Origin IGS: accaaccttgtgattctacgattttaaaataaaaatataagaaaaaccgacgacactttatgtcctcggttcttttttcgttcttgcaaacaaagaagcctagcaattttgctaggcttctttgtt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aacaaagaagcctagcaaaattgctaggcttctttgtttgcaagaacgaaaaaagaaccgaggacataaagtgtcgtcggtttttcttatatttttattttaaaatcgtagaatcacaaggttggt Mask Tandem Repeat Region ================================================ accaaccttgtgattctacgattttaaaataaaaatataagaaaaaccgacgacactttatgtcctcggttcttttttcgttcttgcaaacaaagaagcctagcaattttgctaggcttctttgtt Find is-nt database================================================ Query_seq: SSA_1543:SSA_1544|SSA_1543:SSA_1544:hypothetical protein:Conserved uncharacterized protein:-><-:1548278..1548403 126 accaaccttgtgattctacgattttaaaataaaaatataagaaaaaccgacgacactttatgtcctcggttcttttttcgttcttgcaaacaaagaagcctagcaattttgctaggcttctttgtt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1543:SSA_1544|SSA_1543:SSA_1544:hypothetical protein:Conserved uncharacterized protein:-><-:1548278..1548403 126 accaaccttgtgattctacgattttaaaataaaaatataagaaaaaccgacgacactttatgtcctcggttcttttttcgttcttgcaaacaaagaagcctagcaattttgctaggcttctttgtt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1543:SSA_1544|SSA_1543:SSA_1544:hypothetical protein:Conserved uncharacterized protein:-><-:1548278..1548403 126 accaaccttgtgattctacgattttaaaataaaaatataagaaaaaccgacgacactttatgtcctcggttcttttttcgttcttgcaaacaaagaagcctagcaattttgctaggcttctttgtt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 accaaccttgtgattctacgattttaaaataaaaatataagaaaaaccgacgacactttatgtcctcggttcttttttcgttcttgcaaacaaagaagcctagcaattttgctaggcttctttgtt Predict ORF larger than 30AA ================================================ Protein_Len: 30 Strand: + Start: 37 End: 126 .................................... M R K T D D T L C P R F F F R S C K Q R S L A I L L G F F V Protein_Len: 35 Strand: - Start: 2 End: 106 . W G Q S E V I K F Y F Y L F F R R C K I D E T R K E N K C V F F G L M .................... accaaccttgtgattctacgattttaaaataaaaatataagaaaaaccgacgacactttatgtcctcggttcttttttcgttcttgcaaacaaagaagcctagcaattttgctaggcttctttgtt 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================================================ accaaccttgtgattctacgattttaaaataaaaatataagaaaaaccgacgacactttatgtcctcggttcttttttcgttcttgcaaacaaagaagcctagcaattttgctaggcttctttgtt Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 84 HP_score: -6.0 Tail_Score: -5.37865 Start: 44 End: 72 Full_Region: ATAAAAATATAAGAA AAACCGACGACA CTTTA TGTCCTCGGTTC TTTTTTCGTTCTTGC ...........................................AAACCGACGACACTTTATGTCCTCGGTTC...................................................... TransTerm Strand: - Conf: 90 HP_score: -8.4 Tail_Score: -5.35365 Start: 47 End: 69 Full_Region: agaacgaaaaaagaa ccgaggacat aaa gtgtcgtcgg tttttcttatatttt ..............................................ccgaggacataaagtgtcgtcgg......................................................... Find igs database================================================ Query_seq: SSA_1543:SSA_1544|SSA_1543:SSA_1544:hypothetical