Origin IGS: gcttttaatatatatctaattttttgcttattagtaaataaatcaaatcgttttccttatctaaaggcagttgcaaagttagtaaaaaaaagtcagactaaaaattaatccgtgaactaaaatattatgttgaattacgctaaagtcttattcgcttggtgcttagcgcatctttagactttcaagtaagcagaaaagctt .........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 aagcttttctgcttacttgaaagtctaaagatgcgctaagcaccaagcgaataagactttagcgtaattcaacataatattttagttcacggattaatttttagtctgacttttttttactaactttgcaactgcctttagataaggaaaacgatttgatttatttactaataagcaaaaaattagatatatattaaaagc Mask Tandem Repeat Region ================================================ gcttttaatatatatctaattttttgcttattagtaaataaatcaaatcgttttccttatctaaaggcagttgcaaagttagtaaaaaaaagtcagactaaaaattaatccgtgaactaaaatattatgttgaattacgctaaagtcttattcgcttggtgcttagcgcatctttagactttcaagtaagcagaaaagctt Find is-nt database================================================ Query_seq: PI1454:PI1455|PI1454:PI1455:chromosomal replication initiator protein, DnaA:hypothetical protein:->->:1378202..1378402 201 gcttttaatatatatctaattttttgcttattagtaaataaatcaaatcgttttccttatctaaaggcagttgcaaagttagtaaaaaaaagtcagactaaaaattaatccgtgaactaaaatattatgttgaattacgctaaagtcttattcgcttggtgcttagcgcatctttagactttcaagtaagcagaaaagctt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI1454:PI1455|PI1454:PI1455:chromosomal replication initiator protein, DnaA:hypothetical protein:->->:1378202..1378402 201 gcttttaatatatatctaattttttgcttattagtaaataaatcaaatcgttttccttatctaaaggcagttgcaaagttagtaaaaaaaagtcagactaaaaattaatccgtgaactaaaatattatgttgaattacgctaaagtcttattcgcttggtgcttagcgcatctttagactttcaagtaagcagaaaagctt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI1454:PI1455|PI1454:PI1455:chromosomal replication initiator protein, DnaA:hypothetical protein:->->:1378202..1378402 201 gcttttaatatatatctaattttttgcttattagtaaataaatcaaatcgttttccttatctaaaggcagttgcaaagttagtaaaaaaaagtcagactaaaaattaatccgtgaactaaaatattatgttgaattacgctaaagtcttattcgcttggtgcttagcgcatctttagactttcaagtaagcagaaaagctt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gcttttaatatatatctaattttttgcttattagtaaataaatcaaatcgttttccttatctaaaggcagttgcaaagttagtaaaaaaaagtcagactaaaaattaatccgtgaactaaaatattatgttgaattacgctaaagtcttattcgcttggtgcttagcgcatctttagactttcaagtaagcagaaaagctt Predict ORF larger than 30AA ================================================ Protein_Len: 32 Strand: + Start: 10 End: 105 ......... M Y L I F C L L V N K S N R F P Y L K A V A K L V K K S Q T K N ................................................................................................ gcttttaatatatatctaattttttgcttattagtaaataaatcaaatcgttttccttatctaaaggcagttgcaaagttagtaaaaaaaagtcagactaaaaattaatccgtgaactaaaatattatgttgaattacgctaaagtcttattcgcttggtgcttagcgcatctttagactttcaagtaagcagaaaagctt 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================================================ gcttttaatatatatctaattttttgcttattagtaaataaatcaaatcgttttccttatctaaaggcagttgcaaagttagtaaaaaaaagtcagactaaaaattaatccgtgaactaaaatattatgttgaattacgctaaagtcttattcgcttggtgcttagcgcatctttagactttcaagtaagcagaaaagctt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PI1454:PI1455|PI1454:PI1455:chromosomal