Origin IGS: gtgcctatttatatcggcaaatatactccaaataaatgaaaatattttttgcgataggatttattataatataaattccgatttgtcaatccgataatctttatttcgatagatatatatctataattttcttatttgtgtacgataatccaaataaacaaagatgtgcttttaaccgttttgtttctatttcat .........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 atgaaatagaaacaaaacggttaaaagcacatctttgtttatttggattatcgtacacaaataagaaaattatagatatatatctatcgaaataaagattatcggattgacaaatcggaatttatattataataaatcctatcgcaaaaaatattttcatttatttggagtatatttgccgatataaataggcac Mask Tandem Repeat Region ================================================ gtgcctatttatatcggcaaatatactccaaataaatgaaaatattttttgcgataggatttattataatataaattccgatttgtcaatccgataatctttatttcgatagatatatatctataattttcttatttgtgtacgataatccaaataaacaaagatgtgcttttaaccgttttgtttctatttcat Find is-nt database================================================ Query_seq: PG1526:PG1527|PG1526:PG1527:hypothetical protein:hypothetical protein:<-<-:1605462..1605656 195 gtgcctatttatatcggcaaatatactccaaataaatgaaaatattttttgcgataggatttattataatataaattccgatttgtcaatccgataatctttatttcgatagatatatatctataattttcttatttgtgtacgataatccaaataaacaaagatgtgcttttaaccgttttgtttctatttcat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG1526:PG1527|PG1526:PG1527:hypothetical protein:hypothetical protein:<-<-:1605462..1605656 195 gtgcctatttatatcggcaaatatactccaaataaatgaaaatattttttgcgataggatttattataatataaattccgatttgtcaatccgataatctttatttcgatagatatatatctataattttcttatttgtgtacgataatccaaataaacaaagatgtgcttttaaccgttttgtttctatttcat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG1526:PG1527|PG1526:PG1527:hypothetical protein:hypothetical protein:<-<-:1605462..1605656 195 gtgcctatttatatcggcaaatatactccaaataaatgaaaatattttttgcgataggatttattataatataaattccgatttgtcaatccgataatctttatttcgatagatatatatctataattttcttatttgtgtacgataatccaaataaacaaagatgtgcttttaaccgttttgtttctatttcat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gtgcctatttatatcggcaaatatactccaaataaatgaaaatattttttgcgataggatttattataatataaattccgatttgtcaatccgataatctttatttcgatagatatatatctataattttcttatttgtgtacgataatccaaataaacaaagatgtgcttttaaccgttttgtttctatttcat Predict ORF larger than 30AA ================================================ Protein_Len: 40 Strand: + Start: 75 End: 194 .......................................................................... M P I C Q S D N L Y F D R Y I S I I F L F V Y D N P N K Q R C A F N R F V S I S . Protein_Len: 35 Strand: - Start: 12 End: 116 ........... I P L Y V G F L H F Y K K R Y S K N Y Y L N R N T L G I I K I E I S M ............................................................................... gtgcctatttatatcggcaaatatactccaaataaatgaaaatattttttgcgataggatttattataatataaattccgatttgtcaatccgataatctttatttcgatagatatatatctataattttcttatttgtgtacgataatccaaataaacaaagatgtgcttttaaccgttttgtttctatttcat 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================================================ gtgcctatttatatcggcaaatatactccaaataaatgaaaatattttttgcgataggatttattataatataaattccgatttgtcaatccgataatctttatttcgatagatatatatctataattttcttatttgtgtacgataatccaaataaacaaagatgtgcttttaaccgttttgtttctatttcat Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PG1526:PG1527|PG1526:PG1527:hypothetical protein:hypothetical protein:<-<-:1605462..1605656 195 