Origin IGS: ggtacaaacttagttctcttcactattctgctgcgagacagcaattaggtatctgcactctttttattttgcaaatgtactaatatttagataaacagaacagaaaattaaaagaaaatacgaaattaaccctgtaaaaaccaacaaattaagctgtaaatgccattttt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aaaaatggcatttacagcttaatttgttggtttttacagggttaatttcgtattttcttttaattttctgttctgtttatctaaatattagtacatttgcaaaataaaaagagtgcagatacctaattgctgtctcgcagcagaatagtgaagagaactaagtttgtacc Mask Tandem Repeat Region ================================================ ggtacaaacttagttctcttcactattctgctgcgagacagcaattaggtatctgcactctttttattttgcaaatgtactaatatttagataaacagaacagaaaattaaaagaaaatacgaaattaaccctgtaaaaaccaacaaattaagctgtaaatgccattttt Find is-nt database================================================ Query_seq: PI1390:PI1391|PI1390:PI1391:hypothetical protein:hypothetical protein:->->:1311390..1311559 170 ggtacaaacttagttctcttcactattctgctgcgagacagcaattaggtatctgcactctttttattttgcaaatgtactaatatttagataaacagaacagaaaattaaaagaaaatacgaaattaaccctgtaaaaaccaacaaattaagctgtaaatgccattttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI1390:PI1391|PI1390:PI1391:hypothetical protein:hypothetical protein:->->:1311390..1311559 170 ggtacaaacttagttctcttcactattctgctgcgagacagcaattaggtatctgcactctttttattttgcaaatgtactaatatttagataaacagaacagaaaattaaaagaaaatacgaaattaaccctgtaaaaaccaacaaattaagctgtaaatgccattttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI1390:PI1391|PI1390:PI1391:hypothetical protein:hypothetical protein:->->:1311390..1311559 170 ggtacaaacttagttctcttcactattctgctgcgagacagcaattaggtatctgcactctttttattttgcaaatgtactaatatttagataaacagaacagaaaattaaaagaaaatacgaaattaaccctgtaaaaaccaacaaattaagctgtaaatgccattttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ggtacaaacttagttctcttcactattctgctgcgagacagcaattaggtatctgcactctttttattttgcaaatgtactaatatttagataaacagaacagaaaattaaaagaaaatacgaaattaaccctgtaaaaaccaacaaattaagctgtaaatgccattttt Predict ORF larger than 30AA ================================================ ggtacaaacttagttctcttcactattctgctgcgagacagcaattaggtatctgcactctttttattttgcaaatgtactaatatttagataaacagaacagaaaattaaaagaaaatacgaaattaaccctgtaaaaaccaacaaattaagctgtaaatgccattttt 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================================================ ggtacaaacttagttctcttcactattctgctgcgagacagcaattaggtatctgcactctttttattttgcaaatgtactaatatttagataaacagaacagaaaattaaaagaaaatacgaaattaaccctgtaaaaaccaacaaattaagctgtaaatgccattttt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PI1390:PI1391|PI1390:PI1391:hypothetical protein:hypothetical protein:->->:1311390..1311559 170 ggtacaaacttagttctcttcactattctgctgcgagacagcaattaggtatctgcactctttttattttgcaaatgtactaatatttagataaacagaacagaaaattaaaagaaaatacgaaattaaccctgtaaaaaccaacaaattaagctgtaaatgccattttt Intra-Species Hit: Count: 1 Min: 1 Max: 170 Len: 170 Subject: pint_PI1390_PI1391|hypothetical protein:hypothetical protein|POSITIVE:POSITIVE|[1311390,1311559]|170 HSP 1 e-value: 7.0E-92 bit: 337.0 Len: 170 Query Start:1 Query End:170 Subject Strand: POSITIVE Subject Start: 1 Subject End: 170 ggtacaaacttagttctcttcactattctgctgcgagacagcaattaggtatctgcactctttttattttgcaaatgtactaatatttagataaacagaacagaaaattaaaagaaaatacgaaattaaccctgtaaaaaccaacaaattaagctgtaaatgccattttt ggtacaaacttagttctcttcactattctgctgcgagacagcaattaggtatctgcactctttttattttgcaaatgtactaatatttagataaacagaacagaaaattaaaagaaaatacgaaattaaccctgtaaaaaccaacaaattaagctgtaaatgccattttt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GGUACAAACUUAGUUCUCUUCACUAUUCUGCUGCGAGACAGCAAUUAGGUAUCUGCACUCUUUUUAUUUUGCAAAUGUACUAAUAUUUAGAUAAACAGAACAGAAAAUUAAAAGAAAAUACGAAAUUAACCCUGUAAAAACCAACAAAUUAAGCUGUAAAUGCCAUUUUU ((((((..(((((((.............(((((.....)))))....(((.((((...(((.(((((((...((((((....))))))))))))).))).))))..............((((..........))))...)))....))))))).)))....)))...... (-23.40) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAAAUGGCAUUUACAGCUUAAUUUGUUGGUUUUUACAGGGUUAAUUUCGUAUUUUCUUUUAAUUUUCUGUUCUGUUUAUCUAAAUAUUAGUACAUUUGCAAAAUAAAAAGAGUGCAGAUACCUAAUUGCUGUCUCGCAGCAGAAUAGUGAAGAGAACUAAGUUUGUACC ............