Origin IGS: atcgtacaatttgtacttgatagagctactaccacaatttaaaactaatatcttcataatataattcttgttttctgatttgaaaaaatgcaggagttaaagaatcgttacaccctctaactcctcctaattccttaaatta .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 taatttaaggaattaggaggagttagagggtgtaacgattctttaactcctgcattttttcaaatcagaaaacaagaattatattatgaagatattagttttaaattgtggtagtagctctatcaagtacaaattgtacgat Mask Tandem Repeat Region ================================================ atcgtacaatttgtacttgatagagctactaccacaatttaaaactaatatcttcataatataattcttgttttctgatttgaaaaaatgcaggagttaaagaatcgttacaccctctaactcctcctaattccttaaatta Find is-nt database================================================ Query_seq: PI0197:PI0199|PI0197:PI0199:acetate kinase:phosphate acetyltransferase:->->:189888..190029 142 atcgtacaatttgtacttgatagagctactaccacaatttaaaactaatatcttcataatataattcttgttttctgatttgaaaaaatgcaggagttaaagaatcgttacaccctctaactcctcctaattccttaaatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI0197:PI0199|PI0197:PI0199:acetate kinase:phosphate acetyltransferase:->->:189888..190029 142 atcgtacaatttgtacttgatagagctactaccacaatttaaaactaatatcttcataatataattcttgttttctgatttgaaaaaatgcaggagttaaagaatcgttacaccctctaactcctcctaattccttaaatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI0197:PI0199|PI0197:PI0199:acetate kinase:phosphate acetyltransferase:->->:189888..190029 142 atcgtacaatttgtacttgatagagctactaccacaatttaaaactaatatcttcataatataattcttgttttctgatttgaaaaaatgcaggagttaaagaatcgttacaccctctaactcctcctaattccttaaatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 atcgtacaatttgtacttgatagagctactaccacaatttaaaactaatatcttcataatataattcttgttttctgatttgaaaaaatgcaggagttaaagaatcgttacaccctctaactcctcctaattccttaaatta Predict ORF larger than 30AA ================================================ Protein_Len: 31 Strand: - Start: 1 End: 93 D Y L K Y K I S S S G C N L V L I K M I Y N K N E S K F F H M ................................................. atcgtacaatttgtacttgatagagctactaccacaatttaaaactaatatcttcataatataattcttgttttctgatttgaaaaaatgcaggagttaaagaatcgttacaccctctaactcctcctaattccttaaatta 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: 58 End: 87 .........................................................TTTTTCAAATCAGAAAACAAGAATTATATT....................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ atcgtacaatttgtacttgatagagctactaccacaatttaaaactaatatcttcataatataattcttgttttctgatttgaaaaaatgcaggagttaaagaatcgttacaccctctaactcctcctaattccttaaatta Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PI0197:PI0199|PI0197:PI0199:acetate kinase:phosphate acetyltransferase:->->:189888..190029 142 atcgtacaatttgtacttgatagagctactaccacaatttaaaactaatatcttcataatataattcttgttttctgatttgaaaaaatgcaggagttaaagaatcgttacaccctctaactcctcctaattccttaaatta Intra-Species Hit: Count: 1 Min: 1 Max: 142 Len: 142 Subject: pint_PI0197_PI0199|acetate kinase:phosphate acetyltransferase|POSITIVE:POSITIVE|[189888,190029]|142 HSP 1 e-value: 3.0E-75 bit: 281.0 Len: 142 Query Start:1 Query End:142 Subject Strand: POSITIVE Subject Start: 1 Subject End: 142 atcgtacaatttgtacttgatagagctactaccacaatttaaaactaatatcttcataatataattcttgttttctgatttgaaaaaatgcaggagttaaagaatcgttacaccctctaactcctcctaattccttaaatta atcgtacaatttgtacttgatagagctactaccacaatttaaaactaatatcttcataatataattcttgttttctgatttgaaaaaatgcaggagttaaagaatcgttacaccctctaactcctcctaattccttaaatta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUCGUACAAUUUGUACUUGAUAGAGCUACUACCACAAUUUAAAACUAAUAUCUUCAUAAUAUAAUUCUUGUUUUCUGAUUUGAAAAAAUGCAGGAGUUAAAGAAUCGUUACACCCUCUAACUCCUCCUAAUUCCUUAAAUUA ...((((.....))))....(((((......................((((.......)))).((((((..((((((((((....)))).))))))...)))))).........)))))....................... (-17.80) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAUUUAAGGAAUUAGGAGGAGUUAGAGGGUGUAACGAUUCUUUAACUCCUGCAUUUUUUCAAAUCAGAAAACAAGAAUUAUAUUAUGAAGAUAUUAGUUUUAAAUUGUGGUAGUAGCUCUAUCAAGUACAAAUUGUACGAU ((((((((((.....(.((((((((((((((......)))))))))))))).)