replication initiator protein, DnaA:hypothetical protein:->->:1378202..1378402 201 gcttttaatatatatctaattttttgcttattagtaaataaatcaaatcgttttccttatctaaaggcagttgcaaagttagtaaaaaaaagtcagactaaaaattaatccgtgaactaaaatattatgttgaattacgctaaagtcttattcgcttggtgcttagcgcatctttagactttcaagtaagcagaaaagctt Intra-Species Hit: Count: 1 Min: 1 Max: 201 Len: 201 Subject: pint_PI1454_PI1455|chromosomal replication initiator protein, DnaA:hypothetical protein|POSITIVE:POSITIVE|[1378202,1378402]|201 HSP 1 e-value: 6.0E-96 bit: 351.0 Len: 201 Query Start:1 Query End:201 Subject Strand: POSITIVE Subject Start: 1 Subject End: 201 gcttttaatatatatctaattttttgcttattagtaaataaatcaaatcgttttccttatctaaaggcagttgcaaagttagtnnnnnnnngtcagactaaaaattaatccgtgaactaaaatattatgttgaattacgctaaagtcttattcgcttggtgcttagcgcatctttagactttcaagtaagcagaaaagctt gcttttaatatatatctaattttttgcttattagtaaataaatcaaatcgttttccttatctaaaggcagttgcaaagttagtaaaaaaaagtcagactaaaaattaatccgtgaactaaaatattatgttgaattacgctaaagtcttattcgcttggtgcttagcgcatctttagactttcaagtaagcagaaaagctt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GCUUUUAAUAUAUAUCUAAUUUUUUGCUUAUUAGUAAAUAAAUCAAAUCGUUUUCCUUAUCUAAAGGCAGUUGCAAAGUUAGUAAAAAAAAGUCAGACUAAAAAUUAAUCCGUGAACUAAAAUAUUAUGUUGAAUUACGCUAAAGUCUUAUUCGCUUGGUGCUUAGCGCAUCUUUAGACUUUCAAGUAAGCAGAAAAGCUU ...................(((((((((((((........................(((.((((..((....))....)))))))...((((((.................(((((.(((.((.((((((......))).))).)).))))))))..(((((.....)))))....))))))..))))))))))))).... (-32.40) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAGCUUUUCUGCUUACUUGAAAGUCUAAAGAUGCGCUAAGCACCAAGCGAAUAAGACUUUAGCGUAAUUCAACAUAAUAUUUUAGUUCACGGAUUAAUUUUUAGUCUGACUUUUUUUUACUAACUUUGCAACUGCCUUUAGAUAAGGAAAACGAUUUGAUUUAUUUACUAAUAAGCAAAAAAUUAGAUAUAUAUUAAAAGC ..((((((....((((...(((((((....((.((((........)))).)).)))))))...)))).........(((((((((((..(((((((.....)))))))..(((((((((((((....((....))..)))).)))))))))...((((.((((((....)))))))))).))))))).))))...)))))) (-32.90) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 273 84 55 217 188 pint:PI0454|5end_hypothetical_protein_426653..426883_POSITIVE 268 168 125 89 44 pint:PI1663|5end_hypothetical_protein_1577127..1577357_POSITIVE 258 200 153 76 22 pint:PI2045|5end_hypothetical_protein_1998494..1998724_POSITIVE 257 170 125 216 173 pint:PI2123|5end_adenine_phosphoribosyltransferase_2071711..2071941_POSITIVE 254 168 125 222 170 pint:PI0136|5end_surface_antigen_BspA_127105..127335_POSITIVE 253 200 153 132 79 pint:PI0062|5end_endopeptidase_60963..61193_POSITIVE 252 199 154 89 46 pint:PI0342|5end_hypothetical_protein_317556..317786_POSITIVE 250 199 151 46 2 pint:PI1871|5end_glycosyl_transferase,_group_1_family_protein_1815788..1816018_POSITIVE 249 170 125 152 98 pint:PI2069|5end_ISPg3-related_transposase,_C-terminal_fragment_2028985..2029215_POSITIVE 249 170 125 152 98 