Origin IGS: cttcttgctcctttatgctagataccttatattatatcataattccaaaaaagctaagcaaatcctgtcaactcacttgaatagacacacttgcttagcttatattt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aaatataagctaagcaagtgtgtctattcaagtgagttgacaggatttgcttagcttttttggaattatgatataatataaggtatctagcataaaggagcaagaag Mask Tandem Repeat Region ================================================ cttcttgctcctttatgctagataccttatattatatcataattccaaaaaagctaagcaaatcctgtcaactcacttgaatagacacacttgcttagcttatattt Find is-nt database================================================ Query_seq: SSA_1864:SSA_1865|SSA_1864:SSA_1865:Nicotinate phosphoribosyltransferase (NAPRTase), subgroup A, putative:Thioredoxin reductase, putative:<-<-:1860961..1861067 107 cttcttgctcctttatgctagataccttatattatatcataattccaaaaaagctaagcaaatcctgtcaactcacttgaatagacacacttgcttagcttatattt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1864:SSA_1865|SSA_1864:SSA_1865:Nicotinate phosphoribosyltransferase (NAPRTase), subgroup A, putative:Thioredoxin reductase, putative:<-<-:1860961..1861067 107 cttcttgctcctttatgctagataccttatattatatcataattccaaaaaagctaagcaaatcctgtcaactcacttgaatagacacacttgcttagcttatattt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1864:SSA_1865|SSA_1864:SSA_1865:Nicotinate phosphoribosyltransferase (NAPRTase), subgroup A, putative:Thioredoxin reductase, putative:<-<-:1860961..1861067 107 cttcttgctcctttatgctagataccttatattatatcataattccaaaaaagctaagcaaatcctgtcaactcacttgaatagacacacttgcttagcttatattt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 cttcttgctcctttatgctagataccttatattatatcataattccaaaaaagctaagcaaatcctgtcaactcacttgaatagacacacttgcttagcttatattt Predict ORF larger than 30AA ================================================ Protein_Len: 34 Strand: + Start: 5 End: 106 .... M L L Y A R Y L I L Y H N S K K A K Q I L S T H L N R H T C L A Y I . cttcttgctcctttatgctagataccttatattatatcataattccaaaaaagctaagcaaatcctgtcaactcacttgaatagacacacttgcttagcttatattt 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: 4 End: 33 ...CTTGCTCCTTTATGCTAGATACCTTATATT.......................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ cttcttgctcctttatgctagataccttatattatatcataattccaaaaaagctaagcaaatcctgtcaactcacttgaatagacacacttgcttagcttatattt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_1864:SSA_1865|SSA_1864:SSA_1865:Nicotinate phosphoribosyltransferase (NAPRTase), subgroup A, putative:Thioredoxin reductase, putative:<-<-:1860961..1861067 107 cttcttgctcctttatgctagataccttatattatatcataattccaaaaaagctaagcaaatcctgtcaactcacttgaatagacacacttgcttagcttatattt Intra-Species Hit: Count: 1 Min: 1 Max: 107 Len: 107 Subject: NC_009009_SSA_1864_SSA_1865|Nicotinate phosphoribosyltransferase (NAPRTase), subgroup A, putative:Thioredoxin reductase, putative|NEGATIVE:NEGATIVE|[1860961,1861067]|107 HSP 1 e-value: 2.0E-54 bit: 212.0 Len: 107 Query Start:1 Query End:107 Subject Strand: POSITIVE Subject Start: 1 Subject End: 107 cttcttgctcctttatgctagataccttatattatatcataattccaaaaaagctaagcaaatcctgtcaactcacttgaatagacacacttgcttagcttatattt cttcttgctcctttatgctagataccttatattatatcataattccaaaaaagctaagcaaatcctgtcaactcacttgaatagacacacttgcttagcttatattt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUUCUUGCUCCUUUAUGCUAGAUACCUUAUAUUAUAUCAUAAUUCCAAAAAAGCUAAGCAAAUCCUGUCAACUCACUUGAAUAGACACACUUGCUUAGCUUAUAUUU ..(((.((........)).)))............................(((((((((((....((((...((....))...))))...)))))))))))...... (-21.70) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAUAUAAGCUAAGCAAGUGUGUCUAUUCAAGUGAGUUGACAGGAUUUGCUUAGCUUUUUUGGAAUUAUGAUAUAAUAUAAGGUAUCUAGCAUAAAGGAGCAAGAAG ......(((((((((((((.((((.((((....)))).))))..)))))))))))))............(((((........)))))..((........))