Origin IGS: tgagttccttgtgtggaactcagcccgaatattatttgatgtaagaagttttagcgaacaataataaaagaaagatgatgatacaggaagttccaacgtcttttttta .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 taaaaaaagacgttggaacttcctgtatcatcatctttcttttattattgttcgctaaaacttcttacatcaaataatattcgggctgagttccacacaaggaactca Mask Tandem Repeat Region ================================================ tgagttccttgtgtggaactcagcccgaatattatttgatgtaagaagttttagcgaacaataataaaagaaagatgatgatacaggaagttccaacgtcttttttta Find is-nt database================================================ Query_seq: PI1057:PI1058|PI1057:PI1058:hypothetical protein:possible FHA domain protein:->->:977609..977716 108 tgagttccttgtgtggaactcagcccgaatattatttgatgtaagaagttttagcgaacaataataaaagaaagatgatgatacaggaagttccaacgtcttttttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI1057:PI1058|PI1057:PI1058:hypothetical protein:possible FHA domain protein:->->:977609..977716 108 tgagttccttgtgtggaactcagcccgaatattatttgatgtaagaagttttagcgaacaataataaaagaaagatgatgatacaggaagttccaacgtcttttttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI1057:PI1058|PI1057:PI1058:hypothetical protein:possible FHA domain protein:->->:977609..977716 108 tgagttccttgtgtggaactcagcccgaatattatttgatgtaagaagttttagcgaacaataataaaagaaagatgatgatacaggaagttccaacgtcttttttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tgagttccttgtgtggaactcagcccgaatattatttgatgtaagaagttttagcgaacaataataaaagaaagatgatgatacaggaagttccaacgtcttttttta Predict ORF larger than 30AA ================================================ Protein_Len: 32 Strand: - Start: 1 End: 96 S N R T H F E A R I N N S T L L K L S C Y Y F F S S S V P L E M ............ tgagttccttgtgtggaactcagcccgaatattatttgatgtaagaagttttagcgaacaataataaaagaaagatgatgatacaggaagttccaacgtcttttttta 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: 61 End: 90 ............................................................CTTCCTGTATCATCATCTTTCTTTTATTAT.................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tgagttccttgtgtggaactcagcccgaatattatttgatgtaagaagttttagcgaacaataataaaagaaagatgatgatacaggaagttccaacgtcttttttta Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PI1057:PI1058|PI1057:PI1058:hypothetical protein:possible FHA domain protein:->->:977609..977716 108 tgagttccttgtgtggaactcagcccgaatattatttgatgtaagaagttttagcgaacaataataaaagaaagatgatgatacaggaagttccaacgtcttttttta Intra-Species Hit: Count: 1 Min: 1 Max: 100 Len: 100 Subject: pint_PI1057_PI1058|hypothetical protein:possible FHA domain protein|POSITIVE:POSITIVE|[977609,977716]|108 HSP 1 e-value: 3.0E-50 bit: 198.0 Len: 100 Query Start:1 Query End:100 Subject Strand: POSITIVE Subject Start: 1 Subject End: 100 tgagttccttgtgtggaactcagcccgaatattatttgatgtaagaagttttagcgaacaataataaaagaaagatgatgatacaggaagttccaacgtc........ tgagttccttgtgtggaactcagcccgaatattatttgatgtaagaagttttagcgaacaataataaaagaaagatgatgatacaggaagttccaacgtc........ Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGAGUUCCUUGUGUGGAACUCAGCCCGAAUAUUAUUUGAUGUAAGAAGUUUUAGCGAACAAUAAUAAAAGAAAGAUGAUGAUACAGGAAGUUCCAACGUC ((((((((......))))))))...............(((((.....((((....))))..........................((.....)).))))) (-17.80) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GACGUUGGAACUUCCUGUAUCAUCAUCUUUCUUUUAUUAUUGUUCGCUAAAACUUCUUACAUCAAAUAAUAUUCGGGCUGAGUUCCACACAAGGAACUCA ((..(.((.....)).)..))........(((..(((((((.......................)))))))...)))..