Origin IGS: tgattatgtttcttttttcgtaattttgcaaacataattcaggttattatggcacaagaacaaatacagatacaagagcaacgacaactgcaagtgcagcgactttcgcagcaacag .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 ctgttgctgcgaaagtcgctgcacttgcagttgtcgttgctcttgtatctgtatttgttcttgtgccataataacctgaattatgtttgcaaaattacgaaaaaagaaacataatca Mask Tandem Repeat Region ================================================ tgattatgtttcttttttcgtaattttgcaaacataattcaggttattatggcacaagaacaaatacagatacaagagcaacgacaactgcaagtgcagcgactttcgcagcaacag Find is-nt database================================================ Query_seq: PI2174:PI2175|PI2174:PI2175:hypothetical protein:RNA polymerase sigma-54:->->:2115030..2115146 117 tgattatgtttcttttttcgtaattttgcaaacataattcaggttattatggcacaagaacaaatacagatacaagagcaacgacaactgcaagtgcagcgactttcgcagcaacag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI2174:PI2175|PI2174:PI2175:hypothetical protein:RNA polymerase sigma-54:->->:2115030..2115146 117 tgattatgtttcttttttcgtaattttgcaaacataattcaggttattatggcacaagaacaaatacagatacaagagcaacgacaactgcaagtgcagcgactttcgcagcaacag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI2174:PI2175|PI2174:PI2175:hypothetical protein:RNA polymerase sigma-54:->->:2115030..2115146 117 tgattatgtttcttttttcgtaattttgcaaacataattcaggttattatggcacaagaacaaatacagatacaagagcaacgacaactgcaagtgcagcgactttcgcagcaacag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tgattatgtttcttttttcgtaattttgcaaacataattcaggttattatggcacaagaacaaatacagatacaagagcaacgacaactgcaagtgcagcgactttcgcagcaacag Predict ORF larger than 30AA ================================================ Protein_Len: 37 Strand: - Start: 7 End: 117 ...... T E K K T I K C V Y N L N N H C L F L Y L Y L L L S L Q L H L S K R L L M tgattatgtttcttttttcgtaattttgcaaacataattcaggttattatggcacaagaacaaatacagatacaagagcaacgacaactgcaagtgcagcgactttcgcagcaacag 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: 3 End: 32 ..TTTGCAAAATTACGAAAAAAGAAACATAAT..................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tgattatgtttcttttttcgtaattttgcaaacataattcaggttattatggcacaagaacaaatacagatacaagagcaacgacaactgcaagtgcagcgactttcgcagcaacag Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PI2174:PI2175|PI2174:PI2175:hypothetical protein:RNA polymerase sigma-54:->->:2115030..2115146 117 tgattatgtttcttttttcgtaattttgcaaacataattcaggttattatggcacaagaacaaatacagatacaagagcaacgacaactgcaagtgcagcgactttcgcagcaacag Intra-Species Hit: Count: 1 Min: 1 Max: 117 Len: 117 Subject: pint_PI2174_PI2175|hypothetical protein:RNA polymerase sigma-54|POSITIVE:POSITIVE|[2115030,2115146]|117 HSP 1 e-value: 2.0E-60 bit: 232.0 Len: 117 Query Start:1 Query End:117 Subject Strand: POSITIVE Subject Start: 1 Subject End: 117 tgattatgtttcttttttcgtaattttgcaaacataattcaggttattatggcacaagaacaaatacagatacaagagcaacgacaactgcaagtgcagcgactttcgcagcaacag tgattatgtttcttttttcgtaattttgcaaacataattcaggttattatggcacaagaacaaatacagatacaagagcaacgacaactgcaagtgcagcgactttcgcagcaacag Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGAUUAUGUUUCUUUUUUCGUAAUUUUGCAAACAUAAUUCAGGUUAUUAUGGCACAAGAACAAAUACAGAUACAAGAGCAACGACAACUGCAAGUGCAGCGACUUUCGCAGCAACAG ......(((.(((..(((.((..((.(((...((((((.......))))))))).))..)))))...))).)))...(((........)))...(((.(((.....))).))).... (-18.10) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUGUUGCUGCGAAAGUCGCUGCACUUGCAGUUGUCGUUGCUCUUGUAUCUGUAUUUGUUCUUGUGCCAUAAUAACCUGAAUUAUGUUUGCAAAAUUACGAAAAAAGAAACAUAAUCA .....((.((((.....(((((....)))))..)))).))...(((.(((...(((((.....(((((((((.......))))))...))).....)))))...))).)))