Origin IGS: ctgatttataatagctgtgtttgtgacattctcaacttcagacagagtttctgacaaagagcagatactgagaaattaaaaagctccaagccattgctttttagagacaacggtttggagcttttctccgttttattgctttgtcccga .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tcgggacaaagcaataaaacggagaaaagctccaaaccgttgtctctaaaaagcaatggcttggagctttttaatttctcagtatctgctctttgtcagaaactctgtctgaagttgagaatgtcacaaacacagctattataaatcag Mask Tandem Repeat Region ================================================ ctgatttataatagctgtgtttgtgacattctcaacttcagacagagtttctgacaaagagcagatactgagaaattaaaaagctccaagccattgctttttagagacaacggtttggagcttttctccgttttattgctttgtcccga Find is-nt database================================================ Query_seq: PG1314:PG1315|PG1314:PG1315:chorismate synthase:peptidyl-prolyl cis-trans isomerase SlyD, FKBP-type:<-<-:1395559..1395707 149 ctgatttataatagctgtgtttgtgacattctcaacttcagacagagtttctgacaaagagcagatactgagaaattaaaaagctccaagccattgctttttagagacaacggtttggagcttttctccgttttattgctttgtcccga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG1314:PG1315|PG1314:PG1315:chorismate synthase:peptidyl-prolyl cis-trans isomerase SlyD, FKBP-type:<-<-:1395559..1395707 149 ctgatttataatagctgtgtttgtgacattctcaacttcagacagagtttctgacaaagagcagatactgagaaattaaaaagctccaagccattgctttttagagacaacggtttggagcttttctccgttttattgctttgtcccga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG1314:PG1315|PG1314:PG1315:chorismate synthase:peptidyl-prolyl cis-trans isomerase SlyD, FKBP-type:<-<-:1395559..1395707 149 ctgatttataatagctgtgtttgtgacattctcaacttcagacagagtttctgacaaagagcagatactgagaaattaaaaagctccaagccattgctttttagagacaacggtttggagcttttctccgttttattgctttgtcccga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ctgatttataatagctgtgtttgtgacattctcaacttcagacagagtttctgacaaagagcagatactgagaaattaaaaagctccaagccattgctttttagagacaacggtttggagcttttctccgttttattgctttgtcccga Predict ORF larger than 30AA ================================================ Protein_Len: 34 Strand: - Start: 9 End: 110 ........ L L Q T Q S M R L K L C L K Q C L A S V S F N F L E L G N S K L S M ....................................... ctgatttataatagctgtgtttgtgacattctcaacttcagacagagtttctgacaaagagcagatactgagaaattaaaaagctccaagccattgctttttagagacaacggtttggagcttttctccgttttattgctttgtcccga 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================================================ ctgatttataatagctgtgtttgtgacattctcaacttcagacagagtttctgacaaagagcagatactgagaaattaaaaagctccaagccattgctttttagagacaacggtttggagcttttctccgttttattgctttgtcccga Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 74 HP_score: -9.8 Tail_Score: -2.86514 Start: 78 End: 126 Full_Region: AGATACTGAGAAATT AAAAAGCTCCAAGCCATTGCTT TTTA GAGACAACGGTTTGGAGCTTTTC TCCGTTTTATTGCTT .............................................................................AAAAAGCTCCAAGCCATTGCTTTTTAGAGACAACGGTTTGGAGCTTTTC....................... TransTerm Strand: + Conf: 89 HP_score: -9.7 Tail_Score: -4.5538 Start: 83 End: 121 Full_Region: CTGAGAAATTAAAAA GCTCCAAGCCATTGCTT TTTA GAGACAACGGTTTGGAGC TTTTCTCCGTTTTAT ..................................................................................GCTCCAAGCCATTGCTTTTTAGAGACAACGGTTTGGAGC............................ TransTerm Strand: - Conf: 91 HP_score: -9.0 Tail_Score: -5.04601 Start: 83 End: 121 Full_Region: ataaaacggagaaaa gctccaaaccgttgtct ctaaaa agcaatggcttggagc tttttaatttctcag ..................................................................................gctccaaaccgttgtctctaaaaagcaatggcttggagc............................ Find igs database================================================ Query_seq: PG1314:PG1315|PG1314:PG1315:chorismate synthase:peptidyl-prolyl cis-trans isomerase SlyD, FKBP-type:<-<-:1395559..1395707 149 ctgatttataatagctgtgtttgtgacattctcaacttcagacagagtttctgacaaagagcagatactgagaaattaaaaagctccaagccattgctttttagagacaacggtttggagcttttctccgttttattgctttgtcccga Intra-Species Hit: Count: 1 Min: 1 Max: 149 Len: 149 Subject: NC_002950_PG1314_PG1315|chorismate synthase:peptidyl-prolyl cis-trans isomerase SlyD, FKBP-type|NEGATIVE:NEGATIVE|[1395559,1395707]|149 HSP 1 e-value: 2.0E-79 bit: 295.0 Len: 149 Query Start:1 Query End:149 Subject Strand: POSITIVE Subject Start: 1 Subject End: 149 ctgatttataatagctgtgtttgtgacattctcaacttcagacagagtttctgacaaagagcagatactgagaaattaaaaagctccaagccattgctttttagagacaacggtttggagcttttctccgttttattgctttgtcccga ctgatttataatagctgtgtttgtgacattctcaacttcagacagagtttctgacaaagagcagatactgagaaattaaaaagctccaagccattgctttttagagacaacggtttggagcttttctccgttttattgctttgtcccga Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUGAUUUAUAAUAGCUGUGUUUGUGACAUUCUCAACUUCAGACAGAGUUUCUGACAAAGAGCAGAUACUGAGAAAUUAAAAAGCUCCAAGCCAUUGCUUUUUAGAGACAACGGUUUGGAGCUUUUCUCCGUUUUAUUGCUUUGUCCCGA ............((((.(((((((((.....)))....)))))).))))...(((((((.......((.((((((......(((((((((((.((((((....))).))).))))))))))))))))).)).......))))))).... (-46.04) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCGGGACAAAGCAAUAAAACGGAGAAAAGCUCCAAACCGUUGUCUCUAAAAAGCAAUGGCUUGGAGCUUUUUAAUUUCUCAGUAUCUGCUCUUUGUCAGAAACUCUGUCUGAAGUUGAGAAUGUCACAAACACAGCUAUUAUAAAUCAG ....((((..........((.((((((((((((((.((((((.((......)))))))).))))))))......)))))).)).....(((....(((((.......)))))....)))..))))........................ (-38.80) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 938 130 81 221 172 NC_002950:PG1314|5end_chorismate_synthase_1395468..1395698_NEGATIVE 327 128 83 164 104 NC_002950:PG1735|5end_MutT/nudix_family_protein_1823082..1823312_NEGATIVE 320 129 83 52 12 NC_002950:PG0930|5end_hypothetical_protein_987542..987772_NEGATIVE 318 140 91 156 115 NC_002950:PG0713|5end_anthranilate_synthase_component_II_767749..767979_NEGATIVE 315 127 81 77 27 NC_002950:PG0086|5end_ATP-dependent_RNA_helicase,_DEAD/DEAH_box_family_102359..102589_NEGATIVE 308 140 91 122 64 NC_002950:PG0006|5end_MATE_efflux_family_protein_6332..6562_NEGATIVE 296 55 14 215 158 NC_002950:PG1408|5end_heavy_metal_efflux_pump,_CzcD_family_1491861..1492091_POSITIVE 292 129 83 220 178 NC_002950:PG2223|5end_glycosyl_transferase,_group_2_family_protein_2337713..2337943_POSITIVE 287 120 81 80 43 