Origin IGS: atgggttcactttcattagttggagaaggaaaataagtggaaaacagcagataaataatttttatccgtatcctacaatttgactatacgagtattcaccagttaaaatgtaagtgagtcagggatc .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 gatccctgactcacttacattttaactggtgaatactcgtatagtcaaattgtaggatacggataaaaattatttatctgctgttttccacttattttccttctccaactaatgaaagtgaacccat Mask Tandem Repeat Region ================================================ atgggttcactttcattagttggagaaggaaaataagtggaaaacagcagataaataatttttatccgtatcctacaatttgactatacgagtattcaccagttaaaatgtaagtgagtcagggatc Find is-nt database================================================ Query_seq: SMT_1598:SMT_1599|SMT_1598:SMT_1599:malolactic regulator, LysR family:putative transcriptional regulator:<-<-:1589330..1589456 127 atgggttcactttcattagttggagaaggaaaataagtggaaaacagcagataaataatttttatccgtatcctacaatttgactatacgagtattcaccagttaaaatgtaagtgagtcagggatc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_1598:SMT_1599|SMT_1598:SMT_1599:malolactic regulator, LysR family:putative transcriptional regulator:<-<-:1589330..1589456 127 atgggttcactttcattagttggagaaggaaaataagtggaaaacagcagataaataatttttatccgtatcctacaatttgactatacgagtattcaccagttaaaatgtaagtgagtcagggatc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_1598:SMT_1599|SMT_1598:SMT_1599:malolactic regulator, LysR family:putative transcriptional regulator:<-<-:1589330..1589456 127 atgggttcactttcattagttggagaaggaaaataagtggaaaacagcagataaataatttttatccgtatcctacaatttgactatacgagtattcaccagttaaaatgtaagtgagtcagggatc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 atgggttcactttcattagttggagaaggaaaataagtggaaaacagcagataaataatttttatccgtatcctacaatttgactatacgagtattcaccagttaaaatgtaagtgagtcagggatc Predict ORF larger than 30AA ================================================ atgggttcactttcattagttggagaaggaaaataagtggaaaacagcagataaataatttttatccgtatcctacaatttgactatacgagtattcaccagttaaaatgtaagtgagtcagggatc 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================================================ atgggttcactttcattagttggagaaggaaaataagtggaaaacagcagataaataatttttatccgtatcctacaatttgactatacgagtattcaccagttaaaatgtaagtgagtcagggatc Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 42 HP_score: -2.6 Tail_Score: -2.81966 Start: 48 End: 68 Full_Region: ATAAGTGGAAAACAG CAGATAAA TAATT TTTATCCG TATCCTACAATTTGA ...............................................CAGATAAATAATTTTTATCCG........................................................... TransTerm Strand: - Conf: 51 HP_score: -4.8 Tail_Score: -2.8169 Start: 48 End: 68 Full_Region: tcaaattgtaggata cggataaa aatta tttatctg ctgttttccacttat ...............................................cggataaaaattatttatctg........................................................... TransTerm Strand: - Conf: 46 HP_score: -3.8 Tail_Score: -2.94739 Start: 50 End: 66 Full_Region: aaattgtaggatacg gataaa aatta tttatc tgctgttttccactt .................................................gataaaaattatttatc............................................................. Find igs database================================================ Query_seq: SMT_1598:SMT_1599|SMT_1598:SMT_1599:malolactic regulator, LysR family:putative transcriptional regulator:<-<-:1589330..1589456 127 atgggttcactttcattagttggagaaggaaaataagtggaaaacagcagataaataatttttatccgtatcctacaatttgactatacgagtattcaccagttaaaatgtaagtgagtcagggatc Intra-Species Hit: Count: 1 Min: 1 Max: 127 Len: 127 Subject: smit_SMT_1598_SMT_1599|malolactic regulator, LysR family:putative transcriptional regulator|NEGATIVE:NEGATIVE|[1589330,1589456]|127 HSP 1 e-value: 2.0E-66 bit: 252.0 Len: 127 Query Start:1 Query End:127 Subject Strand: POSITIVE Subject Start: 1 Subject End: 127 atgggttcactttcattagttggagaaggaaaataagtggaaaacagcagataaataatttttatccgtatcctacaatttgactatacgagtattcaccagttaaaatgtaagtgagtcagggatc atgggttcactttcattagttggagaaggaaaataagtggaaaacagcagataaataatttttatccgtatcctacaatttgactatacgagtattcaccagttaaaatgtaagtgagtcagggatc Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUGGGUUCACUUUCAUUAGUUGGAGAAGGAAAAUAAGUGGAAAACAGCAGAUAAAUAAUUUUUAUCCGUAUCCUACAAUUUGACUAUACGAGUAUUCACCAGUUAAAAUGUAAGUGAGUCAGGGAUC ...(..((((((.(((((..(((...((((......((.....)).((.((((((.....)))))).)).))))...(((((......))))).....)))..))..))).))))))..)