Origin IGS: agcgagctttgggttccaaatgtatacaaattcaggaatatagaaggtgcggcatcagacttctaaccggtttgtgcattccggtcttaattgcaacggtttgacaaatttagggtggaaaactacgaaatgggattctaaaatttagtttttttatatctgttattgagattcgtctcaatttgat .........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 atcaaattgagacgaatctcaataacagatataaaaaaactaaattttagaatcccatttcgtagttttccaccctaaatttgtcaaaccgttgcaattaagaccggaatgcacaaaccggttagaagtctgatgccgcaccttctatattcctgaatttgtatacatttggaacccaaagctcgct Mask Tandem Repeat Region ================================================ agcgagctttgggttccaaatgtatacaaattcaggaatatagaaggtgcggcatcagacttctaaccggtttgtgcattccggtcttaattgcaacggtttgacaaatttagggtggaaaactacgaaatgggattctaaaatttagtttttttatatctgttattgagattcgtctcaatttgat Find is-nt database================================================ Query_seq: PG0771:PG0772|PG0771:PG0772:hypothetical protein:hypothetical protein:->->:824928..825114 187 agcgagctttgggttccaaatgtatacaaattcaggaatatagaaggtgcggcatcagacttctaaccggtttgtgcattccggtcttaattgcaacggtttgacaaatttagggtggaaaactacgaaatgggattctaaaatttagtttttttatatctgttattgagattcgtctcaatttgat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG0771:PG0772|PG0771:PG0772:hypothetical protein:hypothetical protein:->->:824928..825114 187 agcgagctttgggttccaaatgtatacaaattcaggaatatagaaggtgcggcatcagacttctaaccggtttgtgcattccggtcttaattgcaacggtttgacaaatttagggtggaaaactacgaaatgggattctaaaatttagtttttttatatctgttattgagattcgtctcaatttgat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG0771:PG0772|PG0771:PG0772:hypothetical protein:hypothetical protein:->->:824928..825114 187 agcgagctttgggttccaaatgtatacaaattcaggaatatagaaggtgcggcatcagacttctaaccggtttgtgcattccggtcttaattgcaacggtttgacaaatttagggtggaaaactacgaaatgggattctaaaatttagtttttttatatctgttattgagattcgtctcaatttgat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 agcgagctttgggttccaaatgtatacaaattcaggaatatagaaggtgcggcatcagacttctaaccggtttgtgcattccggtcttaattgcaacggtttgacaaatttagggtggaaaactacgaaatgggattctaaaatttagtttttttatatctgttattgagattcgtctcaatttgat Predict ORF larger than 30AA ================================================ Protein_Len: 31 Strand: + Start: 9 End: 101 ........ M G S K C I Q I Q E Y R R C G I R L L T G L C I P V L I A T V ...................................................................................... Protein_Len: 33 Strand: + Start: 47 End: 145 .............................................. M R H Q T S N R F V H S G L N C N G L T N L G W K T T K W D S K I .......................................... agcgagctttgggttccaaatgtatacaaattcaggaatatagaaggtgcggcatcagacttctaaccggtttgtgcattccggtcttaattgcaacggtttgacaaatttagggtggaaaactacgaaatgggattctaaaatttagtttttttatatctgttattgagattcgtctcaatttgat 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: 153 End: 182 ........................................................................................................................................................ATTGAGACGAATCTCAATAACAGATATAAA..... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ agcgagctttgggttccaaatgtatacaaattcaggaatatagaaggtgcggcatcagacttctaaccggtttgtgcattccggtcttaattgcaacggtttgacaaatttagggtggaaaactacgaaatgggattctaaaatttagtttttttatatctgttattgagattcgtctcaatttgat Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 89 HP_score: -4.0 Tail_Score: -5.77988 Start: 138 End: 148 Full_Region: CTACGAAATGGGATT CTAA AAT TTAG TTTTTTTATATCTGT .........................................................................................................................................CTAAAATTTAG....................................... Find igs database================================================ Query_seq: PG0771:PG0772|PG0771:PG0772:hypothetical protein:hypothetical protein:->->:824928..825114 187 agcgagctttgggttccaaatgtatacaaattcaggaatatagaaggtgcggcatcagacttctaaccggtttgtgcattccggtcttaattgcaacggtttgacaaatttagggtggaaaactacgaaatgggattctaaaatttagtttttttatatctgttattgagattcgtctcaatttgat Intra-Species Hit: Count: 1 Min: 1 Max: 187 Len: 187 Subject: NC_002950_PG0771_PG0772|hypothetical protein:hypothetical protein|POSITIVE:POSITIVE|[824928,825114]|187 HSP 1 e-value: 2.0E-89 bit: 329.0 Len: 187 Query Start:1 Query End:187 Subject Strand: POSITIVE Subject Start: 1 Subject End: 187 agcgagctttgggttccaaatgtatacaaattcaggaatatagaaggtgcggcatcagacttctaaccggtttgtgcattccggtcttaattgcaacggtttgacaaatttagggtggaaaactacgaaatgggattctaaaatttagnnnnnnnatatctgttattgagattcgtctcaatttgat agcgagctttgggttccaaatgtatacaaattcaggaatatagaaggtgcggcatcagacttctaaccggtttgtgcattccggtcttaattgcaacggtttgacaaatttagggtggaaaactacgaaatgggattctaaaatttagtttttttatatctgttattgagattcgtctcaatttgat Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGCGAGCUUUGGGUUCCAAAUGUAUACAAAUUCAGGAAUAUAGAAGGUGCGGCAUCAGACUUCUAACCGGUUUGUGCAUUCCGGUCUUAAUUGCAACGGUUUGACAAAUUUAGGGUGGAAAACUACGAAAUGGGAUUCUAAAAUUUAGUUUUUUUAUAUCUGUUAUUGAGAUUCGUCUCAAUUUGAU .(((..((((..(((((.(((........)))..)))))...)))).))).(((.((((((.......))))))))).(((((.(((.((((.(((....)))...)))).))).))))).....((((.(((((((((......(((...........)))......)))...)))))).)))).. (-37.70) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUCAAAUUGAGACGAAUCUCAAUAACAGAUAUAAAAAAACUAAAUUUUAGAAUCCCAUUUCGUAGUUUUCCACCCUAAAUUUGUCAAACCGUUGCAAUUAAGACCGGAAUGCACAAACCGGUUAGAAGUCUGAUGCCGCACCUUCUAUAUUCCUGAAUUUGUAUACAUUUGGAACCCAAAGCUCGCU .....(((((((....)))))))..(((((.....(((((((.......(((......))).)))))))...........(((.(((....))))))....((((((..........))))))....)))))..((.(((..(((.........)))..))).....(((((...)))))....)). (-27.40) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 384 86 43 231 178 NC_002950:PG0093|5end_HlyD_family_secretion_protein_109638..109868_NEGATIVE 374 86 50 196 148 NC_002950:PG0649|5end_hypothetical_protein_701820..702050_POSITIVE 364 116 73 212 174 NC_002950:PG1589|5end_dihydropteroate_synthase_1667438..1667668_NEGATIVE 359 79 33 167 115 NC_002950:PG1731|5end_3-dehydroquinate_dehydratase_1820103..1820333_NEGATIVE 341 116 72 199 155 NC_002950:PG0912|5end_polysaccharide_transport_protein,_putative_975356..975586_NEGATIVE 327 77 32 182 132 NC_002950:PG0525|5end_CTP_synthetase_568999..569229_POSITIVE 318 101 63 231 189 NC_002950:PG1401|5end_beta-eliminating_lyase_1484778..1485008_NEGATIVE 318 83 41 50 6 NC_002950:PG0736|5end_ribonuclease_HII_785608..785838_POSITIVE 