(((((((((.(((.....(((((((.((((..((((.((((..((((((.((((..(((..(((....(((.....))).)))...))))))).))))))))))))))))))..((((((.....))))))....)))))))))).)))).))))).. (-29.40) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 365 43 9 66 29 pint:PI1550|5end_conserved_hypothetical_protein_1467360..1467590_POSITIVE 272 60 12 188 127 pint:PI0442|5end_50S_ribosomal_protein_L1_411644..411874_POSITIVE 268 49 1 69 11 pint:PI1050|5end_conserved_hypothetical_protein_967246..967476_POSITIVE 266 60 17 48 2 pint:PI1390|5end_hypothetical_protein_1311154..1311384_POSITIVE 266 72 32 118 79 pint:PI0839|5end_conserved_hypothetical_protein_773843..774073_POSITIVE 257 56 25 190 163 pint:PI1310|5end_LysM_domain_protein_1227262..1227492_POSITIVE 255 62 28 58 19 pint:PI0774|5end_phosphoserine_aminotransferase_(phosphoserine_transaminase)_709497..709727_POSITIVE 253 56 13 216 166 pint:PI2135|5end_conserved_hypothetical_protein_2082754..2082984_POSITIVE 253 56 13 67 17 pint:PI2136|5end_hypothetical_protein_2082605..2082835_POSITIVE 252 78 32 198 146 pint:PI1768|5end_conserved_hypothetical_protein_1695456..1695686_POSITIVE 251 49 10 44 1 pint:PI2021|5end_DNA_repair_protein_1977925..1978155_POSITIVE 251 59 16 213 167 pint:PI0433|5end_hypothetical_protein_404724..404954_POSITIVE 243 110 61 120 69 pint:PI0284|5end_flavoprotein_A_268848..269078_POSITIVE 241 58 17 83 34 pint:PI0876|5end_hypothetical_protein_810767..810997_POSITIVE 240 70 22 82 27 pint:PI0144|5end_conserved_hypothetical_protein_135420..135650_POSITIVE 239 61 23 154 120 pint:PI2063|5end_conserved_hypothetical_protein_2023946..2024176_POSITIVE 238 71 31 50 15 pint:PI0611|5end_hypothetical_protein_559387..559617_POSITIVE 237 67 21 118 58 pint:PI0932|5end_conserved_hypothetical_protein;_possible_hemin_receptor_863854..864084_POSITIVE 236 56 16 127 98 pint:PI1402|5end_3-deoxy-7-phosphoheptulonate_synthase_1322935..1323165_POSITIVE 236 43 8 227 192 pint:PI0336|5end_hypothetical_protein_314499..314729_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 293 73 31 141 98 pint:PI0949|3end_endonuclease_883279..883429_POSITIVE 269 60 13 143 93 pint:PI1390|3end_hypothetical_protein_1311329..1311479_POSITIVE 268 49 1 84 26 pint:PI1049|3end_hypothetical_protein_967341..967491_POSITIVE 266 72 32 122 83 pint:PI0838|3end_DNA_replication_and_repair_protein_773927..774077_POSITIVE 260 80 33 151 96 pint:PI1050|3end_conserved_hypothetical_protein_969698..969848_POSITIVE 256 80 32 140 92 pint:PI1548|3end_conserved_hypothetical_protein_1466886..1467036_POSITIVE 253 58 12 145 97 pint:PI0422|3end_conserved_hypothetical_protein_388025..388175_POSITIVE 251 59 16 82 36 pint:PI0431|3end_Xaa-Pro_aminopeptidase_404673..404823_POSITIVE 246 79 33 71 15 pint:PI0685|3end_elongation_factor_G_623048..623198_POSITIVE 245 59 26 81 46 pint:PI0809|3end_hypothetical_protein_747108..747258_POSITIVE 245 79 31 138 88 pint:PI0664|3end_dihydroorotate_dehydrogenase,_electron_transfer_subunit_607819..607969_POSITIVE 243 110 61 73 22 pint:PI0283|3end_Zn-dependent_peptidase_268881..269031_POSITIVE 239 61 23 136 102 pint:PI2062|3end_type_I_restriction-modification_system_2024008..2024158_POSITIVE 236 43 8 68 33 pint:PI0335|3end_hypothetical_protein_314420..314570_POSITIVE 233 55 13 149 118 pint:PI1649|3end_hypothetical_protein_1563441..1563591_POSITIVE 233 80 40 69 17 pint:PI0616|3end_electron_transfer_flavoprotein,_beta-subunit_566440..566590_POSITIVE 232 57 11 117 62 pint:PI0928|3end_hypothetical_protein_860272..860422_POSITIVE 232 65 23 140 88 pint:PI0300|3end_transposase_285761..285911_POSITIVE 231 50 9 135 87 pint:PI1780|3end_1-deoxy-D-xylulose_5-phosphate_reductoisomerase_1713097..1713247_POSITIVE 231 58 23 50 10 pint:PI0666|3end_chorismate_synthase_610171..610321_POSITIVE