Origin IGS: ttcctccgttattccacaactattatatcacaatcatagtgtatatcaggatatatcaagctctattattcgttagatactcaattttaacttttcccttttccttaaaataatagtataatagagatagaatttagaatcgaggtgcacct .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aggtgcacctcgattctaaattctatctctattatactattattttaaggaaaagggaaaagttaaaattgagtatctaacgaataatagagcttgatatatcctgatatacactatgattgtgatataatagttgtggaataacggaggaa Mask Tandem Repeat Region ================================================ ttcctccgttattccacaactattatatcacaatcatagtgtatatcaggatatatcaagctctattattcgttagatactcaattttaacttttcccttttccttaaaataatagtataatagagatagaatttagaatcgaggtgcacct Find is-nt database================================================ Query_seq: SMT_1428:SMT_1429|SMT_1428:SMT_1429:hypothetical protein predicted by Glimmer/Critica:hypothetical protein predicted by Glimmer/Critica:<-->:1414713..1414864 152 ttcctccgttattccacaactattatatcacaatcatagtgtatatcaggatatatcaagctctattattcgttagatactcaattttaacttttcccttttccttaaaataatagtataatagagatagaatttagaatcgaggtgcacct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_1428:SMT_1429|SMT_1428:SMT_1429:hypothetical protein predicted by Glimmer/Critica:hypothetical protein predicted by Glimmer/Critica:<-->:1414713..1414864 152 ttcctccgttattccacaactattatatcacaatcatagtgtatatcaggatatatcaagctctattattcgttagatactcaattttaacttttcccttttccttaaaataatagtataatagagatagaatttagaatcgaggtgcacct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_1428:SMT_1429|SMT_1428:SMT_1429:hypothetical protein predicted by Glimmer/Critica:hypothetical protein predicted by Glimmer/Critica:<-->:1414713..1414864 152 ttcctccgttattccacaactattatatcacaatcatagtgtatatcaggatatatcaagctctattattcgttagatactcaattttaacttttcccttttccttaaaataatagtataatagagatagaatttagaatcgaggtgcacct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ttcctccgttattccacaactattatatcacaatcatagtgtatatcaggatatatcaagctctattattcgttagatactcaattttaacttttcccttttccttaaaataatagtataatagagatagaatttagaatcgaggtgcacct Predict ORF larger than 30AA ================================================ ttcctccgttattccacaactattatatcacaatcatagtgtatatcaggatatatcaagctctattattcgttagatactcaattttaacttttcccttttccttaaaataatagtataatagagatagaatttagaatcgaggtgcacct 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: 84 Start: 93 End: 122 ............................................................................................TTTCCCTTTTCCTTAAAATAATAGTATAAT.............................. PromScan Matrix: RpoD-17 Strand: + Score: 81 Start: 104 End: 133 .......................................................................................................CTTAAAATAATAGTATAATAGAGATAGAAT................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ ttcctccgttattccacaactattatatcacaatcatagtgtatatcaggatatatcaagctctattattcgttagatactcaattttaacttttcccttttccttaaaataatagtataatagagatagaatttagaatcgaggtgcacct Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SMT_1428:SMT_1429|SMT_1428:SMT_1429:hypothetical protein predicted by Glimmer/Critica:hypothetical protein predicted by Glimmer/Critica:<-->:1414713..1414864 152 ttcctccgttattccacaactattatatcacaatcatagtgtatatcaggatatatcaagctctattattcgttagatactcaattttaacttttcccttttccttaaaataatagtataatagagatagaatttagaatcgaggtgcacct Intra-Species Hit: Count: 1 Min: 1 Max: 152 Len: 152 Subject: smit_SMT_1428_SMT_1429|hypothetical protein predicted by Glimmer/Critica:hypothetical protein predicted by Glimmer/Critica|NEGATIVE:POSITIVE|[1414713,1414864]|152 HSP 1 e-value: 3.0E-81 bit: 301.0 Len: 152 Query Start:1 Query End:152 Subject Strand: POSITIVE Subject Start: 1 Subject End: 152 ttcctccgttattccacaactattatatcacaatcatagtgtatatcaggatatatcaagctctattattcgttagatactcaattttaacttttcccttttccttaaaataatagtataatagagatagaatttagaatcgaggtgcacct ttcctccgttattccacaactattatatcacaatcatagtgtatatcaggatatatcaagctctattattcgttagatactcaattttaacttttcccttttccttaaaataatagtataatagagatagaatttagaatcgaggtgcacct Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUCCUCCGUUAUUCCACAACUAUUAUAUCACAAUCAUAGUGUAUAUCAGGAUAUAUCAAGCUCUAUUAUUCGUUAGAUACUCAAUUUUAACUUUUCCCUUUUCCUUAAAAUAAUAGUAUAAUAGAGAUAGAAUUUAGAAUCGAGGUGCACCU ..((((.(((.........((..((((.(((.......)))))))..))......((...(((((((((..((((((........)))))).......(((.....)))........)))))))))...))......))).))))