Origin IGS: taagggtgctatatccggatacttctttgtagtcaaaatagggattcgttttttcgtttatcagtataacagccatagacccgtttggttgtcatccggcagtacacactgtattatgaaaacgattgagggctgactccgggattcggaaccagcccttatcgtcatacccaaacaaatgtatctatcagata .........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 tatctgatagatacatttgtttgggtatgacgataagggctggttccgaatcccggagtcagccctcaatcgttttcataatacagtgtgtactgccggatgacaaccaaacgggtctatggctgttatactgataaacgaaaaaacgaatccctattttgactacaaagaagtatccggatatagcaccctta Mask Tandem Repeat Region ================================================ taagggtgctatatccggatacttctttgtagtcaaaatagggattcgttttttcgtttatcagtataacagccatagacccgtttggttgtcatccggcagtacacactgtattatgaaaacgattgagggctgactccgggattcggaaccagcccttatcgtcatacccaaacaaatgtatctatcagata Find is-nt database================================================ Query_seq: PG0434:PG0435|PG0434:PG0435:hypothetical protein:capsular polysaccharide biosythesis protein, putative:<-<-:472604..472797 194 taagggtgctatatccggatacttctttgtagtcaaaatagggattcgttttttcgtttatcagtataacagccatagacccgtttggttgtcatccggcagtacacactgtattatgaaaacgattgagggctgactccgggattcggaaccagcccttatcgtcatacccaaacaaatgtatctatcagata Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG0434:PG0435|PG0434:PG0435:hypothetical protein:capsular polysaccharide biosythesis protein, putative:<-<-:472604..472797 194 taagggtgctatatccggatacttctttgtagtcaaaatagggattcgttttttcgtttatcagtataacagccatagacccgtttggttgtcatccggcagtacacactgtattatgaaaacgattgagggctgactccgggattcggaaccagcccttatcgtcatacccaaacaaatgtatctatcagata Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG0434:PG0435|PG0434:PG0435:hypothetical protein:capsular polysaccharide biosythesis protein, putative:<-<-:472604..472797 194 taagggtgctatatccggatacttctttgtagtcaaaatagggattcgttttttcgtttatcagtataacagccatagacccgtttggttgtcatccggcagtacacactgtattatgaaaacgattgagggctgactccgggattcggaaccagcccttatcgtcatacccaaacaaatgtatctatcagata Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taagggtgctatatccggatacttctttgtagtcaaaatagggattcgttttttcgtttatcagtataacagccatagacccgtttggttgtcatccggcagtacacactgtattatgaaaacgattgagggctgactccgggattcggaaccagcccttatcgtcatacccaaacaaatgtatctatcagata Predict ORF larger than 30AA ================================================ Protein_Len: 41 Strand: + Start: 11 End: 133 .......... M S G Y F F V V K I G I R F F V Y Q Y N S H R P V W L S S G S T H C I M K T I E G ............................................................. Protein_Len: 30 Strand: - Start: 95 End: 184 .............................................................................................. G A T C V T N H F R N L A S E P I R F W G K D D Y G F L H M .......... Protein_Len: 39 Strand: - Start: 64 End: 180 ............................................................... Y L L W L G T Q N D D P L V C Q I I F V I S P Q S R S E S G A R I T M G L C M .............. taagggtgctatatccggatacttctttgtagtcaaaatagggattcgttttttcgtttatcagtataacagccatagacccgtttggttgtcatccggcagtacacactgtattatgaaaacgattgagggctgactccgggattcggaaccagcccttatcgtcatacccaaacaaatgtatctatcagata 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: 83 Start: 88 End: 117 .......................................................................................GTTGTCATCCGGCAGTACACACTGTATTAT............................................................................