Origin IGS: tcaggtcttaagaccctctaagagaaacggtgtgccgagatcgcccaaacagcgactccggcacaccgctttttttattgctcgcaggcttatacgactacctttttctccggaggcttcttgtcatacgtcttggagaagatagacggttcgggtctattcggaagaggaaggcggagga .........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 tcctccgccttcctcttccgaatagacccgaaccgtctatcttctccaagacgtatgacaagaagcctccggagaaaaaggtagtcgtataagcctgcgagcaataaaaaaagcggtgtgccggagtcgctgtttgggcgatctcggcacaccgtttctcttagagggtcttaagacctga Mask Tandem Repeat Region ================================================ tcaggtcttaagaccctctaagagaaacggtgtgccgagatcgcccaaacagcgactccggcacaccgctttttttattgctcgcaggcttatacgactacctttttctccggaggcttcttgtcatacgtcttggagaagatagacggttcgggtctattcggaagaggaaggcggagga Find is-nt database================================================ Query_seq: PG0138:PG0139|PG0138:PG0139:malonyl CoA-acyl carrier protein transacylase:membrane-bound lytic murein transglycosylase D, putative:-><-:161695..161875 181 tcaggtcttaagaccctctaagagaaacggtgtgccgagatcgcccaaacagcgactccggcacaccgctttttttattgctcgcaggcttatacgactacctttttctccggaggcttcttgtcatacgtcttggagaagatagacggttcgggtctattcggaagaggaaggcggagga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG0138:PG0139|PG0138:PG0139:malonyl CoA-acyl carrier protein transacylase:membrane-bound lytic murein transglycosylase D, putative:-><-:161695..161875 181 tcaggtcttaagaccctctaagagaaacggtgtgccgagatcgcccaaacagcgactccggcacaccgctttttttattgctcgcaggcttatacgactacctttttctccggaggcttcttgtcatacgtcttggagaagatagacggttcgggtctattcggaagaggaaggcggagga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG0138:PG0139|PG0138:PG0139:malonyl CoA-acyl carrier protein transacylase:membrane-bound lytic murein transglycosylase D, putative:-><-:161695..161875 181 tcaggtcttaagaccctctaagagaaacggtgtgccgagatcgcccaaacagcgactccggcacaccgctttttttattgctcgcaggcttatacgactacctttttctccggaggcttcttgtcatacgtcttggagaagatagacggttcgggtctattcggaagaggaaggcggagga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tcaggtcttaagaccctctaagagaaacggtgtgccgagatcgcccaaacagcgactccggcacaccgctttttttattgctcgcaggcttatacgactacctttttctccggaggcttcttgtcatacgtcttggagaagatagacggttcgggtctattcggaagaggaaggcggagga Predict ORF larger than 30AA ================================================ Protein_Len: 37 Strand: + Start: 32 End: 142 ............................... M P R S P K Q R L R H T A F F I A R R L I R L P F S P E A S C H T S W R R ....................................... Protein_Len: 50 Strand: + Start: 30 End: 179 ............................. M C R D R P N S D S G T P L F L L L A G L Y D Y L F L R R L L V I R L G E D R R F G S I R K R K A E .. Protein_Len: 47 Strand: + Start: 40 End: 180 ....................................... M A Q T A T P A H R F F Y C S Q A Y T T T F F S G G F L S Y V L E K I D G S G L F G R G R R R . Protein_Len: 31 Strand: - Start: 4 End: 93 ... * T K L G E L L F P T G L D G L C R S R C V A K K I A R L S M ........................................................................................ tcaggtcttaagaccctctaagagaaacggtgtgccgagatcgcccaaacagcgactccggcacaccgctttttttattgctcgcaggcttatacgactacctttttctccggaggcttcttgtcatacgtcttggagaagatagacggttcgggtctattcggaagaggaaggcggagga 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================================================ tcaggtcttaagaccctctaagagaaacggtgtgccgagatcgcccaaacagcgactccggcacaccgctttttttattgctcgcaggcttatacgactacctttttctccggaggcttcttgtcatacgtcttggagaagatagacggttcgggtctattcggaagaggaaggcggagga Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 100 HP_score: -11.2 Tail_Score: -5.84381 Start: 27 End: 69 Full_Region: GACCCTCTAAGAGAA ACGGTGTGCCGAGATCGC CCAAACA GCGACTCCGGCACACCGC TTTTTTTATTGCTCG ..........................ACGGTGTGCCGAGATCGCCCAAACAGCGACTCCGGCACACCGC................................................................................................................ TransTerm Strand: - Conf: 100 HP_score: -17.6 Tail_Score: -4.19177 Start: 28 End: 68 Full_Region: gagcaataaaaaaag cggtgtgccggagtcgct gtttg ggcgatctcggcacaccg tttctcttagagggt ...........................cggtgtgccggagtcgctgtttgggcgatctcggcacaccg................................................................................................................. Find igs database================================================ Query_seq: PG0138:PG0139|PG0138:PG0139:malonyl CoA-acyl carrier protein transacylase:membrane-bound lytic murein transglycosylase D, putative:-><-:161695..161875 181 tcaggtcttaagaccctctaagagaaacggtgtgccgagatcgcccaaacagcgactccggcacaccgctttttttattgctcgcaggcttatacgactacctttttctccggaggcttcttgtcatacgtcttggagaagatagacggttcgggtctattcggaagaggaaggcggagga Intra-Species Hit: Count: 1 Min: 1 Max: 181 Len: 181 Subject: NC_002950_PG0138_PG0139|malonyl CoA-acyl carrier protein transacylase:membrane-bound lytic murein transglycosylase D, putative|POSITIVE:NEGATIVE|[161695,161875]|181 HSP 1 e-value: 7.0E-86 bit: 317.0 Len: 181 Query Start:1 Query End:181 Subject Strand: POSITIVE Subject Start: 1 Subject End: 181 tcaggtcttaagaccctctaagagaaacggtgtgccgagatcgcccaaacagcgactccggcacaccgcnnnnnnnattgctcgcaggcttatacgactacctttttctccggaggcttcttgtcatacgtcttggagaagatagacggttcgggtctattcggaagaggaaggcggagga tcaggtcttaagaccctctaagagaaacggtgtgccgagatcgcccaaacagcgactccggcacaccgctttttttattgctcgcaggcttatacgactacctttttctccggaggcttcttgtcatacgtcttggagaagatagacggttcgggtctattcggaagaggaaggcggagga Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCAGGUCUUAAGACCCUCUAAGAGAAACGGUGUGCCGAGAUCGCCCAAACAGCGACUCCGGCACACCGCUUUUUUUAUUGCUCGCAGGCUUAUACGACUACCUUUUUCUCCGGAGGCUUCUUGUCAUACGUCUUGGAGAAGAUAGACGGUUCGGGUCUAUUCGGAAGAGGAAGGCGGAGGA ((..(((((.((((((..((((((((.((((((((((.((((((.......)))).)))))))))))).))))))))..(((....)))......((((..(((((((((((.((((............))))))))))))).))..)))).)))))).(((....))).))))).))... (-66.10) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCCUCCGCCUUCCUCUUCCGAAUAGACCCGAACCGUCUAUCUUCUCCAAGACGUAUGACAAGAAGCCUCCGGAGAAAAAGGUAGUCGUAUAAGCCUGCGAGCAAUAAAAAAAGCGGUGUGCCGGAGUCGCUGUUUGGGCGAUCUCGGCACACCGUUUCUCUUAGAGGGUCUUAAGACCUGA ......(((((..(((.(((.((((((.......))))))(((((...............)))))....))))))..)))))..(((((......)))))..........(((((((((((((..((((((.....))))))..)))))))))))))........(((((....))))).. (-62.56) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 450 70 21 173 128 NC_002950:PG1281|5end_hypothetical_protein_1358848..1359078_POSITIVE 435 89 42 169 114 NC_002950:PG0359|5end_flavin_reductase_domain_protein_392851..393081_POSITIVE 432 69 33 64 26 NC_002950:PG1313|5end_dipeptidase-related_protein_1392282..1392512_POSITIVE 421 67 21 228 188 NC_002950:PG0768|5end_hypothetical_protein_822381..822611_NEGATIVE 420 180 147 78 40 NC_002950:PG1675|5end_hypothetical_protein_1760182..1760412_POSITIVE 406 