Origin IGS: ctgtttgaaatagttgcaacaaaacaacgttagctacaaaagtacaaataaattgcagtccgtcagggagattcggagcgatctcttttggaaattttcagtctcttccctctataatttgaatccctgagatatgaattcgtgcttgttttgataattgaatgtagcaatcatgaagctatacgtacattaggagttcaagtgcgattgccctgagtgatctacaccctct .........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 agagggtgtagatcactcagggcaatcgcacttgaactcctaatgtacgtatagcttcatgattgctacattcaattatcaaaacaagcacgaattcatatctcagggattcaaattatagagggaagagactgaaaatttccaaaagagatcgctccgaatctccctgacggactgcaatttatttgtacttttgtagctaacgttgttttgttgcaactatttcaaacag Mask Tandem Repeat Region ================================================ ctgtttgaaatagttgcaacaaaacaacgttagctacaaaagtacaaataaattgcagtccgtcagggagattcggagcgatctcttttggaaattttcagtctcttccctctataatttgaatccctgagatatgaattcgtgcttgttttgataattgaatgtagcaatcatgaagctatacgtacattaggagttcaagtgcgattgccctgagtgatctacaccctct Find is-nt database================================================ Query_seq: PG0076:PG0078|PG0076:PG0078:N-acetylmuramoyl-L-alanine amidase, family 4:hypothetical protein:<-<-:91424..91655 232 ctgtttgaaatagttgcaacaaaacaacgttagctacaaaagtacaaataaattgcagtccgtcagggagattcggagcgatctcttttggaaattttcagtctcttccctctataatttgaatccctgagatatgaattcgtgcttgttttgataattgaatgtagcaatcatgaagctatacgtacattaggagttcaagtgcgattgccctgagtgatctacaccctct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG0076:PG0078|PG0076:PG0078:N-acetylmuramoyl-L-alanine amidase, family 4:hypothetical protein:<-<-:91424..91655 232 ctgtttgaaatagttgcaacaaaacaacgttagctacaaaagtacaaataaattgcagtccgtcagggagattcggagcgatctcttttggaaattttcagtctcttccctctataatttgaatccctgagatatgaattcgtgcttgttttgataattgaatgtagcaatcatgaagctatacgtacattaggagttcaagtgcgattgccctgagtgatctacaccctct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG0076:PG0078|PG0076:PG0078:N-acetylmuramoyl-L-alanine amidase, family 4:hypothetical protein:<-<-:91424..91655 232 ctgtttgaaatagttgcaacaaaacaacgttagctacaaaagtacaaataaattgcagtccgtcagggagattcggagcgatctcttttggaaattttcagtctcttccctctataatttgaatccctgagatatgaattcgtgcttgttttgataattgaatgtagcaatcatgaagctatacgtacattaggagttcaagtgcgattgccctgagtgatctacaccctct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ctgtttgaaatagttgcaacaaaacaacgttagctacaaaagtacaaataaattgcagtccgtcagggagattcggagcgatctcttttggaaattttcagtctcttccctctataatttgaatccctgagatatgaattcgtgcttgttttgataattgaatgtagcaatcatgaagctatacgtacattaggagttcaagtgcgattgccctgagtgatctacaccctct Predict ORF larger than 30AA ================================================ Protein_Len: 38 Strand: + Start: 14 End: 127 ............. M Q Q N N V S Y K S T N K L Q S V R E I R S D L F W K F S V S S L Y N L N P ......................................................................................................... Protein_Len: 35 Strand: - Start: 66 End: 170 ................................................................. P S E S R D R K S I K L R K G R Y N S D R L Y S N T S T K I I S H L M .............................................................. ctgtttgaaatagttgcaacaaaacaacgttagctacaaaagtacaaataaattgcagtccgtcagggagattcggagcgatctcttttggaaattttcagtctcttccctctataatttgaatccctgagatatgaattcgtgcttgttttgataattgaatgtagcaatcatgaagctatacgtacattaggagttcaagtgcgattgccctgagtgatctacaccctct 