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ taagggtgctatatccggatacttctttgtagtcaaaatagggattcgttttttcgtttatcagtataacagccatagacccgtttggttgtcatccggcagtacacactgtattatgaaaacgattgagggctgactccgggattcggaaccagcccttatcgtcatacccaaacaaatgtatctatcagata Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 100 HP_score: -12.4 Tail_Score: -4.30844 Start: 123 End: 164 Full_Region: tttgtttgggtatga cgataagggctggttccg aatcc cggagtcagccctcaatcg ttttcataatacagt ..........................................................................................................................cgataagggctggttccgaatcccggagtcagccctcaatcg.............................. Find igs database================================================ Query_seq: PG0434:PG0435|PG0434:PG0435:hypothetical protein:capsular polysaccharide biosythesis protein, putative:<-<-:472604..472797 194 taagggtgctatatccggatacttctttgtagtcaaaatagggattcgttttttcgtttatcagtataacagccatagacccgtttggttgtcatccggcagtacacactgtattatgaaaacgattgagggctgactccgggattcggaaccagcccttatcgtcatacccaaacaaatgtatctatcagata Intra-Species Hit: Count: 1 Min: 1 Max: 194 Len: 194 Subject: NC_002950_PG0434_PG0435|hypothetical protein:capsular polysaccharide biosythesis protein, putative|NEGATIVE:NEGATIVE|[472604,472797]|194 HSP 1 e-value: 1.0E-106 bit: 385.0 Len: 194 Query Start:1 Query End:194 Subject Strand: POSITIVE Subject Start: 1 Subject End: 194 taagggtgctatatccggatacttctttgtagtcaaaatagggattcgttttttcgtttatcagtataacagccatagacccgtttggttgtcatccggcagtacacactgtattatgaaaacgattgagggctgactccgggattcggaaccagcccttatcgtcatacccaaacaaatgtatctatcagata taagggtgctatatccggatacttctttgtagtcaaaatagggattcgttttttcgtttatcagtataacagccatagacccgtttggttgtcatccggcagtacacactgtattatgaaaacgattgagggctgactccgggattcggaaccagcccttatcgtcatacccaaacaaatgtatctatcagata Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAGGGUGCUAUAUCCGGAUACUUCUUUGUAGUCAAAAUAGGGAUUCGUUUUUUCGUUUAUCAGUAUAACAGCCAUAGACCCGUUUGGUUGUCAUCCGGCAGUACACACUGUAUUAUGAAAACGAUUGAGGGCUGACUCCGGGAUUCGGAACCAGCCCUUAUCGUCAUACCCAAACAAAUGUAUCUAUCAGAUA .....((((((((..((((.((.(((((((.......)))))))...))...))))..))).))))).......(((((..((((((.(((((((...(((((....)))))...))))..(((((.((((((((..((((.....))))..)))))))))))))......))).))))))..)))))...... (-54.80) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAUCUGAUAGAUACAUUUGUUUGGGUAUGACGAUAAGGGCUGGUUCCGAAUCCCGGAGUCAGCCCUCAAUCGUUUUCAUAAUACAGUGUGUACUGCCGGAUGACAACCAAACGGGUCUAUGGCUGUUAUACUGAUAAACGAAAAAACGAAUCCCUAUUUUGACUACAAAGAAGUAUCCGGAUAUAGCACCCUUA ((((((...(((((.((((((((..(((((((((.(((((((..((((.....))))..)))))))..))))...)))))...(((((((.((.((((...(((..((....)))))..)))).))))))))).))))))))..............(((((....)))))..)))))))))))........... (-61.70) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 973 110 61 201 152 NC_002950:PG0434|5end_hypothetical_protein_472513..472743_NEGATIVE 379 167 122 199 148 NC_002950:PG1633|5end_galactokinase_1713385..1713615_POSITIVE 374 163 122 198 151 NC_002950:PG0387|5end_elongation_factor_Tu_420643..420873_POSITIVE 366 164 127 166 118 NC_002950:PG0635|5end_ribosomal_protein_L11_methyltransferase_687773..688003_NEGATIVE 364 173 131 162 116 NC_002950:PG0139|5end_membrane-bound_lytic_murein_transglycosylase_D,_putative_163141..163371_NEGATIVE 357 112 72 162 124 