Origin IGS: gcaaaaaagttagacttgtaaggtctagcttttttgcttacttgtggatagacagactaaggatggaaggagatgagttgatctcttagttaggaaatcttcattcatttttggtataataaagtatcaattcatggaggtgtttcg .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 cgaaacacctccatgaattgatactttattataccaaaaatgaatgaagatttcctaactaagagatcaactcatctccttccatccttagtctgtctatccacaagtaagcaaaaaagctagaccttacaagtctaacttttttgc Mask Tandem Repeat Region ================================================ gcaaaaaagttagacttgtaaggtctagcttttttgcttacttgtggatagacagactaaggatggaaggagatgagttgatctcttagttaggaaatcttcattcatttttggtataataaagtatcaattcatggaggtgtttcg Find is-nt database================================================ Query_seq: SSA_0987:SSA_0988|SSA_0987:SSA_0988:ABC-type choline transporter, membrane-spanning permease, putative:TfoX N-terminal domain family protein, putative:->->:990655..990801 147 gcaaaaaagttagacttgtaaggtctagcttttttgcttacttgtggatagacagactaaggatggaaggagatgagttgatctcttagttaggaaatcttcattcatttttggtataataaagtatcaattcatggaggtgtttcg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0987:SSA_0988|SSA_0987:SSA_0988:ABC-type choline transporter, membrane-spanning permease, putative:TfoX N-terminal domain family protein, putative:->->:990655..990801 147 gcaaaaaagttagacttgtaaggtctagcttttttgcttacttgtggatagacagactaaggatggaaggagatgagttgatctcttagttaggaaatcttcattcatttttggtataataaagtatcaattcatggaggtgtttcg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0987:SSA_0988|SSA_0987:SSA_0988:ABC-type choline transporter, membrane-spanning permease, putative:TfoX N-terminal domain family protein, putative:->->:990655..990801 147 gcaaaaaagttagacttgtaaggtctagcttttttgcttacttgtggatagacagactaaggatggaaggagatgagttgatctcttagttaggaaatcttcattcatttttggtataataaagtatcaattcatggaggtgtttcg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gcaaaaaagttagacttgtaaggtctagcttttttgcttacttgtggatagacagactaaggatggaaggagatgagttgatctcttagttaggaaatcttcattcatttttggtataataaagtatcaattcatggaggtgtttcg Predict ORF larger than 30AA ================================================ Protein_Len: 31 Strand: - Start: 28 End: 120 ........................... S K Q K S T S L C V L S P L L H T S R K T L F D E N M K P I M ........................... gcaaaaaagttagacttgtaaggtctagcttttttgcttacttgtggatagacagactaaggatggaaggagatgagttgatctcttagttaggaaatcttcattcatttttggtataataaagtatcaattcatggaggtgtttcg 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: 81 Start: 91 End: 120 ..........................................................................................TAGGAAATCTTCATTCATTTTTGGTATAAT........................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ gcaaaaaagttagacttgtaaggtctagcttttttgcttacttgtggatagacagactaaggatggaaggagatgagttgatctcttagttaggaaatcttcattcatttttggtataataaagtatcaattcatggaggtgtttcg Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 48 HP_score: -3.3 Tail_Score: -3.34522 Start: 70 End: 85 Full_Region: GACTAAGGATGGAAG GAGAT GAGTTG ATCTC TTAGTTAGGAAATCT .....................................................................GAGATGAGTTGATCTC.............................................................. Find igs database================================================ Query_seq: SSA_0987:SSA_0988|SSA_0987:SSA_0988:ABC-type choline transporter, membrane-spanning permease, putative:TfoX N-terminal domain family protein, putative:->->:990655..990801 147 gcaaaaaagttagacttgtaaggtctagcttttttgcttacttgtggatagacagactaaggatggaaggagatgagttgatctcttagttaggaaatcttcattcatttttggtataataaagtatcaattcatggaggtgtttcg Intra-Species Hit: Count: 1 Min: 1 Max: 147 Len: 147 Subject: NC_009009_SSA_0987_SSA_0988|ABC-type choline transporter, membrane-spanning permease, putative:TfoX N-terminal domain family protein, putative|POSITIVE:POSITIVE|[990655,990801]|147 HSP 1 e-value: 3.0E-78 bit: 291.0 Len: 147 Query Start:1 Query End:147 Subject Strand: POSITIVE Subject Start: 1 Subject End: 147 gcaaaaaagttagacttgtaaggtctagcttttttgcttacttgtggatagacagactaaggatggaaggagatgagttgatctcttagttaggaaatcttcattcatttttggtataataaagtatcaattcatggaggtgtttcg gcaaaaaagttagacttgtaaggtctagcttttttgcttacttgtggatagacagactaaggatggaaggagatgagttgatctcttagttaggaaatcttcattcatttttggtataataaagtatcaattcatggaggtgtttcg Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GCAAAAAAGUUAGACUUGUAAGGUCUAGCUUUUUUGCUUACUUGUGGAUAGACAGACUAAGGAUGGAAGGAGAUGAGUUGAUCUCUUAGUUAGGAAAUCUUCAUUCAUUUUUGGUAUAAUAAAGUAUCAAUUCAUGGAGGUGUUUCG ((((((((((((((((.....)))))))))))))))).(((((((((((.((...((((((((((((.((((((...(((((......)))))...)))))).))))))))))))...........)).))))))..)))))..... (-44.94) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CGAAACACCUCCAUGAAUUGAUACUUUAUUAUACCAAAAAUGAAUGAAGAUUUCCUAACUAAGAGAUCAACUCAUCUCCUUCCAUCCUUAGUCUGUCUAUCCACAAGUAAGCAAAAAAGCUAGACCUUACAAGUCUAACUUUUUUGC .................(((...(((((((............))))))).....(..((((((.(((................)))))))))..)........)))....(((((((((.(((((.......))))).))))))))) (-22.59) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 294 50 1 211 152 NC_009009:SSA_2105|5end_hypothetical_protein_2107802..2108032_NEGATIVE 273 67 21 60 9 NC_009009:SSA_2132|5end_Ure_cluster_protein,_putative_2134170..2134400_POSITIVE 268 70 21 75 19 NC_009009:SSA_1402|5end_ABC-type_multidrug_transport_system,_ATPase_and_permease_components,_putative_1416220..1416450_NEGATIVE 266 65 21 189 141 NC_009009:SSA_0665|5end_NTP_pyrophosphohydrolases_including_oxidative_damage_repair_enzymes_(MutT/NUDIX_family)_649603..649833_NEGATIVE 263 66 23 185 139 NC_009009:SSA_0981|5end_3-isopropylmalate_dehydratase_small_subunit,_putative_985396..985626_POSITIVE 258 79 34 136 95 NC_009009:SSA_0589|5end_Acetylornithine_deacetylase/succinyl-diaminopimelate_desuccinylase_(M20/M25/M40_family_peptidase),_putative_580745..580975_POSITIVE 257 65 24 141 94 NC_009009:SSA_0607|5end_ABC_transporter,_permease_component,_putative_596926..597156_NEGATIVE 256 66 22 171 122 NC_009009:SSA_1188|5end_Ribonuclease_HII,_putative_1216819..1217049_NEGATIVE 254 70 23 129 77 NC_009009:SSA_1229|5end_hypothetical_protein_1252421..1252651_NEGATIVE 254 107 61 158 104 NC_009009:SSA_1132|5end_TatC,_sec-independent_protein_translocase,_putative_1158645..1158875_POSITIVE 254 43 8 60 23 NC_009009:SSA_1131|5end_High-affinity_Fe_2+/Pb2+_permease,_putative_1157183..1157413_POSITIVE 251 59 15 90 44 