Origin IGS: aactactattatatcattttctttgaataaaatcagcaaaagaaaggagagactagggaaaagaggggaaatttcctagcttttccaataatctctcacatgttttatatgt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 acatataaaacatgtgagagattattggaaaagctaggaaatttcccctcttttccctagtctctcctttcttttgctgattttattcaaagaaaatgatataatagtagtt Mask Tandem Repeat Region ================================================ aactactattatatcattttctttgaataaaatcagcaaaagaaaggagagactagggaaaagaggggaaatttcctagcttttccaataatctctcacatgttttatatgt Find is-nt database================================================ Query_seq: SMT_1333:SMT_1334|SMT_1333:SMT_1334:glycosyltransferase:hypothetical protein:<-<-:1308726..1308837 112 aactactattatatcattttctttgaataaaatcagcaaaagaaaggagagactagggaaaagaggggaaatttcctagcttttccaataatctctcacatgttttatatgt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_1333:SMT_1334|SMT_1333:SMT_1334:glycosyltransferase:hypothetical protein:<-<-:1308726..1308837 112 aactactattatatcattttctttgaataaaatcagcaaaagaaaggagagactagggaaaagaggggaaatttcctagcttttccaataatctctcacatgttttatatgt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_1333:SMT_1334|SMT_1333:SMT_1334:glycosyltransferase:hypothetical protein:<-<-:1308726..1308837 112 aactactattatatcattttctttgaataaaatcagcaaaagaaaggagagactagggaaaagaggggaaatttcctagcttttccaataatctctcacatgttttatatgt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aactactattatatcattttctttgaataaaatcagcaaaagaaaggagagactagggaaaagaggggaaatttcctagcttttccaataatctctcacatgttttatatgt Predict ORF larger than 30AA ================================================ aactactattatatcattttctttgaataaaatcagcaaaagaaaggagagactagggaaaagaggggaaatttcctagcttttccaataatctctcacatgttttatatgt 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================================================ aactactattatatcattttctttgaataaaatcagcaaaagaaaggagagactagggaaaagaggggaaatttcctagcttttccaataatctctcacatgttttatatgt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SMT_1333:SMT_1334|SMT_1333:SMT_1334:glycosyltransferase:hypothetical protein:<-<-:1308726..1308837 112 aactactattatatcattttctttgaataaaatcagcaaaagaaaggagagactagggaaaagaggggaaatttcctagcttttccaataatctctcacatgttttatatgt Intra-Species Hit: Count: 1 Min: 1 Max: 112 Len: 112 Subject: smit_SMT_1333_SMT_1334|glycosyltransferase:hypothetical protein|NEGATIVE:NEGATIVE|[1308726,1308837]|112 HSP 1 e-value: 2.0E-57 bit: 222.0 Len: 112 Query Start:1 Query End:112 Subject Strand: POSITIVE Subject Start: 1 Subject End: 112 aactactattatatcattttctttgaataaaatcagcaaaagaaaggagagactagggaaaagaggggaaatttcctagcttttccaataatctctcacatgttttatatgt aactactattatatcattttctttgaataaaatcagcaaaagaaaggagagactagggaaaagaggggaaatttcctagcttttccaataatctctcacatgttttatatgt Inter-species Hit: Count: 1 Min: 1 Max: 112 Len: 112 Subject: NC_003028_SP_1074_SP_1075|hypothetical protein:glycosyl transferase CpoA|POSITIVE:POSITIVE|[1011636,1011776]|141 HSP 1 e-value: 6.0E-42 bit: 170.0 Len: 112 Query Start:1 Query End:112 Subject Strand: NEGATIVE Subject Start: 1 Subject End: 114 aactactattatatcattttctttgaataaaatcagcaaaagaaaggagagactag-ggaaaagaggggaaatttcctagcttttccaataatctctcacatg-ttttatatgt aactactattatatcattttctttgaataaaatcagcaaaagaaaggagagactagaggaaaagaggggaaatttcctcgcttttccaacagtctctcacatgcttttatatgt Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AACUACUAUUAUAUCAUUUUCUUUGAAUAAAAUCAGCAAAAGAAAGGAGAGACUAGGGAAAAGAGGGGAAAUUUCCUAGCUUUUCCAAUAAUCUCUCACAUGUUUUAUAUGU .........((((.((((((((((..............))))))).((((((....(((((((..((((....))))..))))))).....))))))..)))...))))... (-27.24) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACAUAUAAAACAUGUGAGAGAUUAUUGGAAAAGCUAGGAAAUUUCCCCUCUUUUCCCUAGUCUCUCCUUUCUUUUGCUGAUUUUAUUCAAAGAAAAUGAUAUAAUAGUAGUU ...((((........(((((((((..(((((((...(((....)))...))))))).))))))))).((((((....(((......)))))))))....))))