...... (-27.10) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 888 100 51 191 142 NC_009009:SSA_1864|5end_Nicotinate_phosphoribosyltransferase_(NAPRTase),_subgroup_A,_putative_1860870..1861100_NEGATIVE 290 99 53 203 136 NC_009009:SSA_1544|5end_Conserved_uncharacterized_protein_1548796..1549026_NEGATIVE 289 41 3 130 93 NC_009009:SSA_1613|5end_hypothetical_protein_1616975..1617205_NEGATIVE 269 46 1 164 127 NC_009009:SSA_2205|5end_Transcription_antitermination_factor_NusG,_putative_2206100..2206330_NEGATIVE 252 78 42 80 48 NC_009009:SSA_1111|5end_Branched-chain_amino_acid_transport_system_II_carrier_protein,_putative_1136532..1136762_POSITIVE 245 100 51 142 75 NC_009009:SSA_0585|5end_hypothetical_protein_576937..577167_POSITIVE 244 47 2 137 96 NC_009009:SSA_1787|5end_Diaminopimelate_decarboxylase,_putative_1771551..1771781_NEGATIVE 243 91 53 56 16 NC_009009:SSA_1899|5end_hypothetical_protein_1894739..1894969_NEGATIVE 239 100 53 70 12 NC_009009:SSA_1521|5end_Phosphoenolpyruvate_carboxylase,_putative_1530683..1530913_NEGATIVE 236 99 58 140 112 NC_009009:SSA_0964|5end_DEAD_RNA_helicase,_putative_974114..974344_NEGATIVE 235 40 1 78 28 NC_009009:SSA_1459|5end_RNA_methyltransferase,_putative_1467481..1467711_NEGATIVE 234 39 2 129 92 NC_009009:SSA_1072|5end_Glutamate_5-kinase,_putative_1089755..1089985_POSITIVE 233 99 52 73 22 NC_009009:SSA_2270|5end_Aspartyl-tRNA_synthetase,_putative_2272068..2272298_NEGATIVE 231 60 11 144 86 NC_009009:SSA_0037|5end_Phosphoribosylamine-glycine_ligase;_phosphoribosyl_glycinamide_synthetase_(GARS),_putative_44272..44502_POSITIVE 230 100 52 184 132 NC_009009:SSA_1203|5end_hypothetical_protein_1226985..1227215_POSITIVE 227 93 51 178 134 NC_009009:SSA_0632|5end_Anthranilate_synthase_component_I,_putative_621458..621688_POSITIVE 223 65 22 137 81 NC_009009:SSA_0877|5end_Phosphoglycolate_phosphatase,_putative_871008..871238_POSITIVE 220 28 1 200 172 NC_009009:SSA_2070|5end_Zinc_metalloprotease,_putative_2074574..2074804_NEGATIVE 220 84 45 221 173 NC_009009:SSA_0915|5end_hypothetical_protein_927542..927772_POSITIVE 220 99 52 165 122 NC_009009:SSA_0136|5end_ABC_transporter,_Zn_porter,_putative_131014..131244_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 243 91 53 45 5 NC_009009:SSA_1900|3end_N_utilization_substance_protein_A,_putative_1894750..1894900_NEGATIVE 237 47 3 135 89 NC_009009:SSA_2239|3end_Conserved_uncharacterized_cytosolic_protein_2236922..2237072_NEGATIVE 230 66 21 85 32 NC_009009:SSA_0664|3end_Conserved_uncharacterized_protein_648784..648934_NEGATIVE 224 100 52 109 58 NC_009009:SSA_1390|3end_hypothetical_protein_1405633..1405783_NEGATIVE 218 47 6 64 11 NC_009009:SSA_2245|3end_RecA_protein,_putative_2239961..2240111_NEGATIVE 217 84 54 82 50 NC_009009:SSA_1840|3end_RNA_binding_protein,_putative_1834060..1834210_NEGATIVE 213 26 1 126 96 NC_009009:SSA_2023|3end_Fructan_beta-fructosidase_precursor,_putative_2024609..2024759_NEGATIVE 213 43 1 58 11 NC_009009:SSA_0846|3end_DNA-polymerase_III_alpha-chain,_putative_833367..833517_POSITIVE 211 100 61 60 20 NC_009009:SSA_2359|3end_Glucose_inhibited_division_protein_A,_putative_2360613..2360763_NEGATIVE 209 87 52 109 81 NC_009009:SSA_2353|3end_ABC-type_nitrate/sulfonate/bicarbonate_transport_system,_permease_component,_putative_2354550..2354700_NEGATIVE 209 41 3 108 64 NC_009009:SSA_1590|3end_Transcriptional_regulator,_TetR/AcrR_family,_putative_1593342..1593492_POSITIVE 209 47 1 147 103 NC_009009:SSA_1232|3end_Topoisomerase_IV_subunit_B,_putative_1254806..1254956_NEGATIVE 204 100 61 123 82 NC_009009:SSA_1462|3end_Prephenate_dehydratase,_putative_1468934..1469084_NEGATIVE 204 98 52 64 14 NC_009009:SSA_0435|3end_Urocanate_hydratase,_putative_436689..436839_NEGATIVE 204 98 55 142 102 NC_009009:SSA_0325|3end_Membrane-anchored_glycerophosphoryl_diester_phosphodiesterase,_putative_319437..319587_POSITIVE 202 60 11 63 6 NC_009009:SSA_0713|3end_1-acyl-sn-glycerol-3-phosphate_acyltransferase,_putative_700028..700178_POSITIVE 201 64 26 150 110 NC_009009:SSA_1063|3end_Peptidoglycan-binding_domain-containing_protein,_putative_1080260..1080410_POSITIVE 201 99 51 51 8 NC_009009:SSA_0733|3end_hypothetical_protein_716937..717087_POSITIVE 200 46 8 97 56 NC_009009:SSA_1334|3end_hypothetical_protein_1348482..1348632_NEGATIVE 200 79 45 151 116 NC_009009:SSA_1112|3end_Cell_wall_surface_anchor_family_protein,_putative_1139738..1139888_POSITIVE