Origin IGS: acaatacctccaaatctatagtaactattgtaccacttattttcatcaactcattttcttcttttcaagagctagttatagtttcaaactatagacttatcgagtaaagctaaaaagaatccagaaaagcttccagattcttttgtgaaaatgattgctagagt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 actctagcaatcattttcacaaaagaatctggaagcttttctggattctttttagctttactcgataagtctatagtttgaaactataactagctcttgaaaagaagaaaatgagttgatgaaaataagtggtacaatagttactatagatttggaggtattgt Mask Tandem Repeat Region ================================================ acaatacctccaaatctatagtaactattgtaccacttattttcatcaactcattttcttcttttcaagagctagttatagtttcaaactatagacttatcgagtaaagctaaaaagaatccagaaaagcttccagattcttttgtgaaaatgattgctagagt Find is-nt database================================================ Query_seq: SMT_818:SMT_819|SMT_818:SMT_819:cystathionine gamma-synthase:hypothetical protein predicted by Glimmer/Critica:<-<-:729892..730055 164 acaatacctccaaatctatagtaactattgtaccacttattttcatcaactcattttcttcttttcaagagctagttatagtttcaaactatagacttatcgagtaaagctaaaaagaatccagaaaagcttccagattcttttgtgaaaatgattgctagagt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_818:SMT_819|SMT_818:SMT_819:cystathionine gamma-synthase:hypothetical protein predicted by Glimmer/Critica:<-<-:729892..730055 164 acaatacctccaaatctatagtaactattgtaccacttattttcatcaactcattttcttcttttcaagagctagttatagtttcaaactatagacttatcgagtaaagctaaaaagaatccagaaaagcttccagattcttttgtgaaaatgattgctagagt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_818:SMT_819|SMT_818:SMT_819:cystathionine gamma-synthase:hypothetical protein predicted by Glimmer/Critica:<-<-:729892..730055 164 acaatacctccaaatctatagtaactattgtaccacttattttcatcaactcattttcttcttttcaagagctagttatagtttcaaactatagacttatcgagtaaagctaaaaagaatccagaaaagcttccagattcttttgtgaaaatgattgctagagt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 acaatacctccaaatctatagtaactattgtaccacttattttcatcaactcattttcttcttttcaagagctagttatagtttcaaactatagacttatcgagtaaagctaaaaagaatccagaaaagcttccagattcttttgtgaaaatgattgctagagt Predict ORF larger than 30AA ================================================ acaatacctccaaatctatagtaactattgtaccacttattttcatcaactcattttcttcttttcaagagctagttatagtttcaaactatagacttatcgagtaaagctaaaaagaatccagaaaagcttccagattcttttgtgaaaatgattgctagagt 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================================================ acaatacctccaaatctatagtaactattgtaccacttattttcatcaactcattttcttcttttcaagagctagttatagtttcaaactatagacttatcgagtaaagctaaaaagaatccagaaaagcttccagattcttttgtgaaaatgattgctagagt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SMT_818:SMT_819|SMT_818:SMT_819:cystathionine gamma-synthase:hypothetical protein predicted by Glimmer/Critica:<-<-:729892..730055 164 acaatacctccaaatctatagtaactattgtaccacttattttcatcaactcattttcttcttttcaagagctagttatagtttcaaactatagacttatcgagtaaagctaaaaagaatccagaaaagcttccagattcttttgtgaaaatgattgctagagt Intra-Species Hit: Count: 1 Min: 1 Max: 164 Len: 164 Subject: smit_SMT_818_SMT_819|cystathionine gamma-synthase:hypothetical protein predicted by Glimmer/Critica|NEGATIVE:NEGATIVE|[729892,730055]|164 HSP 1 e-value: 3.0E-88 bit: 325.0 Len: 164 Query Start:1 Query End:164 Subject Strand: POSITIVE Subject Start: 1 Subject End: 164 acaatacctccaaatctatagtaactattgtaccacttattttcatcaactcattttcttcttttcaagagctagttatagtttcaaactatagacttatcgagtaaagctaaaaagaatccagaaaagcttccagattcttttgtgaaaatgattgctagagt acaatacctccaaatctatagtaactattgtaccacttattttcatcaactcattttcttcttttcaagagctagttatagtttcaaactatagacttatcgagtaaagctaaaaagaatccagaaaagcttccagattcttttgtgaaaatgattgctagagt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACAAUACCUCCAAAUCUAUAGUAACUAUUGUACCACUUAUUUUCAUCAACUCAUUUUCUUCUUUUCAAGAGCUAGUUAUAGUUUCAAACUAUAGACUUAUCGAGUAAAGCUAAAAAGAAUCCAGAAAAGCUUCCAGAUUCUUUUGUGAAAAUGAUUGCUAGAGU .......(((......((((((....)))))).((.((((((((((..((((...(((((......)))))..(((((((((.....))))).))))....)))).......(((((((((..(((....)))..))))))))))))))))))).))...))). (-28.30) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACUCUAGCAAUCAUUUUCACAAAAGAAUCUGGAAGCUUUUCUGGAUUCUUUUUAGCUUUACUCGAUAAGUCUAUAGUUUGAAACUAUAACUAGCUCUUGAAAAGAAGAAAAUGAGUUGAUGAAAAUAAGUGGUACAAUAGUUACUAUAGAUUUGGAGGUAUUGU .(((((.(((((((((((..(((((((((..(((....)))..)))))))))...((((.(..((..(((.((((((.....)))))))))...))..).))))