(((((((......))))))). (-15.20) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 442 50 1 173 124 pint:PI1244|5end_hypothetical_protein_1168803..1169033_POSITIVE 290 37 8 138 101 pint:PI0985|5end_aspartyl-tRNA_synthetase_910174..910404_POSITIVE 276 100 53 226 174 pint:PI1449|5end_conserved_hypothetical_protein_1372018..1372248_POSITIVE 268 50 1 98 49 pint:PI1909|5end_DNA_gyrase,_B_subunit_1853223..1853453_POSITIVE 257 43 3 175 138 pint:PI1774|5end_hypothetical_protein_1706184..1706414_POSITIVE 242 50 11 49 2 pint:PI1728|5end_ATP-dependent_Clp_protease,_proteolytic_subunit_1646916..1647146_POSITIVE 238 98 55 133 82 pint:PI0543|5end_adenylate_kinase_495073..495303_POSITIVE 237 41 1 77 34 pint:PI0257|5end_conjugative_transposon_protein,_TraF_249348..249578_POSITIVE 236 99 52 184 132 pint:PI1583|5end_phosphoribosylaminoimidazolecarboxamide_formyltransferase_(AICAR)/IMP_cyclohydrolase_(ATIC)_1510530..1510760_POSITIVE 235 57 12 63 17 pint:PI1438|5end_penicillin_tolerance_protein/steroid_biosynthesis_1356263..1356493_POSITIVE 232 48 2 104 39 pint:PI1936|5end_conserved_hypothetical_protein;_possible_serine-type_protease_1887039..1887269_POSITIVE 231 46 7 103 62 pint:PI0856|5end_hypothetical_protein_789581..789811_POSITIVE 225 98 55 183 140 pint:PI0198|5end_hypothetical_protein_190719..190949_POSITIVE 220 46 1 162 114 pint:PI1828|5end_peptidase,_M23/M37_family,_C-terminal_1768419..1768649_POSITIVE 219 85 44 127 84 pint:PI0034|5end_FKBP-type_peptidyl-prolyl_cis-trans_isomerase_37151..37381_POSITIVE 217 88 41 145 103 pint:PI1895|5end_penicillin-binding_protein_2_1838460..1838690_POSITIVE 217 90 54 212 173 pint:PI0156|5end_conserved_hypothetical_protein_148716..148946_POSITIVE 216 99 57 142 93 pint:PI0786|5end_conserved_hypothetical_protein;_possible_glycosyltransferase_723240..723470_POSITIVE 214 47 1 151 98 pint:PI1973|5end_conserved_hypothetical_protein_1930429..1930659_POSITIVE 214 49 2 166 125 pint:PI0828|5end_GMP_synthase_(glutamine_amidotransferase)_764077..764307_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 442 50 1 50 1 pint:PI1243|3end_conserved_hypothetical_protein_1168760..1168910_POSITIVE 301 26 1 94 69 pint:PI1057|3end_hypothetical_protein_977548..977698_POSITIVE 276 100 53 84 32 pint:PI1447|3end_probable_OPT_oligopeptide_transporter_protein_1371956..1372106_POSITIVE 249 55 12 89 45 pint:PI1380|3end_conserved_hypothetical_protein_1303242..1303392_POSITIVE 237 41 1 69 26 pint:PI0256|3end_conjugative_transposon_protein,_TraE_249420..249570_POSITIVE 235 57 12 127 81 pint:PI1437|3end_hypothetical_protein_1356407..1356557_POSITIVE 232 48 2 96 31 pint:PI1935|3end_possible__internalin-related_protein_1887111..1887261_POSITIVE 224 58 16 52 5 pint:PI0984|3end_hypothetical_protein_910144..910294_POSITIVE 221 99 53 131 82 pint:PI1952|3end_hypothetical_protein_1907039..1907189_POSITIVE 220 99 51 144 95 pint:PI1617|3end_hypothetical_protein_1543164..1543314_POSITIVE 220 99 51 119 70 pint:PI1618|3end_hypothetical_protein_1543139..1543289_POSITIVE 217 88 41 89 47 pint:PI1894|3end_UDP-N-acetylmuramoylalanyl-D-glutamyl-2,6-diamino_pimelate_ligase_1838484..1838634_POSITIVE 217 90 54 103 64 pint:PI0155|3end_conserved_hypothetical_protein_148687..148837_POSITIVE 216 99 57 125 76 pint:PI0784|3end_possible_amidase_enhancer_precursor_723303..723453_POSITIVE 214 47 1 145 92 pint:PI1972|3end_hypothetical_protein_1930503..1930653_POSITIVE 214 49 2 54 13 pint:PI0826|3end_hypothetical_protein_764045..764195_POSITIVE 212 58 11 85 45 pint:PI0071|3end_hypothetical_protein_70229..70379_POSITIVE 211 33 7 146 115 pint:PI1071|3end_DNA_topoisomerase_III_990226..990376_POSITIVE 211 48 4 69 22 pint:PI0396|3end_possible_tetracycline_resistance_element_mobilization_regulatory_protein,_C-terminal_fragment_362396..362546_POSITIVE 210 49 3 55 10 pint:PI1342|3end_conserved_hypothetical_protein_1257799..1257949_POSITIVE