Origin IGS: gtgcttctcgtttctctttacttggctttattataccacatttccatgattttattctacctttttgatataatactatggaatacaatcacaaggagagaacg .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 cgttctctccttgtgattgtattccatagtattatatcaaaaaggtagaataaaatcatggaaatgtggtataataaagccaagtaaagagaaacgagaagcac Mask Tandem Repeat Region ================================================ gtgcttctcgtttctctttacttggctttattataccacatttccatgattttattctacctttttgatataatactatggaatacaatcacaaggagagaacg Find is-nt database================================================ Query_seq: SMT_1355:SMT_1356|SMT_1355:SMT_1356:conserved hypothetical protein TIGR00043:fibronectin-binding protein-like protein A:<-->:1332570..1332673 104 gtgcttctcgtttctctttacttggctttattataccacatttccatgattttattctacctttttgatataatactatggaatacaatcacaaggagagaacg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_1355:SMT_1356|SMT_1355:SMT_1356:conserved hypothetical protein TIGR00043:fibronectin-binding protein-like protein A:<-->:1332570..1332673 104 gtgcttctcgtttctctttacttggctttattataccacatttccatgattttattctacctttttgatataatactatggaatacaatcacaaggagagaacg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_1355:SMT_1356|SMT_1355:SMT_1356:conserved hypothetical protein TIGR00043:fibronectin-binding protein-like protein A:<-->:1332570..1332673 104 gtgcttctcgtttctctttacttggctttattataccacatttccatgattttattctacctttttgatataatactatggaatacaatcacaaggagagaacg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gtgcttctcgtttctctttacttggctttattataccacatttccatgattttattctacctttttgatataatactatggaatacaatcacaaggagagaacg Predict ORF larger than 30AA ================================================ Protein_Len: 34 Strand: + Start: 1 End: 102 M L L V S L Y L A L L Y H I S M I L F Y L F D I I L W N T I T R R E .. gtgcttctcgtttctctttacttggctttattataccacatttccatgattttattctacctttttgatataatactatggaatacaatcacaaggagagaacg 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: 82 Start: 45 End: 74 ............................................CATGATTTTATTCTACCTTTTTGATATAAT.............................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ gtgcttctcgtttctctttacttggctttattataccacatttccatgattttattctacctttttgatataatactatggaatacaatcacaaggagagaacg Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SMT_1355:SMT_1356|SMT_1355:SMT_1356:conserved hypothetical protein TIGR00043:fibronectin-binding protein-like protein A:<-->:1332570..1332673 104 gtgcttctcgtttctctttacttggctttattataccacatttccatgattttattctacctttttgatataatactatggaatacaatcacaaggagagaacg Intra-Species Hit: Count: 1 Min: 1 Max: 104 Len: 104 Subject: smit_SMT_1355_SMT_1356|conserved hypothetical protein TIGR00043:fibronectin-binding protein-like protein A|NEGATIVE:POSITIVE|[1332570,1332673]|104 HSP 1 e-value: 1.0E-52 bit: 206.0 Len: 104 Query Start:1 Query End:104 Subject Strand: POSITIVE Subject Start: 1 Subject End: 104 gtgcttctcgtttctctttacttggctttattataccacatttccatgattttattctacctttttgatataatactatggaatacaatcacaaggagagaacg gtgcttctcgtttctctttacttggctttattataccacatttccatgattttattctacctttttgatataatactatggaatacaatcacaaggagagaacg Inter-species Hit: Count: 2 Min: 1 Max: 104 Len: 104 Subject: NC_008533_SPD_0854_SPD_0855|adherence and virulence protein A:conserved hypothetical protein TIGR00043|NEGATIVE:POSITIVE|[870383,870486]|104 HSP 1 e-value: 1.0E-52 bit: 206.0 Len: 104 Query Start:1 Query End:104 Subject Strand: NEGATIVE Subject Start: 1 Subject End: 104 gtgcttctcgtttctctttacttggctttattataccacatttccatgattttattctacctttttgatataatactatggaatacaatcacaaggagagaacg gtgcttctcgtttctctttacttggctttattataccacatttccatgattttattctacctttttgatataatactatggaatacaatcacaaggagagaacg Subject: NC_003028_SP_0966_SP_0967|adherence and virulence protein A:hypothetical protein|NEGATIVE:POSITIVE|[914745,914848]|104 HSP 1 e-value: 1.0E-52 bit: 206.0 Len: 104 Query Start:1 Query End:104 Subject Strand: NEGATIVE Subject Start: 1 Subject End: 104 gtgcttctcgtttctctttacttggctttattataccacatttccatgattttattctacctttttgatataatactatggaatacaatcacaaggagagaacg gtgcttctcgtttctctttacttggctttattataccacatttccatgattttattctacctttttgatataatactatggaatacaatcacaaggagagaacg Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GUGCUUCUCGUUUCUCUUUACUUGGCUUUAUUAUACCACAUUUCCAUGAUUUUAUUCUACCUUUUUGAUAUAAUACUAUGGAAUACAAUCACAAGGAGAGAACG ........(((((((((((...(((..........)))...(((((((...((((((.........)).))))