Origin IGS: ctgtctctcctttgaaaaaaacagtgctataccacaatagtataacactattttaatctctttacgaacattctaaacgatatctggatttttcatatcctagatagaaagtctgtagctaga .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tctagctacagactttctatctaggatatgaaaaatccagatatcgtttagaatgttcgtaaagagattaaaatagtgttatactattgtggtatagcactgtttttttcaaaggagagacag Mask Tandem Repeat Region ================================================ ctgtctctcctttgaaaaaaacagtgctataccacaatagtataacactattttaatctctttacgaacattctaaacgatatctggatttttcatatcctagatagaaagtctgtagctaga Find is-nt database================================================ Query_seq: SMT_1663:SMT_1664|SMT_1663:SMT_1664:DNA-binding response regulator:hypothetical protein:<-<-:1653143..1653265 123 ctgtctctcctttgaaaaaaacagtgctataccacaatagtataacactattttaatctctttacgaacattctaaacgatatctggatttttcatatcctagatagaaagtctgtagctaga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_1663:SMT_1664|SMT_1663:SMT_1664:DNA-binding response regulator:hypothetical protein:<-<-:1653143..1653265 123 ctgtctctcctttgaaaaaaacagtgctataccacaatagtataacactattttaatctctttacgaacattctaaacgatatctggatttttcatatcctagatagaaagtctgtagctaga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_1663:SMT_1664|SMT_1663:SMT_1664:DNA-binding response regulator:hypothetical protein:<-<-:1653143..1653265 123 ctgtctctcctttgaaaaaaacagtgctataccacaatagtataacactattttaatctctttacgaacattctaaacgatatctggatttttcatatcctagatagaaagtctgtagctaga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ctgtctctcctttgaaaaaaacagtgctataccacaatagtataacactattttaatctctttacgaacattctaaacgatatctggatttttcatatcctagatagaaagtctgtagctaga Predict ORF larger than 30AA ================================================ ctgtctctcctttgaaaaaaacagtgctataccacaatagtataacactattttaatctctttacgaacattctaaacgatatctggatttttcatatcctagatagaaagtctgtagctaga 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================================================ ctgtctctcctttgaaaaaaacagtgctataccacaatagtataacactattttaatctctttacgaacattctaaacgatatctggatttttcatatcctagatagaaagtctgtagctaga Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 95 HP_score: -8.3 Tail_Score: -5.40072 Start: 22 End: 50 Full_Region: gtaaagagattaaaa tagtgttatacta ttg tggtatagcactg tttttttcaaaggag .....................tagtgttatactattgtggtatagcactg......................................................................... TransTerm Strand: - Conf: 84 HP_score: -8.7 Tail_Score: -4.34482 Start: 24 End: 48 Full_Region: aaagagattaaaata gtgttatacta ttg tggtatagcac tgtttttttcaaagg .......................gtgttatactattgtggtatagcac........................................................................... Find igs database================================================ Query_seq: SMT_1663:SMT_1664|SMT_1663:SMT_1664:DNA-binding response regulator:hypothetical protein:<-<-:1653143..1653265 123 ctgtctctcctttgaaaaaaacagtgctataccacaatagtataacactattttaatctctttacgaacattctaaacgatatctggatttttcatatcctagatagaaagtctgtagctaga Intra-Species Hit: Count: 1 Min: 22 Max: 123 Len: 102 Subject: smit_SMT_1663_SMT_1664|DNA-binding response regulator:hypothetical protein|NEGATIVE:NEGATIVE|[1653143,1653265]|123 HSP 1 e-value: 2.0E-51 bit: 202.0 Len: 102 Query Start:22 Query End:123 Subject Strand: POSITIVE Subject Start: 22 Subject End: 123 .....................cagtgctataccacaatagtataacactattttaatctctttacgaacattctaaacgatatctggatttttcatatcctagatagaaagtctgtagctaga .....................cagtgctataccacaatagtataacactattttaatctctttacgaacattctaaacgatatctggatttttcatatcctagatagaaagtctgtagctaga Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CAGUGCUAUACCACAAUAGUAUAACACUAUUUUAAUCUCUUUACGAACAUUCUAAACGAUAUCUGGAUUUUUCAUAUCCUAGAUAGAAAGUCUGUAGCUAGA .((((.(((((.......))))).)))).......(((..(((((.((.(((((.......(((((((.......)))).)))))))).)).)))))..))) (-19.41) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCUAGCUACAGACUUUCUAUCUAGGAUAUGAAAAAUCCAGAUAUCGUUUAGAAUGUUCGUAAAGAGAUUAAAAUAGUGUUAUACUAUUGUGGUAUAGCACUG (((...(((..((.((((((((.((((.......))))))).......))))).))..)))...)))......