NC_002950:PG0540|5end_AcrB/AcrD/AcrF_family_protein_591623..591853_POSITIVE 342 166 121 177 124 NC_002950:PG0757|5end_hypothetical_protein_806370..806600_NEGATIVE 340 100 51 107 64 NC_002950:PG0897|5end_alpha-amylase_family_protein_962472..962702_NEGATIVE 337 167 122 231 178 NC_002950:PG1499|5end_hypothetical_protein_1575524..1575754_POSITIVE 337 164 122 174 140 NC_002950:PG0525|5end_CTP_synthetase_568999..569229_POSITIVE 322 166 121 184 142 NC_002950:PG1254|5end_acetyltransferase,_GNAT_family_1332121..1332351_NEGATIVE 319 158 111 231 181 NC_002950:PG1312|5end_capA_protein,_putative_1390286..1390516_POSITIVE 319 108 73 34 3 NC_002950:PG0499|5end_hypothetical_protein_538709..538939_POSITIVE 316 166 124 176 139 NC_002950:PG0282|5end_ABC_transporter,_ATP-binding_protein_316915..317145_NEGATIVE 315 106 65 225 176 NC_002950:PG1947|5end_TPR_domain_protein_2032932..2033162_POSITIVE 314 162 123 142 98 NC_002950:PG0031|5end_hypothetical_protein_37579..37809_NEGATIVE 312 165 129 203 160 NC_002950:PG0334|5end_glycosyl_transferase,_group_2_family_protein_369751..369981_NEGATIVE 312 170 123 166 116 NC_002950:PG0229|5end_hypothetical_protein_264872..265102_POSITIVE 310 164 122 102 53 NC_002950:PG2090|5end_cation_efflux_family_protein_2190230..2190460_POSITIVE 310 167 124 231 185 NC_002950:PG1102|5end_hypothetical_protein_1173637..1173867_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 416 161 121 38 4 NC_002950:PG1121|3end_asparaginyl-tRNA_synthetase_1196146..1196296_NEGATIVE 379 167 122 149 98 NC_002950:PG1632|3end_aldose_1-epimerase_1713415..1713565_POSITIVE 377 162 123 71 29 NC_002950:PG0506|3end_arginine-specific_cysteine_proteinase_547625..547775_POSITIVE 376 168 121 72 10 NC_002950:PG0349|3end_hydrolase,_haloacid_dehalogenase-like_family_385291..385441_POSITIVE 356 165 128 76 26 NC_002950:PG0350|3end_internalin-related_protein_385356..385506_NEGATIVE 355 160 116 58 1 NC_002950:PG2010|3end_phosphomannomutase,_putative_2100952..2101102_POSITIVE 354 167 123 99 48 NC_002950:PG0572|3end_hypothetical_protein_627434..627584_NEGATIVE 349 165 127 67 28 NC_002950:PG2106|3end_hypothetical_protein_2215457..2215607_POSITIVE 347 172 131 151 106 NC_002950:PG0140|3end_hypothetical_protein_163151..163301_NEGATIVE 342 166 121 80 27 NC_002950:PG0758|3end_peptidyl-dipeptidase_Dcp_806467..806617_NEGATIVE 339 175 131 66 9 NC_002950:PG1297|3end_ribosomal_protein_S1_1377710..1377860_POSITIVE 337 164 122 58 24 NC_002950:PG0524|3end_hypothetical_protein_568963..569113_POSITIVE 332 158 117 64 21 NC_002950:PG1729|3end_thiol_peroxidase_1818342..1818492_NEGATIVE 332 166 123 89 45 NC_002950:PG1391|3end_hypothetical_protein_1472961..1473111_POSITIVE 332 165 121 72 17 NC_002950:PG0159|3end_endopeptidase_PepO_181095..181245_NEGATIVE 331 165 122 50 11 NC_002950:PG2124|3end_glyceraldehyde_3-phosphate_dehydrogenase,_type_I_2231264..2231414_POSITIVE 324 159 111 131 79 NC_002950:PG1884|3end_alpha-L-fucosidase_precursor,_putative_1978968..1979118_NEGATIVE 321 160 115 51 4 NC_002950:PG0721|3end_NLP/P60_family_protein_774535..774685_POSITIVE 316 160 113 63 14 NC_002950:PG0775|3end_acyl-CoA_dehydrogenase_family_protein_827432..827582_NEGATIVE 316 166 124 96 59 NC_002950:PG0283|3end_efflux_transporter,_MFP_component,_RND_family_316995..317145_NEGATIVE