Origin IGS: cagcctgctcagcacacacagcctccatcgacaacagtatcaaaaaagggtattcgttaaagcctctgaaagaccgataacgaatacccttttttgttgcaacagctcgctaaggcgagaagttcataactgaaaaagagacataagtccgactcttttgaagtcagacttatatcttaccccacaaatgattcgggggatgctaaatagccgttgga .........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 tccaacggctatttagcatcccccgaatcatttgtggggtaagatataagtctgacttcaaaagagtcggacttatgtctctttttcagttatgaacttctcgccttagcgagctgttgcaacaaaaaagggtattcgttatcggtctttcagaggctttaacgaatacccttttttgatactgttgtcgatggaggctgtgtgtgctgagcaggctg Mask Tandem Repeat Region ================================================ cagcctgctcagcacacacagcctccatcgacaacagtatcaaaaaagggtattcgttaaagcctctgaaagaccgataacgaatacccttttttgttgcaacagctcgctaaggcgagaagttcataactgaaaaagagacataagtccgactcttttgaagtcagacttatatcttaccccacaaatgattcgggggatgctaaatagccgttgga Find is-nt database================================================ Query_seq: PG1827:PG1828|PG1827:PG1828:RNA polymerase sigma-70 factor, ECF subfamily:lipoprotein, putative:-><-:1920796..1921013 218 cagcctgctcagcacacacagcctccatcgacaacagtatcaaaaaagggtattcgttaaagcctctgaaagaccgataacgaatacccttttttgttgcaacagctcgctaaggcgagaagttcataactgaaaaagagacataagtccgactcttttgaagtcagacttatatcttaccccacaaatgattcgggggatgctaaatagccgttgga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG1827:PG1828|PG1827:PG1828:RNA polymerase sigma-70 factor, ECF subfamily:lipoprotein, putative:-><-:1920796..1921013 218 cagcctgctcagcacacacagcctccatcgacaacagtatcaaaaaagggtattcgttaaagcctctgaaagaccgataacgaatacccttttttgttgcaacagctcgctaaggcgagaagttcataactgaaaaagagacataagtccgactcttttgaagtcagacttatatcttaccccacaaatgattcgggggatgctaaatagccgttgga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG1827:PG1828|PG1827:PG1828:RNA polymerase sigma-70 factor, ECF subfamily:lipoprotein, putative:-><-:1920796..1921013 218 cagcctgctcagcacacacagcctccatcgacaacagtatcaaaaaagggtattcgttaaagcctctgaaagaccgataacgaatacccttttttgttgcaacagctcgctaaggcgagaagttcataactgaaaaagagacataagtccgactcttttgaagtcagacttatatcttaccccacaaatgattcgggggatgctaaatagccgttgga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 cagcctgctcagcacacacagcctccatcgacaacagtatcaaaaaagggtattcgttaaagcctctgaaagaccgataacgaatacccttttttgttgcaacagctcgctaaggcgagaagttcataactgaaaaagagacataagtccgactcttttgaagtcagacttatatcttaccccacaaatgattcgggggatgctaaatagccgttgga Predict ORF larger than 30AA ================================================ Protein_Len: 42 Strand: + Start: 5 End: 130 .... M L S T H S L H R Q Q Y Q K R V F V K A S E R P I T N T L F C C N S S L R R E V H N ........................................................................................ Protein_Len: 38 Strand: - Start: 60 End: 173 ........................................................... L R Q F V S L S Y G K K N C C S A L A L L E Y S F F L C L D S E K S T L S M ............................................. cagcctgctcagcacacacagcctccatcgacaacagtatcaaaaaagggtattcgttaaagcctctgaaagaccgataacgaatacccttttttgttgcaacagctcgctaaggcgagaagttcataactgaaaaagagacataagtccgactcttttgaagtcagacttatatcttaccccacaaatgattcgggggatgctaaatagccgttgga 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================================================ cagcctgctcagcacacacagcctccatcgacaacagtatcaaaaaagggtattcgttaaagcctctgaaagaccgataacgaatacccttttttgttgcaacagctcgctaaggcgagaagttcataactgaaaaagagacataagtccgactcttttgaagtcagacttatatcttaccccacaaatgattcgggggatgctaaatagccgttgga Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 91 HP_score: -6.7 Tail_Score: -5.4505 Start: 48 End: 89 Full_Region: AACAGTATCAAAAAA GGGTATTCGTTAAAGCCTCT GAA AGACCGATAACGAATACCC TTTTTTGTTGCAACA ...............................................GGGTATTCGTTAAAGCCTCTGAAAGACCGATAACGAATACCC................................................................................................................................. TransTerm Strand: - Conf: 100 HP_score: -8.9 Tail_Score: -5.2112 Start: 48 End: 89 Full_Region: tgttgcaacaaaaaa gggtattcgttatcggtctt tca gaggctttaacgaataccc ttttttgatactgtt ...............................................gggtattcgttatcggtctttcagaggctttaacgaataccc................................................................................................................................. TransTerm Strand: - Conf: 100 HP_score: -9.2 Tail_Score: -4.78149 Start: 138 End: 178 Full_Region: aatcatttgtggggt aagatataagtctgactt caaaa gagtcggacttatgtctc tttttcagttatgaa .........................................................................................................................................aagatataagtctgacttcaaaagagtcggacttatgtctc........................................ TransTerm Strand: - Conf: 100 HP_score: -11.8 Tail_Score: -4.00465 Start: 140 End: 176 Full_Region: tcatttgtggggtaa gatataagtctgactt caaaa gagtcggacttatgtc tctttttcagttatg ...........................................................................................................................................gatataagtctgacttcaaaagagtcggacttatgtc.......................................... Find igs database================================================ Query_seq: PG1827:PG1828|PG1827:PG1828:RNA polymerase sigma-70 factor, ECF subfamily:lipoprotein, putative:-><-:1920796..1921013 218 cagcctgctcagcacacacagcctccatcgacaacagtatcaaaaaagggtattcgttaaagcctctgaaagaccgataacgaatacccttttttgttgcaacagctcgctaaggcgagaagttcataactgaaaaagagacataagtccgactcttttgaagtcagacttatatcttaccccacaaatgattcgggggatgctaaatagccgttgga Intra-Species Hit: Count: 1 Min: 1 Max: 218 Len: 218 Subject: NC_002950_PG1827_PG1828|RNA polymerase sigma-70 factor, ECF subfamily:lipoprotein, putative|POSITIVE:NEGATIVE|[1920796,1921013]|218 HSP 1 e-value: 1.0E-120 bit: 432.0 Len: 218 Query Start:1 Query End:218 Subject Strand: POSITIVE Subject Start: 1 Subject End: 218 cagcctgctcagcacacacagcctccatcgacaacagtatcaaaaaagggtattcgttaaagcctctgaaagaccgataacgaatacccttttttgttgcaacagctcgctaaggcgagaagttcataactgaaaaagagacataagtccgactcttttgaagtcagacttatatcttaccccacaaatgattcgggggatgctaaatagccgttgga cagcctgctcagcacacacagcctccatcgacaacagtatcaaaaaagggtattcgttaaagcctctgaaagaccgataacgaatacccttttttgttgcaacagctcgctaaggcgagaagttcataactgaaaaagagacataagtccgactcttttgaagtcagacttatatcttaccccacaaatgattcgggggatgctaaatagccgttgga Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CAGCCUGCUCAGCACACACAGCCUCCAUCGACAACAGUAUCAAAAAAGGGUAUUCGUUAAAGCCUCUGAAAGACCGAUAACGAAUACCCUUUUUUGUUGCAACAGCUCGCUAAGGCGAGAAGUUCAUAACUGAAAAAGAGACAUAAGUCCGACUCUUUUGAAGUCAGACUUAUAUCUUACCCCACAAAUGAUUCGGGGGAUGCUAAAUAGCCGUUGGA ((((..(((.((((.......(((((((((....((((..(((((((((((((((((((..(..((.....)).)..))))))))))))))))))).((.(((..(((((....)))))..)))))..)))).....((((.(((((((.(((((....).)))).))))))).))))..........))))..))))).))))....))).)))).. (-70.30) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCCAACGGCUAUUUAGCAUCCCCCGAAUCAUUUGUGGGGUAAGAUAUAAGUCUGACUUCAAAAGAGUCGGACUUAUGUCUCUUUUUCAGUUAUGAACUUCUCGCCUUAGCGAGCUGUUGCAACAAAAAAGGGUAUUCGUUAUCGGUCUUUCAGAGGCUUUAACGAAUACCCUUUUUUGAUACUGUUGUCGAUGGAGGCUGUGUGUGCUGAGCAGGCUG .....(((((.(((((((((((((((.....))).))))..(((((((((((((((((.....)))))))))))))))))......((((..(((((..(((((....)))))..))).)).(((((((((((((((((((..((((((...)))))).)))))))))))))))))))..))))..(((......))).....))))))))