Origin IGS: ttcttttaattagaaactatcttaacataggaccaatagcttgtataatatatattttatataagtcctataaagagaatataatgcgatttttcaaactaaaatatattaccctcatgaggtagctccacatcaatttcaaacaagaatccgaaacgagaaaaagaagccttttggcttcgatttt .........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 aaaatcgaagccaaaaggcttctttttctcgtttcggattcttgtttgaaattgatgtggagctacctcatgagggtaatatattttagtttgaaaaatcgcattatattctctttataggacttatataaaatatatattatacaagctattggtcctatgttaagatagtttctaattaaaagaa Mask Tandem Repeat Region ================================================ ttcttttaattagaaactatcttaacataggaccaatagcttgtataatatatattttatataagtcctataaagagaatataatgcgatttttcaaactaaaatatattaccctcatgaggtagctccacatcaatttcaaacaagaatccgaaacgagaaaaagaagccttttggcttcgatttt Find is-nt database================================================ Query_seq: SSA_1929:SSA_1930|SSA_1929:SSA_1930:Macrophage infectivity potentiator protein, putative:Acetyl-CoA carboxylase alpha subunit, putative:<-<-:1917680..1917866 187 ttcttttaattagaaactatcttaacataggaccaatagcttgtataatatatattttatataagtcctataaagagaatataatgcgatttttcaaactaaaatatattaccctcatgaggtagctccacatcaatttcaaacaagaatccgaaacgagaaaaagaagccttttggcttcgatttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1929:SSA_1930|SSA_1929:SSA_1930:Macrophage infectivity potentiator protein, putative:Acetyl-CoA carboxylase alpha subunit, putative:<-<-:1917680..1917866 187 ttcttttaattagaaactatcttaacataggaccaatagcttgtataatatatattttatataagtcctataaagagaatataatgcgatttttcaaactaaaatatattaccctcatgaggtagctccacatcaatttcaaacaagaatccgaaacgagaaaaagaagccttttggcttcgatttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1929:SSA_1930|SSA_1929:SSA_1930:Macrophage infectivity potentiator protein, putative:Acetyl-CoA carboxylase alpha subunit, putative:<-<-:1917680..1917866 187 ttcttttaattagaaactatcttaacataggaccaatagcttgtataatatatattttatataagtcctataaagagaatataatgcgatttttcaaactaaaatatattaccctcatgaggtagctccacatcaatttcaaacaagaatccgaaacgagaaaaagaagccttttggcttcgatttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ttcttttaattagaaactatcttaacataggaccaatagcttgtataatatatattttatataagtcctataaagagaatataatgcgatttttcaaactaaaatatattaccctcatgaggtagctccacatcaatttcaaacaagaatccgaaacgagaaaaagaagccttttggcttcgatttt Predict ORF larger than 30AA ================================================ Protein_Len: 38 Strand: + Start: 9 End: 122 ........ M R N Y L N I G P I A C I I Y I L Y K S Y K E N I M R F F K L K Y I T L M R ................................................................. Protein_Len: 33 Strand: + Start: 89 End: 187 ........................................................................................ M F Q T K I Y Y P H E V A P H Q F Q T R I R N E K K K P F G F D F Protein_Len: 38 Strand: - Start: 71 End: 184 ...................................................................... L S F I I R N K L S F Y I V R M L Y S W M L K L C S D S V L F L L R K A E M ... ttcttttaattagaaactatcttaacataggaccaatagcttgtataatatatattttatataagtcctataaagagaatataatgcgatttttcaaactaaaatatattaccctcatgaggtagctccacatcaatttcaaacaagaatccgaaacgagaaaaagaagccttttggcttcgatttt 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================================================ ttcttttaattagaaactatcttaacataggaccaatagcttgtataatatatattttatataagtcctataaagagaatataatgcgatttttcaaactaaaatatattaccctcatgaggtagctccacatcaatttcaaacaagaatccgaaacgagaaaaagaagccttttggcttcgatttt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_1929:SSA_1930|SSA_1929:SSA_1930:Macrophage infectivity potentiator protein, putative:Acetyl-CoA carboxylase alpha subunit, putative:<-<-:1917680..1917866 187 ttcttttaattagaaactatcttaacataggaccaatagcttgtataatatatattttatataagtcctataaagagaatataatgcgatttttcaaactaaaatatattaccctcatgaggtagctccacatcaatttcaaacaagaatccgaaacgagaaaaagaagccttttggcttcgatttt Intra-Species Hit: Count: 1 Min: 1 Max: 187 Len: 187 Subject: NC_009009_SSA_1929_SSA_1930|Macrophage infectivity potentiator protein, putative:Acetyl-CoA carboxylase alpha subunit, putative|NEGATIVE:NEGATIVE|[1917680,1917866]|187 HSP 1 e-value: 1.0E-102 bit: 371.0 Len: 187 Query Start:1 Query End:187 Subject Strand: POSITIVE Subject Start: 1 Subject End: 187 ttcttttaattagaaactatcttaacataggaccaatagcttgtataatatatattttatataagtcctataaagagaatataatgcgatttttcaaactaaaatatattaccctcatgaggtagctccacatcaatttcaaacaagaatccgaaacgagaaaaagaagccttttggcttcgatttt ttcttttaattagaaactatcttaacataggaccaatagcttgtataatatatattttatataagtcctataaagagaatataatgcgatttttcaaactaaaatatattaccctcatgaggtagctccacatcaatttcaaacaagaatccgaaacgagaaaaagaagccttttggcttcgatttt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUCUUUUAAUUAGAAACUAUCUUAACAUAGGACCAAUAGCUUGUAUAAUAUAUAUUUUAUAUAAGUCCUAUAAAGAGAAUAUAAUGCGAUUUUUCAAACUAAAAUAUAUUACCCUCAUGAGGUAGCUCCACAUCAAUUUCAAACAAGAAUCCGAAACGAGAAAAAGAAGCCUUUUGGCUUCGAUUUU (((((...........((((((((..(((((((.......((((((((........)))))))))))))))...(((....(((((..(((((.......))))).)))))..))).)))))))).......((...(((......)))...))...)))))...((((((....))))))...... (-34.21) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAAUCGAAGCCAAAAGGCUUCUUUUUCUCGUUUCGGAUUCUUGUUUGAAAUUGAUGUGGAGCUACCUCAUGAGGGUAAUAUAUUUUAGUUUGAAAAAUCGCAUUAUAUUCUCUUUAUAGGACUUAUAUAAAAUAUAUAUUAUACAAGCUAUUGGUCCUAUGUUAAGAUAGUUUCUAAUUAAAAGAA ......((((((....))))))...((((.(((((((((....)))))))))((((..(((((((.((...(((((.((((((.....(.((....)).)....)))))))))))(((((((((.(((.....((((...)))).....))).)))))))))...)).)))))))..))))..)))) (-38.70) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 796 130 81 221 172 NC_009009:SSA_1929|5end_Macrophage_infectivity_potentiator_protein,_putative_1917589..1917819_NEGATIVE 272 159 111 64 12 NC_009009:SSA_0659|5end_hypothetical_protein_643003..643233_POSITIVE 262 67 25 143 88 NC_009009:SSA_2336|5end_Transcriptional_regulator,_PadR_family,_putative_2338367..2338597_POSITIVE 259 159 120 191 138 NC_009009:SSA_1806|5end_Replication_initiation/membrane_attachment_protein_DnaB,_putative_1790749..1790979_NEGATIVE 259 149 112 168 130 NC_009009:SSA_1370|5end_CAAX_amino_terminal_protease_family,_putative_1386968..1387198_NEGATIVE 259 160 112 185 128 NC_009009:SSA_0479|5end_CbiQ_protein,_putative_480425..480655_POSITIVE 258 40 3 176 134 NC_009009:SSA_0474|5end_Uroporphyrin-III_C-methyltransferase/uroporphyrinogen-III_synthase,_putative_476270..476500_POSITIVE 255 145 112 74 36 NC_009009:SSA_1459|5end_RNA_methyltransferase,_putative_1467481..1467711_NEGATIVE 252 154 112 75 25 NC_009009:SSA_0053|5end_Beta-galactosidase,_putative_56748..56978_POSITIVE 241 160 113 