....... (-20.20) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGGUGCACCUCGAUUCUAAAUUCUAUCUCUAUUAUACUAUUAUUUUAAGGAAAAGGGAAAAGUUAAAAUUGAGUAUCUAACGAAUAAUAGAGCUUGAUAUAUCCUGAUAUACACUAUGAUUGUGAUAUAAUAGUUGUGGAAUAACGGAGGAA .......((((..((....(((((((..((((((((...........((((.....((....))...((..(((.((((........)))))))..))...))))......(((.......))).))))))))..)))))))))..)))).. (-26.10) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 816 50 1 141 92 smit:SMT_1428|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1414622..1414852_NEGATIVE 232 50 2 130 91 smit:SMT_1539|5end_sensor_histidine_kinase,_putative_1524310..1524540_NEGATIVE 224 62 25 114 72 smit:SMT_223|5end_D-fructose-6-phosphate_amidotransferase_156543..156773_POSITIVE 217 48 9 157 122 smit:SMT_683|5end_similar_to_CDP-ribitol_pyrophosphorylase_592572..592802_NEGATIVE 205 49 3 43 4 smit:SMT_1526|5end_K07720_two-component_system,_response_regulator_YesN_1510554..1510784_NEGATIVE 205 47 1 140 96 smit:SMT_1232|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1192935..1193165_POSITIVE 203 129 82 140 80 smit:SMT_1528|5end_K03310_alanine_or_glycine:cation_symporter,_AGCS_family_1512667..1512897_NEGATIVE 199 107 61 219 177 smit:SMT_1696|5end_hypothetical_protein_1678182..1678412_POSITIVE 198 50 1 148 96 smit:SMT_1170|5end_acetyltransferase,_CysE/LacA/LpxA/NodL_family_1118126..1118356_NEGATIVE 198 59 19 166 117 smit:SMT_588|5end_hypothetical_protein_505477..505707_NEGATIVE 197 40 1 139 95 smit:SMT_919|5end_hypothetical_protein_872499..872729_NEGATIVE 196 98 59 198 154 smit:SMT_910|5end_type_I_restriction_enzyme_R_protein_861889..862119_NEGATIVE 196 100 56 102 63 smit:SMT_693|5end_hypothetical_protein_603819..604049_POSITIVE 196 100 55 103 63 smit:SMT_209|5end_acetyltransferase,_GNAT_family_142673..142903_POSITIVE 195 147 116 226 197 smit:SMT_782|5end_GMP_synthase_694519..694749_NEGATIVE 194 84 43 191 152 smit:SMT_1953|5end_hypothetical_protein_1886897..1887127_POSITIVE 194 43 6 75 45 smit:SMT_576|5end_transcriptional_regulator,_LysR_family_495157..495387_POSITIVE 194 100 55 128 71 smit:SMT_536|5end_oxidoreductase,_aldo/keto_reductase_family_454451..454681_POSITIVE 193 118 74 119 82 smit:SMT_157|5end_hypothetical_protein_103525..103755_POSITIVE 192 89 47 77 26 smit:SMT_336|5end_hypothetical_protein_275222..275452_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 282 49 3 134 69 smit:SMT_1170|3end_acetyltransferase,_CysE/LacA/LpxA/NodL_family_1117569..1117719_NEGATIVE 232 50 2 133 94 smit:SMT_1540|3end_hypothetical_protein_1524307..1524457_NEGATIVE 214 105 61 115 69 smit:SMT_340|3end_chaperone_protein_280566..280716_POSITIVE 205 107 61 142 86 smit:SMT_258|3end_alpha-glucosidase,_family_31_of_glycosyl_hydrolase_197342..197492_POSITIVE 198 97 51 45 3 smit:SMT_284|3end_putative_capsular_polysaccharide_biosynthesis_protein,glycosyl_transferase_family_2,_YveT_227459..227609_POSITIVE 197 40 1 50 6 smit:SMT_920|3end_serine/threonine_protein_kinase_872588..872738_NEGATIVE 194 84 43 146 107 smit:SMT_1952|3end_hypothetical_protein_1886932..1887082_POSITIVE 191 50 4 52 5 smit:SMT_1171|3end_hypothetical_protein_1118222..1118372_NEGATIVE 189 64 21 79 28 smit:SMT_859|3end_K02086_DNA_replication_protein_803381..803531_NEGATIVE 188 45 12 73 34 smit:SMT_802|3end_aldo/keto_reductase_family_711486..711636_NEGATIVE 187 97 68 135 106 smit:SMT_736|3end_hypothetical_protein_641500..641650_NEGATIVE 186 79 33 116 68 smit:SMT_737|3end_hypothetical_protein_642270..642420_NEGATIVE 184 43 3 143 111 smit:SMT_627|3end_glucose-1-phosphate_adenylyltransferase_532921..533071_POSITIVE 184 52 13 62 16 smit:SMT_422|3end_K02004_365876..366026_POSITIVE 184 97 53 105 57 smit:SMT_396|3end_putative_nicotinate_phosphoribosyltransferase_326602..326752_POSITIVE 183 103 61 107 65 smit:SMT_1680|3end_hypothetical_protein_1664173..1664323_POSITIVE 183 24 1 136 115 smit:SMT_1231|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1193034..1193184_POSITIVE 183 84 45 47 13 smit:SMT_681|3end_choline_kinase_589952..590102_NEGATIVE 183 41 3 144 99 smit:SMT_379|3end_acetyltransferase,_GNAT_family_316456..316606_POSITIVE 183 41 3 144 99 smit:SMT_370|3end_acetyltransferase,_GNAT_family_305328..305478_POSITIVE