Origin IGS: acatggctaaacaagttatctacaagggaatgtcttgctggttgttagagttggaagaatcttttcctgccagggtacaaatcatctcccctgacgatctttctaaggcaatgcaagaaggcttcagctgctggggctacccaaatgagattatgaaagaagtctctgctgaagaatacgcttgtttaacacgttttggaaaatttccactgaattgattgaaatagaaactaggagaaataaaaa .........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 tttttatttctcctagtttctatttcaatcaattcagtggaaattttccaaaacgtgttaaacaagcgtattcttcagcagagacttctttcataatctcatttgggtagccccagcagctgaagccttcttgcattgccttagaaagatcgtcaggggagatgatttgtaccctggcaggaaaagattcttccaactctaacaaccagcaagacattcccttgtagataacttgtttagccatgt Mask Tandem Repeat Region ================================================ acatggctaaacaagttatctacaagggaatgtcttgctggttgttagagttggaagaatcttttcctgccagggtacaaatcatctcccctgacgatctttctaaggcaatgcaagaaggcttcagctgctggggctacccaaatgagattatgaaagaagtctctgctgaagaatacgcttgtttaacacgttttggaaaatttccactgaattgattgaaatagaaactaggagaaataaaaa Find is-nt database================================================ Query_seq: SSA_1166:SSA_1167|SSA_1166:SSA_1167:hypothetical protein:SRP54, signal recognition particle GTPase protein, putative:->->:1192411..1192656 246 acatggctaaacaagttatctacaagggaatgtcttgctggttgttagagttggaagaatcttttcctgccagggtacaaatcatctcccctgacgatctttctaaggcaatgcaagaaggcttcagctgctggggctacccaaatgagattatgaaagaagtctctgctgaagaatacgcttgtttaacacgttttggaaaatttccactgaattgattgaaatagaaactaggagaaataaaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1166:SSA_1167|SSA_1166:SSA_1167:hypothetical protein:SRP54, signal recognition particle GTPase protein, putative:->->:1192411..1192656 246 acatggctaaacaagttatctacaagggaatgtcttgctggttgttagagttggaagaatcttttcctgccagggtacaaatcatctcccctgacgatctttctaaggcaatgcaagaaggcttcagctgctggggctacccaaatgagattatgaaagaagtctctgctgaagaatacgcttgtttaacacgttttggaaaatttccactgaattgattgaaatagaaactaggagaaataaaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1166:SSA_1167|SSA_1166:SSA_1167:hypothetical protein:SRP54, signal recognition particle GTPase protein, putative:->->:1192411..1192656 246 acatggctaaacaagttatctacaagggaatgtcttgctggttgttagagttggaagaatcttttcctgccagggtacaaatcatctcccctgacgatctttctaaggcaatgcaagaaggcttcagctgctggggctacccaaatgagattatgaaagaagtctctgctgaagaatacgcttgtttaacacgttttggaaaatttccactgaattgattgaaatagaaactaggagaaataaaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 acatggctaaacaagttatctacaagggaatgtcttgctggttgttagagttggaagaatcttttcctgccagggtacaaatcatctcccctgacgatctttctaaggcaatgcaagaaggcttcagctgctggggctacccaaatgagattatgaaagaagtctctgctgaagaatacgcttgtttaacacgttttggaaaatttccactgaattgattgaaatagaaactaggagaaataaaaa Predict ORF larger than 30AA ================================================ Protein_Len: 60 Strand: + Start: 3 End: 215 .. M A K Q V I Y K G M S C W L L E L E E S F P A R V Q I I S P D D L S K A M Q E G F S C W G Y P N E I M K E V S A E E Y A ............................... Protein_Len: 34 Strand: - Start: 140 End: 241 ........................................................................................................................................... G F S I I F S T E A S S Y A Q K V R K P F N G S F Q N F Y F S P S M ..... Protein_Len: 33 Strand: - Start: 48 End: 146 ............................................... L Q F F R K R G P Y L D D G R V I K R L C H L F A E A A P A V W M .................................................................................................... Protein_Len: 35 Strand: - Start: 23 End: 127 ...................... L P I D Q Q N N S N S S D K G A L T C I M E G S S R E L A I C S P K M ....................................................................................................................... acatggctaaacaagttatctacaagggaatgtcttgctggttgttagagttggaagaatcttttcctgccagggtacaaatcatctcccctgacgatctttctaaggcaatgcaagaaggcttcagctgctggggctacccaaatgagattatgaaagaagtctctgctgaagaatacgcttgtttaacacgttttggaaaatttccactgaattgattgaaatagaaactaggagaaataaaaa 