....... (-24.80) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAUCCCUGACUCACUUACAUUUUAACUGGUGAAUACUCGUAUAGUCAAAUUGUAGGAUACGGAUAAAAAUUAUUUAUCUGCUGUUUUCCACUUAUUUUCCUUCUCCAACUAAUGAAAGUGAACCCAU ..........((((((.((((.....(((.(((...((.((((((...)))))).))..((((((((.....))))))))....................))).)))...)))).))))))...... (-22.50) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 843 50 1 141 92 smit:SMT_1598|5end_malolactic_regulator,_LysR_family_1589239..1589469_NEGATIVE 319 50 1 168 120 smit:SMT_1761|5end_transcriptional_activator,_putative_1736458..1736688_POSITIVE 242 29 3 68 43 smit:SMT_1581|5end_transcriptional_regulator,_biotin_repressor_family_1573635..1573865_NEGATIVE 223 44 6 171 130 smit:SMT_1290|5end_autolysin_1252564..1252794_POSITIVE 218 30 6 187 155 smit:SMT_2082|5end_ATP-dependent_nuclease_subunit_B_1982286..1982516_NEGATIVE 216 49 1 122 74 smit:SMT_2019|5end_dTDP-glucose_4,6-dehydratase_1937054..1937284_POSITIVE 216 52 11 161 119 smit:SMT_899|5end_5,10-methylenetetrahydrofolate_reductase_848263..848493_NEGATIVE 213 106 61 96 50 smit:SMT_1975|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1906138..1906368_POSITIVE 213 119 82 82 45 smit:SMT_959|5end_1-acyl-sn-glycerol-3-phosphate_acyltransferase_905283..905513_POSITIVE 213 119 82 82 45 smit:SMT_955|5end_acyltransferase_family_protein_904096..904326_POSITIVE 211 47 7 162 127 smit:SMT_1302|5end_hypothetical_protein_1263883..1264113_POSITIVE 210 104 61 199 155 smit:SMT_1395|5end_K07025_putative_hydrolase_of_the_HAD_superfamily_1371310..1371540_POSITIVE 206 120 71 186 145 smit:SMT_2077|5end_chloride_channel_protein_1979429..1979659_NEGATIVE 204 101 61 194 152 smit:SMT_1566|5end_K03475_PTS_system,_unknown_pentitol_phosphotransferase_enzyme_IIC_component_1557918..1558148_POSITIVE 203 85 61 135 111 smit:SMT_628|5end_glucose-1-phosphate_adenylyltransferase,_GlgD_subunit_532831..533061_POSITIVE 201 48 2 228 187 smit:SMT_391|5end_PTS_system,_galactose-specific_IIC_component_322647..322877_POSITIVE 195 38 1 69 39 smit:SMT_2066|5end_K02074_zinc/manganese_transport_system_ATP-binding_protein_1973105..1973335_POSITIVE 195 38 1 69 39 smit:SMT_1321|5end_K02074_zinc/manganese_transport_system_ATP-binding_protein_1290674..1290904_POSITIVE 195 69 21 114 57 smit:SMT_624|5end_K07584_hypothetical_protein_529870..530100_POSITIVE 194 97 66 230 203 smit:SMT_1358|5end_dihydroorotate_dehydrogenase_B_1337192..1337422_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 223 44 6 81 40 smit:SMT_1289|3end_hypothetical_protein_1252554..1252704_POSITIVE 218 102 66 135 102 smit:SMT_1902|3end_proton-translocating_NADH-quinone_oxidoreductase,_chain_L_1852028..1852178_NEGATIVE 216 52 11 57 15 smit:SMT_900|3end_5-methyltetrahydropteroyltriglutamate--_homocysteine_methyltransferase_848367..848517_NEGATIVE 203 49 1 49 3 smit:SMT_1865|3end_D-alanyl_carrier_protein_1827377..1827527_POSITIVE 203 49 1 49 3 smit:SMT_1312|3end_D-alanyl_carrier_protein_1277361..1277511_POSITIVE 203 81 45 82 47 smit:SMT_1010|3end_hypothetical_protein_948761..948911_POSITIVE 203 85 61 145 121 smit:SMT_627|3end_glucose-1-phosphate_adenylyltransferase_532921..533071_POSITIVE 199 47 8 35 2 smit:SMT_1301|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1263836..1263986_POSITIVE 195 38 1 69 39 smit:SMT_2065|3end_transcriptional_regulator,_MarR_family_1973185..1973335_POSITIVE 195 38 1 69 39 smit:SMT_1320|3end_transcriptional_regulator,_MarR_family_1290754..1290904_POSITIVE 194 102 65 62 18 smit:SMT_239|3end_hypothetical_protein_177788..177938_POSITIVE 191 49 3 68 13 smit:SMT_1540|3end_hypothetical_protein_1524307..1524457_NEGATIVE 191 98 65 34 3 smit:SMT_188|3end_LSU_ribosomal_protein_L30P_123767..123917_POSITIVE 190 24 3 141 121 smit:SMT_805|3end_hypothetical_protein_predicted_by_Glimmer/Critica_715692..715842_NEGATIVE 189 102 64 125 97 smit:SMT_802|3end_aldo/keto_reductase_family_711486..711636_NEGATIVE 184 49 9 70 33 smit:SMT_1360|3end_lactoylglutathione_lyase_1338252..1338402_NEGATIVE 184 120 71 121 76 smit:SMT_515|3end_hypothetical_protein_442526..442676_POSITIVE 183 30 1 116 93 smit:SMT_1479|3end_K02074_zinc/manganese_transport_system_ATP-binding_protein_1461253..1461403_NEGATIVE 179 110 68 52 4 smit:SMT_1315|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1280952..1281102_POSITIVE 179 42 1 46 3 smit:SMT_1046|3end_chaperonin_GroEL_987638..987788_NEGATIVE