Origin IGS: atctctacaaattattgtaatcgattccaaagatgtatgcaagttgtttgttgaaaaaagcccacttttttgataaaattttctgggttgtatgtaaaaaagaaaacaagtggagttt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aaactccacttgttttcttttttacatacaacccagaaaattttatcaaaaaagtgggcttttttcaacaaacaacttgcatacatctttggaatcgattacaataatttgtagagat Mask Tandem Repeat Region ================================================ atctctacaaattattgtaatcgattccaaagatgtatgcaagttgtttgttgaaaaaagcccacttttttgataaaattttctgggttgtatgtaaaaaagaaaacaagtggagttt Find is-nt database================================================ Query_seq: SSA_1752:SSA_1753|SSA_1752:SSA_1753:Phosphotransferase system, trehalose-specific IIBC component, putative:Transcriptional regulator, GntR family (repressor of trehalose operon), putative:<-->:1741966..1742083 118 atctctacaaattattgtaatcgattccaaagatgtatgcaagttgtttgttgaaaaaagcccacttttttgataaaattttctgggttgtatgtaaaaaagaaaacaagtggagttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1752:SSA_1753|SSA_1752:SSA_1753:Phosphotransferase system, trehalose-specific IIBC component, putative:Transcriptional regulator, GntR family (repressor of trehalose operon), putative:<-->:1741966..1742083 118 atctctacaaattattgtaatcgattccaaagatgtatgcaagttgtttgttgaaaaaagcccacttttttgataaaattttctgggttgtatgtaaaaaagaaaacaagtggagttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1752:SSA_1753|SSA_1752:SSA_1753:Phosphotransferase system, trehalose-specific IIBC component, putative:Transcriptional regulator, GntR family (repressor of trehalose operon), putative:<-->:1741966..1742083 118 atctctacaaattattgtaatcgattccaaagatgtatgcaagttgtttgttgaaaaaagcccacttttttgataaaattttctgggttgtatgtaaaaaagaaaacaagtggagttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 atctctacaaattattgtaatcgattccaaagatgtatgcaagttgtttgttgaaaaaagcccacttttttgataaaattttctgggttgtatgtaaaaaagaaaacaagtggagttt Predict ORF larger than 30AA ================================================ Protein_Len: 31 Strand: + Start: 24 End: 116 ....................... M P K M Y A S C L L K K A H F F D K I F W V V C K K E N K W S .. Protein_Len: 34 Strand: - Start: 8 End: 109 ....... L N N Y D I G F I Y A L Q K N F F A W K K S L I K Q T T H L F S F M ......... Protein_Len: 31 Strand: - Start: 1 End: 93 D R C I I T I S E L S T H L N N T S F L G S K Q Y F K R P Q M ......................... atctctacaaattattgtaatcgattccaaagatgtatgcaagttgtttgttgaaaaaagcccacttttttgataaaattttctgggttgtatgtaaaaaagaaaacaagtggagttt 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: 89 Start: 50 End: 79 .................................................GTTGAAAAAAGCCCACTTTTTTGATAAAAT....................................... PromScan Matrix: RpoD-17 Strand: - Score: 82 Start: 14 End: 43 .............CTTGCATACATCTTTGGAATCGATTACAAT........................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ atctctacaaattattgtaatcgattccaaagatgtatgcaagttgtttgttgaaaaaagcccacttttttgataaaattttctgggttgtatgtaaaaaagaaaacaagtggagttt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_1752:SSA_1753|SSA_1752:SSA_1753:Phosphotransferase system, trehalose-specific IIBC component, putative:Transcriptional regulator, GntR family (repressor of trehalose operon), putative:<-->:1741966..1742083 118 atctctacaaattattgtaatcgattccaaagatgtatgcaagttgtttgttgaaaaaagcccacttttttgataaaattttctgggttgtatgtaaaaaagaaaacaagtggagttt Intra-Species Hit: Count: 1 Min: 1 Max: 118 Len: 118 Subject: NC_009009_SSA_1752_SSA_1753|Phosphotransferase system, trehalose-specific IIBC component, putative:Transcriptional regulator, GntR family (repressor of trehalose operon), putative|NEGATIVE:POSITIVE|[1741966,1742083]|118 HSP 1 e-value: 5.0E-61 bit: 234.0 Len: 118 Query Start:1 Query End:118 Subject Strand: POSITIVE Subject Start: 1 Subject End: 118 atctctacaaattattgtaatcgattccaaagatgtatgcaagttgtttgttgaaaaaagcccacttttttgataaaattttctgggttgtatgtaaaaaagaaaacaagtggagttt atctctacaaattattgtaatcgattccaaagatgtatgcaagttgtttgttgaaaaaagcccacttttttgataaaattttctgggttgtatgtaaaaaagaaaacaagtggagttt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUCUCUACAAAUUAUUGUAAUCGAUUCCAAAGAUGUAUGCAAGUUGUUUGUUGAAAAAAGCCCACUUUUUUGAUAAAAUUUUCUGGGUUGUAUGUAAAAAAGAAAACAAGUGGAGUUU ..((((((......((((((((.........)))...)))))..(((((.(((.....((((((....(((....))).....)))))).....)))......))))).))))))... (-18.50) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAACUCCACUUGUUUUCUUUUUUACAUACAACCCAGAAAAUUUUAUCAAAAAAGUGGGCUUUUUUCAACAAACAACUUGCAUACAUCUUUGGAAUCGAUUACAAUAAUUUGUAGAGAU ....