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================================================ acatggctaaacaagttatctacaagggaatgtcttgctggttgttagagttggaagaatcttttcctgccagggtacaaatcatctcccctgacgatctttctaaggcaatgcaagaaggcttcagctgctggggctacccaaatgagattatgaaagaagtctctgctgaagaatacgcttgtttaacacgttttggaaaatttccactgaattgattgaaatagaaactaggagaaataaaaa Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_1166:SSA_1167|SSA_1166:SSA_1167:hypothetical protein:SRP54, signal recognition particle GTPase protein, putative:->->:1192411..1192656 246 acatggctaaacaagttatctacaagggaatgtcttgctggttgttagagttggaagaatcttttcctgccagggtacaaatcatctcccctgacgatctttctaaggcaatgcaagaaggcttcagctgctggggctacccaaatgagattatgaaagaagtctctgctgaagaatacgcttgtttaacacgttttggaaaatttccactgaattgattgaaatagaaactaggagaaataaaaa Intra-Species Hit: Count: 1 Min: 1 Max: 246 Len: 246 Subject: NC_009009_SSA_1166_SSA_1167|hypothetical protein:SRP54, signal recognition particle GTPase protein, putative|POSITIVE:POSITIVE|[1192411,1192656]|246 HSP 1 e-value: 1.0E-137 bit: 488.0 Len: 246 Query Start:1 Query End:246 Subject Strand: POSITIVE Subject Start: 1 Subject End: 246 acatggctaaacaagttatctacaagggaatgtcttgctggttgttagagttggaagaatcttttcctgccagggtacaaatcatctcccctgacgatctttctaaggcaatgcaagaaggcttcagctgctggggctacccaaatgagattatgaaagaagtctctgctgaagaatacgcttgtttaacacgttttggaaaatttccactgaattgattgaaatagaaactaggagaaataaaaa acatggctaaacaagttatctacaagggaatgtcttgctggttgttagagttggaagaatcttttcctgccagggtacaaatcatctcccctgacgatctttctaaggcaatgcaagaaggcttcagctgctggggctacccaaatgagattatgaaagaagtctctgctgaagaatacgcttgtttaacacgttttggaaaatttccactgaattgattgaaatagaaactaggagaaataaaaa Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACAUGGCUAAACAAGUUAUCUACAAGGGAAUGUCUUGCUGGUUGUUAGAGUUGGAAGAAUCUUUUCCUGCCAGGGUACAAAUCAUCUCCCCUGACGAUCUUUCUAAGGCAAUGCAAGAAGGCUUCAGCUGCUGGGGCUACCCAAAUGAGAUUAUGAAAGAAGUCUCUGCUGAAGAAUACGCUUGUUUAACACGUUUUGGAAAAUUUCCACUGAAUUGAUUGAAAUAGAAACUAGGAGAAAUAAAAA ......(((.....((((...(((((.(....((((((..(((.((((((..((((((...))))))...(((((.............))))).......)))))))))...))))))...(((((((...((((....))))...((((((.(....).)))))).)))))))....).))))).))))..((((..(..(((((.....)))))..)..))))......)))............ (-59.82) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUUUAUUUCUCCUAGUUUCUAUUUCAAUCAAUUCAGUGGAAAUUUUCCAAAACGUGUUAAACAAGCGUAUUCUUCAGCAGAGACUUCUUUCAUAAUCUCAUUUGGGUAGCCCCAGCAGCUGAAGCCUUCUUGCAUUGCCUUAGAAAGAUCGUCAGGGGAGAUGAUUUGUACCCUGGCAGGAAAAGAUUCUUCCAACUCUAACAACCAGCAAGACAUUCCCUUGUAGAUAACUUGUUUAGCCAUGU ..............((((((((((...........)))))))))).......((((((((((((((..(((((((((((.((((.(........).))))..(((((....)))))..)))))))...((((((......(((((......(((((((..((....))...))))))).((((.......))))...)))))......))))))............)))).))))))))).))))) (-61.30) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 347 137 91 208 157 NC_009009:SSA_1657|5end_hypothetical_protein_1653231..1653461_NEGATIVE 333 142 103 211 171 NC_009009:SSA_0811|5end_hypothetical_protein_792469..792699_POSITIVE 331 80 35 72 25 NC_009009:SSA_0739|5end_Carbamate_kinase,_putative_721087..721317_POSITIVE 327 170 126 54 1 NC_009009:SSA_2053|5end_hypothetical_protein_2057747..2057977_NEGATIVE 322 138 91 183 134 NC_009009:SSA_1448|5end_ATP_phosphoribosyltransferase_regulatory_subunit,_putative_1450817..1451047_NEGATIVE 321 69 27 223 179 NC_009009:SSA_1304|5end_hypothetical_protein_1323449..1323679_NEGATIVE 319 150 103 189 135 NC_009009:SSA_1051|5end_Spermidine/putrescine_ABC_transporter,_spermidine/putrescine-binding_protein,_putative_1065658..1065888_POSITIVE 317 109 62 229 178 