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================================================ ctgtttgaaatagttgcaacaaaacaacgttagctacaaaagtacaaataaattgcagtccgtcagggagattcggagcgatctcttttggaaattttcagtctcttccctctataatttgaatccctgagatatgaattcgtgcttgttttgataattgaatgtagcaatcatgaagctatacgtacattaggagttcaagtgcgattgccctgagtgatctacaccctct Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PG0076:PG0078|PG0076:PG0078:N-acetylmuramoyl-L-alanine amidase, family 4:hypothetical protein:<-<-:91424..91655 232 ctgtttgaaatagttgcaacaaaacaacgttagctacaaaagtacaaataaattgcagtccgtcagggagattcggagcgatctcttttggaaattttcagtctcttccctctataatttgaatccctgagatatgaattcgtgcttgttttgataattgaatgtagcaatcatgaagctatacgtacattaggagttcaagtgcgattgccctgagtgatctacaccctct Intra-Species Hit: Count: 1 Min: 1 Max: 232 Len: 232 Subject: NC_002950_PG0076_PG0078|N-acetylmuramoyl-L-alanine amidase, family 4:hypothetical protein|NEGATIVE:NEGATIVE|[91424,91655]|232 HSP 1 e-value: 1.0E-128 bit: 460.0 Len: 232 Query Start:1 Query End:232 Subject Strand: POSITIVE Subject Start: 1 Subject End: 232 ctgtttgaaatagttgcaacaaaacaacgttagctacaaaagtacaaataaattgcagtccgtcagggagattcggagcgatctcttttggaaattttcagtctcttccctctataatttgaatccctgagatatgaattcgtgcttgttttgataattgaatgtagcaatcatgaagctatacgtacattaggagttcaagtgcgattgccctgagtgatctacaccctct ctgtttgaaatagttgcaacaaaacaacgttagctacaaaagtacaaataaattgcagtccgtcagggagattcggagcgatctcttttggaaattttcagtctcttccctctataatttgaatccctgagatatgaattcgtgcttgttttgataattgaatgtagcaatcatgaagctatacgtacattaggagttcaagtgcgattgccctgagtgatctacaccctct Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUGUUUGAAAUAGUUGCAACAAAACAACGUUAGCUACAAAAGUACAAAUAAAUUGCAGUCCGUCAGGGAGAUUCGGAGCGAUCUCUUUUGGAAAUUUUCAGUCUCUUCCCUCUAUAAUUUGAAUCCCUGAGAUAUGAAUUCGUGCUUGUUUUGAUAAUUGAAUGUAGCAAUCAUGAAGCUAUACGUACAUUAGGAGUUCAAGUGCGAUUGCCCUGAGUGAUCUACACCCUCU .((((((.....((((........))))....(((.....))).))))))..............((((((((((((.((((((......((((............)))).......(((((((..(((((..((((..((((((.(((((...............))))).))))))......))))..)))))..)))))))..)))))).))))...))))...)))).. (-48.46) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGAGGGUGUAGAUCACUCAGGGCAAUCGCACUUGAACUCCUAAUGUACGUAUAGCUUCAUGAUUGCUACAUUCAAUUAUCAAAACAAGCACGAAUUCAUAUCUCAGGGAUUCAAAUUAUAGAGGGAAGAGACUGAAAAUUUCCAAAAGAGAUCGCUCCGAAUCUCCCUGACGGACUGCAAUUUAUUUGUACUUUUGUAGCUAACGUUGUUUUGUUGCAACUAUUUCAAACAG ...((((((((((((.(((((((....)).))))).........((.......))....))))..)))))))).............((((((((......((((((((((((..........(((((...........)))))....(((....))).)))..))))))).))..(((((.....)))))..))))).)))...(((((......)))))............ (-45.30) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 954 110 61 201 152 NC_002950:PG0076|5end_N-acetylmuramoyl-L-alanine_amidase,_family_4_91333..91563_NEGATIVE 546 180 132 227 180 NC_002950:PG0499|5end_hypothetical_protein_538709..538939_POSITIVE 534 180 132 226 180 NC_002950:PG1059|5end_hypothetical_protein_1126495..1126725_NEGATIVE 478 180 132 226 180 NC_002950:PG2220|5end_hypothetical_protein_2334935..2335165_POSITIVE 468 150 101 196 147 NC_002950:PG1363|5end_hypothetical_protein_1443804..1444034_POSITIVE 392 108 61 231 185 NC_002950:PG2065|5end_conserved_hypothetical_protein_TIGR00048_2161000..2161230_POSITIVE 