Origin IGS: tcagtttcctgccgccgcctcctctccgacaagagaggaggcggcagcggacaggactctgagtgacgagccgccctctatccggatgcagaccggcagacgagggggagggaagtcgaagagccgggcatatcgtctttcggtcttctccgtgcggcttacggtttcgtcctgctataccttattattataagtatcaatcctcaatattcgttacggcagcattc .........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 gaatgctgccgtaacgaatattgaggattgatacttataataataaggtatagcaggacgaaaccgtaagccgcacggagaagaccgaaagacgatatgcccggctcttcgacttccctccccctcgtctgccggtctgcatccggatagagggcggctcgtcactcagagtcctgtccgctgccgcctcctctcttgtcggagaggaggcggcggcaggaaactga Mask Tandem Repeat Region ================================================ tcagtttcctgccgccgcctcctctccgacaagagaggaggcggcagcggacaggactctgagtgacgagccgccctctatccggatgcagaccggcagacgagggggagggaagtcgaagagccgggcatatcgtctttcggtcttctccgtgcggcttacggtttcgtcctgctataccttattattataagtatcaatcctcaatattcgttacggcagcattc Find is-nt database================================================ Query_seq: PG0332:PG0333|PG0332:PG0333:transcription termination factor Rho:hypothetical protein:->->:367736..367962 227 tcagtttcctgccgccgcctcctctccgacaagagaggaggcggcagcggacaggactctgagtgacgagccgccctctatccggatgcagaccggcagacgagggggagggaagtcgaagagccgggcatatcgtctttcggtcttctccgtgcggcttacggtttcgtcctgctataccttattattataagtatcaatcctcaatattcgttacggcagcattc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG0332:PG0333|PG0332:PG0333:transcription termination factor Rho:hypothetical protein:->->:367736..367962 227 tcagtttcctgccgccgcctcctctccgacaagagaggaggcggcagcggacaggactctgagtgacgagccgccctctatccggatgcagaccggcagacgagggggagggaagtcgaagagccgggcatatcgtctttcggtcttctccgtgcggcttacggtttcgtcctgctataccttattattataagtatcaatcctcaatattcgttacggcagcattc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG0332:PG0333|PG0332:PG0333:transcription termination factor Rho:hypothetical protein:->->:367736..367962 227 tcagtttcctgccgccgcctcctctccgacaagagaggaggcggcagcggacaggactctgagtgacgagccgccctctatccggatgcagaccggcagacgagggggagggaagtcgaagagccgggcatatcgtctttcggtcttctccgtgcggcttacggtttcgtcctgctataccttattattataagtatcaatcctcaatattcgttacggcagcattc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tcagtttcctgccgccgcctcctctccgacaagagaggaggcggcagcggacaggactctgagtgacgagccgccctctatccggatgcagaccggcagacgagggggagggaagtcgaagagccgggcatatcgtctttcggtcttctccgtgcggcttacggtttcgtcctgctataccttattattataagtatcaatcctcaatattcgttacggcagcattc Predict ORF larger than 30AA ================================================ Protein_Len: 44 Strand: + Start: 59 End: 190 .......................................................... M S D E P P S I R M Q T G R R G G G K S K S R A Y R L S V F S V R L T V S S C Y T L L L ..................................... Protein_Len: 32 Strand: + Start: 130 End: 225 ................................................................................................................................. M S S F G L L R A A Y G F V L L Y L I I I S I N P Q Y S L R Q H .. Protein_Len: 55 Strand: + Start: 63 End: 227 .............................................................. M T S R P L S G C R P A D E G E G S R R A G H I V F R S S P C G L R F R P A I P Y Y Y K Y Q S S I F V T A A F Protein_Len: 59 Strand: - Start: 2 End: 178 . L K R G G G G R R C S L L R C R V P S Q T V L R G R D P H L G A S S P S P L R L A P C I T K R D E G H P K R N R G A M ................................................. Protein_Len: 33 Strand: - Start: 4 End: 99 ... * N G A A A E E G V L S S