Origin IGS: atataatctccagtctattaatatcttttatattttaacacacttagaatgaggattcaaaaagaccggtcgcccagtctttcatcttgtattaaagtttttcatctgtcttgccatgtcgcggttttgctcgcggcgtttgatggacccgtgattctcacaagaattatttgtcagtagttttatcgttttccctgtagact .........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 agtctacagggaaaacgataaaactactgacaaataattcttgtgagaatcacgggtccatcaaacgccgcgagcaaaaccgcgacatggcaagacagatgaaaaactttaatacaagatgaaagactgggcgaccggtctttttgaatcctcattctaagtgtgttaaaatataaaagatattaatagactggagattatat Mask Tandem Repeat Region ================================================ atataatctccagtctattaatatcttttatattttaacacacttagaatgaggattcaaaaagaccggtcgcccagtctttcatcttgtattaaagtttttcatctgtcttgccatgtcgcggttttgctcgcggcgtttgatggacccgtgattctcacaagaattatttgtcagtagttttatcgttttccctgtagact Find is-nt database================================================ Query_seq: SSA_1598:SSA_1599|SSA_1598:SSA_1599:hypothetical protein:hypothetical protein:<-<-:1605329..1605531 203 atataatctccagtctattaatatcttttatattttaacacacttagaatgaggattcaaaaagaccggtcgcccagtctttcatcttgtattaaagtttttcatctgtcttgccatgtcgcggttttgctcgcggcgtttgatggacccgtgattctcacaagaattatttgtcagtagttttatcgttttccctgtagact Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1598:SSA_1599|SSA_1598:SSA_1599:hypothetical protein:hypothetical protein:<-<-:1605329..1605531 203 atataatctccagtctattaatatcttttatattttaacacacttagaatgaggattcaaaaagaccggtcgcccagtctttcatcttgtattaaagtttttcatctgtcttgccatgtcgcggttttgctcgcggcgtttgatggacccgtgattctcacaagaattatttgtcagtagttttatcgttttccctgtagact Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1598:SSA_1599|SSA_1598:SSA_1599:hypothetical protein:hypothetical protein:<-<-:1605329..1605531 203 atataatctccagtctattaatatcttttatattttaacacacttagaatgaggattcaaaaagaccggtcgcccagtctttcatcttgtattaaagtttttcatctgtcttgccatgtcgcggttttgctcgcggcgtttgatggacccgtgattctcacaagaattatttgtcagtagttttatcgttttccctgtagact Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 atataatctccagtctattaatatcttttatattttaacacacttagaatgaggattcaaaaagaccggtcgcccagtctttcatcttgtattaaagtttttcatctgtcttgccatgtcgcggttttgctcgcggcgtttgatggacccgtgattctcacaagaattatttgtcagtagttttatcgttttccctgtagact Predict ORF larger than 30AA ================================================ Protein_Len: 43 Strand: + Start: 49 End: 177 ................................................ M R I Q K D R S P S L S S C I K V F H L S C H V A V L L A A F D G P V I L T R I I C Q .......................... Protein_Len: 34 Strand: - Start: 85 End: 186 .................................................................................... R T N F N K M Q R A M D R N Q E R R K I S G H N E C S N N T L L K M ................. atataatctccagtctattaatatcttttatattttaacacacttagaatgaggattcaaaaagaccggtcgcccagtctttcatcttgtattaaagtttttcatctgtcttgccatgtcgcggttttgctcgcggcgtttgatggacccgtgattctcacaagaattatttgtcagtagttttatcgttttccctgtagact 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: 85 Start: 32 End: 61 ...............................TTTGAATCCTCATTCTAAGTGTGTTAAAAT.............................................................................................................................................