gtgcctatttatatcggcaaatatactccaaataaatgaaaatattttttgcgataggatttattataatataaattccgatttgtcaatccgataatctttatttcgatagatatatatctataattttcttatttgtgtacgataatccaaataaacaaagatgtgcttttaaccgttttgtttctatttcat Intra-Species Hit: Count: 1 Min: 1 Max: 195 Len: 195 Subject: NC_002950_PG1526_PG1527|hypothetical protein:hypothetical protein|NEGATIVE:NEGATIVE|[1605462,1605656]|195 HSP 1 e-value: 1.0E-106 bit: 387.0 Len: 195 Query Start:1 Query End:195 Subject Strand: POSITIVE Subject Start: 1 Subject End: 195 gtgcctatttatatcggcaaatatactccaaataaatgaaaatattttttgcgataggatttattataatataaattccgatttgtcaatccgataatctttatttcgatagatatatatctataattttcttatttgtgtacgataatccaaataaacaaagatgtgcttttaaccgttttgtttctatttcat gtgcctatttatatcggcaaatatactccaaataaatgaaaatattttttgcgataggatttattataatataaattccgatttgtcaatccgataatctttatttcgatagatatatatctataattttcttatttgtgtacgataatccaaataaacaaagatgtgcttttaaccgttttgtttctatttcat Inter-species Hit: Count: 1 Min: 1 Max: 195 Len: 195 Subject: tfor_TF0869_TF0870|conserved hypothetical protein; possible transcriptional regulator:conserved hypothetical protein|POSITIVE:POSITIVE|[922075,922265]|191 HSP 1 e-value: 1.0E-56 bit: 220.0 Len: 195 Query Start:1 Query End:195 Subject Strand: POSITIVE Subject Start: 1 Subject End: 188 gtgcctatttatatcggcaaatatactccaaataaatgaaaatattttttgcgataggatttattataatataaattccgatttgtcaatccgataatctttatttcgatagatatatatctataattttcttattt-gtgtacgataatccaaataaacaaagatgtgcttttaaccgttttgtttctatttcat gtgcctatttatatcggcaaatatactccaaataaatgaaaatattttttgcgataggatttattaaaagataaattccgatttgtcaatccgataatctttatttcgatatata--------tagttatcttattttgtttatgataaccccaataaataaagatatgcttttaaccgttttatttctatttcat Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GUGCCUAUUUAUAUCGGCAAAUAUACUCCAAAUAAAUGAAAAUAUUUUUUGCGAUAGGAUUUAUUAUAAUAUAAAUUCCGAUUUGUCAAUCCGAUAAUCUUUAUUUCGAUAGAUAUAUAUCUAUAAUUUUCUUAUUUGUGUACGAUAAUCCAAAUAAACAAAGAUGUGCUUUUAACCGUUUUGUUUCUAUUUCAU .((((.((....)).))))....(((..(((((((..((((((........(((..((((((((......)))))))).((((.(((.....)))))))......))).(((((....)))))..))))))))))))).))).............((((((((..((.......))..))))))))......... (-27.50) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUGAAAUAGAAACAAAACGGUUAAAAGCACAUCUUUGUUUAUUUGGAUUAUCGUACACAAAUAAGAAAAUUAUAGAUAUAUAUCUAUCGAAAUAAAGAUUAUCGGAUUGACAAAUCGGAAUUUAUAUUAUAAUAAAUCCUAUCGCAAAAAAUAUUUUCAUUUAUUUGGAGUAUAUUUGCCGAUAUAAAUAGGCAC ..........................((..((((((((((...(((((((((......................))))...)))))...))))))))))((((((...........(((.(((((......)))))))).........(((((((((((......))))).)))))).)))))).......)).. (-29.65) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 748 100 51 191 142 NC_002950:PG1526|5end_hypothetical_protein_1605371..1605601_NEGATIVE 234 51 11 206 170 NC_002950:PG1271|5end_acetylornithine_aminotransferase,_putative_1351443..1351673_NEGATIVE 233 122 81 135 90 NC_002950:PG0625|5end_GTP_cyclohydrolase_I_678588..678818_POSITIVE 221 108 67 231 185 NC_002950:PG1925|5end_ribosomal_protein_S14_2018675..2018905_NEGATIVE 213 100 53 94 49 NC_002950:PG0563|5end_hypothetical_protein_621438..621668_NEGATIVE 210 140 102 223 178 NC_002950:PG1008|5end_hypothetical_protein_1067644..1067874_NEGATIVE 208 98 51 130 75 NC_002950:PG1924|5end_ribosomal_protein_S8_2018355..2018585_NEGATIVE 