...))))))).........)))))))).))) (-16.20) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CGUUCUCUCCUUGUGAUUGUAUUCCAUAGUAUUAUAUCAAAAAGGUAGAAUAAAAUCAUGGAAAUGUGGUAUAAUAAAGCCAAGUAAAGAGAAACGAGAAGCAC ((((((((.(((((.((((((((((((..((((.((((.....)))).)))).....)))))......)))))))...).))))...)))).))))........ (-18.60) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 829 50 1 141 92 smit:SMT_1355|5end_conserved_hypothetical_protein_TIGR00043_1332479..1332709_NEGATIVE 289 44 4 138 92 smit:SMT_953|5end_hypothetical_protein_901576..901806_NEGATIVE 256 50 1 94 47 smit:SMT_1723|5end_hypothetical_protein_1709081..1709311_POSITIVE 254 56 16 100 62 smit:SMT_1855|5end_K03650_tRNA_modification_GTPase_1819711..1819941_POSITIVE 234 36 1 77 38 smit:SMT_1854|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1818375..1818605_POSITIVE 229 47 3 208 156 smit:SMT_267|5end_putative_cell_division_protein_205150..205380_POSITIVE 220 49 4 150 96 smit:SMT_1612|5end_K06024_segregation_and_condensation_protein_B_1600052..1600282_POSITIVE 219 39 5 72 33 smit:SMT_1447|5end_hypothetical_protein_1430476..1430706_NEGATIVE 219 47 4 144 95 smit:SMT_599|5end_glucosamine-1-phosphate_N-acetyltransferase_/_UDP-N-acetylglucosamine_pyrophosphorylase_514918..515148_POSITIVE 217 45 2 137 80 smit:SMT_1693|5end_dimethyladenosine_transferase_1675800..1676030_POSITIVE 216 46 4 183 137 smit:SMT_1984|5end_phosphinothricin_N-acetyltransferase_1914028..1914258_NEGATIVE 216 46 4 183 137 smit:SMT_1869|5end_phosphinothricin_N-acetyltransferase_1829215..1829445_NEGATIVE 216 40 6 136 104 smit:SMT_1093|5end_K03073_preprotein_translocase_SecE_subunit_1033926..1034156_NEGATIVE 213 56 11 189 135 smit:SMT_1459|5end_K02037_phosphate_transport_system_permease_protein_1440522..1440752_POSITIVE 212 49 3 105 37 smit:SMT_2023|5end_tryptophan_synthase,_alpha_subunit_1939315..1939545_POSITIVE 212 50 2 145 97 smit:SMT_1796|5end_dihydroorotate_dehydrogenase_A_1770816..1771046_NEGATIVE 211 28 1 115 78 smit:SMT_1568|5end_putative_transketolase_C-terminal_section_1560122..1560352_POSITIVE 211 70 22 111 63 smit:SMT_663|5end_phosphate_acetyltransferase_574990..575220_NEGATIVE 209 40 6 125 86 smit:SMT_1702|5end_penicillin-binding_protein_2B_1684592..1684822_POSITIVE 208 50 2 214 159 smit:SMT_301|5end_hypothetical_protein_244086..244316_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 235 44 14 37 9 smit:SMT_954|3end_cation-transporting_ATPase,_E1-E2_family_901677..901827_NEGATIVE 220 49 4 131 77 smit:SMT_1611|3end_K05896_segregation_and_condensation_protein_A_1600113..1600263_POSITIVE 217 45 2 72 15 smit:SMT_1692|3end_hypothetical_protein_1675815..1675965_POSITIVE 211 28 1 118 81 smit:SMT_1567|3end_transketolase,_N-terminal_subunit_1560205..1560355_POSITIVE 211 70 22 67 19 smit:SMT_664|3end_ribosomal_large_subunit_pseudouridine_synthase,_RluD_subfamily_575034..575184_NEGATIVE 208 41 1 143 112 smit:SMT_214|3end_leucyl-tRNA_synthetase_147066..147216_POSITIVE 206 38 1 143 102 smit:SMT_1704|3end_D-alanine-D-alanine_ligase_1688554..1688704_POSITIVE 206 66 21 140 105 smit:SMT_812|3end_acetyltransferase,_GNAT_family_721664..721814_NEGATIVE 204 49 5 131 90 smit:SMT_771|3end_spermidine/putrescine_transport_system_permease_protein_PotB_681356..681506_NEGATIVE 203 49 6 130 86 smit:SMT_1275|3end_rod_shape-determining_protein_MreC_1239492..1239642_POSITIVE 197 23 5 106 88 smit:SMT_1206|3end_similar_to_sensor_histidine_kinase_(AgrC_from_Staphylococcus)_1165697..1165847_NEGATIVE 196 48 1 63 14 smit:SMT_1560|3end_DNA_polymerase_III_alpha_subunit_1545511..1545661_NEGATIVE 195 49 2 80 15 smit:SMT_1869|3end_phosphinothricin_N-acetyltransferase_1828796..1828946_NEGATIVE 194 68 35 142 103 smit:SMT_1154|3end_tryptophanyl-tRNA_synthetase_1098154..1098304_NEGATIVE 194 38 7 98 64 smit:SMT_1150|3end_hypothetical_protein_1094288..1094438_NEGATIVE 194 45 3 120 94 smit:SMT_963|3end_K02015_iron_complex_transport_system_permease_protein_908586..908736_NEGATIVE 194 40 8 55 19 smit:SMT_607|3end_K03294_basic_amino_acid/polyamine_antiporter,_APA_family_520816..520966_POSITIVE 192 50 8 126 82 smit:SMT_189|3end_50S_ribosomal_protein_L15_124352..124502_POSITIVE 191 69 23 109 71 smit:SMT_1803|3end_K03693_penicillin_binding_protein_1779346..1779496_POSITIVE 187 60 19 120 74 smit:SMT_1993|3end_hypothetical_protein_1919207..1919357_NEGATIVE