Origin IGS: ttagtctagacttgcttgcaatgaactaggaatctagtaggaatatcaaaataagaaaaaacagccgaagtaatcctttcggctgtttttgatggggaaaa .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 ttttccccatcaaaaacagccgaaaggattacttcggctgttttttcttattttgatattcctactagattcctagttcattgcaagcaagtctagactaa Mask Tandem Repeat Region ================================================ ttagtctagacttgcttgcaatgaactaggaatctagtaggaatatcaaaataagaaaaaacagccgaagtaatcctttcggctgtttttgatggggaaaa Find is-nt database================================================ Query_seq: SMT_201:SMT_202|SMT_201:SMT_202:phosphoglycerate mutase:K02011 iron(III) transport system permease protein:-><-:132162..132262 101 ttagtctagacttgcttgcaatgaactaggaatctagtaggaatatcaaaataagaaaaaacagccgaagtaatcctttcggctgtttttgatggggaaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_201:SMT_202|SMT_201:SMT_202:phosphoglycerate mutase:K02011 iron(III) transport system permease protein:-><-:132162..132262 101 ttagtctagacttgcttgcaatgaactaggaatctagtaggaatatcaaaataagaaaaaacagccgaagtaatcctttcggctgtttttgatggggaaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_201:SMT_202|SMT_201:SMT_202:phosphoglycerate mutase:K02011 iron(III) transport system permease protein:-><-:132162..132262 101 ttagtctagacttgcttgcaatgaactaggaatctagtaggaatatcaaaataagaaaaaacagccgaagtaatcctttcggctgtttttgatggggaaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ttagtctagacttgcttgcaatgaactaggaatctagtaggaatatcaaaataagaaaaaacagccgaagtaatcctttcggctgtttttgatggggaaaa Predict ORF larger than 30AA ================================================ ttagtctagacttgcttgcaatgaactaggaatctagtaggaatatcaaaataagaaaaaacagccgaagtaatcctttcggctgtttttgatggggaaaa 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================================================ ttagtctagacttgcttgcaatgaactaggaatctagtaggaatatcaaaataagaaaaaacagccgaagtaatcctttcggctgtttttgatggggaaaa Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 93 HP_score: -8.9 Tail_Score: -4.72272 Start: 62 End: 85 Full_Region: CAAAATAAGAAAAAA CAGCCGAAG TAATCC TTTCGGCTG TTTTTGATGGGGAAA .............................................................CAGCCGAAGTAATCCTTTCGGCTG................ Find igs database================================================ Query_seq: SMT_201:SMT_202|SMT_201:SMT_202:phosphoglycerate mutase:K02011 iron(III) transport system permease protein:-><-:132162..132262 101 ttagtctagacttgcttgcaatgaactaggaatctagtaggaatatcaaaataagaaaaaacagccgaagtaatcctttcggctgtttttgatggggaaaa Intra-Species Hit: Count: 3 Min: 1 Max: 101 Len: 101 Subject: smit_SMT_1993_SMT_1994|hypothetical protein:phosphoglycerate mutase|NEGATIVE:NEGATIVE|[1919891,1920147]|257 HSP 1 e-value: 6.0E-51 bit: 200.0 Len: 101 Query Start:1 Query End:101 Subject Strand: NEGATIVE Subject Start: 157 Subject End: 257 ttagtctagacttgcttgcaatgaactaggaatctagtaggaatatcaaaataagaaaaaacagccgaagtaatcctttcggctgtttttgatggggaaaa ttagtctagacttgcttgcaatgaactaggaatctagtaggaatatcaaaataagaaaaaacagccgaagtaatcctttcggctgtttttgatggggaaaa Subject: smit_SMT_201_SMT_202|phosphoglycerate mutase:K02011 iron(III) transport system permease protein|POSITIVE:NEGATIVE|[132162,132262]|101 HSP 1 e-value: 6.0E-51 bit: 200.0 Len: 101 Query Start:1 Query End:101 Subject Strand: POSITIVE Subject Start: 1 Subject End: 101 ttagtctagacttgcttgcaatgaactaggaatctagtaggaatatcaaaataagaaaaaacagccgaagtaatcctttcggctgtttttgatggggaaaa ttagtctagacttgcttgcaatgaactaggaatctagtaggaatatcaaaataagaaaaaacagccgaagtaatcctttcggctgtttttgatggggaaaa Subject: smit_SMT_2061_SMT_2062|K02011 iron(III) transport system permease protein:phosphoglycerate mutase|POSITIVE:NEGATIVE|[1970863,1971002]|140 HSP 1 e-value: 9.0E-50 bit: 196.0 Len: 101 Query Start:1 Query End:101 Subject Strand: NEGATIVE Subject Start: 1 Subject End: 101 ttagtctagacttgcttgcaatgaactaggaatctagtaggaatatcaaaataagaaaaaacagccgaagtaatcctttcggctgtttttgatggggaaaa ttaktctagacttgcttgcaatgaactaggaatctagtaggaatatcaaaataagaaaaaacagccgaagtaatcctttcggctgtttttgatggggaaaa Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUAGUCUAGACUUGCUUGCAAUGAACUAGGAAUCUAGUAGGAAUAUCAAAAUAAGAAAAAACAGCCGAAGUAAUCCUUUCGGCUGUUUUUGAUGGGGAAAA ....(((....(((....)))...(((((....))))).)))...((...((....((((((((((((((......)))))))))))))).))