372 109 61 86 44 NC_002950:PG1831|5end_ATP-dependent_DNA_helicase_RecQ_1925422..1925652_NEGATIVE 368 105 62 61 5 NC_002950:PG0336|5end_hypothetical_protein_371292..371522_NEGATIVE 334 227 181 214 165 NC_002950:PG0754|5end_DNA_topoisomerase_I_800943..801173_POSITIVE 330 100 51 43 2 NC_002950:PG0507|5end_hypothetical_protein_547916..548146_POSITIVE 329 215 171 182 137 NC_002950:PG1787|5end_hypothetical_protein_1875908..1876138_NEGATIVE 324 112 71 107 63 NC_002950:PG1665|5end_ABC_transporter,_permease_protein,_putative_1747110..1747340_POSITIVE 321 219 171 66 16 NC_002950:PG0879|5end_hypothetical_protein_942536..942766_NEGATIVE 316 80 42 66 19 NC_002950:PG0704|5end_phosphoglycerate_mutase_family_protein_758928..759158_POSITIVE 312 109 61 173 125 NC_002950:PG0525|5end_CTP_synthetase_568999..569229_POSITIVE 309 81 54 63 36 NC_002950:PG1566|5end_glutamyl-tRNA_synthetase_1647401..1647631_NEGATIVE 302 113 71 65 20 NC_002950:PG1919|5end_ribosomal_protein_L15_2016281..2016511_NEGATIVE 301 100 53 90 31 NC_002950:PG2227|5end_hypothetical_protein_2342008..2342238_POSITIVE 298 109 61 181 129 NC_002950:PG1846|5end_hypothetical_protein_1946037..1946267_POSITIVE 298 89 58 161 125 NC_002950:PG0790|5end_GTP-binding_protein_Obg_842583..842813_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 336 91 55 45 12 NC_002950:PG1304|3end_hypothetical_protein_1382134..1382284_NEGATIVE 329 230 197 49 14 NC_002950:PG2094|3end_hypothetical_protein_2193321..2193471_NEGATIVE 324 112 71 84 40 NC_002950:PG1664|3end_ABC_transporter,_permease_protein,_putative_1747167..1747317_POSITIVE 316 80 42 64 17 NC_002950:PG0703|3end_cobalamin_(5'-phosphate)_synthase,_putative_759006..759156_POSITIVE 312 109 61 57 9 NC_002950:PG0524|3end_hypothetical_protein_568963..569113_POSITIVE 304 95 53 61 15 NC_002950:PG0707|3end_TonB-dependent_receptor,_putative_761086..761236_NEGATIVE 301 100 53 93 34 NC_002950:PG2226|3end_hypothetical_protein_2342091..2342241_POSITIVE 298 89 58 151 115 NC_002950:PG0791|3end_adenylate_kinase_842593..842743_NEGATIVE 297 90 54 72 31 NC_002950:PG0337|3end_hypothetical_protein_371377..371527_NEGATIVE 295 90 54 121 76 NC_002950:PG0790|3end_GTP-binding_protein_Obg_841399..841549_NEGATIVE 294 85 55 148 120 NC_002950:PG0059|3end_hypothetical_protein_71989..72139_POSITIVE 293 79 41 135 97 NC_002950:PG1341|3end_hypothetical_protein_1422665..1422815_POSITIVE 290 92 59 139 98 NC_002950:PG1766|3end_phosphoribosylglycinamide_formyltransferase_1854078..1854228_POSITIVE 290 100 57 42 3 NC_002950:PG1382|3end_hypothetical_protein_1462550..1462700_POSITIVE 287 89 44 107 44 NC_002950:PG0163|3end_diphosphate--fructose-6-phosphate_1-phosphotransferase_185236..185386_NEGATIVE 286 230 192 57 16 NC_002950:PG1773|3end_PAP2_superfamily_protein_1861232..1861382_POSITIVE 282 91 53 98 63 NC_002950:PG1095|3end_RNA_methyltransferase,_TrmA_family_1161702..1161852_POSITIVE 280 81 51 60 27 NC_002950:PG1223|3end_hypothetical_protein_1299744..1299894_POSITIVE 280 93 54 115 72 NC_002950:PG0619|3end_alkyl_hydroperoxide_reductase,_F_subunit_672731..672881_POSITIVE 279 94 54 43 4 NC_002950:PG1117|3end_MATE_efflux_family_protein_1191541..1191691_POSITIVE