...... (-25.30) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 349 110 66 129 88 pint:PI0203|5end_conserved_hypothetical_protein_195109..195339_POSITIVE 349 110 66 90 49 pint:PI0201|5end_hypothetical_protein_195070..195300_POSITIVE 307 110 68 34 2 pint:PI0536|5end_hypothetical_protein_492163..492393_POSITIVE 306 110 72 60 22 pint:PI1263|5end_probable_integrase_1184502..1184732_POSITIVE 295 109 64 152 94 pint:PI0094|5end_protoporphyrinogen_oxidase_89571..89801_POSITIVE 295 109 64 78 20 pint:PI0091|5end_hypothetical_protein_89497..89727_POSITIVE 291 98 56 125 70 pint:PI1036|5end_ATP-dependent__Lon_protease_954446..954676_POSITIVE 288 102 61 191 139 pint:PI0980|5end_conserved_hypothetical_protein_905703..905933_POSITIVE 288 86 41 132 85 pint:PI0829|5end_nucleotidyl_transferase_family;_possible_mannose-1-phosphate_guanyltransferase_765665..765895_POSITIVE 285 110 68 144 103 pint:PI1893|5end_phospho-N-acetylmuramoyl-pentapeptide-transferase__1835624..1835854_POSITIVE 277 108 67 164 109 pint:PI1627|5end_hypothetical_protein_1550445..1550675_POSITIVE 273 109 64 61 15 pint:PI0950|5end_50S_ribosomal_protein_L31_883327..883557_POSITIVE 273 110 67 83 36 pint:PI0720|5end_conserved_hypothetical_protein_653949..654179_POSITIVE 272 108 61 143 88 pint:PI0625|5end_possible_membrane_transport_protein_573104..573334_POSITIVE 270 109 66 205 156 pint:PI0478|5end_50S_ribosomal_protein_L30_440923..441153_POSITIVE 269 108 70 127 86 pint:PI1381|5end_conserved_hypothetical_protein_1303060..1303290_POSITIVE 268 110 61 231 181 pint:PI0843|5end_carboxyl-terminal_protease_776145..776375_POSITIVE 268 110 66 212 159 pint:PI0684|5end_coproporphyrinogen_III_oxidase_619357..619587_POSITIVE 268 110 66 147 94 pint:PI0683|5end_hypothetical_protein_619292..619522_POSITIVE 267 100 57 154 118 pint:PI1460|5end_ribonucleotide_reductase,_alpha_subunit,_N-terminal_region_1382215..1382445_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 349 110 66 129 88 pint:PI0202|3end_DNA_helicase_195189..195339_POSITIVE 291 98 56 132 77 pint:PI1035|3end_queuine_tRNA-ribosyltransferase_(tRNA-guanine_transglycosylase)_954533..954683_POSITIVE 288 102 61 86 34 pint:PI0979|3end_transcriptional_regulator,_tetR_family_905678..905828_POSITIVE 288 86 41 82 35 pint:PI0828|3end_GMP_synthase_(glutamine_amidotransferase)_765695..765845_POSITIVE 280 109 64 59 1 pint:PI1734|3end_possible_carboxyl-terminal_protease-related_protein_1653829..1653979_POSITIVE 279 103 66 70 35 pint:PI0375|3end_hypothetical_protein_346082..346232_POSITIVE 276 110 73 149 115 pint:PI1788|3end_hypothetical_protein_1718707..1718857_POSITIVE 273 110 67 64 17 pint:PI0719|3end_conserved_hypothetical_protein_654010..654160_POSITIVE 268 110 66 147 94 pint:PI0682|3end_hypothetical_protein_619372..619522_POSITIVE 266 109 64 150 94 pint:PI0092|3end_regulatory_protein_RecX_89651..89801_POSITIVE 263 107 67 116 72 pint:PI2137|3end_RNA_methylase_SpoU_family_2083807..2083957_POSITIVE 263 90 42 126 84 pint:PI1639|3end_conserved_hypothetical_protein_1558133..1558283_POSITIVE 262 90 42 132 97 pint:PI2025|3end_conserved_hypothetical_protein_1979452..1979602_POSITIVE 259 108 66 62 1 pint:PI0853|3end_glycosyl_transferase,_group_2_family_protein_786593..786743_POSITIVE 257 109 67 148 106 pint:PI1891|3end_hypothetical_protein_1835917..1836067_POSITIVE 257 102 64 143 115 pint:PI1864|3end_chromate_transport_protein_1811009..1811159_POSITIVE 254 88 49 71 32 pint:PI0892|3end_acyl-ACP_thioesterase_823939..824089_POSITIVE 251 100 52 86 42 pint:PI0764|3end_permease_699145..699295_POSITIVE 249 109 78 84 47 pint:PI1818|3end_hypothetical_protein_1757270..1757420_POSITIVE 247 109 76 38 5 pint:PI2135|3end_conserved_hypothetical_protein_2083253..2083403_POSITIVE