......... (-24.80) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 895 80 31 171 122 smit:SMT_1333|5end_glycosyltransferase_1308635..1308865_NEGATIVE 326 80 35 152 107 smit:SMT_2055|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1965785..1966015_POSITIVE 292 62 24 171 134 smit:SMT_673|5end_K01926_AT-rich_DNA-binding_protein_580902..581132_POSITIVE 282 100 51 77 30 smit:SMT_1622|5end_K03499_trk_system_potassium_uptake_protein_TrkA_1608243..1608473_POSITIVE 276 78 31 131 74 smit:SMT_423|5end_sensory_transduction_protein_kinase_366012..366242_POSITIVE 266 108 61 230 184 smit:SMT_1063|5end_preprotein_translocase_SecA_subunit_1000714..1000944_POSITIVE 266 95 51 183 135 smit:SMT_1006|5end_6-pyruvoyl_tetrahydrobiopterin_synthase,_putative_946599..946829_POSITIVE 265 81 45 56 17 smit:SMT_606|5end_cytochrome_c-type_biogenesis_protein_CcdA_519390..519620_POSITIVE 264 106 63 185 136 smit:SMT_1338|5end_K05832_putative_ABC_transport_system_permease_protein_1313675..1313905_NEGATIVE 257 94 51 78 38 smit:SMT_1903|5end_hypothetical_protein_1852411..1852641_POSITIVE 256 84 46 220 185 smit:SMT_1222|5end_pneumococcal_surface_protein_A_1187008..1187238_NEGATIVE 256 98 65 207 181 smit:SMT_1176|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1128993..1129223_NEGATIVE 251 93 60 226 193 smit:SMT_1287|5end_50S_ribosomal_protein_L9_1250358..1250588_POSITIVE 245 108 63 91 44 smit:SMT_265|5end_DNA-binding_protein_204073..204303_NEGATIVE 243 99 51 212 145 smit:SMT_395|5end_hypothetical_protein_324459..324689_POSITIVE 242 85 41 144 107 smit:SMT_1307|5end_glycerol_uptake_facilitator_protein_1271664..1271894_POSITIVE 236 88 41 71 30 smit:SMT_2035|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1947167..1947397_POSITIVE 235 83 49 163 130 smit:SMT_298|5end_penicillin-binding_protein_1A_242902..243132_NEGATIVE 233 76 35 217 163 smit:SMT_890|5end_K02029_polar_amino_acid_transport_system_permease_protein_836953..837183_POSITIVE 233 88 50 162 104 smit:SMT_810|5end_oxidoreductase_720015..720245_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 326 80 35 54 9 smit:SMT_2054|3end_dTDP-glucose_4,6-dehydratase_1965767..1965917_POSITIVE 319 99 54 104 46 smit:SMT_1648|3end_hypothetical_protein_1634883..1635033_POSITIVE 292 62 24 88 51 smit:SMT_672|3end_hypothetical_protein_580899..581049_POSITIVE 286 80 31 149 109 smit:SMT_1857|3end_hypothetical_protein_1821145..1821295_POSITIVE 276 80 32 60 9 smit:SMT_1774|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1750151..1750301_NEGATIVE 274 69 30 79 37 smit:SMT_1211|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1171470..1171620_POSITIVE 273 83 41 148 104 smit:SMT_1961|3end_K07485_transposase_1894885..1895035_POSITIVE 266 108 61 84 38 smit:SMT_1062|3end_hypothetical_protein_1000648..1000798_POSITIVE 264 106 63 109 60 smit:SMT_1339|3end_hypothetical_protein_1313751..1313901_NEGATIVE 256 84 46 77 42 smit:SMT_1223|3end_pneumococcal_surface_protein_A_1187151..1187301_NEGATIVE 249 76 45 38 1 smit:SMT_1113|3end_hypothetical_protein_1051811..1051961_NEGATIVE 246 98 54 76 32 smit:SMT_1163|3end_hypothetical_protein_1109096..1109246_NEGATIVE 245 84 46 100 51 smit:SMT_1123|3end_hypothetical_protein_1060229..1060379_POSITIVE 242 85 41 73 36 smit:SMT_1306|3end_alpha-glycerophosphate_oxidase_1271673..1271823_POSITIVE 238 59 14 75 33 smit:SMT_516|3end_hypothetical_protein_442527..442677_NEGATIVE 238 84 45 82 39 smit:SMT_412|3end_hypothetical_protein_predicted_by_Glimmer/Critica_356436..356586_NEGATIVE 236 88 41 81 40 smit:SMT_2034|3end_hydrolase,_haloacid_dehalogenase-like_family_1947257..1947407_POSITIVE 236 63 22 71 29 smit:SMT_1004|3end_thioredoxin_945824..945974_POSITIVE 232 83 46 92 56 smit:SMT_1289|3end_hypothetical_protein_1252554..1252704_POSITIVE 229 67 27 73 35 smit:SMT_446|3end_ABC-type_cobalt_transport_system,_ATPase_component_386335..386485_POSITIVE