((((((((((((.....)))))))))))) (-25.81) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 803 100 51 212 163 smit:SMT_1663|5end_DNA-binding_response_regulator_1653052..1653282_NEGATIVE 234 100 58 188 139 smit:SMT_1652|5end_Cof_family_protein_1640534..1640764_POSITIVE 232 50 2 102 51 smit:SMT_1562|5end_hypothetical_protein_1554992..1555222_NEGATIVE 223 98 57 183 134 smit:SMT_1133|5end_cytidine/deoxycytidylate_deaminase_family_protein,_putative_1074990..1075220_NEGATIVE 220 84 44 149 112 smit:SMT_1789|5end_hypothetical_protein_1765318..1765548_POSITIVE 218 100 60 153 102 smit:SMT_945|5end_cytidylate_kinase_895908..896138_NEGATIVE 212 100 56 187 144 smit:SMT_1296|5end_K03696_ATP-dependent_Clp_protease_ATP-binding_subunit_ClpC_1257290..1257520_POSITIVE 211 87 41 53 10 smit:SMT_1750|5end_anthranilate_phosphoribosyltransferase_1728011..1728241_POSITIVE 211 96 62 57 24 smit:SMT_516|5end_hypothetical_protein_442847..443077_NEGATIVE 211 90 45 111 52 smit:SMT_457|5end_hypothetical_protein_396166..396396_POSITIVE 211 69 35 131 96 smit:SMT_205|5end_K02012_iron(III)_transport_system_substrate-binding_protein_137174..137404_NEGATIVE 210 98 52 223 180 smit:SMT_1159|5end_hypothetical_protein_1104544..1104774_NEGATIVE 208 97 56 57 12 smit:SMT_393|5end_hypothetical_protein_predicted_by_Glimmer/Critica_323973..324203_POSITIVE 207 93 62 112 81 smit:SMT_885|5end_single-stranded-DNA-specific_exonuclease_RecJ_832660..832890_NEGATIVE 203 79 44 209 175 smit:SMT_671|5end_hypothetical_protein_580249..580479_POSITIVE 203 100 56 132 77 smit:SMT_434|5end_orotidine_5'-phosphate_decarboxylase_376107..376337_POSITIVE 200 99 63 115 76 smit:SMT_1792|5end_K03307_solute:Na+_symporter,_SSS_family_1767774..1768004_NEGATIVE 200 99 63 115 76 smit:SMT_1175|5end_K03307_solute:Na+_symporter,_SSS_family_1127660..1127890_NEGATIVE 199 99 51 68 16 smit:SMT_831|5end_transcriptional_activator,_putative_772791..773021_POSITIVE 198 100 57 208 159 smit:SMT_1021|5end_K05846_osmoprotectant_transport_system_permease_protein_957999..958229_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 218 100 60 143 92 smit:SMT_946|3end_hypothetical_protein_895918..896068_NEGATIVE 210 98 52 147 104 smit:SMT_1160|3end_K03152_4-methyl-5(b-hydroxyethyl)-thiazole_monophosphate_biosynthesis_1104620..1104770_NEGATIVE 200 99 63 113 74 smit:SMT_1176|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1127662..1127812_NEGATIVE 196 80 36 77 38 smit:SMT_1995|3end_phosphoglycerate_mutase_1920535..1920685_NEGATIVE 195 80 34 62 18 smit:SMT_2080|3end_glycosyl_transferase_CpsE_1980915..1981065_POSITIVE 195 86 44 103 37 smit:SMT_630|3end_phosphoserine_phosphatase_536183..536333_POSITIVE 195 80 34 62 18 smit:SMT_279|3end_glycosyl_transferase_CpsE_222421..222571_POSITIVE 193 100 51 88 37 smit:SMT_1251|3end_hypothetical_protein_1211329..1211479_NEGATIVE 193 96 66 29 2 smit:SMT_587|3end_ATP_synthase_epsilon_chain_504449..504599_POSITIVE 192 96 58 100 62 smit:SMT_1329|3end_GTP-binding_protein_CgtA_1304478..1304628_NEGATIVE 191 87 43 42 1 smit:SMT_1749|3end_anthranilate_synthase_component_II_1728080..1728230_POSITIVE 188 87 49 103 53 smit:SMT_447|3end_ABC-type_cobalt_transport_system,_permease_component_CbiQ_related_transporter_386987..387137_POSITIVE 187 98 57 142 85 smit:SMT_315|3end_acetyl-coenzyme_A_carboxylase_carboxyl_transferase_subunit_beta_256627..256777_POSITIVE 184 99 63 136 101 smit:SMT_1569|3end_dihydroxy-acid_dehydratase_1563068..1563218_POSITIVE 182 99 74 43 20 smit:SMT_230|3end_hypothetical_protein_predicted_by_Glimmer/Critica_165666..165816_NEGATIVE 182 99 59 91 52 smit:SMT_216|3end_Holliday_junction_DNA_helicase_RuvB_149335..149485_POSITIVE 180 66 28 129 92 smit:SMT_1655|3end_glucose-6-phosphate_1-dehydrogenase_1643534..1643684_NEGATIVE 179 93 56 91 45 smit:SMT_1254|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1220574..1220724_NEGATIVE 178 65 24 73 25 smit:SMT_1669|3end_potassium_uptake_protein_KtrB_1658302..1658452_NEGATIVE 178 88 44 146 95 smit:SMT_1255|3end_cell_division_protein_FtsH_1220987..1221137_NEGATIVE