Origin IGS: agctgctccctcatagtcatttttctacaattataccataaaaaagcgatcagactcaaagcaaaaaaagtgtgagtatctgctccccttacgtttgttcaaaagaaatggaatagcgaattaagataggcatgatgacagacttctgccttccattattgcctcaagcaacgataagaaaatataaagcacattgcttcgtcttttttcccttttgtgataagctaagattagtgaattgagagggttttcgt .........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 acgaaaaccctctcaattcactaatcttagcttatcacaaaagggaaaaaagacgaagcaatgtgctttatattttcttatcgttgcttgaggcaataatggaaggcagaagtctgtcatcatgcctatcttaattcgctattccatttcttttgaacaaacgtaaggggagcagatactcacactttttttgctttgagtctgatcgcttttttatggtataattgtagaaaaatgactatgagggagcagct Mask Tandem Repeat Region ================================================ agctgctccctcatagtcatttttctacaattataccataaaaaagcgatcagactcaaagcaaaaaaagtgtgagtatctgctccccttacgtttgttcaaaagaaatggaatagcgaattaagataggcatgatgacagacttctgccttccattattgcctcaagcaacgataagaaaatataaagcacattgcttcgtcttttttcccttttgtgataagctaagattagtgaattgagagggttttcgt Find is-nt database================================================ Query_seq: SSA_1824:SSA_1825|SSA_1824:SSA_1825:hypothetical protein:hypothetical protein:<-->:1812837..1813090 254 agctgctccctcatagtcatttttctacaattataccataaaaaagcgatcagactcaaagcaaaaaaagtgtgagtatctgctccccttacgtttgttcaaaagaaatggaatagcgaattaagataggcatgatgacagacttctgccttccattattgcctcaagcaacgataagaaaatataaagcacattgcttcgtcttttttcccttttgtgataagctaagattagtgaattgagagggttttcgt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1824:SSA_1825|SSA_1824:SSA_1825:hypothetical protein:hypothetical protein:<-->:1812837..1813090 254 agctgctccctcatagtcatttttctacaattataccataaaaaagcgatcagactcaaagcaaaaaaagtgtgagtatctgctccccttacgtttgttcaaaagaaatggaatagcgaattaagataggcatgatgacagacttctgccttccattattgcctcaagcaacgataagaaaatataaagcacattgcttcgtcttttttcccttttgtgataagctaagattagtgaattgagagggttttcgt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1824:SSA_1825|SSA_1824:SSA_1825:hypothetical protein:hypothetical protein:<-->:1812837..1813090 254 agctgctccctcatagtcatttttctacaattataccataaaaaagcgatcagactcaaagcaaaaaaagtgtgagtatctgctccccttacgtttgttcaaaagaaatggaatagcgaattaagataggcatgatgacagacttctgccttccattattgcctcaagcaacgataagaaaatataaagcacattgcttcgtcttttttcccttttgtgataagctaagattagtgaattgagagggttttcgt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 agctgctccctcatagtcatttttctacaattataccataaaaaagcgatcagactcaaagcaaaaaaagtgtgagtatctgctccccttacgtttgttcaaaagaaatggaatagcgaattaagataggcatgatgacagacttctgccttccattattgcctcaagcaacgataagaaaatataaagcacattgcttcgtcttttttcccttttgtgataagctaagattagtgaattgagagggttttcgt Predict ORF larger than 30AA ================================================ Protein_Len: 40 Strand: + Start: 120 End: 239 ....................................................................................................................... M K I G M M T D F C L P L L P Q A T I R K Y K A H C F V F F P F C D K L R L V N ............... Protein_Len: 36 Strand: - Start: 124 End: 231 ........................................................................................................................... S L C S S L S R G E M I A E L L S L F I Y L V N S R R K E R K H Y A L M ....................... agctgctccctcatagtcatttttctacaattataccataaaaaagcgatcagactcaaagcaaaaaaagtgtgagtatctgctccccttacgtttgttcaaaagaaatggaatagcgaattaagataggcatgatgacagacttctgccttccattattgcctcaagcaacgataagaaaatataaagcacattgcttcgtcttttttcccttttgtgataagctaagattagtgaattgagagggttttcgt 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================================================ agctgctccctcatagtcatttttctacaattataccataaaaaagcgatcagactcaaagcaaaaaaagtgtgagtatctgctccccttacgtttgttcaaaagaaatggaatagcgaattaagataggcatgatgacagacttctgccttccattattgcctcaagcaacgataagaaaatataaagcacattgcttcgtcttttttcccttttgtgataagctaagattagtgaattgagagggttttcgt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_1824:SSA_1825|SSA_1824:SSA_1825:hypothetical protein:hypothetical protein:<-->:1812837..1813090 254 agctgctccctcatagtcatttttctacaattataccataaaaaagcgatcagactcaaagcaaaaaaagtgtgagtatctgctccccttacgtttgttcaaaagaaatggaatagcgaattaagataggcatgatgacagacttctgccttccattattgcctcaagcaacgataagaaaatataaagcacattgcttcgtcttttttcccttttgtgataagctaagattagtgaattgagagggttttcgt Intra-Species Hit: Count: 1 Min: 1 Max: 254 Len: 254 Subject: NC_009009_SSA_1824_SSA_1825|hypothetical protein:hypothetical protein|NEGATIVE:POSITIVE|[1812837,1813090]|254 HSP 1 e-value: 1.0E-129 bit: 462.0 Len: 254 Query Start:1 Query End:254 Subject Strand: POSITIVE Subject Start: 1 Subject End: 254 agctgctccctcatagtcatttttctacaattataccataaaaaagcgatcagactcaaagcnnnnnnngtgtgagtatctgctccccttacgtttgttcaaaagaaatggaatagcgaattaagataggcatgatgacagacttctgccttccattattgcctcaagcaacgataagaaaatataaagcacattgcttcgtcttttttcccttttgtgataagctaagattagtgaattgagagggttttcgt agctgctccctcatagtcatttttctacaattataccataaaaaagcgatcagactcaaagcaaaaaaagtgtgagtatctgctccccttacgtttgttcaaaagaaatggaatagcgaattaagataggcatgatgacagacttctgccttccattattgcctcaagcaacgataagaaaatataaagcacattgcttcgtcttttttcccttttgtgataagctaagattagtgaattgagagggttttcgt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGCUGCUCCCUCAUAGUCAUUUUUCUACAAUUAUACCAUAAAAAAGCGAUCAGACUCAAAGCAAAAAAAGUGUGAGUAUCUGCUCCCCUUACGUUUGUUCAAAAGAAAUGGAAUAGCGAAUUAAGAUAGGCAUGAUGACAGACUUCUGCCUUCCAUUAUUGCCUCAAGCAACGAUAAGAAAAUAUAAAGCACAUUGCUUCGUCUUUUUUCCCUUUUGUGAUAAGCUAAGAUUAGUGAAUUGAGAGGGUUUUCGU ....((((.((((...(((((..(((....((((..(((((((..(.((..((((...(((((......(((((..((((((((...((((((((.((((...(....).))))))))...))))..((((((((((.(((....))).....))))).)))))..))))..)))).............)))))))))).))))..)).)..)))))))))))....)))..)))))..)))).))))...... (-51.86) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACGAAAACCCUCUCAAUUCACUAAUCUUAGCUUAUCACAAAAGGGAAAAAAGACGAAGCAAUGUGCUUUAUAUUUUCUUAUCGUUGCUUGAGGCAAUAAUGGAAGGCAGAAGUCUGUCAUCAUGCCUAUCUUAAUUCGCUAUUCCAUUUCUUUUGAACAAACGUAAGGGGAGCAGAUACUCACACUUUUUUUGCUUUGAGUCUGAUCGCUUUUUUAUGGUAUAAUUGUAGAAAAAUGACUAUGAGGGAGCAGCU .......(((((.....(((....(((.....(((((.(((((((.....(((((((((((((((...(((.((..((((.((((.(..((((....((((((((((((....))))).....((..((....))..))..)))))))))))..)....))))))))..))....)))..))))......)))))))..)))).....))))))).))))).......)))....)))....)))))....... (-55.30) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 881 100 51 191 142 NC_009009:SSA_1824|5end_hypothetical_protein_1812746..1812976_NEGATIVE 340 119 71 226 181 NC_009009:SSA_1447|5end_ATP_phosphoribosyltransferase,_putative_1449831..1450061_NEGATIVE 337 119 73 136 81 NC_009009:SSA_0618|5end_hypothetical_protein_611973..612203_NEGATIVE 311 180 131 167 121 NC_009009:SSA_2157|5end_ATP-dependent_serine_protease,_putative_2158241..2158471_NEGATIVE 296 47 2 86 22 NC_009009:SSA_1405|5end_Copper_homeostasis_protein_CutC,_putative_1419393..1419623_NEGATIVE 295 105 69 207 170 NC_009009:SSA_1173|5end_Lipoate_protein_ligase_A,_putative_1201081..1201311_NEGATIVE 292 118 78 78 21 NC_009009:SSA_0188|5end_hypothetical_protein_190798..191028_POSITIVE 283 177 135 