Origin IGS: ctgttacattcatgagacaagtataccatacagtaaccgatttcaacaagtgataaatccctatttttacactttcttttctaaaacagtctatattttatcccaaactgtattatatttttgaaaaaattaaagccttttttctttttttcagaaaaaagggtataataaaagaaaataagcagtaaaaaggggaccagac .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 gtctggtcccctttttactgcttattttcttttattatacccttttttctgaaaaaaagaaaaaaggctttaattttttcaaaaatataatacagtttgggataaaatatagactgttttagaaaagaaagtgtaaaaatagggatttatcacttgttgaaatcggttactgtatggtatacttgtctcatgaatgtaacag Mask Tandem Repeat Region ================================================ ctgttacattcatgagacaagtataccatacagtaaccgatttcaacaagtgataaatccctatttttacactttcttttctaaaacagtctatattttatcccaaactgtattatatttttgaaaaaattaaagccttttttctttttttcagaaaaaagggtataataaaagaaaataagcagtaaaaaggggaccagac Find is-nt database================================================ Query_seq: SMT_1624:SMT_1625|SMT_1624:SMT_1625:formate acetyltransferase:DNA polymerase IV:<-->:1613863..1614064 202 ctgttacattcatgagacaagtataccatacagtaaccgatttcaacaagtgataaatccctatttttacactttcttttctaaaacagtctatattttatcccaaactgtattatatttttgaaaaaattaaagccttttttctttttttcagaaaaaagggtataataaaagaaaataagcagtaaaaaggggaccagac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_1624:SMT_1625|SMT_1624:SMT_1625:formate acetyltransferase:DNA polymerase IV:<-->:1613863..1614064 202 ctgttacattcatgagacaagtataccatacagtaaccgatttcaacaagtgataaatccctatttttacactttcttttctaaaacagtctatattttatcccaaactgtattatatttttgaaaaaattaaagccttttttctttttttcagaaaaaagggtataataaaagaaaataagcagtaaaaaggggaccagac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_1624:SMT_1625|SMT_1624:SMT_1625:formate acetyltransferase:DNA polymerase IV:<-->:1613863..1614064 202 ctgttacattcatgagacaagtataccatacagtaaccgatttcaacaagtgataaatccctatttttacactttcttttctaaaacagtctatattttatcccaaactgtattatatttttgaaaaaattaaagccttttttctttttttcagaaaaaagggtataataaaagaaaataagcagtaaaaaggggaccagac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ctgttacattcatgagacaagtataccatacagtaaccgatttcaacaagtgataaatccctatttttacactttcttttctaaaacagtctatattttatcccaaactgtattatatttttgaaaaaattaaagccttttttctttttttcagaaaaaagggtataataaaagaaaataagcagtaaaaaggggaccagac Predict ORF larger than 30AA ================================================ Protein_Len: 38 Strand: + Start: 8 End: 121 ....... M H E T S I P Y S N R F Q Q V I N P Y F Y T F F S K T V Y I L S Q T V L Y F ................................................................................. Protein_Len: 43 Strand: + Start: 57 End: 185 ........................................................ M P I F T L S F L K Q S I F Y P K L Y Y I F E K I K A F F L F F R K K G I I K E N K Q ................. Protein_Len: 39 Strand: - Start: 84 End: 200 ................................................................................... F L R Y K I G F Q I I N K F F N F G K K K K E S F L T Y Y F F I L L L F P V M .. Protein_Len: 31 Strand: - Start: 2 End: 94 . T V N M L C T Y W V T V S K L L H Y I G I K V S E K R F C D M ............................................................................................................ ctgttacattcatgagacaagtataccatacagtaaccgatttcaacaagtgataaatccctatttttacactttcttttctaaaacagtctatattttatcccaaactgtattatatttttgaaaaaattaaagccttttttctttttttcagaaaaaagggtataataaaagaaaataagcagtaaaaaggggaccagac 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: 140 End: 169 ...........................................................................................................................................TTTTCTTTTTTTCAGAAAAAAGGGTATAAT................................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ ctgttacattcatgagacaagtataccatacagtaaccgatttcaacaagtgataaatccctatttttacactttcttttctaaaacagtctatattttatcccaaactgtattatatttttgaaaaaattaaagccttttttctttttttcagaaaaaagggtataataaaagaaaataagcagtaaaaaggggaccagac Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 74 HP_score: -4.8 Tail_Score: -5.02476 Start: 130 End: 168 Full_Region: gcttattttctttta ttatacccttttttct gaaaaaa agaaaaaaggctttaa ttttttcaaaaatat .................................................................................................................................ttatacccttttttctgaaaaaaagaaaaaaggctttaa.................................. TransTerm Strand: - Conf: 70 HP_score: -8.2 Tail_Score: -3.24575 Start: 136 End: 162 Full_Region: tttcttttattatac ccttttttct gaaaaaa agaaaaaagg ctttaattttttcaa .......................................................................................................................................ccttttttctgaaaaaaagaaaaaagg........................................ Find igs database================================================ Query_seq: SMT_1624:SMT_1625|SMT_1624:SMT_1625:formate acetyltransferase:DNA polymerase IV:<-->:1613863..1614064 202 ctgttacattcatgagacaagtataccatacagtaaccgatttcaacaagtgataaatccctatttttacactttcttttctaaaacagtctatattttatcccaaactgtattatatttttgaaaaaattaaagccttttttctttttttcagaaaaaagggtataataaaagaaaataagcagtaaaaaggggaccagac Intra-Species Hit: Count: 1 Min: 1 Max: 137 Len: 137 Subject: smit_SMT_1624_SMT_1625|formate acetyltransferase:DNA polymerase IV|NEGATIVE:POSITIVE|[1613863,1614064]|202 HSP 1 e-value: 4.0E-72 bit: 272.0 Len: 137 Query Start:1 Query End:137 Subject Strand: POSITIVE Subject Start: 1 Subject End: 137 ctgttacattcatgagacaagtataccatacagtaaccgatttcaacaagtgataaatccctatttttacactttcttttctaaaacagtctatattttatcccaaactgtattatatttttgaaaaaattaaagcc................................................................. ctgttacattcatgagacaagtataccatacagtaaccgatttcaacaagtgataaatccctatttttacactttcttttctaaaacagtctatattttatcccaaactgtattatatttttgaaaaaattaaagcc................................................................. Inter-species Hit: Count: 3 Min: 1 Max: 135 Len: 135 Subject: NC_008533_SPD_0419_SPD_0420|DNA-damage inducible protein P:formate acetyltransferase|NEGATIVE:POSITIVE|[419249,419642]|394 HSP 1 e-value: 3.0E-54 bit: 212.0 Len: 135 Query Start:1 Query End:135 Subject Strand: NEGATIVE Subject Start: 228 Subject End: 362 ctgttacattcatgagacaagtataccatacagtaaccgatttcaacaagtgataaatccctatttttacactttcttttctaaaacagtctatattttatcccaaactgtattatatttttgaaaaaattaaag................................................................... ctgttacattcataagacaagtataccataaagtaaccgatttcaacaagtgcaaaatccctatttttacactttcttttctaaaacagtctatattttatttcaaactgtattatatttttgaaaaaaataaag................................................................... Subject: NC_003098_spr0414_spr0415|DNA polymerase IV:Pyruvate formate-lyase|NEGATIVE:POSITIVE|[411728,412112]|385 HSP 1 e-value: 3.0E-54 bit: 212.0 Len: 135 Query Start:1 Query End:135 Subject Strand: NEGATIVE Subject Start: 219 Subject End: 353 ctgttacattcatgagacaagtataccatacagtaaccgatttcaacaagtgataaatccctatttttacactttcttttctaaaacagtctatattttatcccaaactgtattatatttttgaaaaaattaaag................................................................... ctgttacattcataagacaagtataccataaagtaaccgatttcaacaagtgcaaaatccctatttttacactttcttttctaaaacagtctatattttatttcaaactgtattatatttttgaaaaaaataaag................................................................... Subject: NC_003028_SP_0458_SP_0459|DNA polymerase IV:formate acetyltransferase|NEGATIVE:POSITIVE|[431934,432307]|374 HSP 1 e-value: 1.0E-53 bit: 210.0 Len: 130 Query Start:1 Query End:130 Subject Strand: NEGATIVE Subject Start: 213 Subject End: 342 ctgttacattcatgagacaagtataccatacagtaaccgatttcaacaagtgataaatccctatttttacactttcttttctaaaacagtctatattttatcccaaactgtattatatttttgaaaaaat........................................................................ ctgttacattcataagacaagtataccatatagtaaccgatttcaacaagtgaaaattccctatttttacactttcttttctaaaacagtctatattttatttcaaactgtattatatttttgaaaaaat........................................................................ Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUGUUACAUUCAUGAGACAAGUAUACCAUACAGUAACCGAUUUCAACAAGUGAUAAAUCCCUAUUUUUACACUUUCUUUUCUAAAACAGUCUAUAUUUUAUCCCAAACUGUAUUAUAUUUUUGAAAAAAUUAAAG ..(((((..((....))...((((...)))).)))))...((((((.(((((.((((........))))))))).......(((.(((((................))))).))).....))))))......... (-13.09) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUUUAAUUUUUUCAAAAAUAUAAUACAGUUUGGGAUAAAAUAUAGACUGUUUUAGAAAAGAAAGUGUAAAAAUAGGGAUUUAUCACUUGUUGAAAUCGGUUACUGUAUGGUAUACUUGUCUCAUGAAUGUAACAG .........