protein:Conserved uncharacterized protein:-><-:1548278..1548403 126 accaaccttgtgattctacgattttaaaataaaaatataagaaaaaccgacgacactttatgtcctcggttcttttttcgttcttgcaaacaaagaagcctagcaattttgctaggcttctttgtt Intra-Species Hit: Count: 1 Min: 1 Max: 126 Len: 126 Subject: NC_009009_SSA_1543_SSA_1544|hypothetical protein:Conserved uncharacterized protein|POSITIVE:NEGATIVE|[1548278,1548403]|126 HSP 1 e-value: 9.0E-66 bit: 250.0 Len: 126 Query Start:1 Query End:126 Subject Strand: POSITIVE Subject Start: 1 Subject End: 126 accaaccttgtgattctacgattttaaaataaaaatataagaaaaaccgacgacactttatgtcctcggttcttttttcgttcttgcaaacaaagaagcctagcaattttgctaggcttctttgtt accaaccttgtgattctacgattttaaaataaaaatataagaaaaaccgacgacactttatgtcctcggttcttttttcgttcttgcaaacaaagaagcctagcaattttgctaggcttctttgtt HSP 2 e-value: 2.0E-8 bit: 60.0 Len: 38 Query Start:89 Query End:126 Subject Strand: NEGATIVE Subject Start: 89 Subject End: 126 ........................................................................................aacaaagaagcctagcaattttgctaggcttctttgtt ........................................................................................aacaaagaagcctagcaaaattgctaggcttctttgtt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACCAACCUUGUGAUUCUACGAUUUUAAAAUAAAAAUAUAAGAAAAACCGACGACACUUUAUGUCCUCGGUUCUUUUUUCGUUCUUGCAAACAAAGAAGCCUAGCAAUUUUGCUAGGCUUCUUUGUU ........((..(....((((.................(((((.((((((.((((.....)))).)))))).)))))))))..)..)).((((((((((((((((....)))))))))))))))). (-42.22) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AACAAAGAAGCCUAGCAAAAUUGCUAGGCUUCUUUGUUUGCAAGAACGAAAAAAGAACCGAGGACAUAAAGUGUCGUCGGUUUUUCUUAUAUUUUUAUUUUAAAAUCGUAGAAUCACAAGGUUGGU (((((((((((((((((....))))))))))))))))).......((((...(((((((((.(((((...))))).)))))))))...(((....))).......))))..((((....))))... (-44.80) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 317 89 46 61 15 NC_009009:SSA_0950|5end_hypothetical_protein_956302..956532_POSITIVE 311 101 62 189 146 NC_009009:SSA_1616|5end_PhoH-like_protein,_putative_1620258..1620488_NEGATIVE 289 100 52 122 82 NC_009009:SSA_1382|5end_hypothetical_protein_1400270..1400500_NEGATIVE 278 100 51 200 145 NC_009009:SSA_0860|5end_N-acetylmuramidase/lysin,_putative_847615..847845_POSITIVE 276 119 77 72 35 NC_009009:SSA_1045|5end_hypothetical_protein_1060841..1061071_POSITIVE 275 118 71 229 179 NC_009009:SSA_1113|5end_Two-component_response_transcriptional_regulator_(CheY-like_receiver_domain_and_a_winged-helix_DNA-binding_domains),_putative_1139742..1139972_POSITIVE 271 75 34 212 175 NC_009009:SSA_0805|5end_Collagen-binding_surface_protein,_putative_787476..787706_POSITIVE 265 83 46 206 173 NC_009009:SSA_0152|5end_hypothetical_protein_145799..146029_POSITIVE 263 84 44 111 70 NC_009009:SSA_0674|5end_Exodeoxyribonuclease_VII_large_subunit,_putative_657071..657301_POSITIVE 262 117 74 93 53 NC_009009:SSA_1463|5end_Shikimate_kinase,_putative_1470240..1470470_NEGATIVE 259 88 55 131 85 NC_009009:SSA_1308|5end_hypothetical_protein_1326818..1327048_NEGATIVE 258 106 62 61 25 