165 122 NC_009009:SSA_1377|5end_Asparaginyl-tRNA_synthetase,_putative_1397614..1397844_NEGATIVE 281 170 128 202 158 NC_009009:SSA_0334|5end_Diphosphomevalonate_decarboxylase,_putative_327855..328085_POSITIVE 280 170 129 68 31 NC_009009:SSA_1855|5end_hypothetical_protein_1852051..1852281_NEGATIVE 280 150 104 203 143 NC_009009:SSA_1472|5end_hypothetical_protein_1478655..1478885_NEGATIVE 280 90 44 170 112 NC_009009:SSA_1085|5end_Dihydrodipicolinate_reductase,_putative_1102564..1102794_POSITIVE 275 227 188 121 87 NC_009009:SSA_0973|5end_hypothetical_protein_980296..980526_POSITIVE 273 99 52 199 140 NC_009009:SSA_0128|5end_Adenylate_kinase,_putative_119201..119431_POSITIVE 272 177 134 84 39 NC_009009:SSA_1775|5end_Potassium_uptake_protein,_Trk_family,_putative_1761284..1761514_POSITIVE 272 228 197 118 86 NC_009009:SSA_0485|5end_Porphobilinogen_deaminase,_putative_485732..485962_POSITIVE 272 218 173 122 78 NC_009009:SSA_0069|5end_Hypothetical_protein,_possibly_membrane-associated_73037..73267_POSITIVE 268 164 127 219 181 NC_009009:SSA_0716|5end_Competence_protein,_putative_701390..701620_POSITIVE 267 170 125 51 4 NC_009009:SSA_1891|5end_Oxidoreductase,_aldo/keto_reductase_family,_putative_1888991..1889221_NEGATIVE 267 125 82 43 7 NC_009009:SSA_0355|5end_DNA_mismatch_repair_protein,_putative_346847..347077_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 301 169 124 122 70 NC_009009:SSA_1960|3end_hypothetical_protein_1956571..1956721_NEGATIVE 295 105 69 140 103 NC_009009:SSA_1174|3end_Dihydrolipoamide_dehydrogenase,_putative_1201148..1201298_NEGATIVE 283 177 135 143 100 NC_009009:SSA_1378|3end_hypothetical_protein_1397636..1397786_NEGATIVE 280 170 129 42 5 NC_009009:SSA_1856|3end_hypothetical_protein_1852077..1852227_NEGATIVE 280 150 104 129 69 NC_009009:SSA_1473|3end_hypothetical_protein_1478729..1478879_NEGATIVE 280 90 44 129 71 NC_009009:SSA_1084|3end_Conserved_uncharacterized_protein_1102603..1102753_POSITIVE 277 89 45 87 38 NC_009009:SSA_1731|3end_ATP-dependent_Clp_protease,_proteolytic_subunit,_putative_1716218..1716368_NEGATIVE 275 227 188 109 75 NC_009009:SSA_0972|3end_hypothetical_protein_980364..980514_POSITIVE 272 228 197 131 99 NC_009009:SSA_0484|3end_Glutamyl-tRNA_reductase,_putative_485825..485975_POSITIVE 267 198 151 91 34 NC_009009:SSA_1892|3end_hypothetical_protein_1889068..1889218_NEGATIVE 261 118 73 145 102 NC_009009:SSA_0325|3end_Membrane-anchored_glycerophosphoryl_diester_phosphodiesterase,_putative_319437..319587_POSITIVE 258 125 83 133 84 NC_009009:SSA_2223|3end_Capsular_polysaccharide_biosynthesis_protein_Wzd_(chain_length_regulator),_putative_2224008..2224158_NEGATIVE 257 169 133 36 1 NC_009009:SSA_0502|3end_Peptide_ABC_transporter,_permease_protein,_putative_502323..502473_POSITIVE 256 249 201 144 96 NC_009009:SSA_0861|3end_hypothetical_protein_851742..851892_NEGATIVE 251 164 124 88 27 NC_009009:SSA_1117|3end_hypothetical_protein_1143386..1143536_POSITIVE 250 111 73 151 103 NC_009009:SSA_0620|3end_hypothetical_protein_611951..612101_NEGATIVE 248 174 133 144 102 NC_009009:SSA_2369|3end_hypothetical_protein_2370239..2370389_NEGATIVE 248 100 53 114 58 NC_009009:SSA_1338|3end_hypothetical_protein_1351200..1351350_NEGATIVE 245 89 45 82 31 NC_009009:SSA_1666|3end_Collagen-binding_surface_protein,_putative_1665375..1665525_NEGATIVE 245 169 132 110 70 NC_009009:SSA_0101|3end_Conserved_uncharacterized_protein_104113..104263_POSITIVE