((((((.....(((.((((((((..........)))))))).))).......(((((((((........)))).))))).))))))...(((((..((((..((....))..))))...))))).. (-21.90) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 822 50 1 141 92 smit:SMT_1624|5end_formate_acetyltransferase_1613772..1614002_NEGATIVE 246 94 54 123 82 smit:SMT_157|5end_hypothetical_protein_103525..103755_POSITIVE 242 80 33 122 76 smit:SMT_1636|5end_5-formyltetrahydrofolate_cyclo-ligase_family_protein_1622568..1622798_POSITIVE 228 60 12 193 145 smit:SMT_862|5end_hypothetical_protein_predicted_by_Glimmer/Critica_808587..808817_POSITIVE 225 44 2 186 133 smit:SMT_193|5end_50S_ribosomal_protein_L36_126743..126973_POSITIVE 223 46 1 209 161 smit:SMT_1828|5end_PTS_system,_galactose-specific_IIC_component_1797668..1797898_POSITIVE 223 46 1 109 61 smit:SMT_1827|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1797568..1797798_POSITIVE 217 69 26 133 84 smit:SMT_1125|5end_K08987_putative_membrane_protein_1061145..1061375_NEGATIVE 216 104 67 97 49 smit:SMT_825|5end_aspartate_aminotransferase_749594..749824_NEGATIVE 216 118 71 189 139 smit:SMT_355|5end_hypothetical_protein_291622..291852_POSITIVE 216 116 78 55 15 smit:SMT_164|5end_hypothetical_membrane_spanning_protein_109095..109325_POSITIVE 214 80 38 198 159 smit:SMT_2164|5end_K06147_ATP-binding_cassette,_subfamily_B,_bacterial_2037861..2038091_POSITIVE 203 69 26 96 56 smit:SMT_1529|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1512880..1513110_NEGATIVE 201 48 1 206 148 smit:SMT_320|5end_alcohol_dehydrogenase,_zinc-containing_259492..259722_NEGATIVE 201 50 2 185 124 smit:SMT_152|5end_sensor_histidine_kinase,_putative_100759..100989_POSITIVE 201 99 56 143 97 smit:SMT_136|5end_hypothetical_protein_predicted_by_Glimmer/Critica_87314..87544_POSITIVE 200 53 11 97 60 smit:SMT_1464|5end_K02030_polar_amino_acid_transport_system_substrate-binding_protein_1444721..1444951_POSITIVE 200 56 11 169 134 smit:SMT_963|5end_K02015_iron_complex_transport_system_permease_protein_909632..909862_NEGATIVE 200 44 9 231 193 smit:SMT_196|5end_30S_ribosomal_protein_S11_127260..127490_POSITIVE 198 50 7 127 85 smit:SMT_109|5end_beta-galactosidase_53925..54155_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 242 80 33 110 64 smit:SMT_1635|3end_putative_N-acetyldiaminopimelate_deacetylase_1622636..1622786_POSITIVE 223 46 1 83 35 smit:SMT_1826|3end_ATP_synthase_beta_chain_1797622..1797772_POSITIVE 217 69 26 121 72 smit:SMT_1126|3end_K08987_putative_membrane_protein_1061157..1061307_NEGATIVE 216 104 67 100 52 smit:SMT_826|3end_hypothetical_protein_749591..749741_NEGATIVE 214 99 57 131 83 smit:SMT_444|3end_thiamine-phosphate_pyrophosphorylase_384048..384198_POSITIVE 208 108 67 136 91 smit:SMT_998|3end_peptide_chain_release_factor_3_939699..939849_NEGATIVE 190 110 62 131 74 smit:SMT_754|3end_3-dehydroquinate_synthase_657977..658127_NEGATIVE 189 93 53 56 11 smit:SMT_629|3end_glycogen_synthase_535480..535630_POSITIVE 187 107 63 118 68 smit:SMT_1294|3end_K02049_sulfonate/nitrate/taurine_transport_system_ATP-binding_protein_1256791..1256941_POSITIVE 181 48 2 68 28 smit:SMT_1737|3end_peptidyl-prolyl_cis-trans_isomerase_1720598..1720748_POSITIVE 179 52 12 40 10 smit:SMT_1116|3end_K02244_competence_protein_ComGB_1052798..1052948_NEGATIVE 177 88 41 127 71 smit:SMT_354|3end_hypothetical_protein_291671..291821_POSITIVE 175 38 2 82 38 smit:SMT_419|3end_hypothetical_protein_predicted_by_Glimmer/Critica_362510..362660_POSITIVE 173 101 63 75 46 smit:SMT_1773|3end_hypothetical_protein_1749905..1750055_POSITIVE 173 92 61 72 35 smit:SMT_1287|3end_50S_ribosomal_protein_L9_1250890..1251040_POSITIVE 173 87 50 49 12 smit:SMT_292|3end_dTDP-glucose_4,6-dehydratase_235933..236083_POSITIVE 172 94 61 36 1 smit:SMT_156|3end_hypothetical_protein_103518..103668_POSITIVE 171 106 70 66 24 smit:SMT_1460|3end_K02038_phosphate_transport_system_permease_protein_1442393..1442543_POSITIVE 170 38 7 89 41 smit:SMT_425|3end_hypothetical_cytosolic_protein_368424..368574_POSITIVE 169 79 36 144 100 smit:SMT_978|3end_hypothetical_protein_925765..925915_NEGATIVE