Origin IGS: aatgataattaaggggtgcttgttcgtttgaacttgctgagaatagacccataaacctgatacggataatgccgtcgtagggaaactccccttctattttattattcaaaatacataat .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 attatgtattttgaataataaaatagaaggggagtttccctacgacggcattatccgtatcaggtttatgggtctattctcagcaagttcaaacgaacaagcaccccttaattatcatt Mask Tandem Repeat Region ================================================ aatgataattaaggggtgcttgttcgtttgaacttgctgagaatagacccataaacctgatacggataatgccgtcgtagggaaactccccttctattttattattcaaaatacataat Find is-nt database================================================ Query_seq: PI1450:PI1451|PI1450:PI1451:hypothetical protein:outer membrane receptor proteins, tonB dependent (possibly iron transport related):->->:1372952..1373070 119 aatgataattaaggggtgcttgttcgtttgaacttgctgagaatagacccataaacctgatacggataatgccgtcgtagggaaactccccttctattttattattcaaaatacataat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI1450:PI1451|PI1450:PI1451:hypothetical protein:outer membrane receptor proteins, tonB dependent (possibly iron transport related):->->:1372952..1373070 119 aatgataattaaggggtgcttgttcgtttgaacttgctgagaatagacccataaacctgatacggataatgccgtcgtagggaaactccccttctattttattattcaaaatacataat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI1450:PI1451|PI1450:PI1451:hypothetical protein:outer membrane receptor proteins, tonB dependent (possibly iron transport related):->->:1372952..1373070 119 aatgataattaaggggtgcttgttcgtttgaacttgctgagaatagacccataaacctgatacggataatgccgtcgtagggaaactccccttctattttattattcaaaatacataat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aatgataattaaggggtgcttgttcgtttgaacttgctgagaatagacccataaacctgatacggataatgccgtcgtagggaaactccccttctattttattattcaaaatacataat Predict ORF larger than 30AA ================================================ Protein_Len: 37 Strand: - Start: 2 End: 112 . H Y N L P A Q E N S S A S F L G M F R I R I I G D Y P F E G E I K N N L M ....... aatgataattaaggggtgcttgttcgtttgaacttgctgagaatagacccataaacctgatacggataatgccgtcgtagggaaactccccttctattttattattcaaaatacataat 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================================================ aatgataattaaggggtgcttgttcgtttgaacttgctgagaatagacccataaacctgatacggataatgccgtcgtagggaaactccccttctattttattattcaaaatacataat Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PI1450:PI1451|PI1450:PI1451:hypothetical protein:outer membrane receptor proteins, tonB dependent (possibly iron transport related):->->:1372952..1373070 119 aatgataattaaggggtgcttgttcgtttgaacttgctgagaatagacccataaacctgatacggataatgccgtcgtagggaaactccccttctattttattattcaaaatacataat Intra-Species Hit: Count: 1 Min: 1 Max: 119 Len: 119 Subject: pint_PI1450_PI1451|hypothetical protein:outer membrane receptor proteins, tonB dependent (possibly iron transport related)|POSITIVE:POSITIVE|[1372952,1373070]|119 HSP 1 e-value: 1.0E-61 bit: 236.0 Len: 119 Query Start:1 Query End:119 Subject Strand: POSITIVE Subject Start: 1 Subject End: 119 aatgataattaaggggtgcttgttcgtttgaacttgctgagaatagacccataaacctgatacggataatgccgtcgtagggaaactccccttctattttattattcaaaatacataat aatgataattaaggggtgcttgttcgtttgaacttgctgagaatagacccataaacctgatacggataatgccgtcgtagggaaactccccttctattttattattcaaaatacataat Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUGAUAAUUAAGGGGUGCUUGUUCGUUUGAACUUGCUGAGAAUAGACCCAUAAACCUGAUACGGAUAAUGCCGUCGUAGGGAAACUCCCCUUCUAUUUUAUUAUUCAAAAUACAUAAU ((((((((..((((((.((..((((....))))..))..................((((..((((......))))..))))......)))))).....))))))))............. (-27.60) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUUAUGUAUUUUGAAUAAUAAAAUAGAAGGGGAGUUUCCCUACGACGGCAUUAUCCGUAUCAGGUUUAUGGGUCUAUUCUCAGCAAGUUCAAACGAACAAGCACCCCUUAAUUAUCAUU ......(((((((.....))))))).((((((.(((..(((...((((......))))...)))....((((......))))