Origin IGS: cttcggacacgtggcggatgcctcatcgagtaggccaaaaatgcctacctttggggcagttgtaaaaacttaatatcaatatctaacaagaggatacagcg .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 cgctgtatcctcttgttagatattgatattaagtttttacaactgccccaaaggtaggcatttttggcctactcgatgaggcatccgccacgtgtccgaag Mask Tandem Repeat Region ================================================ cttcggacacgtggcggatgcctcatcgagtaggccaaaaatgcctacctttggggcagttgtaaaaacttaatatcaatatctaacaagaggatacagcg Find is-nt database================================================ Query_seq: PG0229:PG0230|PG0229:PG0230:hypothetical protein:transaldolase:->->:265411..265511 101 cttcggacacgtggcggatgcctcatcgagtaggccaaaaatgcctacctttggggcagttgtaaaaacttaatatcaatatctaacaagaggatacagcg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG0229:PG0230|PG0229:PG0230:hypothetical protein:transaldolase:->->:265411..265511 101 cttcggacacgtggcggatgcctcatcgagtaggccaaaaatgcctacctttggggcagttgtaaaaacttaatatcaatatctaacaagaggatacagcg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG0229:PG0230|PG0229:PG0230:hypothetical protein:transaldolase:->->:265411..265511 101 cttcggacacgtggcggatgcctcatcgagtaggccaaaaatgcctacctttggggcagttgtaaaaacttaatatcaatatctaacaagaggatacagcg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 cttcggacacgtggcggatgcctcatcgagtaggccaaaaatgcctacctttggggcagttgtaaaaacttaatatcaatatctaacaagaggatacagcg Predict ORF larger than 30AA ================================================ cttcggacacgtggcggatgcctcatcgagtaggccaaaaatgcctacctttggggcagttgtaaaaacttaatatcaatatctaacaagaggatacagcg 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================================================ cttcggacacgtggcggatgcctcatcgagtaggccaaaaatgcctacctttggggcagttgtaaaaacttaatatcaatatctaacaagaggatacagcg Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PG0229:PG0230|PG0229:PG0230:hypothetical protein:transaldolase:->->:265411..265511 101 cttcggacacgtggcggatgcctcatcgagtaggccaaaaatgcctacctttggggcagttgtaaaaacttaatatcaatatctaacaagaggatacagcg Intra-Species Hit: Count: 1 Min: 1 Max: 101 Len: 101 Subject: NC_002950_PG0229_PG0230|hypothetical protein:transaldolase|POSITIVE:POSITIVE|[265411, 265511]|101 HSP 1 e-value: 6.0E-51 bit: 200.0 Len: 101 Query Start:1 Query End:101 Subject Strand: POSITIVE Subject Start: 1 Subject End: 101 cttcggacacgtggcggatgcctcatcgagtaggccaaaaatgcctacctttggggcagttgtaaaaacttaatatcaatatctaacaagaggatacagcg cttcggacacgtggcggatgcctcatcgagtaggccaaaaatgcctacctttggggcagttgtaaaaacttaatatcaatatctaacaagaggatacagcg Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUUCGGACACGUGGCGGAUGCCUCAUCGAGUAGGCCAAAAAUGCCUACCUUUGGGGCAGUUGUAAAAACUUAAUAUCAAUAUCUAACAAGAGGAUACAGCG (....)...(((.((((.(((((((..(.((((((.......)))))))..))))))).))))..........((((....(((....))).))))..))) (-27.40) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CGCUGUAUCCUCUUGUUAGAUAUUGAUAUUAAGUUUUUACAACUGCCCCAAAGGUAGGCAUUUUUGGCCUACUCGAUGAGGCAUCCGCCACGUGUCCGAAG .((.(((....((((.((........)).))))....)))...((((.((..(((((((.......)))))).)..)).))))...))