Origin IGS: cggtctaaatatatagtttttgattaaattgtcagacaatttcttgaaatatgagaaaaaaactggtataatttacaggaaataatctctatctaggagagaaaacaaaggagtcacc .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 ggtgactcctttgttttctctcctagatagagattatttcctgtaaattataccagtttttttctcatatttcaagaaattgtctgacaatttaatcaaaaactatatatttagaccg Mask Tandem Repeat Region ================================================ cggtctaaatatatagtttttgattaaattgtcagacaatttcttgaaatatgagaaaaaaactggtataatttacaggaaataatctctatctaggagagaaaacaaaggagtcacc Find is-nt database================================================ Query_seq: SSA_1128:SSA_1129|SSA_1128:SSA_1129:Voltage gated chloride channel EriC, putative:Periplasmic iron transport lipoprotein, putative:->->:1154947..1155064 118 cggtctaaatatatagtttttgattaaattgtcagacaatttcttgaaatatgagaaaaaaactggtataatttacaggaaataatctctatctaggagagaaaacaaaggagtcacc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1128:SSA_1129|SSA_1128:SSA_1129:Voltage gated chloride channel EriC, putative:Periplasmic iron transport lipoprotein, putative:->->:1154947..1155064 118 cggtctaaatatatagtttttgattaaattgtcagacaatttcttgaaatatgagaaaaaaactggtataatttacaggaaataatctctatctaggagagaaaacaaaggagtcacc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1128:SSA_1129|SSA_1128:SSA_1129:Voltage gated chloride channel EriC, putative:Periplasmic iron transport lipoprotein, putative:->->:1154947..1155064 118 cggtctaaatatatagtttttgattaaattgtcagacaatttcttgaaatatgagaaaaaaactggtataatttacaggaaataatctctatctaggagagaaaacaaaggagtcacc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 cggtctaaatatatagtttttgattaaattgtcagacaatttcttgaaatatgagaaaaaaactggtataatttacaggaaataatctctatctaggagagaaaacaaaggagtcacc Predict ORF larger than 30AA ================================================ cggtctaaatatatagtttttgattaaattgtcagacaatttcttgaaatatgagaaaaaaactggtataatttacaggaaataatctctatctaggagagaaaacaaaggagtcacc Predict Promoter with matrix: RpoD-15 score > 80================================================ Predict Promoter with matrix: RpoD-16 score > 80================================================ Predict Promoter with matrix: RpoD-17 score > 80================================================ PromScan Matrix: RpoD-17 Strand: + Score: 91 Start: 43 End: 72 ..........................................CTTGAAATATGAGAAAAAAACTGGTATAAT.............................................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ cggtctaaatatatagtttttgattaaattgtcagacaatttcttgaaatatgagaaaaaaactggtataatttacaggaaataatctctatctaggagagaaaacaaaggagtcacc Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_1128:SSA_1129|SSA_1128:SSA_1129:Voltage gated chloride channel EriC, putative:Periplasmic iron transport lipoprotein, putative:->->:1154947..1155064 118 cggtctaaatatatagtttttgattaaattgtcagacaatttcttgaaatatgagaaaaaaactggtataatttacaggaaataatctctatctaggagagaaaacaaaggagtcacc Intra-Species Hit: Count: 1 Min: 1 Max: 118 Len: 118 Subject: NC_009009_SSA_1128_SSA_1129|Voltage gated chloride channel EriC, putative:Periplasmic iron transport lipoprotein, putative|POSITIVE:POSITIVE|[1154947,1155064]|118 HSP 1 e-value: 2.0E-48 bit: 192.0 Len: 118 Query Start:1 Query End:118 Subject Strand: POSITIVE Subject Start: 1 Subject End: 118 cggtctaaatatatagtttttgattaaattgtcagacaatttcttgaaatatgagnnnnnnnctggtataatttacaggaaataatctctatctaggagagaaaacaaaggagtcacc cggtctaaatatatagtttttgattaaattgtcagacaatttcttgaaatatgagaaaaaaactggtataatttacaggaaataatctctatctaggagagaaaacaaaggagtcacc Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CGGUCUAAAUAUAUAGUUUUUGAUUAAAUUGUCAGACAAUUUCUUGAAAUAUGAGAAAAAAACUGGUAUAAUUUACAGGAAAUAAUCUCUAUCUAGGAGAGAAAACAAAGGAGUCACC ............(((((((......)))))))..(((.((((((((((((((.((.......)).))))...)).))))))))..(((((.....)))))............)))... (-16.80) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GGUGACUCCUUUGUUUUCUCUCCUAGAUAGAGAUUAUUUCCUGUAAAUUAUACCAGUUUUUUUCUCAUAUUUCAAGAAAUUGUCUGACAAUUUAAUCAAAAACUAUAUAUUUAGACCG (((.....((((((((........))))))))...........(((((.(((..(((((((...............((((((.....))))))