Origin IGS: ttttttactccttattttatctgtactattttaccacattttgtgatttttatatagttaaatcactgaaatttttcttttttccttttagtaaaatagcagagcaggcaagctcatttcacagaaaaaccagccccatcatcagataggactgggaatgcatacttcaatcatcttttacaagatccac .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 gtggatcttgtaaaagatgattgaagtatgcattcccagtcctatctgatgatggggctggtttttctgtgaaatgagcttgcctgctctgctattttactaaaaggaaaaaagaaaaatttcagtgatttaactatataaaaatcacaaaatgtggtaaaatagtacagataaaataaggagtaaaaaa Mask Tandem Repeat Region ================================================ ttttttactccttattttatctgtactattttaccacattttgtgatttttatatagttaaatcactgaaatttttcttttttccttttagtaaaatagcagagcaggcaagctcatttcacagaaaaaccagccccatcatcagataggactgggaatgcatacttcaatcatcttttacaagatccac Find is-nt database================================================ Query_seq: SSA_1620:SSA_1621|SSA_1620:SSA_1621:Uridylate kinase, putative:Amino acid transporter, putative:<-<-:1623072..1623261 190 ttttttactccttattttatctgtactattttaccacattttgtgatttttatatagttaaatcactgaaatttttcttttttccttttagtaaaatagcagagcaggcaagctcatttcacagaaaaaccagccccatcatcagataggactgggaatgcatacttcaatcatcttttacaagatccac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1620:SSA_1621|SSA_1620:SSA_1621:Uridylate kinase, putative:Amino acid transporter, putative:<-<-:1623072..1623261 190 ttttttactccttattttatctgtactattttaccacattttgtgatttttatatagttaaatcactgaaatttttcttttttccttttagtaaaatagcagagcaggcaagctcatttcacagaaaaaccagccccatcatcagataggactgggaatgcatacttcaatcatcttttacaagatccac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1620:SSA_1621|SSA_1620:SSA_1621:Uridylate kinase, putative:Amino acid transporter, putative:<-<-:1623072..1623261 190 ttttttactccttattttatctgtactattttaccacattttgtgatttttatatagttaaatcactgaaatttttcttttttccttttagtaaaatagcagagcaggcaagctcatttcacagaaaaaccagccccatcatcagataggactgggaatgcatacttcaatcatcttttacaagatccac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ttttttactccttattttatctgtactattttaccacattttgtgatttttatatagttaaatcactgaaatttttcttttttccttttagtaaaatagcagagcaggcaagctcatttcacagaaaaaccagccccatcatcagataggactgggaatgcatacttcaatcatcttttacaagatccac Predict ORF larger than 30AA ================================================ Protein_Len: 42 Strand: + Start: 21 End: 146 .................... M Y Y F T T F C D F Y I V K S L K F F F F P F S K I A E Q A S S F H R K T S P I I R ............................................ ttttttactccttattttatctgtactattttaccacattttgtgatttttatatagttaaatcactgaaatttttcttttttccttttagtaaaatagcagagcaggcaagctcatttcacagaaaaaccagccccatcatcagataggactgggaatgcatacttcaatcatcttttacaagatccac 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: 29 End: 58 ............................TTTTACCACATTTTGTGATTTTTATATAGT.................................................