NC_002950:PG0250|5end_hypothetical_protein_284081..284311_NEGATIVE 284 129 81 89 41 NC_002950:PG1221|5end_oxidoreductase,_short_chain_dehydrogenase/reductase_family_1298129..1298359_POSITIVE 283 120 71 213 164 NC_002950:PG0766|5end_polyribonucleotide_nucleotidyltransferase_818405..818635_NEGATIVE 282 139 92 216 171 NC_002950:PG0307|5end_NADH-ubiquinone_oxidoreductase_342560..342790_POSITIVE 277 126 83 206 165 NC_002950:PG2075|5end_hypothetical_protein_2176466..2176696_NEGATIVE 277 130 83 220 171 NC_002950:PG0399|5end_lipoprotein,_putative_436237..436467_NEGATIVE 276 121 82 49 8 NC_002950:PG1091|5end_DHH_subfamily_1_protein_1157017..1157247_POSITIVE 271 130 83 127 80 NC_002950:PG1937|5end_50S_ribosomal_protein_L4_2024136..2024366_NEGATIVE 270 130 83 192 142 NC_002950:PG1009|5end_hypothetical_protein_1068495..1068725_NEGATIVE 268 88 45 225 181 NC_002950:PG1473|5end_conjugative_transposon_protein_TraQ_1550225..1550455_NEGATIVE 268 139 91 78 43 NC_002950:PG0897|5end_alpha-amylase_family_protein_962472..962702_NEGATIVE 268 99 55 180 133 NC_002950:PG0704|5end_phosphoglycerate_mutase_family_protein_758928..759158_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 322 130 81 112 61 NC_002950:PG2037|3end_hypothetical_protein_2137591..2137741_NEGATIVE 310 139 91 67 8 NC_002950:PG1247|3end_3-dehydroquinate_synthase_1325585..1325735_POSITIVE 307 129 82 75 31 NC_002950:PG0731|3end_hypothetical_protein_782020..782170_NEGATIVE 292 140 103 68 29 NC_002950:PG1410|3end_hypothetical_protein_1493436..1493586_POSITIVE 284 129 81 79 31 NC_002950:PG1220|3end_erythronate-4-phosphate_dehydrogenase_1298199..1298349_POSITIVE 283 120 71 61 12 NC_002950:PG0767|3end_4-alpha-glucanotransferase_818557..818707_NEGATIVE 282 98 52 59 8 NC_002950:PG1678|3end_hypothetical_protein_1763755..1763905_NEGATIVE 274 140 99 142 94 NC_002950:PG0800|3end_hypothetical_protein_854719..854869_NEGATIVE 273 139 93 138 100 NC_002950:PG1316|3end_hypothetical_protein_1396241..1396391_NEGATIVE 272 55 18 62 12 NC_002950:PG2154|3end_hypothetical_protein_2260760..2260910_NEGATIVE 271 130 83 127 80 NC_002950:PG1938|3end_50S_ribosomal_protein_L3_2024136..2024286_NEGATIVE 266 130 83 131 90 NC_002950:PG1789|3end_peptidyl-dipeptidase_Dcp_1877417..1877567_NEGATIVE 265 100 52 67 11 NC_002950:PG0710|3end_peptidyl-prolyl_cis-trans_isomerase,_FKBP-type_765447..765597_NEGATIVE 259 129 82 127 67 NC_002950:PG0377|3end_30S_ribosomal_protein_S2_407845..407995_POSITIVE 257 130 83 72 23 NC_002950:PG0459|3end_ISPg5,_transposase_Orf1_501517..501667_NEGATIVE 257 129 83 62 8 NC_002950:PG0267|3end_arginyl-tRNA_synthetase_300973..301123_POSITIVE 255 132 103 71 32 NC_002950:PG0328|3end_imidazolonepropionase_362155..362305_NEGATIVE 252 130 86 48 15 NC_002950:PG0305|3end_electron_transport_complex,_RnfABCDGE_type,_D_subunit_341969..342119_POSITIVE 250 130 81 119 65 NC_002950:PG0498|3end_S-ribosylhomocysteinase_538527..538677_POSITIVE 248 130 92 116 76 NC_002950:PG1541|3end_2-amino-4-hydroxy-6-_hydroxymethyldihydropteridine_pyrophosphokinase_1620855..1621005_POSITIVE