....((((....)))).))).)))))).......... (-23.90) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 298 66 21 90 43 pint:PI0604|5end_O-succinylbenzoic_acid--CoA_ligase_550825..551055_POSITIVE 282 90 46 205 166 pint:PI0266|5end_DNA_primase_(bacterial_type)_257931..258161_POSITIVE 279 96 56 203 158 pint:PI0651|5end_HD_superfamily_hydrolase_592270..592500_POSITIVE 277 93 55 97 50 pint:PI1778|5end_UDP-N-acetylglucosamine_1-carboxyvinyltransferase_1710009..1710239_POSITIVE 270 91 56 99 42 pint:PI1024|5end_conserved_hypothetical_protein;_possible_nitroreductase_family_protein_940167..940397_POSITIVE 265 73 32 68 13 pint:PI1640|5end_hypothetical_protein_1558062..1558292_POSITIVE 263 79 34 59 6 pint:PI2100|5end_conserved_hypothetical_protein_2053351..2053581_POSITIVE 262 94 57 121 85 pint:PI2162|5end_conserved_hypothetical_protein_2108796..2109026_POSITIVE 260 79 31 83 8 pint:PI1477|5end_TonB-dependent_outer_membrane_receptor_1399734..1399964_POSITIVE 260 95 73 30 5 pint:PI0596|5end_hypothetical_protein_546400..546630_POSITIVE 257 60 13 210 154 pint:PI1539|5end_3-phosphoshikimate_1-carboxyvinyltransferase_1459804..1460034_POSITIVE 256 39 11 87 51 pint:PI1636|5end_hypothetical_protein_1554246..1554476_POSITIVE 255 95 52 196 146 pint:PI0506|5end_conserved_hypothetical_protein_465501..465731_POSITIVE 255 95 55 204 165 pint:PI0365|5end_hypothetical_protein_335721..335951_POSITIVE 254 93 55 129 89 pint:PI0528|5end_hypothetical_protein_482791..483021_POSITIVE 253 50 12 50 8 pint:PI1867|5end_helicase_related_protein_1812390..1812620_POSITIVE 253 100 61 42 1 pint:PI0114|5end_hypothetical_protein_108139..108369_POSITIVE 252 79 34 68 18 pint:PI0234|5end_integrase_234473..234703_POSITIVE 251 90 47 197 155 pint:PI0932|5end_conserved_hypothetical_protein;_possible_hemin_receptor_863854..864084_POSITIVE 251 55 13 187 140 pint:PI0822|5end_tRNA_delta(2)-isopentenylpyrophosphate_transferase_761028..761258_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 282 90 46 151 112 pint:PI0265|3end_conjugative_transposon_protein,_TraO_257957..258107_POSITIVE 277 93 55 89 42 pint:PI1777|3end_conserved_hypothetical_protein_1710081..1710231_POSITIVE 268 79 41 67 16 pint:PI2166|3end_hypothetical_protein_2112073..2112223_POSITIVE 267 57 14 66 21 pint:PI2093|3end_hypothetical_protein_2049440..2049590_POSITIVE 265 73 32 59 4 pint:PI1639|3end_conserved_hypothetical_protein_1558133..1558283_POSITIVE 256 39 11 67 31 pint:PI1635|3end_hypothetical_protein_1554306..1554456_POSITIVE 253 100 61 88 47 pint:PI0111|3end_hypothetical_protein_108265..108415_POSITIVE 247 87 47 57 10 pint:PI1272|3end_possible_transcriptional_regulator_1192342..1192492_POSITIVE 247 50 3 136 85 pint:PI0694|3end_Na+/dicarboxylate_or_sulfate_symporter_631177..631327_POSITIVE 243 96 62 51 3 pint:PI0042|3end_hypothetical_protein_43444..43594_POSITIVE 241 84 41 42 3 pint:PI0796|3end_competence_protein_734954..735104_POSITIVE 240 77 35 64 9 pint:PI1734|3end_possible_carboxyl-terminal_protease-related_protein_1653829..1653979_POSITIVE 238 99 72 49 8 pint:PI0335|3end_hypothetical_protein_314420..314570_POSITIVE 234 39 4 52 16 pint:PI0691|3end_hypothetical_protein_628369..628519_POSITIVE 233 59 11 58 20 pint:PI0248|3end_protein_associated_with_conjugate_transformation/chromosome_partioning_246647..246797_POSITIVE 232 50 14 101 68 pint:PI0842|3end_5-formyltetrahydrofolate_cyclo-ligase_776191..776341_POSITIVE 230 80 35 77 13 pint:PI0960|3end_hypothetical_protein_891381..891531_POSITIVE 230 89 55 112 72 pint:PI0758|3end_hypothetical_protein_690506..690656_POSITIVE 229 49 1 126 80 pint:PI1461|3end_conserved_hypothetical_protein_1385073..1385223_POSITIVE 228 52 12 137 99 pint:PI1885|3end_cell_division_protein_1827639..1827789_POSITIVE