pint:PI2070|5end_ISPg3-related_transposase,_N-terminal_fragment_2028985..2029215_POSITIVE 245 192 157 97 57 pint:PI1415|5end_cation_transporting_ATPase/E1-E2_ATPase_1333939..1334169_POSITIVE 245 192 157 71 31 pint:PI1414|5end_conserved_hypothetical_protein_1333913..1334143_POSITIVE 244 200 151 187 128 pint:PI1285|5end_ATP_synthase,_B_subunit_1200348..1200578_POSITIVE 244 187 145 46 2 pint:PI0362|5end_hypothetical_protein_333397..333627_POSITIVE 243 198 153 63 17 pint:PI0586|5end_hypothetical_protein_533757..533987_POSITIVE 242 100 56 57 18 pint:PI0861|5end_glucosamine--fructose-6-phosphate_aminotransferase_(glutamine-fructose-6-phosphate_transaminase_(isomerizing))_796346..796576_POSITIVE 242 183 141 154 109 pint:PI0833|5end_conserved_hypothetical_protein_770059..770289_POSITIVE 241 168 128 200 149 pint:PI1778|5end_UDP-N-acetylglucosamine_1-carboxyvinyltransferase_1710009..1710239_POSITIVE 241 186 145 104 60 pint:PI0785|5end_hypothetical_protein_723744..723974_POSITIVE 240 80 63 18 1 pint:PI1384|5end_conserved_hypothetical_protein_1305171..1305401_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 271 184 148 121 88 pint:PI0356|3end_hypothetical_protein_327288..327438_POSITIVE 268 168 125 123 78 pint:PI1662|3end_hypothetical_protein_1577241..1577391_POSITIVE 256 196 154 146 107 pint:PI1773|3end_alpha-amylase_(neopullulanase)_1706107..1706257_POSITIVE 252 199 154 68 25 pint:PI0341|3end_conserved_hypothetical_protein_317615..317765_POSITIVE 246 169 129 49 17 pint:PI0675|3end_hypothetical_protein_613957..614107_POSITIVE 246 170 123 143 101 pint:PI0163|3end_conserved_hypothetical_protein_158410..158560_POSITIVE 244 200 151 82 23 pint:PI1284|3end_ATP_synthase,_delta_subunit_1200323..1200473_POSITIVE 239 198 153 121 82 pint:PI0606|3end_naphthoate_synthase_553917..554067_POSITIVE 239 178 146 129 93 pint:PI0456|3end_30S_ribosomal_protein_S12_429219..429369_POSITIVE 238 180 131 145 96 pint:PI0324|3end_conserved_hypothetical_protein_305680..305830_POSITIVE 235 87 42 76 33 pint:PI1805|3end_TPR_repeat_containing_protein_1740533..1740683_POSITIVE 234 170 125 138 105 pint:PI0664|3end_dihydroorotate_dehydrogenase,_electron_transfer_subunit_607819..607969_POSITIVE 232 176 133 142 90 pint:PI1651|3end_hypothetical_protein_1564512..1564662_POSITIVE 232 168 153 133 115 pint:PI1579|3end_penicillin-binding_protein_2_1507913..1508063_POSITIVE 231 168 123 61 1 pint:PI1970|3end_hypothetical_protein_1927882..1928032_POSITIVE 231 97 67 47 17 pint:PI1446|3end_conserved_hypothetical_protein_1369832..1369982_POSITIVE 231 174 139 146 104 pint:PI0835|3end_conserved_hypothetical_protein;_possible_protein-export_membrane_protein_771859..772009_POSITIVE 230 170 124 78 32 pint:PI1794|3end_conserved_hypothetical_protein_1726696..1726846_POSITIVE 230 199 156 54 3 pint:PI0257|3end_conjugative_transposon_protein,_TraF_249802..249952_POSITIVE 228 168 128 133 82 pint:PI1504|3end_non-specific_DNA-binding_protein_1424904..1425054_POSITIVE