208 118 79 208 175 NC_002950:PG0352|5end_sialidase,_putative_387187..387417_POSITIVE 207 188 165 49 21 NC_002950:PG1398|5end_hypothetical_protein_1480694..1480924_POSITIVE 201 99 77 77 50 NC_002950:PG1235|5end_epimerase/reductase,_putative_1311256..1311486_NEGATIVE 201 189 162 182 155 NC_002950:PG0475|5end_oxygen-independent_coproporphyrinogen_III_oxidase,_putative_517218..517448_NEGATIVE 201 184 144 45 2 NC_002950:PG0013|5end_hypothetical_protein_15591..15821_POSITIVE 198 94 66 215 189 NC_002950:PG0794|5end_penicillin-binding_protein_1A,_putative_846411..846641_POSITIVE 192 111 79 87 46 NC_002950:PG1041|5end_K+-dependent_Na+/Ca+_exchanger_related-protein_1108923..1109153_NEGATIVE 192 30 1 71 39 NC_002950:PG0556|5end_hypothetical_protein_613278..613508_POSITIVE 191 115 77 96 60 NC_002950:PG0204|5end_hypothetical_protein_240507..240737_NEGATIVE 190 187 162 210 186 NC_002950:PG2098|5end_hypothetical_protein_2206635..2206865_NEGATIVE 189 113 72 168 125 NC_002950:PG1748|5end_transketolase_1834929..1835159_NEGATIVE 188 112 73 58 24 NC_002950:PG1441|5end_lysozyme-related_protein_1527525..1527755_NEGATIVE 187 108 75 38 1 NC_002950:PG1279|5end_D-isomer_specific_2-hydroxyacid_dehydrogenase_family_protein_1356535..1356765_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 233 122 81 131 86 NC_002950:PG0624|3end_hypothetical_protein_678664..678814_POSITIVE 219 112 76 115 83 NC_002950:PG0354|3end_hypothetical_protein_389131..389281_NEGATIVE 213 100 53 116 71 NC_002950:PG0564|3end_hypothetical_protein_621416..621566_NEGATIVE 208 98 51 79 24 NC_002950:PG1925|3end_ribosomal_protein_S14_2018406..2018556_NEGATIVE 208 118 79 55 22 NC_002950:PG0351|3end_hypothetical_protein_387114..387264_POSITIVE 198 94 66 59 33 NC_002950:PG0793|3end_fructose-1,6-bisphosphatase_846335..846485_POSITIVE 194 109 76 131 99 NC_002950:PG0708|3end_peptidyl-prolyl_cis-trans_isomerase,_FKBP-type_763798..763948_NEGATIVE 193 187 146 53 15 NC_002950:PG1014|3end_TPR_domain_protein_1075855..1076005_POSITIVE 191 115 77 90 54 NC_002950:PG0205|3end_peptide_chain_release_factor_3_240513..240663_NEGATIVE 190 19 2 53 34 NC_002950:PG1786|3end_hypothetical_protein_1875322..1875472_POSITIVE 189 111 75 133 100 NC_002950:PG1459|3end_hypothetical_protein_1539632..1539782_NEGATIVE 187 112 77 134 100 NC_002950:PG1213|3end_ribonuclease_H_1293163..1293313_POSITIVE 185 99 52 132 84 NC_002950:PG0087|3end_SIS_domain_protein_102505..102655_NEGATIVE 183 58 15 83 41 NC_002950:PG2223|3end_glycosyl_transferase,_group_2_family_protein_2338761..2338911_POSITIVE 181 189 163 23 2 NC_002950:PG0934|3end_hypothetical_protein_992414..992564_NEGATIVE 181 178 131 134 83 NC_002950:PG0639|3end_signal_peptide_peptidase_SppA,_67K_type_691213..691363_NEGATIVE 180 133 91 125 77 NC_002950:PG1851|3end_phosphopantothenoylcysteine_decarboxylase/phosphopantothenate--cysteine_ligase_1949954..1950104_NEGATIVE 180 119 74 68 18 NC_002950:PG0777|3end_electron_transfer_flavoprotein,_beta_subunit_830193..830343_NEGATIVE 179 115 78 36 2 NC_002950:PG1552|3end_TonB-dependent_receptor_HmuR_1630901..1631051_POSITIVE 178 104 78 33 7 NC_002950:PG1105|3end_RNA_polymerase_sigma-54_factor_1175716..1175866_NEGATIVE