Origin IGS: atatattctccatttcttttttatgatataattgtaacagttacaaacaaaaaaacaagtagatactttttcgatagctagtatcaaaagtagtactattattgatactaaaagataaattttttttaaaaaatagaaagaggatatttt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aaaatatcctctttctattttttaaaaaaaatttatcttttagtatcaataatagtactacttttgatactagctatcgaaaaagtatctacttgtttttttgtttgtaactgttacaattatatcataaaaaagaaatggagaatatat Mask Tandem Repeat Region ================================================ atatattctccatttcttttttatgatataattgtaacagttacaaacaaaaaaacaagtagatactttttcgatagctagtatcaaaagtagtactattattgatactaaaagataaattttttttaaaaaatagaaagaggatatttt Find is-nt database================================================ Query_seq: SMT_1265:SMT_1266|SMT_1265:SMT_1266:hypothetical protein:predicted transcriptional regulator:<-->:1231352..1231501 150 atatattctccatttcttttttatgatataattgtaacagttacaaacaaaaaaacaagtagatactttttcgatagctagtatcaaaagtagtactattattgatactaaaagataaattttttttaaaaaatagaaagaggatatttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_1265:SMT_1266|SMT_1265:SMT_1266:hypothetical protein:predicted transcriptional regulator:<-->:1231352..1231501 150 atatattctccatttcttttttatgatataattgtaacagttacaaacaaaaaaacaagtagatactttttcgatagctagtatcaaaagtagtactattattgatactaaaagataaattttttttaaaaaatagaaagaggatatttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_1265:SMT_1266|SMT_1265:SMT_1266:hypothetical protein:predicted transcriptional regulator:<-->:1231352..1231501 150 atatattctccatttcttttttatgatataattgtaacagttacaaacaaaaaaacaagtagatactttttcgatagctagtatcaaaagtagtactattattgatactaaaagataaattttttttaaaaaatagaaagaggatatttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 atatattctccatttcttttttatgatataattgtaacagttacaaacaaaaaaacaagtagatactttttcgatagctagtatcaaaagtagtactattattgatactaaaagataaattttttttaaaaaatagaaagaggatatttt Predict ORF larger than 30AA ================================================ Protein_Len: 34 Strand: - Start: 44 End: 145 ........................................... L C F F L Y I S K R Y S T D F T T S N N I S F S L N K K F F L F L M ..... Protein_Len: 49 Strand: - Start: 1 End: 147 Y I R W K K K I I Y N Y C N C V F F C T S V K E I A L I L L L V I I S V L L Y I K K L F Y F S S M ... atatattctccatttcttttttatgatataattgtaacagttacaaacaaaaaaacaagtagatactttttcgatagctagtatcaaaagtagtactattattgatactaaaagataaattttttttaaaaaatagaaagaggatatttt 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================================================ atatattctccatttcttttttatgatataattgtaacagttacaaacaaaaaaacaagtagatactttttcgatagctagtatcaaaagtagtactattattgatactaaaagataaattttttttaaaaaatagaaagaggatatttt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SMT_1265:SMT_1266|SMT_1265:SMT_1266:hypothetical protein:predicted transcriptional regulator:<-->:1231352..1231501 150 atatattctccatttcttttttatgatataattgtaacagttacaaacaaaaaaacaagtagatactttttcgatagctagtatcaaaagtagtactattattgatactaaaagataaattttttttaaaaaatagaaagaggatatttt Intra-Species Hit: Count: 1 Min: 1 Max: 150 Len: 150 Subject: smit_SMT_1265_SMT_1266|hypothetical protein:predicted transcriptional regulator|NEGATIVE:POSITIVE|[1231352,1231501]|150 HSP 1 e-value: 4.0E-53 bit: 208.0 Len: 150 Query Start:1 Query End:150 Subject Strand: POSITIVE Subject Start: 1 Subject End: 150 atatattctccatttcttttttatgatataattgtaacagttacaaacnnnnnnncaagtagatactttttcgatagctagtatcaaaagtagtactattattgatactaaaagataaannnnnnnnaaaaaatagaaagaggatatttt atatattctccatttcttttttatgatataattgtaacagttacaaacaaaaaaacaagtagatactttttcgatagctagtatcaaaagtagtactattattgatactaaaagataaattttttttaaaaaatagaaagaggatatttt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUAUAUUCUCCAUUUCUUUUUUAUGAUAUAAUUGUAACAGUUACAAACAAAAAAACAAGUAGAUACUUUUUCGAUAGCUAGUAUCAAAAGUAGUACUAUUAUUGAUACUAAAAGAUAAAUUUUUUUUAAAAAAUAGAAAGAGGAUAUUUU ..((((((((..(((((.((((.........(((((.....)))))..(((((((.((((....))))..........(((((((((.((((....)))).)))))))))..........)))))))..)))).)))))))))))))... (-24.70) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAAUAUCCUCUUUCUAUUUUUUAAAAAAAAUUUAUCUUUUAGUAUCAAUAAUAGUACUACUUUUGAUACUAGCUAUCGAAAAAGUAUCUACUUGUUUUUUUGUUUGUAACUGUUACAAUUAUAUCAUAAAAAAGAAAUGGAGAAUAUAU ...........