178 131 170 123 NC_002950:PG1167|5end_hypothetical_protein_1248427..1248657_POSITIVE 399 69 27 161 114 NC_002950:PG1967|5end_TPR_domain_protein_2057168..2057398_POSITIVE 387 70 28 58 19 NC_002950:PG1902|5end_uridylate_kinase_2002147..2002377_NEGATIVE 378 170 123 228 185 NC_002950:PG1094|5end_phosphomannomutase_1158753..1158983_POSITIVE 377 63 21 159 121 NC_002950:PG2021|5end_hypothetical_protein_2114852..2115082_NEGATIVE 372 69 22 187 148 NC_002950:PG0607|5end_hypothetical_protein_662552..662782_POSITIVE 370 157 112 164 108 NC_002950:PG0074|5end_peptide_chain_release_factor_1_89172..89402_NEGATIVE 369 67 21 200 153 NC_002950:PG0744|5end_RNA_methyltransferase,_TrmH_family_791897..792127_NEGATIVE 368 167 126 173 127 NC_002950:PG1719|5end_ABC_transporter,_ATP-binding_protein,_MsbA_family_1806749..1806979_POSITIVE 366 88 47 100 47 NC_002950:PG1525|5end_isochorismate_synthase,_putative_1603865..1604095_NEGATIVE 361 70 28 227 185 NC_002950:PG0256|5end_CvpA_family_protein_289509..289739_POSITIVE 357 62 21 231 193 NC_002950:PG0619|5end_alkyl_hydroperoxide_reductase,_F_subunit_671104..671334_POSITIVE 356 178 131 225 183 NC_002950:PG1647|5end_cardiolipin_synthetase_1726273..1726503_POSITIVE 356 68 22 230 182 NC_002950:PG1052|5end_transcriptional_regulator,_putative_1119690..1119920_POSITIVE 355 89 51 45 4 NC_002950:PG1959|5end_ribosomal_protein_L33_2048405..2048635_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 526 69 23 55 5 NC_002950:PG2207|3end_hypothetical_protein_2319142..2319292_NEGATIVE 482 70 21 72 27 NC_002950:PG0618|3end_alkyl_hydroperoxide_reductase,_C_subunit_671018..671168_POSITIVE 466 68 21 63 15 NC_002950:PG0138|3end_malonyl_CoA-acyl_carrier_protein_transacylase_161634..161784_POSITIVE 450 70 21 46 1 NC_002950:PG1280|3end_hypothetical_protein_1358801..1358951_POSITIVE 435 89 42 140 85 NC_002950:PG0358|3end_aspartate_carbamoyltransferase_regulatory_subunit_392902..393052_POSITIVE 421 67 21 54 14 NC_002950:PG0769|3end_fibronectin_type_III_domain_protein_822555..822705_NEGATIVE 413 180 131 87 41 NC_002950:PG2161|3end_transcriptional_regulator,_AraC_family_2266717..2266867_NEGATIVE 412 70 26 126 86 NC_002950:PG1675|3end_hypothetical_protein_1760360..1760510_POSITIVE 396 70 22 60 5 NC_002950:PG0537|3end_aminoacyl-histidine_dipeptidase_588394..588544_POSITIVE 374 89 44 150 95 NC_002950:PG0800|3end_hypothetical_protein_854719..854869_NEGATIVE 370 157 112 139 83 NC_002950:PG0075|3end_phosphoribosylformylglycinamidine_cyclo-ligase,_putative_89197..89347_NEGATIVE 370 70 23 122 71 NC_002950:PG0003|3end_hypothetical_protein_1919..2069_NEGATIVE 369 67 21 115 68 NC_002950:PG0745|3end_lactoylglutathione_lyase,_putative_791982..792132_NEGATIVE 360 179 140 120 63 NC_002950:PG2031|3end_hypothetical_protein_2130871..2131021_POSITIVE 359 160 112 146 101 NC_002950:PG1099|3end_hypothetical_protein_1167344..1167494_NEGATIVE 357 180 136 119 65 NC_002950:PG1842|3end_acetyltransferase,_GNAT_family_1939313..1939463_POSITIVE 355 88 42 77 13 NC_002950:PG1247|3end_3-dehydroquinate_synthase_1325585..1325735_POSITIVE 354 60 11 83 21 NC_002950:PG1433|3end_hydrolase_1519126..1519276_POSITIVE 352 180 132 55 8 NC_002950:PG0329|3end_formiminotransferase-cyclodeaminase-related_protein_363527..363677_NEGATIVE 352 69 30 134 77 NC_002950:PG0087|3end_SIS_domain_protein_102505..102655_NEGATIVE