A A A S L V R L S S G G E I R I C V P M ................................................................................................................................ tcagtttcctgccgccgcctcctctccgacaagagaggaggcggcagcggacaggactctgagtgacgagccgccctctatccggatgcagaccggcagacgagggggagggaagtcgaagagccgggcatatcgtctttcggtcttctccgtgcggcttacggtttcgtcctgctataccttattattataagtatcaatcctcaatattcgttacggcagcattc 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================================================ tcagtttcctgccgccgcctcctctccgacaagagaggaggcggcagcggacaggactctgagtgacgagccgccctctatccggatgcagaccggcagacgagggggagggaagtcgaagagccgggcatatcgtctttcggtcttctccgtgcggcttacggtttcgtcctgctataccttattattataagtatcaatcctcaatattcgttacggcagcattc Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PG0332:PG0333|PG0332:PG0333:transcription termination factor Rho:hypothetical protein:->->:367736..367962 227 tcagtttcctgccgccgcctcctctccgacaagagaggaggcggcagcggacaggactctgagtgacgagccgccctctatccggatgcagaccggcagacgagggggagggaagtcgaagagccgggcatatcgtctttcggtcttctccgtgcggcttacggtttcgtcctgctataccttattattataagtatcaatcctcaatattcgttacggcagcattc Intra-Species Hit: Count: 1 Min: 1 Max: 227 Len: 227 Subject: NC_002950_PG0332_PG0333|transcription termination factor Rho:hypothetical protein|POSITIVE:POSITIVE|[367736,367962]|227 HSP 1 e-value: 1.0E-126 bit: 450.0 Len: 227 Query Start:1 Query End:227 Subject Strand: POSITIVE Subject Start: 1 Subject End: 227 tcagtttcctgccgccgcctcctctccgacaagagaggaggcggcagcggacaggactctgagtgacgagccgccctctatccggatgcagaccggcagacgagggggagggaagtcgaagagccgggcatatcgtctttcggtcttctccgtgcggcttacggtttcgtcctgctataccttattattataagtatcaatcctcaatattcgttacggcagcattc tcagtttcctgccgccgcctcctctccgacaagagaggaggcggcagcggacaggactctgagtgacgagccgccctctatccggatgcagaccggcagacgagggggagggaagtcgaagagccgggcatatcgtctttcggtcttctccgtgcggcttacggtttcgtcctgctataccttattattataagtatcaatcctcaatattcgttacggcagcattc Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCAGUUUCCUGCCGCCGCCUCCUCUCCGACAAGAGAGGAGGCGGCAGCGGACAGGACUCUGAGUGACGAGCCGCCCUCUAUCCGGAUGCAGACCGGCAGACGAGGGGGAGGGAAGUCGAAGAGCCGGGCAUAUCGUCUUUCGGUCUUCUCCGUGCGGCUUACGGUUUCGUCCUGCUAUACCUUAUUAUUAUAAGUAUCAAUCCUCAAUAUUCGUUACGGCAGCAUUC ((((..((((((((((((((((((((......)))))))))))))...)).)))))..))))((((((((...(((((..(((((.......)))).)...))))).(((((.........(((.((((..(((((((..(((......)))...))...)))))...)))).)))....(((((....)))))......)))))....)))))))).......... (-90.70) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAAUGCUGCCGUAACGAAUAUUGAGGAUUGAUACUUAUAAUAAUAAGGUAUAGCAGGACGAAACCGUAAGCCGCACGGAGAAGACCGAAAGACGAUAUGCCCGGCUCUUCGACUUCCCUCCCCCUCGUCUGCCGGUCUGCAUCCGGAUAGAGGGCGGCUCGUCACUCAGAGUCCUGUCCGCUGCCGCCUCCUCUCUUGUCGGAGAGGAGGCGGCGGCAGGAAACUGA ...(((((((...........((((........)))).........)))..)))).(((((........(((((.((((..((((((..((((((.......((...........)).......))))))..))))))...))))........))))))))))..((((..((((....(((((((((((((((((....)))))))))))))))))))))