query Start:1 Query End:112 Subject Strand: POSITIVE Subject Start: 1 Subject End: 112 gattattccttttaagtgtaatgaaattattataacacataccaaactaagaatttgcttttatgttataaaatacaaagaatccgctaaaaagaaaagttgaaataagatt gattattccttttaagtgtaatgaaattattataacacataccaaactaagaatttgcttttatgttataaaatacaaagaatccgctaaaaagaaaagttgaaataagatt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAUUAUUCCUUUUAAGUGUAAUGAAAUUAUUAUAACACAUACCAAACUAAGAAUUUGCUUUUAUGUUAUAAAAUACAAAGAAUCCGCUAAAAAGAAAAGUUGAAAUAAGAUU ((((.(((.(((((.((((.((((.....)))).))))......((((((((......))))).)))....................))))).))).))))........... ( -9.50) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUCUUAUUUCAACUUUUCUUUUUAGCGGAUUCUUUGUAUUUUAUAACAUAAAAGCAAAUUCUUAGUUUGGUAUGUGUUAUAAUAAUUUCAUUACACUUAAAAGGAAUAAUC ................((((((((((.(.............((((((((((..(.(((((.....))))).).)))))))))).............)))))))))))..... (-16.37) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 715 90 41 181 132 NC_009009:SSA_1718|5end_Site-specific_DNA-methyltransferase,_putative_1705811..1706041_NEGATIVE 230 110 75 74 43 NC_009009:SSA_1121|5end_Cytochrome_C-type_biogenesis_protein,_putative_1147149..1147379_POSITIVE 204 60 17 161 111 NC_009009:SSA_1868|5end_ABC-type_arginine/histidine_transport_system,_permease_component,_putative_1863902..1864132_NEGATIVE 197 68 35 155 115 NC_009009:SSA_2310|5end_hypothetical_protein_2313418..2313648_NEGATIVE 190 67 38 97 59 NC_009009:SSA_1811|5end_6-phosphogluconate_dehydrogenase,_putative_1796830..1797060_NEGATIVE 182 44 7 128 91 NC_009009:SSA_1318|5end_GTP-binding_protein_lepA,_putative_1335821..1336051_NEGATIVE 181 88 42 194 149 NC_009009:SSA_1083|5end_Conserved_uncharacterized_protein_1101298..1101528_POSITIVE 176 89 47 183 148 NC_009009:SSA_0683|5end_DNA-binding_protein_HU,_putative_664384..664614_POSITIVE 174 44 3 134 97 NC_009009:SSA_0820|5end_Ribosomal_protein_S21,_putative_801249..801479_POSITIVE 170 90 44 150 115 NC_009009:SSA_0418|5end_AraC-type_DNA-binding_domain-containing_protein,_putative_415256..415486_POSITIVE 166 90 46 199 150 NC_009009:SSA_1191|5end_hypothetical_protein_1218323..1218553_NEGATIVE 166 63 23 152 117 NC_009009:SSA_0907|5end_Fibronectin-binding_protein_A,_putative_919217..919447_NEGATIVE 166 39 6 137 107 NC_009009:SSA_0552|5end_Cof_family_protein,_putative_547424..547654_POSITIVE 164 94 51 202 163 NC_009009:SSA_0584|5end_hypothetical_protein_575806..576036_POSITIVE 162 100 60 156 121 NC_009009:SSA_0966|5end_Uridine_kinase,_putative_975063..975293_POSITIVE 161 66 34 203 166 NC_009009:SSA_0379|5end_PTS_system,_beta-glucoside-specific_EII_component,_putative_368822..369052_POSITIVE 161 88 41 66 23 NC_009009:SSA_0308|5end_hypothetical_protein_304385..304615_POSITIVE 160 37 6 130 97 NC_009009:SSA_0852|5end_ATP-dependent_DNA_helicase,_putative_839050..839280_POSITIVE 159 22 6 156 140 NC_009009:SSA_1639|5end_5'-methylthioadenosine/S-adenosylhomocysteine_nucleosidase,_putative_1642031..1642261_NEGATIVE 159 87 44 220 172 NC_009009:SSA_0065|5end_Low_molecular_weight_phosphotyrosine_protein_phosphatase,_putative_67175..67405_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 197 68 35 142 102 NC_009009:SSA_2311|3end_Nitric_oxide_reductase_NorD_/_Von_Willebrand_factor_type_A_(vWA)_domain_protein,_putative_2313431..2313581_NEGATIVE 192 89 50 34 1 NC_009009:SSA_2285|3end_hypothetical_protein_2287825..2287975_POSITIVE 182 95 57 111 69 NC_009009:SSA_0230|3end_hypothetical_protein_223812..223962_NEGATIVE 181 88 42 67 22 NC_009009:SSA_1082|3end_PTS_system,_fructose_specific_II_ABC_components,_putative_1101251..1101401_POSITIVE 176 89 47 70 35 NC_009009:SSA_0682|3end_Conserved_uncharacterized_protein_664351..664501_POSITIVE 170 90 44 52 17 NC_009009:SSA_0417|3end_5,10-methylenetetrahydrofolate_reductase,_putative_415238..415388_POSITIVE 167 88 46 95 55 NC_009009:SSA_0858|3end_DTDP-L-rhamnose_synthase,_putative_846446..846596_POSITIVE 166 90 46 87 38 NC_009009:SSA_1192|3end_hypothetical_protein_1218435..1218585_NEGATIVE 166 65 36 127 100 NC_009009:SSA_0067|3end_Acyltransferase_(yrhL-like_subfamily_of_SGNH-hydrolases),_putative_69890..70040_POSITIVE 161 100 76 56 28 NC_009009:SSA_0506|3end_Iron-sulfur_cluster-binding_protein,_putative_504430..504580_NEGATIVE 161 105 82 76 54 NC_009009:SSA_0175|3end_Penicillin-binding_protein_1B,_putative_174484..174634_POSITIVE 161 105 82 76 54 NC_009009:SSA_0134|3end_Membrane_carboxypeptidase_(penicillin-binding_protein),_putative_174484..174634_POSITIVE 159 22 6 79 63 NC_009009:SSA_1640|3end_hypothetical_protein_1642108..1642258_NEGATIVE 157 88 57 80 46 NC_009009:SSA_0135|3end_Multiple_antibiotic_resistance_operon_transcriptional_repressor_(MarR),_putative_131097..131247_POSITIVE 155 65 25 43 2 NC_009009:SSA_1990|3end_Zn-porter_lipoprotein,_putative_1985402..1985552_NEGATIVE 154 109 75 52 15 NC_009009:SSA_1480|3end_hypothetical_protein_1483960..1484110_NEGATIVE 153 45 1 105 61 NC_009009:SSA_0518|3end_Ethanolamine_utilization_protein_EutA,_putative_518123..518273_POSITIVE 150 101 68 65 37 NC_009009:SSA_2286|3end_Dihydroxy-acid_dehydratase,_putative_2287878..2288028_NEGATIVE 150 103 76 65 34 NC_009009:SSA_0406|3end_hypothetical_protein_402196..402346_NEGATIVE 150 72 31 52 12 NC_009009:SSA_0181|3end_Glycosyltransferase_(vectorial_glycosyl_polymerization_(VGP)_family),_putative_186292..186442_POSITIVE