NC_009009:SSA_1859|5end_Penicillin-binding_protein-like_factor_A/_recombinase,_putative_1853704..1853934_POSITIVE 251 47 18 205 172 NC_009009:SSA_1084|5end_Conserved_uncharacterized_protein_1101675..1101905_POSITIVE 251 57 20 231 191 NC_009009:SSA_0697|5end_hypothetical_protein_680083..680313_POSITIVE 250 99 51 66 2 NC_009009:SSA_1403|5end_Multidrug_ABC_transporter,_ATPase_and_permease_components,_putative_1417964..1418194_NEGATIVE 249 57 15 66 1 NC_009009:SSA_0025|5end_DNA_repair_protein_recO,_putative_29694..29924_POSITIVE 246 59 15 160 112 NC_009009:SSA_0585|5end_hypothetical_protein_576937..577167_POSITIVE 244 60 18 205 167 NC_009009:SSA_0512|5end_Nicotinate-nucleotide--dimethylbenzimidazole_phosphoribosyltransferase,_putative_510439..510669_POSITIVE 239 100 53 59 11 NC_009009:SSA_0741|5end_Acetylornithine_deacetylase/Succinyl-diaminopimelate_desuccinylase,_putative_723773..724003_POSITIVE 235 49 5 159 108 NC_009009:SSA_1349|5end_Transcriptional_regulator,_biotin_repressor_family,_putative_1365918..1366148_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 432 40 1 93 54 NC_009009:SSA_0987|3end_ABC-type_choline_transporter,_membrane-spanning_permease,_putative_990594..990744_POSITIVE 281 70 21 147 93 NC_009009:SSA_2343|3end_hypothetical_protein_2343703..2343853_NEGATIVE 273 67 21 57 6 NC_009009:SSA_2131|3end_DNA-binding_protein,_putative_2134247..2134397_POSITIVE 271 58 12 146 96 NC_009009:SSA_1140|3end_Dihydrolipoamide_acetyl_transferase,_E2_component,_putative_1169207..1169357_POSITIVE 268 70 21 73 17 NC_009009:SSA_1403|3end_Multidrug_ABC_transporter,_ATPase_and_permease_components,_putative_1416222..1416372_NEGATIVE 266 65 21 111 63 NC_009009:SSA_0666|3end_hypothetical_protein_649681..649831_NEGATIVE 262 65 22 124 85 NC_009009:SSA_2027|3end_P-type_ATPase-metal/cation_transport_(probably_copper),_putative_2033109..2033259_NEGATIVE 261 49 1 66 8 NC_009009:SSA_0273|3end_hypothetical_protein_268566..268716_POSITIVE 252 49 2 91 45 NC_009009:SSA_0886|3end_Enolase,_putative_881057..881207_POSITIVE 251 70 25 148 94 NC_009009:SSA_0405|3end_Transcriptional_regulator,_XRE_family,_putative_402115..402265_POSITIVE 249 57 15 73 8 NC_009009:SSA_0023|3end_Aspartate_aminotransferase,_putative_29781..29931_POSITIVE 247 96 53 56 12 NC_009009:SSA_2076|3end_Conserved_uncharacterized_protein_2079390..2079540_NEGATIVE 235 49 5 120 69 NC_009009:SSA_1348|3end_hypothetical_protein_1365959..1366109_POSITIVE 234 85 53 35 8 NC_009009:SSA_0375|3end_D-methionine-binding_lipoprotein_(ABC-type_transporter),_putative_365209..365359_POSITIVE 232 47 4 101 51 NC_009009:SSA_2188|3end_Conserved_uncharacterized_protein_2190232..2190382_POSITIVE 232 78 38 139 91 NC_009009:SSA_2151|3end_M_protein_trans-acting_positive_transcriptional_regulator_(MGA),_putative_2152921..2153071_POSITIVE 232 70 22 146 99 NC_009009:SSA_0483|3end_Siroheme_synthase,_putative_484556..484706_POSITIVE 230 66 21 105 54 NC_009009:SSA_2242|3end_hypothetical_protein_2238121..2238271_NEGATIVE 230 67 21 67 25 NC_009009:SSA_1122|3end_Thioredoxin_family_protein,_putative_1148526..1148676_POSITIVE 229 47 6 37 1 NC_009009:SSA_1274|3end_hypothetical_protein_1295517..1295667_NEGATIVE