Origin IGS: tgttctatcgaatagtatttgtgttcttgtgattgtcttttctcttgtcttttgggtggaaaatgccgtccccgtctcgaagcagggggaataagccgtctcgc .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 gcgagacggcttattccccctgcttcgagacggggacggcattttccacccaaaagacaagagaaaagacaatcacaagaacacaaatactattcgatagaaca Mask Tandem Repeat Region ================================================ tgttctatcgaatagtatttgtgttcttgtgattgtcttttctcttgtcttttgggtggaaaatgccgtccccgtctcgaagcagggggaataagccgtctcgc Find is-nt database================================================ Query_seq: PG2201:PG2202|PG2201:PG2202:peptide deformylase:Holliday junction resolvase-like protein:<-<-:2309503..2309606 104 tgttctatcgaatagtatttgtgttcttgtgattgtcttttctcttgtcttttgggtggaaaatgccgtccccgtctcgaagcagggggaataagccgtctcgc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG2201:PG2202|PG2201:PG2202:peptide deformylase:Holliday junction resolvase-like protein:<-<-:2309503..2309606 104 tgttctatcgaatagtatttgtgttcttgtgattgtcttttctcttgtcttttgggtggaaaatgccgtccccgtctcgaagcagggggaataagccgtctcgc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG2201:PG2202|PG2201:PG2202:peptide deformylase:Holliday junction resolvase-like protein:<-<-:2309503..2309606 104 tgttctatcgaatagtatttgtgttcttgtgattgtcttttctcttgtcttttgggtggaaaatgccgtccccgtctcgaagcagggggaataagccgtctcgc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tgttctatcgaatagtatttgtgttcttgtgattgtcttttctcttgtcttttgggtggaaaatgccgtccccgtctcgaagcagggggaataagccgtctcgc Predict ORF larger than 30AA ================================================ Protein_Len: 30 Strand: - Start: 3 End: 92 .. E I S Y Y K H E Q S Q R K E Q R K P P F H R G R R S A P P M ............ tgttctatcgaatagtatttgtgttcttgtgattgtcttttctcttgtcttttgggtggaaaatgccgtccccgtctcgaagcagggggaataagccgtctcgc 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================================================ tgttctatcgaatagtatttgtgttcttgtgattgtcttttctcttgtcttttgggtggaaaatgccgtccccgtctcgaagcagggggaataagccgtctcgc Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PG2201:PG2202|PG2201:PG2202:peptide deformylase:Holliday junction resolvase-like protein:<-<-:2309503..2309606 104 tgttctatcgaatagtatttgtgttcttgtgattgtcttttctcttgtcttttgggtggaaaatgccgtccccgtctcgaagcagggggaataagccgtctcgc Intra-Species Hit: Count: 1 Min: 1 Max: 104 Len: 104 Subject: NC_002950_PG2201_PG2202|peptide deformylase:Holliday junction resolvase-like protein|NEGATIVE:NEGATIVE|[2309503,2309606]|104 HSP 1 e-value: 1.0E-52 bit: 206.0 Len: 104 Query Start:1 Query End:104 Subject Strand: POSITIVE Subject Start: 1 Subject End: 104 tgttctatcgaatagtatttgtgttcttgtgattgtcttttctcttgtcttttgggtggaaaatgccgtccccgtctcgaagcagggggaataagccgtctcgc tgttctatcgaatagtatttgtgttcttgtgattgtcttttctcttgtcttttgggtggaaaatgccgtccccgtctcgaagcagggggaataagccgtctcgc Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGUUCUAUCGAAUAGUAUUUGUGUUCUUGUGAUUGUCUUUUCUCUUGUCUUUUGGGUGGAAAAUGCCGUCCCCGUCUCGAAGCAGGGGGAAUAAGCCGUCUCGC (((((....)))))..............(.(((.((..(((((((((.((((.((..((............))..)).)))))))))))))...)).))).).. (-22.90) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GCGAGACGGCUUAUUCCCCCUGCUUCGAGACGGGGACGGCAUUUUCCACCCAAAAGACAAGAGAAAAGACAAUCACAAGAACACAAAUACUAUUCGAUAGAACA .((((...(((...(((((...(.....)..))))).))).(((((..............)))))...........................))))........ (-12.64) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 1071 100 51 191 142 NC_002950:PG2201|5end_peptide_deformylase_2309412..2309642_NEGATIVE 388 85 41 194 150 NC_002950:PG1697|5end_type_II_restriction_endonuclease,_putative_1781020..1781250_POSITIVE 368 100 54 98 48 NC_002950:PG0605|5end_hypothetical_protein_662406..662636_NEGATIVE 366 89 44 121 56 NC_002950:PG1969|5end_hypothetical_protein_2059515..2059745_NEGATIVE 362 99 54 197 157 NC_002950:PG1305|5end_glycine_dehydrogenase_1386538..1386768_NEGATIVE 362 88 49 155 112 NC_002950:PG0166|5end_peptidyl-tRNA_hydrolase_188370..188600_NEGATIVE 361 98 51 186 140 NC_002950:PG0607|5end_hypothetical_protein_662552..662782_POSITIVE 361 89 42 102 43 NC_002950:PG0606|5end_hypothetical_protein_662558..662788_NEGATIVE 360 98 52 56 8 NC_002950:PG0924|5end_5'-nucleotidase,_lipoprotein_e(P4)_family_983668..983898_NEGATIVE 358 98 63 60 10 NC_002950:PG0434|5end_hypothetical_protein_472513..472743_NEGATIVE 355 100 51 221 149 NC_002950:PG2107|5end_thiamine_biosynthesis_protein_ThiH_2216658..2216888_NEGATIVE 354 90 41 214 171 NC_002950:PG2069|5end_oxidoreductase,_short_chain_dehydrogenase/reductase_family_2164798..2165028_POSITIVE 348 99 56 71 8 NC_002950:PG0753|5end_protease_798301..798531_POSITIVE 348 97 51 111 48 NC_002950:PG0145|5end_hypothetical_protein_167831..168061_POSITIVE 346 89 41 222 156 NC_002950:PG2098|5end_hypothetical_protein_2206635..2206865_NEGATIVE 340 97 52 192 131 NC_002950:PG0472|5end_iron-sulfur_cluster_binding_protein,_putative_513339..513569_POSITIVE 338 88 45 61 12 NC_002950:PG0287|5end_hypothetical_protein_320457..320687_POSITIVE 333 90 45 147 99 NC_002950:PG1105|5end_RNA_polymerase_sigma-54_factor_1177173..1177403_NEGATIVE 330 78 35 214 162 NC_002950:PG1498|5end_hypothetical_protein_1574656..1574886_POSITIVE 328 98 52 54 7 NC_002950:PG0272|5end_CBS_domain_protein_304399..304629_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 429 90 41 77 30 NC_002950:PG2040|3end_DNA-binding_protein,_histone-like_family_2138398..2138548_NEGATIVE 398 99 54 114 58 NC_002950:PG0143|3end_hydrolase,_carbon-nitrogen_family_165747..165897_NEGATIVE 394 98 51 83 20 NC_002950:PG1118|3end_clpB_protein_1192083..1192233_NEGATIVE 379 99 52 87 16 NC_002950:PG0752|3end_uracil_phosphoribosyltransferase_798397..798547_POSITIVE 368 100 54 53 3 NC_002950:PG0606|3end_hypothetical_protein_662451..662601_NEGATIVE 367 90 41 128 89 NC_002950:PG0317|3end_peptidase,_M49_family_349771..349921_NEGATIVE 360 70 28 123 71 NC_002950:PG1970|3end_hypothetical_protein_2059484..2059634_NEGATIVE 360 98 52 59 11 NC_002950:PG0925|3end_thymidine_kinase_983665..983815_NEGATIVE 352 90 55 75 38 NC_002950:PG1359|3end_hypothetical_protein_1437644..1437794_NEGATIVE 331 90 41 128 66 NC_002950:PG0795|3end_hypothetical_protein_849603..849753_POSITIVE 330 78 35 113 61 NC_002950:PG1497|3end_DNA-binding_protein,_histone-like_family_1574635..1574785_POSITIVE 326 98 51 49 2 NC_002950:PG0560|3end_hypothetical_protein_617748..617898_POSITIVE 323 98 64 67 31 NC_002950:PG0915|3end_hypothetical_protein_977057..977207_POSITIVE 319 88 47 83 32 NC_002950:PG1133|3end_hypothetical_protein_1214103..1214253_POSITIVE 319 100 56 92 40 NC_002950:PG0605|3end_hypothetical_protein_661165..661315_NEGATIVE 318 83 43 137 89 NC_002950:PG0719|3end_sensor_histidine_kinase_771696..771846_NEGATIVE 318 99 59 101 54 NC_002950:PG0016|3end_sigma-54_dependent_DNA-binding_response_regulator_18376..18526_POSITIVE 316 90 46 73 37 NC_002950:PG0678|3end_pyrazinamidase/nicotinamidase,_putative_729471..729621_POSITIVE 311 88 42 119 60 NC_002950:PG2158|3end_hypothetical_protein_2264473..2264623_POSITIVE 308 98 54 142 87 NC_002950:PG2161|3end_transcriptional_regulator,_AraC_family_2266717..2266867_NEGATIVE