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ ttttttactccttattttatctgtactattttaccacattttgtgatttttatatagttaaatcactgaaatttttcttttttccttttagtaaaatagcagagcaggcaagctcatttcacagaaaaaccagccccatcatcagataggactgggaatgcatacttcaatcatcttttacaagatccac Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 100 HP_score: -11.9 Tail_Score: -4.9792 Start: 130 End: 155 Full_Region: ttgaagtatgcattc ccagtcctatc tgat gatggggctgg tttttctgtgaaatg .................................................................................................................................ccagtcctatctgatgatggggctgg................................... Find igs database================================================ Query_seq: SSA_1620:SSA_1621|SSA_1620:SSA_1621:Uridylate kinase, putative:Amino acid transporter, putative:<-<-:1623072..1623261 190 ttttttactccttattttatctgtactattttaccacattttgtgatttttatatagttaaatcactgaaatttttcttttttccttttagtaaaatagcagagcaggcaagctcatttcacagaaaaaccagccccatcatcagataggactgggaatgcatacttcaatcatcttttacaagatccac Intra-Species Hit: Count: 1 Min: 90 Max: 190 Len: 101 Subject: NC_009009_SSA_1620_SSA_1621|Uridylate kinase, putative:Amino acid transporter, putative|NEGATIVE:NEGATIVE|[1623072,1623261]|190 HSP 1 e-value: 1.0E-50 bit: 200.0 Len: 101 Query Start:90 Query End:190 Subject Strand: POSITIVE Subject Start: 90 Subject End: 190 .........................................................................................agtaaaatagcagagcaggcaagctcatttcacagaaaaaccagccccatcatcagataggactgggaatgcatacttcaatcatcttttacaagatccac .........................................................................................agtaaaatagcagagcaggcaagctcatttcacagaaaaaccagccccatcatcagataggactgggaatgcatacttcaatcatcttttacaagatccac Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGUAAAAUAGCAGAGCAGGCAAGCUCAUUUCACAGAAAAACCAGCCCCAUCAUCAGAUAGGACUGGGAAUGCAUACUUCAAUCAUCUUUUACAAGAUCCAC .((((((.....((((......))))..............((((.((.(((....))).)).))))....................))))))......... (-20.10) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GUGGAUCUUGUAAAAGAUGAUUGAAGUAUGCAUUCCCAGUCCUAUCUGAUGAUGGGGCUGGUUUUUCUGUGAAAUGAGCUUGCCUGCUCUGCUAUUUUACU ....(((((....)))))...(((((((.((....(((((((((((....)))))))))))..............((((......)))).))))))))).. (-32.80) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 933 50 1 230 181 NC_009009:SSA_1620|5end_Uridylate_kinase,_putative_1622981..1623211_NEGATIVE 333 68 41 57 26 NC_009009:SSA_1537|5end_Conserved_uncharacterized_protein_1544441..1544671_NEGATIVE 326 57 11 53 13 NC_009009:SSA_0794|5end_Zn-dependent_protease,_putative_775896..776126_POSITIVE 320 56 12 73 25 NC_009009:SSA_2331|5end_D-alanine_transfer_protein,_putative_2334964..2335194_NEGATIVE 307 57 17 181 140 NC_009009:SSA_0943|5end_ABC_transporter_membrane-spanning_permease-phosphate_transport,_putative_950846..951076_POSITIVE 305 50 9 91 40 NC_009009:SSA_1118|5end_Peptide_methionine_sulfoxide_reductase,_putative_1143322..1143552_POSITIVE 296 90 41 51 1 NC_009009:SSA_1440|5end_Phosphoribosyl-ATP_pyrophosphohydrolase,_putative_1444721..1444951_NEGATIVE 294 49 7 160 101 NC_009009:SSA_0796|5end_ABC-NBD_transporters_with_duplicated_ATPase_domains,_putative_777085..777315_POSITIVE 293 66 28 128 86 NC_009009:SSA_1744|5end_Iron_compound_ABC_transporter,_permease_protein,_putative_1730915..1731145_POSITIVE 292 39 2 226 180 NC_009009:SSA_0318|5end_Secreted_metalloendopeptidase_Gcp_311701..311931_POSITIVE 291 87 41 187 117 NC_009009:SSA_1474|5end_Lipoprotein,_putative_1479741..1479971_NEGATIVE 