Origin IGS: ttgatttcctcggaaaatgtattctgctattgagtgtaacagaaaagagaattttttgcacagaattgctttctaggctaggactgaaaattttcagatgtttcagaatggcttttatgatataatcatagcagt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 actgctatgattatatcataaaagccattctgaaacatctgaaaattttcagtcctagcctagaaagcaattctgtgcaaaaaattctcttttctgttacactcaatagcagaatacattttccgaggaaatcaa Mask Tandem Repeat Region ================================================ ttgatttcctcggaaaatgtattctgctattgagtgtaacagaaaagagaattttttgcacagaattgctttctaggctaggactgaaaattttcagatgtttcagaatggcttttatgatataatcatagcagt Find is-nt database================================================ Query_seq: SSA_0872:SSA_0873|SSA_0872:SSA_0873:Zn-dependent hydrolases, including glyoxylases, putative:ATP-dependent DNA helicase; DNA polymerase III, epsilon subunit, putative:<-->:865396..865530 135 ttgatttcctcggaaaatgtattctgctattgagtgtaacagaaaagagaattttttgcacagaattgctttctaggctaggactgaaaattttcagatgtttcagaatggcttttatgatataatcatagcagt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0872:SSA_0873|SSA_0872:SSA_0873:Zn-dependent hydrolases, including glyoxylases, putative:ATP-dependent DNA helicase; DNA polymerase III, epsilon subunit, putative:<-->:865396..865530 135 ttgatttcctcggaaaatgtattctgctattgagtgtaacagaaaagagaattttttgcacagaattgctttctaggctaggactgaaaattttcagatgtttcagaatggcttttatgatataatcatagcagt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0872:SSA_0873|SSA_0872:SSA_0873:Zn-dependent hydrolases, including glyoxylases, putative:ATP-dependent DNA helicase; DNA polymerase III, epsilon subunit, putative:<-->:865396..865530 135 ttgatttcctcggaaaatgtattctgctattgagtgtaacagaaaagagaattttttgcacagaattgctttctaggctaggactgaaaattttcagatgtttcagaatggcttttatgatataatcatagcagt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ttgatttcctcggaaaatgtattctgctattgagtgtaacagaaaagagaattttttgcacagaattgctttctaggctaggactgaaaattttcagatgtttcagaatggcttttatgatataatcatagcagt Predict ORF larger than 30AA ================================================ Protein_Len: 34 Strand: + Start: 21 End: 122 .................... M L L L S V T E K R I F C T E L L S R L G L K I F R C F R M A F M I ............. Protein_Len: 40 Strand: - Start: 2 End: 121 . S K R P F H I R S N L T V S F L I K Q V S N S E L S P S F I K L H K L I A K I M .............. ttgatttcctcggaaaatgtattctgctattgagtgtaacagaaaagagaattttttgcacagaattgctttctaggctaggactgaaaattttcagatgtttcagaatggcttttatgatataatcatagcagt 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: 92 End: 121 ...........................................................................................TTTCAGATGTTTCAGAATGGCTTTTATGAT.............. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ ttgatttcctcggaaaatgtattctgctattgagtgtaacagaaaagagaattttttgcacagaattgctttctaggctaggactgaaaattttcagatgtttcagaatggcttttatgatataatcatagcagt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_0872:SSA_0873|SSA_0872:SSA_0873:Zn-dependent hydrolases, including glyoxylases, putative:ATP-dependent DNA helicase; DNA polymerase III, epsilon subunit, putative:<-->:865396..865530 135 ttgatttcctcggaaaatgtattctgctattgagtgtaacagaaaagagaattttttgcacagaattgctttctaggctaggactgaaaattttcagatgtttcagaatggcttttatgatataatcatagcagt Intra-Species Hit: Count: 1 Min: 1 Max: 135 Len: 135 Subject: NC_009009_SSA_0872_SSA_0873|Zn-dependent hydrolases, including glyoxylases, putative:ATP-dependent DNA helicase; DNA polymerase III, epsilon subunit, putative|NEGATIVE:POSITIVE|[865396,865530]|135 HSP 1 e-value: 4.0E-71 bit: 268.0 Len: 135 Query Start:1 Query End:135 Subject Strand: POSITIVE Subject Start: 1 Subject End: 135 ttgatttcctcggaaaatgtattctgctattgagtgtaacagaaaagagaattttttgcacagaattgctttctaggctaggactgaaaattttcagatgtttcagaatggcttttatgatataatcatagcagt ttgatttcctcggaaaatgtattctgctattgagtgtaacagaaaagagaattttttgcacagaattgctttctaggctaggactgaaaattttcagatgtttcagaatggcttttatgatataatcatagcagt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUGAUUUCCUCGGAAAAUGUAUUCUGCUAUUGAGUGUAACAGAAAAGAGAAUUUUUUGCACAGAAUUGCUUUCUAGGCUAGGACUGAAAAUUUUCAGAUGUUUCAGAAUGGCUUUUAUGAUAUAAUCAUAGCAGU ....((((....)))).......(((((((.((.((((.((.(((((...(((((..((..((((.....))))..)).....(((((....))))).......)))))..))))).)).)))).))))))))). (-28.40) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACUGCUAUGAUUAUAUCAUAAAAGCCAUUCUGAAACAUCUGAAAAUUUUCAGUCCUAGCCUAGAAAGCAAUUCUGUGCAAAAAAUUCUCUUUUCUGUUACACUCAAUAGCAGAAUACAUUUUCCGAGGAAAUCAA .