...))... (-23.40) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUUCCCCAUCAAAAACAGCCGAAAGGAUUACUUCGGCUGUUUUUUCUUAUUUUGAUAUUCCUACUAGAUUCCUAGUUCAUUGCAAGCAAGUCUAGACUAA ...........(((((((((((((.(.....))))))))))))))...................(((((((.((.((.....)).))..)))))))..... (-24.60) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 255 47 3 100 49 smit:SMT_813|5end_acetyltransferase,_GNAT_family_722322..722552_NEGATIVE 245 44 3 39 4 smit:SMT_384|5end_hypothetical_protein_319406..319636_POSITIVE 239 48 2 217 170 smit:SMT_1276|5end_rod_shape-determining_protein_MreD_1239412..1239642_POSITIVE 238 48 4 122 77 smit:SMT_1989|5end_multimodular_transpeptidase-transglycosylase_1917607..1917837_NEGATIVE 235 88 51 147 112 smit:SMT_882|5end_acetyl_esterase_830441..830671_NEGATIVE 234 96 66 202 169 smit:SMT_1806|5end_aminoacylase/N-acyl-L-amino_acid_amidohydrolase/hippurate_hydrolase_1781229..1781459_POSITIVE 234 96 66 202 169 smit:SMT_1635|5end_putative_N-acetyldiaminopimelate_deacetylase_1621426..1621656_POSITIVE 232 99 61 54 21 smit:SMT_265|5end_DNA-binding_protein_204073..204303_NEGATIVE 226 48 4 76 15 smit:SMT_2046|5end_choline_binding_protein_C_1957519..1957749_NEGATIVE 224 98 61 96 45 smit:SMT_2014|5end_tryptophan_synthase_beta_chain_1932471..1932701_POSITIVE 223 42 4 190 151 smit:SMT_392|5end_acetyltransferase,_GNAT_family_323616..323846_POSITIVE 218 66 22 202 157 smit:SMT_2142|5end_hypothetical_protein_predicted_by_Glimmer/Critica_2019999..2020229_POSITIVE 217 100 57 65 8 smit:SMT_1286|5end_hypothetical_protein_1248388..1248618_POSITIVE 217 53 18 168 133 smit:SMT_163|5end_cardiolipin_synthetase_107309..107539_POSITIVE 215 97 64 44 12 smit:SMT_1903|5end_hypothetical_protein_1852411..1852641_POSITIVE 209 96 63 143 105 smit:SMT_1790|5end_hypothetical_protein_1765644..1765874_POSITIVE 208 53 18 228 193 smit:SMT_1379|5end_thymidylate_kinase_1357438..1357668_NEGATIVE 208 88 53 159 124 smit:SMT_1367|5end_K02237_competence_protein_ComEA_1347522..1347752_NEGATIVE 208 53 18 203 168 smit:SMT_150|5end_K02030_polar_amino_acid_transport_system_substrate-binding_protein_98787..99017_POSITIVE 207 50 1 188 142 smit:SMT_269|5end_phospho-N-acetylmuramoyl-pentapeptide-transferas_e_207725..207955_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 844 100 51 89 40 smit:SMT_2061|3end_K02011_iron(III)_transport_system_permease_protein_1970802..1970952_POSITIVE 315 90 57 34 1 smit:SMT_1994|3end_phosphoglycerate_mutase_1920058..1920208_NEGATIVE 315 90 57 34 1 smit:SMT_201|3end_phosphoglycerate_mutase_132101..132251_POSITIVE 255 47 3 90 39 smit:SMT_814|3end_UDP-N-acetyl_muramate-alanine_ligase_722332..722482_NEGATIVE 250 48 3 58 8 smit:SMT_631|3end_glycerate_kinase_537307..537457_POSITIVE 235 88 51 80 45 smit:SMT_883|3end_metallo-beta-lactamase_superfamily_protein_830508..830658_NEGATIVE 234 96 66 134 101 smit:SMT_1805|3end_2,3,4,5-tetrahydropyridine-2-carboxylate_N-succinyltransferase,_putative_1781241..1781391_POSITIVE 234 96 66 134 101 smit:SMT_1634|3end_2,3,4,5-tetrahydropyridine-2-carboxylate_N-succinyltransferase,_putative_1621438..1621588_POSITIVE 229 38 7 103 75 smit:SMT_1949|3end_IS1381_transposase_protein_B_1883987..1884137_POSITIVE 225 45 5 151 105 smit:SMT_235|3end_hypothetical_protein_174391..174541_POSITIVE 224 98 61 66 15 smit:SMT_2013|3end_alpha-glycerophosphate_oxidase_1932521..1932671_POSITIVE 216 98 63 139 97 smit:SMT_1484|3end_exonuclease_RexA_1464256..1464406_NEGATIVE 210 98 62 140 92 smit:SMT_1340|3end_phosphoenolpyruvate_carboxylase_1315171..1315321_NEGATIVE 208 88 53 92 57 smit:SMT_1368|3end_acetyltransferase,_GNAT_family_1347589..1347739_NEGATIVE 208 53 18 121 86 smit:SMT_149|3end_hypothetical_protein_predicted_by_Glimmer/Critica_98785..98935_POSITIVE 207 95 51 115 67 smit:SMT_1671|3end_hypothetical_protein_1659392..1659542_NEGATIVE 206 81 54 43 16 smit:SMT_1678|3end_inorganic_pyrophosphatase_1662991..1663141_POSITIVE 203 97 63 62 22 smit:SMT_2129|3end_cell_division_protein_FtsZ_2010694..2010844_POSITIVE 203 97 69 147 124 smit:SMT_1149|3end_hypothetical_protein_1094040..1094190_NEGATIVE 203 89 54 84 52 smit:SMT_142|3end_hypothetical_protein_93409..93559_NEGATIVE