290 45 4 218 169 NC_009009:SSA_1613|5end_hypothetical_protein_1616975..1617205_NEGATIVE 289 66 23 212 162 NC_009009:SSA_1178|5end_Acetoin_dehydrogenase,_E1_component,_alpha_subunit,_putative_1206417..1206647_NEGATIVE 288 55 11 65 21 NC_009009:SSA_2271|5end_hypothetical_protein_2272450..2272680_NEGATIVE 288 50 1 104 35 NC_009009:SSA_1667|5end_hypothetical_protein_1667704..1667934_NEGATIVE 287 49 7 180 135 NC_009009:SSA_0204|5end_Nisin_biosynthesis_two-component_response_transcriptional_regulator_nisR,_putative_202057..202287_POSITIVE 285 73 42 66 37 NC_009009:SSA_2323|5end_Transporter,_putative_2327604..2327834_POSITIVE 285 47 4 178 124 NC_009009:SSA_1224|5end_hypothetical_protein_1247481..1247711_NEGATIVE 280 86 41 43 3 NC_009009:SSA_2069|5end_Prolyl-tRNA_synthetase,_putative_2073252..2073482_NEGATIVE 280 88 42 190 145 NC_009009:SSA_1709|5end_hypothetical_protein_1698414..1698644_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 320 56 12 80 32 NC_009009:SSA_2332|3end_D-alanyl_carrier_protein,_putative_2334957..2335107_NEGATIVE 306 49 10 133 100 NC_009009:SSA_1065|3end_Beta-hexosamidase_A,_putative_1084130..1084280_POSITIVE 305 50 9 75 24 NC_009009:SSA_1117|3end_hypothetical_protein_1143386..1143536_POSITIVE 304 60 14 108 49 NC_009009:SSA_0687|3end_hypothetical_protein_671290..671440_POSITIVE 294 49 7 60 1 NC_009009:SSA_0795|3end_hypothetical_protein_777065..777215_POSITIVE 293 66 28 138 96 NC_009009:SSA_1743|3end_ABC-type_Fe3+-siderophore_transport_system,_permease_component,_putative_1731005..1731155_POSITIVE 288 50 1 70 1 NC_009009:SSA_1668|3end_NrdI_protein,_putative_1667738..1667888_NEGATIVE 285 47 4 70 16 NC_009009:SSA_1225|3end_Branched-chain_amino_acid_aminotransferase,_putative_1247589..1247739_NEGATIVE 284 69 22 85 36 NC_009009:SSA_2242|3end_hypothetical_protein_2238121..2238271_NEGATIVE 282 49 2 72 26 NC_009009:SSA_0586|3end_Conserved_uncharacterized_protein_578243..578393_POSITIVE 279 73 45 27 2 NC_009009:SSA_2322|3end_Transcriptional_regulator,_TetR/AcrR_family,_putative_2327645..2327795_POSITIVE 279 67 37 142 110 NC_009009:SSA_0411|3end_hypothetical_protein_406480..406630_NEGATIVE 277 55 11 93 36 NC_009009:SSA_0480|3end_Cobalt_ABC_transporter,_ATP-binding_protein,_putative_482057..482207_POSITIVE 276 56 14 111 61 NC_009009:SSA_1058|3end_Thiamine_biosynthesis_protein,_putative_1076211..1076361_POSITIVE 274 46 14 151 115 NC_009009:SSA_2023|3end_Fructan_beta-fructosidase_precursor,_putative_2024609..2024759_NEGATIVE 273 68 43 42 16 NC_009009:SSA_2208|3end_Preprotein_translocase_secE_component,_putative_2207734..2207884_NEGATIVE 270 77 34 80 39 NC_009009:SSA_1639|3end_5'-methylthioadenosine/S-adenosylhomocysteine_nucleosidase,_putative_1641339..1641489_NEGATIVE 269 80 33 77 39 NC_009009:SSA_2092|3end_Phosphotransferase_system_sugar-specific_EII_component,_putative_2095697..2095847_NEGATIVE 269 56 13 44 1 NC_009009:SSA_0376|3end_ABC-type_methionine_transporter,_ATPase_component,_putative_366526..366676_POSITIVE 267 51 11 46 7 NC_009009:SSA_0621|3end_SOS_responce_UmuC_protein,_putative_612322..612472_NEGATIVE