..)))))))).)))..........((((((.......)))))).....)))))....... (-37.10) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 809 140 91 231 182 smit:SMT_818|5end_cystathionine_gamma-synthase_729801..730031_NEGATIVE 303 86 42 72 30 smit:SMT_1203|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1164394..1164624_NEGATIVE 295 95 58 129 91 smit:SMT_1514|5end_methylenetetrahydrofolate_dehydrogenase_(NADP+)_/_methenyltetrahydrofolate_cyclohydrolase_1496640..1496870_NEGATIVE 266 82 48 161 126 smit:SMT_141|5end_K03495_glucose_inhibited_division_protein_A_91408..91638_POSITIVE 264 50 7 130 97 smit:SMT_592|5end_amino_acid_ABC_transporter,_ATP-binding_protein_508759..508989_POSITIVE 257 160 116 183 150 smit:SMT_1218|5end_DNA_polymerase_I_1179357..1179587_NEGATIVE 245 160 117 151 107 smit:SMT_359|5end_transcription_termination-antitermination_factor_294470..294700_POSITIVE 243 159 112 142 101 smit:SMT_1571|5end_CAAX_amino_terminal_protease_family_protein_1563780..1564010_POSITIVE 243 90 41 135 86 smit:SMT_346|5end_K01992_ABC-2_type_transport_system_permease_protein_284720..284950_POSITIVE 235 160 115 90 34 smit:SMT_880|5end_beta-lactam_resistance_factor_828300..828530_NEGATIVE 234 96 54 70 31 smit:SMT_1852|5end_1,4-alpha-glucan_branching_enzyme_1817690..1817920_NEGATIVE 227 69 32 106 69 smit:SMT_1790|5end_hypothetical_protein_1765644..1765874_POSITIVE 226 110 61 198 156 smit:SMT_1160|5end_K03152_4-methyl-5(b-hydroxyethyl)-thiazole_monophosphate_biosynthesis_1105174..1105404_NEGATIVE 225 129 81 176 132 smit:SMT_2166|5end_UDP-N-acetylmuramoylalanyl-D-glutamyl-2,6-_diaminopimelate--D-alanyl-D-alanine_ligase_2039569..2039799_POSITIVE 225 68 23 230 187 smit:SMT_999|5end_hypothetical_protein_predicted_by_Glimmer/Critica_941642..941872_NEGATIVE 222 87 41 54 1 smit:SMT_1733|5end_DNA_repair_protein_RecN_1716889..1717119_POSITIVE 222 77 49 115 86 smit:SMT_1612|5end_K06024_segregation_and_condensation_protein_B_1600052..1600282_POSITIVE 222 44 16 36 1 smit:SMT_829|5end_putative_mucus_binding_protein_764939..765169_NEGATIVE 220 76 34 122 82 smit:SMT_1058|5end_primosomal_protein_DnaI_996486..996716_POSITIVE 217 80 33 141 88 smit:SMT_1273|5end_K02006_cobalt_transport_system_ATP-binding_protein_1236909..1237139_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 264 50 7 120 87 smit:SMT_591|3end_K02029_polar_amino_acid_transport_system_permease_protein_508829..508979_POSITIVE 245 160 117 107 63 smit:SMT_358|3end_hypothetical_protein_294506..294656_POSITIVE 243 90 41 138 89 smit:SMT_345|3end_K01990_ABC-2_type_transport_system_ATP-binding_protein_284803..284953_POSITIVE 235 160 115 85 29 smit:SMT_881|3end_peptidoglycan_branched_peptide_synthesis_protein,_alanine_adding_enzyme_828305..828455_NEGATIVE 234 96 54 73 34 smit:SMT_1853|3end_1,4-alpha-glucan_branching_enzyme_1817687..1817837_NEGATIVE 233 144 104 90 50 smit:SMT_695|3end_heat_shock_protein_HtpX_605984..606134_NEGATIVE 230 160 122 85 43 smit:SMT_769|3end_spermidine/putrescine-binding_periplasmic_protein_679519..679669_NEGATIVE 224 76 33 127 77 smit:SMT_901|3end_hypothetical_protein_851141..851291_NEGATIVE 222 77 49 96 67 smit:SMT_1611|3end_K05896_segregation_and_condensation_protein_A_1600113..1600263_POSITIVE 220 76 34 121 81 smit:SMT_1057|3end_replicative_DNA_helicase_996565..996715_POSITIVE 215 67 21 109 55 smit:SMT_748|3end_prephenate_dehydratase_652650..652800_NEGATIVE 215 90 41 116 65 smit:SMT_411|3end_thymidylate_synthase_356415..356565_POSITIVE 214 144 102 68 18 smit:SMT_1814|3end_amino_acid_transporter_1788640..1788790_POSITIVE 212 75 31 59 17 smit:SMT_808|3end_hypothetical_protein_predicted_by_Glimmer/Critica_717897..718047_NEGATIVE 210 100 52 61 12 smit:SMT_1178|3end_choline_binding_protein_A_1135442..1135592_NEGATIVE 210 90 43 76 31 smit:SMT_120|3end_hypothetical_protein_72943..73093_POSITIVE 209 73 33 69 27 smit:SMT_397|3end_NAD(+)_synthetase_327423..327573_POSITIVE 208 112 80 148 109 smit:SMT_688|3end_carbamoyl-phosphate_synthase_small_chain_599576..599726_NEGATIVE 207 100 53 72 27 smit:SMT_1319|3end_muscus_binding_protein_1289974..1290124_POSITIVE 205 78 31 142 95 smit:SMT_857|3end_endo-beta-N-acetylglucosaminidase_800881..801031_NEGATIVE