NC_009009:SSA_1720|5end_Initiation-control_protein,_putative_1707113..1707343_NEGATIVE 315 141 106 61 25 NC_009009:SSA_1948|5end_Oligopeptide-binding_lipoprotein_precursor,_putative_1942170..1942400_NEGATIVE 315 137 91 63 20 NC_009009:SSA_1340|5end_Zn/Mn_ABC-type_porter_lipoprotein,_putative_1356372..1356602_NEGATIVE 313 73 33 170 125 NC_009009:SSA_2277|5end_DNA_segregation_ATPase_FtsK/SpoIIIE_family_protein,_putative_2280407..2280637_NEGATIVE 313 74 37 42 16 NC_009009:SSA_0143|5end_Conserved_uncharacterized_protein_137465..137695_POSITIVE 311 170 121 62 3 NC_009009:SSA_2091|5end_Phosphotransferase_system_sugar-specific_EII_component,_putative_2095562..2095792_NEGATIVE 311 139 91 165 119 NC_009009:SSA_0981|5end_3-isopropylmalate_dehydratase_small_subunit,_putative_985396..985626_POSITIVE 308 169 122 205 153 NC_009009:SSA_1875|5end_hypothetical_protein_1870558..1870788_POSITIVE 305 139 91 195 145 NC_009009:SSA_0643|5end_hypothetical_protein_630194..630424_NEGATIVE 305 109 61 54 2 NC_009009:SSA_0188|5end_hypothetical_protein_190798..191028_POSITIVE 303 107 61 157 104 NC_009009:SSA_2230|5end_Ribonucleotide_reductase,_class_III,_anaerobic,_putative_2231158..2231388_NEGATIVE 303 142 105 184 127 NC_009009:SSA_0087|5end_V-type_sodium_ATPase,_subunit_E,_putative_88329..88559_POSITIVE 302 141 101 200 169 NC_009009:SSA_2323|5end_Transporter,_putative_2327604..2327834_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 330 143 105 148 110 NC_009009:SSA_0227|3end_Collagen-binding_surface_protein,_putative_222970..223120_POSITIVE 324 137 103 108 69 NC_009009:SSA_1993|3end_Conserved_uncharacterized_protein_1990380..1990530_NEGATIVE 322 138 91 127 78 NC_009009:SSA_1449|3end_Histidinol-phosphate/aromatic_aminotransferase_and_cobyric_acid_decarboxylase,_putative_1450873..1451023_NEGATIVE 321 69 27 147 103 NC_009009:SSA_1305|3end_hypothetical_protein_1323525..1323675_NEGATIVE 315 129 83 146 97 NC_009009:SSA_2226|3end_Organic_radical_activating_chaperone,_putative_2227151..2227301_NEGATIVE 307 149 122 135 105 NC_009009:SSA_1874|3end_YorfE_protein,_putative_1870590..1870740_POSITIVE 301 58 15 123 86 NC_009009:SSA_1476|3end_Phosphoglycerol_transferase,_alkaline_phosphatase_superfamily,_putative_1482448..1482598_POSITIVE 301 77 32 85 41 NC_009009:SSA_0581|3end_Conserved_uncharacterized_protein_573774..573924_POSITIVE 298 70 28 121 76 NC_009009:SSA_1757|3end_hypothetical_protein_1745282..1745432_NEGATIVE 298 137 92 138 94 NC_009009:SSA_0956|3end_surface_protein_D_965418..965568_POSITIVE 296 168 127 71 36 NC_009009:SSA_1463|3end_Shikimate_kinase,_putative_1469764..1469914_NEGATIVE 292 134 91 151 99 NC_009009:SSA_0716|3end_Competence_protein,_putative_703710..703860_POSITIVE 291 198 163 87 47 NC_009009:SSA_0028|3end_Phosphoribosylaminoimidazole-succinocarboxamide_synthase,_putative_32670..32820_POSITIVE 290 148 104 82 24 NC_009009:SSA_1794|3end_Two-component_response_transcriptional_regulator_(CheY-like_receiver_and_winged-helix_DNA-binding_domains),_putative_1776345..1776495_NEGATIVE 287 149 103 70 31 NC_009009:SSA_1867|3end_ABC-type_polar_amino_acid_transport_system,_ATPase_component,_putative_1862353..1862503_NEGATIVE 286 170 123 138 95 NC_009009:SSA_0489|3end_Adenosylcobinamide_kinase_/_adenosylcobinamide_phosphate_guanyltransferase,_putative_490319..490469_POSITIVE 285 131 91 147 112 NC_009009:SSA_2082|3end_Carbohydrate_kinase,_FGGY_family,_putative_2085351..2085501_NEGATIVE 281 117 71 60 6 NC_009009:SSA_0685|3end_hypothetical_protein_669432..669582_POSITIVE 281 135 91 149 113 NC_009009:SSA_0500|3end_Peptide_ABC_transporter,_permease_protein,_putative_501524..501674_POSITIVE 280 128 81 147 103 NC_009009:SSA_0837|3end_Glucosyltransferase,_putative_825502..825652_POSITIVE