316 99 53 197 150 NC_002950:PG1057|5end_hypothetical_protein_1123419..1123649_POSITIVE 312 88 42 110 58 NC_002950:PG1002|5end_hypothetical_protein_1058771..1059001_POSITIVE 312 86 45 206 162 NC_002950:PG0976|5end_phosphoribosylaminoimidazole-succinocarboxamide_synthase_1038326..1038556_POSITIVE 312 90 46 186 141 NC_002950:PG0955|5end_hypothetical_protein_1014832..1015062_POSITIVE 310 88 42 187 140 NC_002950:PG0739|5end_ribonuclease_Z_786947..787177_POSITIVE 309 87 47 228 187 NC_002950:PG0155|5end_riboflavin_biosynthesis_protein_RibD_178853..179083_NEGATIVE 301 84 46 200 161 NC_002950:PG1996|5end_deoxyribose-phosphate_aldolase_2085921..2086151_POSITIVE 299 100 51 100 38 NC_002950:PG1481|5end_conjugative_transposon_protein_TraG_1558447..1558677_NEGATIVE 298 138 91 187 151 NC_002950:PG1786|5end_hypothetical_protein_1874358..1874588_POSITIVE 298 76 31 68 29 NC_002950:PG1270|5end_hypothetical_protein_1350207..1350437_NEGATIVE 295 85 43 218 169 NC_002950:PG0364|5end_hypothetical_protein_399615..399845_NEGATIVE 294 85 48 159 127 NC_002950:PG1754|5end_hypothetical_protein_1839679..1839909_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 349 98 51 66 19 NC_002950:PG0380|3end_excinuclease_ABC_subunit_B_411218..411368_POSITIVE 331 99 67 80 52 NC_002950:PG1655|3end_hypothetical_protein_1737384..1737534_POSITIVE 327 77 32 66 16 NC_002950:PG0524|3end_hypothetical_protein_568963..569113_POSITIVE 312 77 33 54 5 NC_002950:PG1156|3end_S4_domain_protein_1237267..1237417_POSITIVE 312 88 42 105 53 NC_002950:PG1001|3end_hypothetical_protein_1058846..1058996_POSITIVE 306 99 55 142 107 NC_002950:PG0656|3end_50S_ribosomal_protein_L34_706945..707095_NEGATIVE 304 100 52 78 14 NC_002950:PG1247|3end_3-dehydroquinate_synthase_1325585..1325735_POSITIVE 302 100 53 61 24 NC_002950:PG1391|3end_hypothetical_protein_1472961..1473111_POSITIVE 299 100 51 103 41 NC_002950:PG1482|3end_conjugative_transposon_protein_TraF_1558444..1558594_NEGATIVE 298 76 31 61 22 NC_002950:PG1271|3end_acetylornithine_aminotransferase,_putative_1350214..1350364_NEGATIVE 294 99 51 106 58 NC_002950:PG2214|3end_hypothetical_protein_2325301..2325451_NEGATIVE 294 85 48 141 109 NC_002950:PG1753|3end_selenide,_water_dikinase_1839741..1839891_POSITIVE 294 83 42 151 108 NC_002950:PG0738|3end_cytidine/deoxycytidylate_deaminase_family_protein_786995..787145_POSITIVE 289 130 82 121 79 NC_002950:PG1523|3end_naphthoate_synthase_1600170..1600320_NEGATIVE 289 88 46 98 59 NC_002950:PG0283|3end_efflux_transporter,_MFP_component,_RND_family_316995..317145_NEGATIVE 286 100 51 122 84 NC_002950:PG0396|3end_transcriptional_regulator,_Crp/Fnr_family_434291..434441_POSITIVE 284 99 51 138 96 NC_002950:PG0222|3end_DNA-binding_protein,_histone-like_family_255913..256063_NEGATIVE 282 88 45 113 67 NC_002950:PG2107|3end_thiamine_biosynthesis_protein_ThiH_2215546..2215696_NEGATIVE 281 85 43 111 72 NC_002950:PG1954|3end_NAD_dependent_epimerase/reductase-related_protein_2045612..2045762_POSITIVE 278 88 42 89 37 NC_002950:PG0561|3end_peptidase,_M20/M25/M40_family_617700..617850_NEGATIVE