..))))) (-87.70) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 356 67 22 161 119 NC_002950:PG1099|5end_hypothetical_protein_1168168..1168398_NEGATIVE 335 39 1 97 44 NC_002950:PG0172|5end_exonuclease_193493..193723_POSITIVE 332 115 73 161 121 NC_002950:PG0526|5end_putative_inner_membrane_protein_translocase_component_YidC_570746..570976_POSITIVE 308 109 61 189 147 NC_002950:PG1381|5end_ABC_transporter,_permease_protein_1460622..1460852_POSITIVE 302 119 74 215 163 NC_002950:PG0501|5end_hypothetical_protein_540344..540574_POSITIVE 299 120 84 63 18 NC_002950:PG1042|5end_glycogen_synthase,_putative_1110638..1110868_NEGATIVE 294 168 121 77 39 NC_002950:PG1763|5end_ribonuclease_III_1851712..1851942_NEGATIVE 289 31 1 46 18 NC_002950:PG1416|5end_enoyl-(acyl-carrier-protein)_reductase_II_1500057..1500287_POSITIVE 288 49 3 104 46 NC_002950:PG1365|5end_16S_rRNA-processing_protein_1446069..1446299_NEGATIVE 287 42 4 187 143 NC_002950:PG2173|5end_outer_membrane_lipoprotein_Omp28_2280813..2281043_NEGATIVE 286 125 81 46 4 NC_002950:PG1969|5end_hypothetical_protein_2059515..2059745_NEGATIVE 286 128 93 50 2 NC_002950:PG0236|5end_hypothetical_protein_273224..273454_POSITIVE 285 118 74 84 37 NC_002950:PG1930|5end_50S_ribosomal_protein_L29_2020409..2020639_NEGATIVE 284 50 2 171 120 NC_002950:PG1088|5end_acetyltransferase,_GNAT_family_1155426..1155656_NEGATIVE 284 204 165 57 2 NC_002950:PG1075|5end_coenzyme_A_transferase,_beta_subunit_1142778..1143008_POSITIVE 284 119 72 62 13 NC_002950:PG0736|5end_ribonuclease_HII_785608..785838_POSITIVE 283 132 99 166 131 NC_002950:PG0357|5end_aspartate_carbamoyltransferase_catalytic_subunit_391440..391670_POSITIVE 282 37 1 78 32 NC_002950:PG0441|5end_hypothetical_protein_478734..478964_POSITIVE 282 132 94 173 126 NC_002950:PG0134|5end_magnesium_transporter_157135..157365_NEGATIVE 281 30 1 226 190 NC_002950:PG0647|5end_iron_compound_ABC_transporter,_permease_protein_700113..700343_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 371 118 71 118 77 NC_002950:PG2214|3end_hypothetical_protein_2325301..2325451_NEGATIVE 357 198 151 96 51 NC_002950:PG1814|3end_DNA_primase_1908606..1908756_NEGATIVE 335 40 3 76 36 NC_002950:PG1055|3end_thiol_protease_1121202..1121352_NEGATIVE 335 39 1 100 47 NC_002950:PG0171|3end_5'-nucleotidase_family_protein_193576..193726_POSITIVE 331 90 47 44 1 NC_002950:PG1827|3end_RNA_polymerase_sigma-70_factor,_ECF_subfamily_1920735..1920885_POSITIVE 328 109 62 53 6 NC_002950:PG0086|3end_ATP-dependent_RNA_helicase,_DEAD/DEAH_box_family_100545..100695_NEGATIVE 290 55 20 141 107 NC_002950:PG0492|3end_hypothetical_protein_534408..534558_NEGATIVE 288 49 3 97 39 NC_002950:PG1366|3end_UDP-N-acetylglucosamine_1-carboxyvinyltransferase_1446076..1446226_NEGATIVE 286 125 81 77 35 NC_002950:PG1970|3end_hypothetical_protein_2059484..2059634_NEGATIVE 286 118 73 98 47 NC_002950:PG0308|3end_electron_transport_complex,_RnfABCDGE_type,_A_subunit_343827..343977_POSITIVE 285 118 74 78 31 NC_002950:PG1931|3end_50S_ribosomal_protein_L16_2020415..2020565_NEGATIVE 284 110 61 81 28 NC_002950:PG1112|3end_hypothetical_protein_1185571..1185721_POSITIVE 284 50 2 74 23 NC_002950:PG1089|3end_DNA-binding_response_regulator_RprY_1155523..1155673_NEGATIVE 284 119 72 51 2 NC_002950:PG0735|3end_aminotransferase,_class_V_785677..785827_POSITIVE 283 69 21 66 25 NC_002950:PG0374|3end_hypothetical_protein_405448..405598_NEGATIVE 283 132 99 119 84 NC_002950:PG0356|3end_hypothetical_protein_391473..391623_POSITIVE 282 37 1 74 28 NC_002950:PG0439|3end_hypothetical_protein_478810..478960_POSITIVE 282 132 94 141 94 NC_002950:PG0135|3end_dimethyladenosine_transferase_157167..157317_NEGATIVE 281 126 89 119 74 NC_002950:PG0750|3end_glycosyl_transferase,_group_2_family_protein_795946..796096_NEGATIVE 274 120 75 118 83 NC_002950:PG0442|3end_hypothetical_protein_481514..481664_NEGATIVE