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ atataatctccagtctattaatatcttttatattttaacacacttagaatgaggattcaaaaagaccggtcgcccagtctttcatcttgtattaaagtttttcatctgtcttgccatgtcgcggttttgctcgcggcgtttgatggacccgtgattctcacaagaattatttgtcagtagttttatcgttttccctgtagact Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 77 HP_score: -6.8 Tail_Score: -4.68994 Start: 64 End: 79 Full_Region: taatacaagatgaaa gactgg gcga ccggtc tttttgaatcctcat ...............................................................gactgggcgaccggtc............................................................................................................................ Find igs database================================================ Query_seq: SSA_1598:SSA_1599|SSA_1598:SSA_1599:hypothetical protein:hypothetical protein:<-<-:1605329..1605531 203 atataatctccagtctattaatatcttttatattttaacacacttagaatgaggattcaaaaagaccggtcgcccagtctttcatcttgtattaaagtttttcatctgtcttgccatgtcgcggttttgctcgcggcgtttgatggacccgtgattctcacaagaattatttgtcagtagttttatcgttttccctgtagact Intra-Species Hit: Count: 1 Min: 1 Max: 203 Len: 203 Subject: NC_009009_SSA_1598_SSA_1599|hypothetical protein:hypothetical protein|NEGATIVE:NEGATIVE|[1605329,1605531]|203 HSP 1 e-value: 1.0E-111 bit: 402.0 Len: 203 Query Start:1 Query End:203 Subject Strand: POSITIVE Subject Start: 1 Subject End: 203 atataatctccagtctattaatatcttttatattttaacacacttagaatgaggattcaaaaagaccggtcgcccagtctttcatcttgtattaaagtttttcatctgtcttgccatgtcgcggttttgctcgcggcgtttgatggacccgtgattctcacaagaattatttgtcagtagttttatcgttttccctgtagact atataatctccagtctattaatatcttttatattttaacacacttagaatgaggattcaaaaagaccggtcgcccagtctttcatcttgtattaaagtttttcatctgtcttgccatgtcgcggttttgctcgcggcgtttgatggacccgtgattctcacaagaattatttgtcagtagttttatcgttttccctgtagact Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUAUAAUCUCCAGUCUAUUAAUAUCUUUUAUAUUUUAACACACUUAGAAUGAGGAUUCAAAAAGACCGGUCGCCCAGUCUUUCAUCUUGUAUUAAAGUUUUUCAUCUGUCUUGCCAUGUCGCGGUUUUGCUCGCGGCGUUUGAUGGACCCGUGAUUCUCACAAGAAUUAUUUGUCAGUAGUUUUAUCGUUUUCCCUGUAGACU ...........(((((((............((((((((.....)))))))).(((..(..((((((.((....)).))))))..((((((.....((....((((..((((....(((((((((......))))))))).....))))..))))..)).))))))......................)...)))..))))))) (-40.80) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGUCUACAGGGAAAACGAUAAAACUACUGACAAAUAAUUCUUGUGAGAAUCACGGGUCCAUCAAACGCCGCGAGCAAAACCGCGACAUGGCAAGACAGAUGAAAAACUUUAAUACAAGAUGAAAGACUGGGCGACCGGUCUUUUUGAAUCCUCAUUCUAAGUGUGUUAAAAUAUAAAAGAUAUUAAUAGACUGGAGAUUAUAU (((((.(((.................(((..........((((((.....))))))..........((((.(.((......))..).))))....))).........(((((((((....((((((((((....)))))))))).((((....))))....)))))))))....................))).))))).... (-44.40) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 943 140 91 231 182 NC_009009:SSA_1598|5end_hypothetical_protein_1605238..1605468_NEGATIVE 888 148 101 154 107 NC_009009:SSA_1600|5end_hypothetical_protein_1606595..1606825_NEGATIVE 731 110 61 231 182 NC_009009:SSA_1596|5end_hypothetical_protein_1603034..1603264_NEGATIVE 381 147 108 203 166 NC_009009:SSA_1341|5end_Carbamoyl-phosphate_synthase_large_chain,_putative_1359827..1360057_NEGATIVE 371 150 104 67 15 NC_009009:SSA_0481|5end_Cobyric_acid_synthase,_putative_481962..482192_POSITIVE 357 150 104 210 149 NC_009009:SSA_1530|5end_ABC-type_antimicrobial_peptide_transport_system,_permease_component,_putative_1538778..1539008_NEGATIVE 349 150 104 56 12 NC_009009:SSA_1911|5end_Conserved_uncharacterized_protein_1903105..1903335_NEGATIVE 345 149 102 221 174 NC_009009:SSA_1707|5end_Conserved_uncharacterized_protein_1697782..1698012_POSITIVE 339 147 103 187 140 NC_009009:SSA_1203|5end_hypothetical_protein_1226985..1227215_POSITIVE 