....))))))).)))))))).))). (-12.71) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 263 80 31 214 167 NC_009009:SSA_0674|5end_Exodeoxyribonuclease_VII_large_subunit,_putative_657071..657301_POSITIVE 234 98 60 63 16 NC_009009:SSA_1728|5end_ABC_transporter_membrane-spanning_permease-branched_chain_amino_acid_transport,_putative_1714293..1714523_NEGATIVE 199 104 70 231 184 NC_009009:SSA_0168|5end_hypothetical_protein_166457..166687_POSITIVE 198 67 28 62 17 NC_009009:SSA_0809|5end_Translation_initiation_inhibitor,_yjgF_family_/_endoribonuclease_L-PSP,_putative_791146..791376_POSITIVE 188 47 10 115 76 NC_009009:SSA_0752|5end_hypothetical_protein_734171..734401_POSITIVE 187 66 31 55 7 NC_009009:SSA_0795|5end_hypothetical_protein_776620..776850_POSITIVE 184 105 62 203 164 NC_009009:SSA_2200|5end_Firmicutes_transcriptional_repressor_of_class_III_stress_genes_(CtsR),_putative_2201573..2201803_NEGATIVE 182 108 61 170 133 NC_009009:SSA_1005|5end_Sugar_ABC_transporter,_permease_protein,_putative_1006028..1006258_POSITIVE 182 55 17 197 166 NC_009009:SSA_0354|5end_Uncharacterized_membrane_protein_346241..346471_POSITIVE 181 47 10 178 142 NC_009009:SSA_0314|5end_Nucleoside-diphosphate-sugar_epimerase,_putative_310019..310249_NEGATIVE 178 64 21 163 107 NC_009009:SSA_1166|5end_hypothetical_protein_1191929..1192159_POSITIVE 176 79 31 135 87 NC_009009:SSA_1419|5end_hypothetical_protein_1429675..1429905_NEGATIVE 172 50 15 85 46 NC_009009:SSA_1856|5end_hypothetical_protein_1852208..1852438_NEGATIVE 172 101 75 98 66 NC_009009:SSA_0299|5end_hypothetical_protein_292759..292989_POSITIVE 169 110 63 72 13 NC_009009:SSA_2122|5end_hypothetical_protein_2127607..2127837_NEGATIVE 169 106 93 128 115 NC_009009:SSA_0412|5end_ABC-type_multidrug_transport_system_(3-component_subtilin_immunity_exporter),_ATPase_component,_putative_408163..408393_NEGATIVE 167 47 10 141 107 NC_009009:SSA_1468|5end_3-dehydroquinate_synthase,_putative_1475452..1475682_NEGATIVE 164 101 63 229 198 NC_009009:SSA_1994|5end_CTP_synthase,_putative_1992474..1992704_NEGATIVE 163 58 23 73 36 NC_009009:SSA_1599|5end_hypothetical_protein_1606416..1606646_NEGATIVE 161 103 64 210 171 NC_009009:SSA_0946|5end_Phosphate_transport_system_regulatory_protein,_putative_953393..953623_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 263 80 31 57 10 NC_009009:SSA_0673|3end_hypothetical_protein_656994..657144_POSITIVE 191 97 54 151 105 NC_009009:SSA_1024|3end_Alpha-amylase,_putative_1041182..1041332_NEGATIVE 189 110 61 55 4 NC_009009:SSA_1367|3end_hypothetical_protein_1383828..1383978_POSITIVE 188 47 10 113 74 NC_009009:SSA_0751|3end_Oligoendopeptidase_F,_putative_734249..734399_POSITIVE 187 66 31 50 2 NC_009009:SSA_0794|3end_Zn-dependent_protease,_putative_776695..776845_POSITIVE 176 79 31 126 78 NC_009009:SSA_1420|3end_Homoserine_O-succinyltransferase,_putative_1429684..1429834_NEGATIVE 168 102 70 102 61 NC_009009:SSA_2373|3end_DNA_replication_and_repair_protein_recF,_putative_2375382..2375532_POSITIVE 168 60 15 51 1 NC_009009:SSA_0098|3end_Hydrolase,_haloacid_dehalogenase-like_family,_putative_100116..100266_POSITIVE 167 57 17 59 16 NC_009009:SSA_2005|3end_Chaperone_protein_dnaJ,_putative_2005251..2005401_NEGATIVE 167 47 10 130 96 NC_009009:SSA_1469|3end_Shikimate_dehydrogenase,_putative_1475463..1475613_NEGATIVE 165 47 27 18 1 NC_009009:SSA_0811|3end_hypothetical_protein_793526..793676_POSITIVE 163 57 28 140 115 NC_009009:SSA_1853|3end_S-ribosylhomocysteine_lyase,_putative_1849360..1849510_POSITIVE 163 48 14 107 70 NC_009009:SSA_0955|3end_Aminopeptidase_N,_putative_961139..961289_POSITIVE 163 57 11 49 11 NC_009009:SSA_0062|3end_Aldose_1-epimerase,_putative_64858..65008_POSITIVE 162 108 63 44 1 NC_009009:SSA_0242|3end_hypothetical_protein_235810..235960_POSITIVE 162 110 70 51 8 NC_009009:SSA_0081|3end_Transcriptional_regulator,_RpiR_family_(phosphosugar-binding),_putative_84220..84370_NEGATIVE 160 100 61 151 119 NC_009009:SSA_1004|3end_ABC_transporter_membrane-spanning_permease-multiple_sugars,_putative_1006094..1006244_POSITIVE 160 106 76 46 15 NC_009009:SSA_0184|3end_Competence_protein_ComYA,_putative_189177..189327_POSITIVE 158 36 1 132 101 NC_009009:SSA_0543|3end_SecA,_putative_539878..540028_POSITIVE 157 90 41 62 15 NC_009009:SSA_1056|3end_Firmicute_fructose-1,6-bisphosphatase,_putative_1073750..1073900_POSITIVE