138 99 NC_009009:SSA_0841|5end_hypothetical_protein_826935..827165_POSITIVE 230 140 107 76 52 NC_009009:SSA_0476|5end_Precorrin-2_C20-methyltransferase,_putative_478500..478730_POSITIVE 229 158 113 196 158 NC_009009:SSA_2315|5end_Conserved_uncharacterized_protein_2316945..2317175_NEGATIVE 224 140 99 85 46 NC_009009:SSA_2356|5end_Replicative_DNA_helicase,_putative_2357958..2358188_NEGATIVE 224 160 112 63 15 NC_009009:SSA_1999|5end_hypothetical_protein_1996974..1997204_NEGATIVE 223 158 111 190 136 NC_009009:SSA_0812|5end_hypothetical_protein_793443..793673_POSITIVE 223 39 1 142 99 NC_009009:SSA_0398|5end_hypothetical_protein_396452..396682_NEGATIVE 220 135 91 153 112 NC_009009:SSA_0789|5end_Proton-translocating_ATPase,_F1_sector,_epsilon_subunit,_putative_772451..772681_POSITIVE 220 160 111 48 6 NC_009009:SSA_0257|5end_N-acetylmuramidase/lysin,_putative_248878..249108_POSITIVE 219 135 113 56 30 NC_009009:SSA_0470|5end_Precorrin-4_methylase,_putative_472879..473109_POSITIVE 216 179 131 206 153 NC_009009:SSA_1987|5end_hypothetical_protein_1983368..1983598_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 259 149 112 85 47 NC_009009:SSA_1371|3end_FmtA-like_protein,_putative_1387051..1387201_NEGATIVE 259 160 112 67 10 NC_009009:SSA_0478|3end_Cobalt_transport_protein_cbiN,_putative_480387..480537_POSITIVE 241 160 113 136 97 NC_009009:SSA_0839|3end_hypothetical_protein_827013..827163_POSITIVE 234 172 143 66 36 NC_009009:SSA_0908|3end_ABC-type_uncharacterized_transport_system,_periplasmic_component,_putative_920787..920937_POSITIVE 230 140 107 66 42 NC_009009:SSA_0475|3end_CbiK_protein,_putative_478570..478720_POSITIVE 228 35 3 151 115 NC_009009:SSA_0473|3end_Precorrin-6x_reductase,_putative_476331..476481_POSITIVE 227 179 132 81 38 NC_009009:SSA_1030|3end_Transcriptional_regulator,_TetR_family,_putative_1047749..1047899_POSITIVE 226 179 149 135 97 NC_009009:SSA_1573|3end_hypothetical_protein_1576054..1576204_NEGATIVE 224 140 99 58 19 NC_009009:SSA_2357|3end_50S_ribosomal_protein_L9,_putative_2357985..2358135_NEGATIVE 224 160 112 50 2 NC_009009:SSA_2000|3end_hypothetical_protein_1996987..1997137_NEGATIVE 223 39 1 124 81 NC_009009:SSA_0400|3end_hypothetical_protein_396470..396620_NEGATIVE 220 135 91 145 104 NC_009009:SSA_0788|3end_Proton-translocating_ATPase,_F1_sector,_beta_subunit,_putative_772523..772673_POSITIVE 219 135 113 56 30 NC_009009:SSA_0469|3end_Precorrin-6B_methylase_2,putative_472959..473109_POSITIVE 215 95 72 66 42 NC_009009:SSA_0800|3end_Glutamine_amidotransferase,_putative_781989..782139_NEGATIVE 213 155 117 73 21 NC_009009:SSA_1622|3end_50S_ribosomal_protein_L1,_putative_1624752..1624902_NEGATIVE 213 180 145 55 25 NC_009009:SSA_1362|3end_ORFB,_transposon_ISSsa2_1378599..1378749_POSITIVE 208 179 146 81 46 NC_009009:SSA_1731|3end_ATP-dependent_Clp_protease,_proteolytic_subunit,_putative_1716218..1716368_NEGATIVE 208 177 131 110 62 NC_009009:SSA_1445|3end_Imidazole_glycerol-phosphate_dehydratase,_putative_1447302..1447452_NEGATIVE 206 179 139 68 27 NC_009009:SSA_0506|3end_Iron-sulfur_cluster-binding_protein,_putative_504430..504580_NEGATIVE 203 154 113 150 114 NC_009009:SSA_1090|3end_Glucokinase,_putative_1108610..1108760_POSITIVE