337 149 109 96 53 NC_009009:SSA_0362|5end_Thioredoxin,_putative_353290..353520_POSITIVE 335 153 113 70 30 NC_009009:SSA_1353|5end_hypothetical_protein_1368519..1368749_NEGATIVE 332 139 92 52 4 NC_009009:SSA_0316|5end_hypothetical_protein_310576..310806_POSITIVE 330 140 95 204 149 NC_009009:SSA_1932|5end_Biotin_carboxylase,_putative_1920874..1921104_NEGATIVE 330 146 104 228 186 NC_009009:SSA_0351|5end_Signal_peptidase_I,_putative_344907..345137_NEGATIVE 330 79 56 35 11 NC_009009:SSA_0314|5end_Nucleoside-diphosphate-sugar_epimerase,_putative_310019..310249_NEGATIVE 328 166 121 208 169 NC_009009:SSA_1438|5end_Acetyltransferase,_putative_1443612..1443842_NEGATIVE 326 159 114 58 1 NC_009009:SSA_1879|5end_Glycyl-tRNA_synthetase_beta_chain,_putative_1874262..1874492_NEGATIVE 326 143 104 215 169 NC_009009:SSA_1544|5end_Conserved_uncharacterized_protein_1548796..1549026_NEGATIVE 323 148 106 122 75 NC_009009:SSA_1606|5end_Dephospho-CoA_kinase,_putative_1612425..1612655_NEGATIVE 322 149 104 83 20 NC_009009:SSA_1014|5end_Phosphatidylserine_decarboxylase_proenzyme_2,_putative_1017846..1018076_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 865 110 61 119 70 NC_009009:SSA_1601|3end_VacB-like_protein,_putative_1606592..1606742_NEGATIVE 603 153 113 41 1 NC_009009:SSA_1597|3end_hypothetical_protein_1603267..1603417_NEGATIVE 395 134 96 151 109 NC_009009:SSA_1869|3end_ATP-dependent_RNA_helicase,_putative_1864152..1864302_NEGATIVE 371 150 104 82 30 NC_009009:SSA_0480|3end_Cobalt_ABC_transporter,_ATP-binding_protein,_putative_482057..482207_POSITIVE 349 150 104 48 4 NC_009009:SSA_1912|3end_hypothetical_protein_1903113..1903263_NEGATIVE 340 150 108 66 16 NC_009009:SSA_0057|3end_Phosphotransferase_system_sugar-specific_EII_component,_putative_61246..61396_POSITIVE 328 176 131 43 3 NC_009009:SSA_1061|3end_50S_ribosomal_protein_L21,_putative_1077986..1078136_POSITIVE 327 140 94 113 68 NC_009009:SSA_0686|3end_Fe2+/Zn2+_uptake_regulation_protein,_putative_670079..670229_POSITIVE 323 148 106 116 69 NC_009009:SSA_1607|3end_Formamidopyrimidine-DNA_glycosylase,_putative_1612431..1612581_NEGATIVE 322 149 104 90 27 NC_009009:SSA_1013|3end_Phosphatidylserine_synthase,_putative_1017933..1018083_POSITIVE 322 146 110 151 105 NC_009009:SSA_0491|3end_Alpha-ribazole-5'-phosphate_phosphatase,_putative_491613..491763_POSITIVE 319 150 103 141 78 NC_009009:SSA_1659|3end_ABC-type_antimicrobial_peptide_transport_system,_permease_component,_putative_1654831..1654981_NEGATIVE 314 143 101 146 95 NC_009009:SSA_1356|3end_Helicase_subunit_of_the_DNA_excision_repair_complex,_subunit_B,_putative_1369927..1370077_NEGATIVE 306 147 106 90 56 NC_009009:SSA_0470|3end_Precorrin-4_methylase,_putative_473732..473882_POSITIVE 305 159 117 55 4 NC_009009:SSA_1880|3end_Glycyl-tRNA_synthetase_alpha_chain,_putative_1874265..1874415_NEGATIVE 299 150 107 137 100 NC_009009:SSA_1873|3end_S-adenosyl-methyltransferase_mraW,_putative_1869194..1869344_NEGATIVE 297 146 101 148 94 NC_009009:SSA_2138|3end_RNA-binding_protein,_Jag_family,_putative_2138462..2138612_NEGATIVE 297 146 110 71 29 NC_009009:SSA_0621|3end_SOS_responce_UmuC_protein,_putative_612322..612472_NEGATIVE 294 88 43 81 35 NC_009009:SSA_1465|3end_Conserved_uncharacterized_protein_1471648..1471798_NEGATIVE 292 154 111 143 95 NC_009009:SSA_0101|3end_Conserved_uncharacterized_protein_104113..104263_POSITIVE