...(((((......)))))..........................)))))))))).(((((.....)))))..((((.....))))... (-33.10) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 244 125 88 222 190 pint:PI2159|5end_immunoreactive_84_kDa_antigen_PG93_2105267..2105497_POSITIVE 235 128 89 127 69 pint:PI0809|5end_hypothetical_protein_746630..746860_POSITIVE 230 97 68 174 140 pint:PI0004|5end_hypothetical_protein_6199..6429_POSITIVE 226 90 45 229 180 pint:PI1745|5end_conserved_hypothetical_protein_1666615..1666845_POSITIVE 223 136 94 178 130 pint:PI0328|5end_conserved_hypothetical_protein_309476..309706_POSITIVE 221 127 92 215 173 pint:PI0715|5end_hypothetical_protein_652311..652541_POSITIVE 216 119 77 183 142 pint:PI1536|5end_hypothetical_protein_1455555..1455785_POSITIVE 213 128 90 188 153 pint:PI1460|5end_ribonucleotide_reductase,_alpha_subunit,_N-terminal_region_1382215..1382445_POSITIVE 210 128 89 45 5 pint:PI1884|5end_conserved_hypothetical_protein_1826883..1827113_POSITIVE 208 127 89 231 177 pint:PI0811|5end_protease/hemagglutinin_PrtT,_streptopain_family_746738..746968_POSITIVE 206 125 81 135 92 pint:PI0518|5end_5'-nucleotidase_precursor_477076..477306_POSITIVE 206 128 87 220 185 pint:PI0248|5end_protein_associated_with_conjugate_transformation/chromosome_partioning_246139..246369_POSITIVE 205 107 65 53 22 pint:PI2113|5end_hypothetical_protein_2063794..2064024_POSITIVE 205 128 89 76 38 pint:PI2055|5end_hypothetical_protein_2012999..2013229_POSITIVE 205 120 88 94 69 pint:PI0049|5end_outer_membrane_receptor_protein_(iron_transport)_48605..48835_POSITIVE 197 34 7 78 52 pint:PI0195|5end_epimerase/reductase_187172..187402_POSITIVE 195 125 92 134 101 pint:PI1816|5end_acid_phosphatase_1754646..1754876_POSITIVE 193 125 92 158 118 pint:PI1028|5end_glutamate_synthase,_small_subunit_943420..943650_POSITIVE 193 128 89 168 124 pint:PI0382|5end_conserved_hypothetical_protein_351510..351740_POSITIVE 192 127 99 40 10 pint:PI0716|5end_conserved_hypothetical_protein_652136..652366_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 274 128 82 81 35 pint:PI1444|3end_protease_ClpB_1368137..1368287_POSITIVE 246 119 71 107 58 pint:PI1572|3end_hypothetical_protein_1498215..1498365_POSITIVE 242 49 13 76 36 pint:PI1681|3end_Mg2+/Co2+_transporter_1598129..1598279_POSITIVE 216 85 45 148 105 pint:PI1744|3end_chromosome_partitioning_protein_1666620..1666770_POSITIVE 216 119 77 49 8 pint:PI1535|3end_response_regulator_1455501..1455651_POSITIVE 206 125 81 63 20 pint:PI0517|3end_apparent_PorT_homolog_477084..477234_POSITIVE 205 128 89 73 35 pint:PI2054|3end_hypothetical_protein_2013076..2013226_POSITIVE 199 54 26 104 73 pint:PI0434|3end_possible_beta-lactamase_406890..407040_POSITIVE 196 130 81 149 92 pint:PI2075|3end_conserved_hypothetical_protein_2035355..2035505_POSITIVE 195 45 1 62 11 pint:PI1633|3end_hypothetical_protein_1552955..1553105_POSITIVE 194 34 2 146 107 pint:PI2117|3end_fumarate_reductase/succinate_dehydrogenase_flavoprotein_subunit,_C-terminal_2066684..2066834_POSITIVE 193 125 92 57 17 pint:PI1027|3end_hypothetical_protein_943399..943549_POSITIVE 193 128 89 132 88 pint:PI0381|3end_probable_transcriptional_regulator,_AraC_family_351554..351704_POSITIVE 185 124 81 80 38 pint:PI0605|3end_chloromuconate_cycloisomerase_553026..553176_POSITIVE 184 106 71 136 101 pint:PI1837|3end_aspartate_ammonia-lyase_1780406..1780556_POSITIVE 183 128 92 65 33 pint:PI1602|3end_conserved_hypothetical_protein;_possible_internalin-related_protein_1533819..1533969_POSITIVE 183 126 92 104 70 pint:PI0749|3end_hypothetical_protein_677469..677619_POSITIVE 180 139 92 75 32 pint:PI0063|3end_transcriptional_regulator,_GntR_family_63620..63770_POSITIVE 177 38 1 64 31 pint:PI2016|3end_ribosomal_large_subunit_pseudouridine_synthase_D_1974933..1975083_POSITIVE 172 123 100 29 1 pint:PI2051|3end_hypothetical_protein_2007835..2007985_POSITIVE