(((((((((......((.(((((..............(((((....))))).....((.(((((.....))))).))..........))))).))......)).))))))).......((((....)))).... (-22.80) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 823 110 61 201 152 NC_009009:SSA_0872|5end_Zn-dependent_hydrolases,_including_glyoxylases,_putative_865305..865535_NEGATIVE 297 70 22 205 155 NC_009009:SSA_0765|5end_hypothetical_protein_745519..745749_POSITIVE 285 115 71 76 24 NC_009009:SSA_0768|5end_Ribonucleoside-diphosphate_reductase_2,_beta_subunit,_putative_749095..749325_NEGATIVE 274 86 45 207 172 NC_009009:SSA_1466|5end_Prephenate_dehydrogenase,_putative_1473111..1473341_NEGATIVE 259 114 71 185 135 NC_009009:SSA_2376|5end_ABC_transporter_with_duplicated_ATPase_domains,_putative_2378744..2378974_POSITIVE 259 114 76 210 173 NC_009009:SSA_2284|5end_Histidyl-tRNA_synthetase,_putative_2287272..2287502_NEGATIVE 251 97 55 146 112 NC_009009:SSA_0692|5end_D-Ala-D-Ala_adding_enzyme,_putative_676370..676600_POSITIVE 243 113 72 193 161 NC_009009:SSA_0047|5end_NAD(P)H_dehydrogenase_(Quinone),_putative_52850..53080_NEGATIVE 241 101 68 58 27 NC_009009:SSA_1651|5end_hypothetical_protein_1649853..1650083_NEGATIVE 240 96 55 56 21 NC_009009:SSA_1587|5end_hypothetical_protein_1589086..1589316_NEGATIVE 240 104 61 195 148 NC_009009:SSA_1445|5end_Imidazole_glycerol-phosphate_dehydratase,_putative_1447886..1448116_NEGATIVE 238 96 51 180 141 NC_009009:SSA_0187|5end_Competence_protein_ComYD,_putative_190350..190580_POSITIVE 237 104 61 155 116 NC_009009:SSA_1899|5end_hypothetical_protein_1894739..1894969_NEGATIVE 236 112 73 70 22 NC_009009:SSA_1743|5end_ABC-type_Fe3+-siderophore_transport_system,_permease_component,_putative_1730170..1730400_POSITIVE 236 113 74 62 24 NC_009009:SSA_1396|5end_hypothetical_protein_1410374..1410604_NEGATIVE 234 87 41 206 170 NC_009009:SSA_0817|5end_Antirepressor_regulating_drug_resistance_(membrane-bound),_putative_797838..798068_POSITIVE 232 99 51 200 161 NC_009009:SSA_0041|5end_hypothetical_protein_47662..47892_POSITIVE 230 87 53 125 82 NC_009009:SSA_1606|5end_Dephospho-CoA_kinase,_putative_1612425..1612655_NEGATIVE 229 86 52 72 33 NC_009009:SSA_1661|5end_hypothetical_protein_1658004..1658234_NEGATIVE 229 70 21 203 149 NC_009009:SSA_0150|5end_hypothetical_protein_143936..144166_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 294 76 31 68 11 NC_009009:SSA_1878|3end_Conserved_uncharacterized_protein_1871943..1872093_NEGATIVE 285 115 71 65 13 NC_009009:SSA_0769|3end_hypothetical_protein_749106..749256_NEGATIVE 253 119 71 138 88 NC_009009:SSA_2285|3end_hypothetical_protein_2287825..2287975_POSITIVE 251 97 55 70 36 NC_009009:SSA_0691|3end_D-ala,D-ala_ligase,_putative_676374..676524_POSITIVE 243 117 71 137 82 NC_009009:SSA_0597|3end_hypothetical_protein_588563..588713_POSITIVE 241 87 47 71 26 NC_009009:SSA_0229|3end_hypothetical_protein_223713..223863_POSITIVE 237 104 61 144 105 NC_009009:SSA_1900|3end_N_utilization_substance_protein_A,_putative_1894750..1894900_NEGATIVE 233 86 49 146 105 NC_009009:SSA_0668|3end_hypothetical_protein_651431..651581_POSITIVE 230 87 53 119 76 NC_009009:SSA_1607|3end_Formamidopyrimidine-DNA_glycosylase,_putative_1612431..1612581_NEGATIVE 223 117 75 93 45 NC_009009:SSA_1502|3end_Conserved_uncharacterized_protein_(contains_LysM,_Lysin_motif)_1505782..1505932_NEGATIVE 223 107 75 90 54 NC_009009:SSA_0020|3end_Ribose-phosphate_pyrophosphokinase_1,_putative_26609..26759_POSITIVE 222 117 74 34 2 NC_009009:SSA_1397|3end_hypothetical_protein_1410995..1411145_POSITIVE 221 115 73 78 40 NC_009009:SSA_0548|3end_Alanine_racemase,_putative_543529..543679_POSITIVE 219 120 73 96 41 NC_009009:SSA_1510|3end_Rhamnosyltransferase,_putative_1514188..1514338_NEGATIVE 219 119 72 127 75 NC_009009:SSA_0932|3end_hypothetical_protein_942804..942954_POSITIVE 218 88 42 52 8 NC_009009:SSA_1832|3end_hypothetical_protein_1822614..1822764_POSITIVE 218 129 81 149 97 NC_009009:SSA_1732|3end_Uracil_phosphoribosyltransferase,_putative_1716916..1717066_NEGATIVE 218 79 40 48 9 NC_009009:SSA_0457|3end_Fructokinase,_putative_461642..461792_POSITIVE 217 105 68 93 45 NC_009009:SSA_1863|3end_NH(3)-dependent_NAD(+)_synthetase,_putative_1858589..1858739_NEGATIVE 217 79 39 90 47 NC_009009:SSA_1751|3end_Dextran_glucosidase,_alpha_amylase_family,_putative_1738110..1738260_NEGATIVE