((((((((((((................((((((((((....((.....)).))))))))))....((((((((((......)))))))))).(((((.....))))).............))))))))))))...... (-22.60) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 736 110 61 201 152 smit:SMT_1265|5end_hypothetical_protein_1231261..1231491_NEGATIVE 217 87 56 203 173 smit:SMT_1140|5end_glycogen_phosphorylase_1083574..1083804_NEGATIVE 206 98 55 203 165 smit:SMT_862|5end_hypothetical_protein_predicted_by_Glimmer/Critica_808587..808817_POSITIVE 205 85 67 92 74 smit:SMT_1795|5end_DNA_polymerase_III,_delta_subunit_1769847..1770077_NEGATIVE 204 119 72 53 1 smit:SMT_1589|5end_hypothetical_protein_1578332..1578562_POSITIVE 198 94 57 106 59 smit:SMT_1948|5end_IS1381_transposase_protein_A_1883184..1883414_POSITIVE 194 27 1 94 71 smit:SMT_204|5end_K02012_iron(III)_transport_system_substrate-binding_protein_135971..136201_NEGATIVE 193 100 51 71 23 smit:SMT_1498|5end_transcriptional_regulator,_LytR_family_1481958..1482188_POSITIVE 193 101 69 93 55 smit:SMT_1454|5end_cytidine_deaminase_1437886..1438116_NEGATIVE 192 105 69 163 120 smit:SMT_1452|5end_ABC-type_uncharacterized_transport_system,_ATPase_component_1436211..1436441_NEGATIVE 191 99 55 57 16 smit:SMT_941|5end_hypothetical_protein_893558..893788_NEGATIVE 187 95 56 44 1 smit:SMT_144|5end_hypothetical_protein_predicted_by_Glimmer/Critica_95553..95783_POSITIVE 185 38 8 67 41 smit:SMT_1262|5end_ribosomal_protein_L11_methyltransferase_1227152..1227382_POSITIVE 185 110 73 75 37 smit:SMT_578|5end_lipoprotein_signal_peptidase_496061..496291_POSITIVE 184 99 59 229 182 smit:SMT_1100|5end_putative_protein-tyrosine_phosphatase_1042567..1042797_NEGATIVE 182 145 102 105 67 smit:SMT_1905|5end_peptidyl-tRNA_hydrolase_1853769..1853999_NEGATIVE 177 92 57 47 13 smit:SMT_1660|5end_serine_protease_1650634..1650864_NEGATIVE 177 107 69 90 43 smit:SMT_1509|5end_phosphopentomutase_1492781..1493011_NEGATIVE 176 45 3 231 181 smit:SMT_1126|5end_K08987_putative_membrane_protein_1061342..1061572_NEGATIVE 175 120 73 193 134 smit:SMT_1210|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1171051..1171281_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 205 85 67 58 40 smit:SMT_1796|3end_dihydroorotate_dehydrogenase_A_1769881..1770031_NEGATIVE 200 42 11 74 46 smit:SMT_773|3end_UDP-N-acetylenolpyruvoylglucosamine_reductase_683460..683610_NEGATIVE 193 100 51 63 15 smit:SMT_1497|3end_acetyltransferase,_GNAT_family_1482030..1482180_POSITIVE 193 101 69 106 68 smit:SMT_1455|3end_deoxyribose-phosphate_aldolase_1437873..1438023_NEGATIVE 191 98 57 49 10 smit:SMT_1588|3end_UDP-N-acetylglucosamine_1-carboxyvinyltransferase_1578425..1578575_POSITIVE 191 99 55 87 46 smit:SMT_942|3end_hypothetical_protein_893528..893678_NEGATIVE 187 50 8 141 97 smit:SMT_1637|3end_hypothetical_protein_1623848..1623998_POSITIVE 185 110 73 78 40 smit:SMT_577|3end_transcriptional_regulator,_LysR_family_496144..496294_POSITIVE 182 145 102 151 113 smit:SMT_1906|3end_peptidyl-tRNA_hydrolase_1853723..1853873_NEGATIVE 177 107 69 66 19 smit:SMT_1510|3end_ribose_5-phosphate_isomerase_1492805..1492955_NEGATIVE 172 105 63 68 17 smit:SMT_490|3end_branched-chain_amino_acid_ABC_transporter,_permease_protein_425493..425643_POSITIVE 171 42 6 143 101 smit:SMT_1286|3end_hypothetical_protein_1250441..1250591_POSITIVE 170 99 56 110 66 smit:SMT_1158|3end_DNA_gyrase_subunit_B_1102011..1102161_NEGATIVE 167 78 58 45 27 smit:SMT_1532|3end_hypothetical_protein_1515994..1516144_NEGATIVE 167 99 57 81 36 smit:SMT_731|3end_hypothetical_protein_predicted_by_Glimmer/Critica_638387..638537_NEGATIVE 165 89 59 44 3 smit:SMT_1276|3end_rod_shape-determining_protein_MreD_1239986..1240136_POSITIVE 165 110 62 78 35 smit:SMT_1105|3end_K03217_preprotein_translocase_YidC_subunit_1046802..1046952_NEGATIVE 164 99 65 69 41 smit:SMT_1900|3end_K03710_GntR_family_transcriptional_regulator_1850620..1850770_POSITIVE 163 92 57 148 115 smit:SMT_2094|3end_serine_protease_1989243..1989393_NEGATIVE 161 118 73 149 95 smit:SMT_1799|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1773612..1773762_POSITIVE