((((((((((((((................)))))))..........)))))))...................................(((..((((((....)))))).))) (-12.09) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 794 70 21 161 112 NC_009009:SSA_1752|5end_Phosphotransferase_system,_trehalose-specific_IIBC_component,_putative_1741875..1742105_NEGATIVE 219 89 47 173 132 NC_009009:SSA_1667|5end_hypothetical_protein_1667704..1667934_NEGATIVE 218 62 21 89 45 NC_009009:SSA_1622|5end_50S_ribosomal_protein_L1,_putative_1625441..1625671_NEGATIVE 215 86 57 36 5 NC_009009:SSA_1625|5end_Lactoylglutathione_lyase,_putative_1626963..1627193_NEGATIVE 212 93 55 225 190 NC_009009:SSA_1612|5end_Diacylglycerol_kinase,_putative_1616497..1616727_NEGATIVE 207 64 22 173 123 NC_009009:SSA_2296|5end_Transcriptional_regulator,_XRE_family,_putative_2298773..2299003_NEGATIVE 207 64 22 160 125 NC_009009:SSA_1208|5end_23S_rRNA_pseudouridine_synthase,_putative_1233185..1233415_NEGATIVE 207 70 22 102 40 NC_009009:SSA_0794|5end_Zn-dependent_protease,_putative_775896..776126_POSITIVE 205 70 23 80 33 NC_009009:SSA_1005|5end_Sugar_ABC_transporter,_permease_protein,_putative_1006028..1006258_POSITIVE 203 90 58 230 197 NC_009009:SSA_1249|5end_hypothetical_protein_1273985..1274215_NEGATIVE 201 89 42 191 141 NC_009009:SSA_1751|5end_Dextran_glucosidase,_alpha_amylase_family,_putative_1739801..1740031_NEGATIVE 201 87 45 148 109 NC_009009:SSA_0854|5end_hypothetical_protein_841335..841565_POSITIVE 201 90 44 122 77 NC_009009:SSA_0683|5end_DNA-binding_protein_HU,_putative_664384..664614_POSITIVE 201 93 60 33 1 NC_009009:SSA_0197|5end_Dihydropteroate_synthase,_putative_195946..196176_POSITIVE 199 67 38 210 184 NC_009009:SSA_0182|5end_Endoglucanase,_putative_186299..186529_POSITIVE 197 84 41 183 143 NC_009009:SSA_1801|5end_hypothetical_protein_1783314..1783544_NEGATIVE 196 93 60 88 54 NC_009009:SSA_0761|5end_Transcriptional_regulator,_XRE_family,_putative_743877..744107_POSITIVE 195 91 52 196 155 NC_009009:SSA_1436|5end_hypothetical_protein_1443125..1443355_NEGATIVE 194 49 1 149 97 NC_009009:SSA_1224|5end_hypothetical_protein_1247481..1247711_NEGATIVE 194 63 25 145 104 NC_009009:SSA_0492|5end_NADH-dependent_flavin_oxidoreductase,_putative_491588..491818_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 219 89 47 139 98 NC_009009:SSA_1668|3end_NrdI_protein,_putative_1667738..1667888_NEGATIVE 205 70 23 66 19 NC_009009:SSA_1004|3end_ABC_transporter_membrane-spanning_permease-multiple_sugars,_putative_1006094..1006244_POSITIVE 204 89 46 49 4 NC_009009:SSA_1529|3end_Lysyl-tRNA_synthetase,_putative_1537441..1537591_POSITIVE 202 95 56 82 40 NC_009009:SSA_0267|3end_ROK_family_protein,_putative_260873..261023_NEGATIVE 201 87 45 151 112 NC_009009:SSA_0852|3end_ATP-dependent_DNA_helicase,_putative_841418..841568_POSITIVE 199 67 38 123 97 NC_009009:SSA_0181|3end_Glycosyltransferase_(vectorial_glycosyl_polymerization_(VGP)_family),_putative_186292..186442_POSITIVE 198 49 1 52 3 NC_009009:SSA_1239|3end_hypothetical_protein_1263151..1263301_NEGATIVE 197 84 41 128 88 NC_009009:SSA_1802|3end_Snf2_family_protein,_putative_1783369..1783519_NEGATIVE 194 66 21 144 99 NC_009009:SSA_0568|3end_Aspartyl-tRNA_synthetase_1,_putative_563490..563640_POSITIVE 194 63 25 90 49 NC_009009:SSA_0491|3end_Alpha-ribazole-5'-phosphate_phosphatase,_putative_491613..491763_POSITIVE 192 64 22 151 111 NC_009009:SSA_0035|3end_Bifunctional_purine_biosynthesis_protein_purH,_putative_41957..42107_POSITIVE 187 64 23 78 32 NC_009009:SSA_1281|3end_Uracil-DNA_glycosylase,_putative_1301608..1301758_NEGATIVE 187 89 41 147 105 NC_009009:SSA_0090|3end_Acetyltransferase,_GNAT_family,_putative_91033..91183_POSITIVE 184 50 18 135 99 NC_009009:SSA_0972|3end_hypothetical_protein_980364..980514_POSITIVE 183 64 22 78 35 NC_009009:SSA_2349|3end_DTDP-4-dehydrorhamnose_3,5-epimerase,_putative_2350677..2350827_NEGATIVE 183 70 22 133 83 NC_009009:SSA_2105|3end_hypothetical_protein_2106756..2106906_NEGATIVE 183 87 43 124 90 NC_009009:SSA_2030|3end_hypothetical_protein_2036514..2036664_NEGATIVE 181 89 41 144 93 NC_009009:SSA_1945|3end_Oligopeptide_transport_ATP-binding_protein,_putative_1936622..1936772_NEGATIVE 181 108 62 60 11 NC_009009:SSA_1573|3end_hypothetical_protein_1576054..1576204_NEGATIVE 179 93 58 105 61 NC_009009:SSA_1915|3end_hypothetical_protein_1905276..1905426_NEGATIVE