............. (-21.20) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 409 50 1 209 156 NC_002950:PG0800|5end_hypothetical_protein_856278..856508_NEGATIVE 393 59 11 114 47 NC_002950:PG1029|5end_hypothetical_protein_1091080..1091310_POSITIVE 390 56 11 152 101 NC_002950:PG0495|5end_hypothetical_protein_535447..535677_POSITIVE 371 59 11 60 13 NC_002950:PG1242|5end_replicative_DNA_helicase_1317435..1317665_POSITIVE 365 58 13 123 80 NC_002950:PG1969|5end_hypothetical_protein_2059515..2059745_NEGATIVE 357 35 1 166 128 NC_002950:PG1485|5end_conjugative_transposon_protein_TraC_1560370..1560600_NEGATIVE 355 48 1 116 59 NC_002950:PG1311|5end_hypothetical_protein_1389709..1389939_POSITIVE 354 59 11 69 6 NC_002950:PG1418|5end_DNA_polymerase_III,_gamma_and_tau_subunits_1503064..1503294_POSITIVE 351 48 2 176 122 NC_002950:PG0075|5end_phosphoribosylformylglycinamidine_cyclo-ligase,_putative_90438..90668_NEGATIVE 350 58 12 199 136 NC_002950:PG2082|5end_POT_family_protein_2183384..2183614_NEGATIVE 347 50 2 213 157 NC_002950:PG1480|5end_conjugative_transposon_protein_TraI_1555895..1556125_NEGATIVE 343 35 1 223 189 NC_002950:PG0431|5end_hypothetical_protein_468978..469208_POSITIVE 342 50 3 160 118 NC_002950:PG0335|5end_tRNA_delta(2)-isopentenylpyrophosphate_transferase_370706..370936_NEGATIVE 336 57 13 63 13 NC_002950:PG1594|5end_ComEC/Rec2-related_protein_1673587..1673817_NEGATIVE 335 59 11 171 104 NC_002950:PG1102|5end_hypothetical_protein_1173637..1173867_NEGATIVE 332 34 2 111 84 NC_002950:PG0980|5end_hypothetical_protein_1040897..1041127_POSITIVE 331 45 2 211 175 NC_002950:PG0923|5end_ribosome-binding_factor_A_982814..983044_NEGATIVE 331 59 11 165 117 NC_002950:PG0326|5end_hypothetical_protein_360974..361204_NEGATIVE 330 60 12 53 1 NC_002950:PG0767|5end_4-alpha-glucanotransferase_820533..820763_NEGATIVE 328 45 1 185 142 NC_002950:PG2107|5end_thiamine_biosynthesis_protein_ThiH_2216658..2216888_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 361 34 1 47 1 NC_002950:PG1966|3end_hypothetical_protein_2056118..2056268_NEGATIVE 359 36 2 127 94 NC_002950:PG1956|3end_4-hydroxybutyrate_CoA-transferase_2046215..2046365_NEGATIVE 343 50 1 144 96 NC_002950:PG1310|3end_exsB_protein_1389826..1389976_POSITIVE 342 50 3 143 101 NC_002950:PG0336|3end_hypothetical_protein_370723..370873_NEGATIVE 337 53 11 71 27 NC_002950:PG1593|3end_shikimate_kinase_1672143..1672293_POSITIVE 336 57 13 56 6 NC_002950:PG1595|3end_ribulose-phosphate_3-epimerase_1673594..1673744_NEGATIVE 332 34 2 124 97 NC_002950:PG0979|3end_hypothetical_protein_1040990..1041140_POSITIVE 326 44 1 142 98 NC_002950:PG1970|3end_hypothetical_protein_2059484..2059634_NEGATIVE 325 56 12 151 120 NC_002950:PG1657|3end_methylmalonyl-CoA_mutase_1741571..1741721_POSITIVE 325 58 11 66 22 NC_002950:PG0286|3end_hypothetical_protein_320454..320604_POSITIVE 323 60 13 71 34 NC_002950:PG2082|3end_POT_family_protein_2181843..2181993_NEGATIVE 323 59 12 51 11 NC_002950:PG0127|3end_ferrochelatase_149667..149817_POSITIVE 321 58 15 151 97 NC_002950:PG1027|3end_hypothetical_protein_1089197..1089347_NEGATIVE 316 48 2 147 98 NC_002950:PG1556|3end_hypothetical_protein_1637001..1637151_POSITIVE 315 58 11 46 1 NC_002950:PG0508|3end_HAD-superfamily_subfamily_IB_hydrolase,_TIGR01490_548136..548286_NEGATIVE 314 57 12 76 23 NC_002950:PG2188|3end_diaminopimelate_decarboxylase_2294633..2294783_NEGATIVE 309 52 12 133 92 NC_002950:PG0141|3end_spoOJ_protein_163878..164028_NEGATIVE 307 50 4 130 72 NC_002950:PG0752|3end_uracil_phosphoribosyltransferase_798397..798547_POSITIVE 307 58 11 63 3 NC_002950:PG0569|3end_hypothetical_protein_624697..624847_NEGATIVE 304 59 11 141 95 NC_002950:PG0699|3end_maltodextrin_phosphorylase_753388..753538_NEGATIVE