..)))) (-91.89) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 565 59 11 113 59 NC_002950:PG0145|5end_hypothetical_protein_167831..168061_POSITIVE 525 118 73 220 167 NC_002950:PG0450|5end_hypothetical_protein_490812..491042_POSITIVE 522 130 84 76 14 NC_002950:PG0275|5end_thioredoxin_family_protein_307464..307694_NEGATIVE 498 57 11 136 77 NC_002950:PG1441|5end_lysozyme-related_protein_1527525..1527755_NEGATIVE 483 150 103 187 136 NC_002950:PG0882|5end_hypothetical_protein_944195..944425_POSITIVE 483 129 81 162 104 NC_002950:PG0489|5end_polysaccharide_biosynthesis-related_protein_529247..529477_POSITIVE 476 89 41 64 3 NC_002950:PG2205|5end_2-dehydropantoate_2-reductase_2316121..2316351_POSITIVE 463 130 82 175 129 NC_002950:PG1815|5end_3-deoxy-manno-octulosonate_cytidylyltransferase_1911433..1911663_NEGATIVE 462 130 82 80 28 NC_002950:PG2126|5end_conserved_hypothetical_protein_TIGR00044_2233112..2233342_NEGATIVE 452 70 22 61 9 NC_002950:PG1735|5end_MutT/nudix_family_protein_1823082..1823312_NEGATIVE 450 79 31 133 84 NC_002950:PG1871|5end_hypothetical_protein_1966859..1967089_NEGATIVE 450 129 81 121 68 NC_002950:PG1655|5end_hypothetical_protein_1737095..1737325_POSITIVE 449 118 71 122 70 NC_002950:PG0606|5end_hypothetical_protein_662558..662788_NEGATIVE 449 49 4 59 7 NC_002950:PG0506|5end_arginine-specific_cysteine_proteinase_545335..545565_POSITIVE 445 109 61 188 123 NC_002950:PG0794|5end_penicillin-binding_protein_1A,_putative_846411..846641_POSITIVE 438 166 121 231 178 NC_002950:PG2062|5end_histidyl-tRNA_synthetase_2158971..2159201_POSITIVE 438 74 32 210 168 NC_002950:PG0305|5end_electron_transport_complex,_RnfABCDGE_type,_D_subunit_340906..341136_POSITIVE 434 158 111 199 157 NC_002950:PG1837|5end_hemagglutinin_protein_HagA_1930337..1930567_POSITIVE 434 60 12 198 136 NC_002950:PG1739|5end_hypothetical_protein_1825709..1825939_NEGATIVE 431 89 41 228 175 NC_002950:PG1911|5end_DNA-directed_RNA_polymerase_alpha_subunit_2011762..2011992_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 763 50 1 82 29 NC_002950:PG0332|3end_transcription_termination_factor_Rho_367675..367825_POSITIVE 483 150 103 77 26 NC_002950:PG0881|3end_recombinase_A_944165..944315_POSITIVE 483 129 81 115 57 NC_002950:PG0488|3end_Holliday_junction_DNA_helicase_RuvB_529280..529430_POSITIVE 477 79 33 83 26 NC_002950:PG1117|3end_MATE_efflux_family_protein_1191541..1191691_POSITIVE 474 74 33 128 71 NC_002950:PG1040|3end_transcriptional_regulator,_putative_1107485..1107635_NEGATIVE 464 57 12 59 1 NC_002950:PG1442|3end_hypothetical_protein_1527602..1527752_NEGATIVE 462 130 82 83 31 NC_002950:PG2127|3end_hypothetical_protein_2233109..2233259_NEGATIVE 457 118 72 151 95 NC_002950:PG2119|3end_oxidoreductase,_Gfo/Idh/MocA_family_2227598..2227748_POSITIVE 456 129 82 113 63 NC_002950:PG1975|3end_hemagglutinin_protein_HagC_2064350..2064500_POSITIVE 452 110 61 81 18 NC_002950:PG1723|3end_ribosomal_protein_S20_1813403..1813553_POSITIVE 451 60 11 100 40 NC_002950:PG0605|3end_hypothetical_protein_661165..661315_NEGATIVE 450 79 31 60 11 NC_002950:PG1872|3end_urocanate_hydratase_1966932..1967082_NEGATIVE 450 129 81 107 54 NC_002950:PG1654|3end_D-alanyl-D-alanine_dipeptidase_1737161..1737311_POSITIVE 450 77 32 63 12 NC_002950:PG0593|3end_htrA_protein_651938..652088_POSITIVE 449 160 111 65 9 NC_002950:PG2212|3end_hypothetical_protein_2324483..2324633_NEGATIVE 446 137 93 123 69 NC_002950:PG1972|3end_hemagglutinin_protein_HagB_2061203..2061353_POSITIVE 441 150 102 121 62 NC_002950:PG1874|3end_hypothetical_protein_1969253..1969403_NEGATIVE 435 90 42 79 27 NC_002950:PG1133|3end_hypothetical_protein_1214103..1214253_POSITIVE 433 170 125 55 2 NC_002950:PG0076|3end_N-acetylmuramoyl-L-alanine_amidase,_family_4_90392..90542_NEGATIVE 424 126 81 87 32 NC_002950:PG1391|3end_hypothetical_protein_1472961..1473111_POSITIVE