NC_009009:SSA_2264|5end_hypothetical_protein_2261757..2261987_NEGATIVE 258 119 71 142 98 NC_009009:SSA_0336|5end_Isopentenyl-diphosphate_delta-isomerase,_putative_329792..330022_POSITIVE 256 112 72 223 188 NC_009009:SSA_2205|5end_Transcription_antitermination_factor_NusG,_putative_2206100..2206330_NEGATIVE 255 89 43 121 65 NC_009009:SSA_2062|5end_hypothetical_protein_2063521..2063751_NEGATIVE 253 88 46 87 44 NC_009009:SSA_0761|5end_Transcriptional_regulator,_XRE_family,_putative_743877..744107_POSITIVE 250 116 72 185 136 NC_009009:SSA_0043|5end_hypothetical_protein_48801..49031_POSITIVE 248 119 83 101 67 NC_009009:SSA_2054|5end_hypothetical_protein_2057899..2058129_NEGATIVE 248 95 51 126 87 NC_009009:SSA_0585|5end_hypothetical_protein_576937..577167_POSITIVE 247 94 56 124 86 NC_009009:SSA_1466|5end_Prephenate_dehydrogenase,_putative_1473111..1473341_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 317 89 46 74 28 NC_009009:SSA_0949|3end_hypothetical_protein_956395..956545_POSITIVE 289 119 85 97 62 NC_009009:SSA_0362|3end_Thioredoxin,_putative_353594..353744_POSITIVE 275 118 71 145 95 NC_009009:SSA_1112|3end_Cell_wall_surface_anchor_family_protein,_putative_1139738..1139888_POSITIVE 271 75 34 83 46 NC_009009:SSA_0804|3end_Phosphoglucomutase/phosphomannomutase_family_protein,_putative_787427..787577_POSITIVE 262 117 74 100 60 NC_009009:SSA_1464|3end_3-phosphoshikimate_1-carboxyvinyltransferase,_putative_1470233..1470383_NEGATIVE 261 110 64 146 81 NC_009009:SSA_1893|3end_N-acetylglucosamine-6-phosphate_deacetylase,_putative_1889421..1889571_NEGATIVE 257 87 41 97 53 NC_009009:SSA_1064|3end_hypothetical_protein_1080325..1080475_NEGATIVE 254 117 86 57 31 NC_009009:SSA_1051|3end_Spermidine/putrescine_ABC_transporter,_spermidine/putrescine-binding_protein,_putative_1066808..1066958_POSITIVE 252 118 76 41 3 NC_009009:SSA_1384|3end_hypothetical_protein_1401715..1401865_NEGATIVE 249 117 71 122 76 NC_009009:SSA_0394|3end_hypothetical_protein_390931..391081_POSITIVE 248 119 83 64 30 NC_009009:SSA_2055|3end_hypothetical_protein_2057936..2058086_NEGATIVE 247 94 56 108 70 NC_009009:SSA_1467|3end_Chorismate_synthase,_putative_1473127..1473277_NEGATIVE 246 119 71 143 95 NC_009009:SSA_0381|3end_hypothetical_protein_373514..373664_POSITIVE 245 116 80 33 5 NC_009009:SSA_2263|3end_Ribonucleotide_reductase_(NrdI_family_protein),_putative_2260688..2260838_NEGATIVE 245 118 71 92 52 NC_009009:SSA_0897|3end_Two_component_system_histidine_kinase,_putative_889811..889961_POSITIVE 242 117 72 110 72 NC_009009:SSA_0686|3end_Fe2+/Zn2+_uptake_regulation_protein,_putative_670079..670229_POSITIVE 241 120 75 85 42 NC_009009:SSA_2129|3end_Arsenical_resistance_operon_transcription_repressor_(ArsR),_putative_2132223..2132373_NEGATIVE 241 110 62 151 94 NC_009009:SSA_0905|3end_CshA-like_fibrillar_surface_protein_B_909060..909210_POSITIVE 241 108 64 127 70 NC_009009:SSA_0509|3end_Propanediol_utilization_protein,_putative_508538..508688_POSITIVE 241 118 76 142 94 NC_009009:SSA_0227|3end_Collagen-binding_surface_protein,_putative_222970..223120_POSITIVE