Origin IGS: taataaaaggagataacaggaactcgtgttcggagaattttgagggtgtgtcaaaacgctatgtttgggcacaccctcttttagatgtgtaaattcctccggactttatttagcctgcttggtgctgttcgaacagactgttgtgaccggatttaatacggttgctctgaagattatttgcagagcaggcttcttttaagatttattttctacctttgtccccgaaaaagtcagtagc .........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 gctactgactttttcggggacaaaggtagaaaataaatcttaaaagaagcctgctctgcaaataatcttcagagcaaccgtattaaatccggtcacaacagtctgttcgaacagcaccaagcaggctaaataaagtccggaggaatttacacatctaaaagagggtgtgcccaaacatagcgttttgacacaccctcaaaattctccgaacacgagttcctgttatctccttttatta Mask Tandem Repeat Region ================================================ taataaaaggagataacaggaactcgtgttcggagaattttgagggtgtgtcaaaacgctatgtttgggcacaccctcttttagatgtgtaaattcctccggactttatttagcctgcttggtgctgttcgaacagactgttgtgaccggatttaatacggttgctctgaagattatttgcagagcaggcttcttttaagatttattttctacctttgtccccgaaaaagtcagtagc Find is-nt database================================================ Query_seq: TF2765:TF2766|TF2765:TF2766:subtilisin-like serine protease:shikimate kinase:->->:2951521..2951758 238 taataaaaggagataacaggaactcgtgttcggagaattttgagggtgtgtcaaaacgctatgtttgggcacaccctcttttagatgtgtaaattcctccggactttatttagcctgcttggtgctgttcgaacagactgttgtgaccggatttaatacggttgctctgaagattatttgcagagcaggcttcttttaagatttattttctacctttgtccccgaaaaagtcagtagc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF2765:TF2766|TF2765:TF2766:subtilisin-like serine protease:shikimate kinase:->->:2951521..2951758 238 taataaaaggagataacaggaactcgtgttcggagaattttgagggtgtgtcaaaacgctatgtttgggcacaccctcttttagatgtgtaaattcctccggactttatttagcctgcttggtgctgttcgaacagactgttgtgaccggatttaatacggttgctctgaagattatttgcagagcaggcttcttttaagatttattttctacctttgtccccgaaaaagtcagtagc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF2765:TF2766|TF2765:TF2766:subtilisin-like serine protease:shikimate kinase:->->:2951521..2951758 238 taataaaaggagataacaggaactcgtgttcggagaattttgagggtgtgtcaaaacgctatgtttgggcacaccctcttttagatgtgtaaattcctccggactttatttagcctgcttggtgctgttcgaacagactgttgtgaccggatttaatacggttgctctgaagattatttgcagagcaggcttcttttaagatttattttctacctttgtccccgaaaaagtcagtagc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taataaaaggagataacaggaactcgtgttcggagaattttgagggtgtgtcaaaacgctatgtttgggcacaccctcttttagatgtgtaaattcctccggactttatttagcctgcttggtgctgttcgaacagactgttgtgaccggatttaatacggttgctctgaagattatttgcagagcaggcttcttttaagatttattttctacctttgtccccgaaaaagtcagtagc Predict ORF larger than 30AA ================================================ Protein_Len: 44 Strand: + Start: 65 End: 196 ................................................................ M G T P S F R C V N S S G L Y L A C L V L F E Q T V V T G F N T V A L K I I C R A G F F .......................................... Protein_Len: 30 Strand: - Start: 113 End: 202 ................................................................................................................ G A Q H Q E F L S N H G S K I R N S Q L N N A S C A E K L M .................................... taataaaaggagataacaggaactcgtgttcggagaattttgagggtgtgtcaaaacgctatgtttgggcacaccctcttttagatgtgtaaattcctccggactttatttagcctgcttggtgctgttcgaacagactgttgtgaccggatttaatacggttgctctgaagattatttgcagagcaggcttcttttaagatttattttctacctttgtccccgaaaaagtcagtagc 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================================================ taataaaaggagataacaggaactcgtgttcggagaattttgagggtgtgtcaaaacgctatgtttgggcacaccctcttttagatgtgtaaattcctccggactttatttagcctgcttggtgctgttcgaacagactgttgtgaccggatttaatacggttgctctgaagattatttgcagagcaggcttcttttaagatttattttctacctttgtccccgaaaaagtcagtagc Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 42 HP_score: -3.3 Tail_Score: -2.57132 Start: 39 End: 81 Full_Region: gaatttacacatcta aaagagggtgtgcccaaac atagc gttttgacacaccctcaaa attctccgaacacga ......................................aaagagggtgtgcccaaacatagcgttttgacacaccctcaaa............................................................................................................................................................. TransTerm Strand: + Conf: 100 HP_score: -16.7 Tail_Score: -4.26188 Start: 42 End: 78 Full_Region: TGTTCGGAGAATTTT GAGGGTGTGTCAAAACG CTA TGTTTGGGCACACCCTC TTTTAGATGTGTAAA .........................................GAGGGTGTGTCAAAACGCTATGTTTGGGCACACCCTC................................................................................................................................................................ Find igs database================================================ Query_seq: TF2765:TF2766|TF2765:TF2766:subtilisin-like serine protease:shikimate kinase:->->:2951521..2951758 238 taataaaaggagataacaggaactcgtgttcggagaattttgagggtgtgtcaaaacgctatgtttgggcacaccctcttttagatgtgtaaattcctccggactttatttagcctgcttggtgctgttcgaacagactgttgtgaccggatttaatacggttgctctgaagattatttgcagagcaggcttcttttaagatttattttctacctttgtccccgaaaaagtcagtagc Intra-Species Hit: Count: 2 Min: 1 Max: 238 Len: 238 Subject: tfor_TF2765_TF2766|subtilisin-like serine protease:shikimate kinase|POSITIVE:POSITIVE|[2951521,2951758]|238 HSP 1 e-value: 1.0E-132 bit: 472.0 Len: 238 Query Start:1 Query End:238 Subject Strand: POSITIVE Subject Start: 1 Subject End: 238 taataaaaggagataacaggaactcgtgttcggagaattttgagggtgtgtcaaaacgctatgtttgggcacaccctcttttagatgtgtaaattcctccggactttatttagcctgcttggtgctgttcgaacagactgttgtgaccggatttaatacggttgctctgaagattatttgcagagcaggcttcttttaagatttattttctacctttgtccccgaaaaagtcagtagc taataaaaggagataacaggaactcgtgttcggagaattttgagggtgtgtcaaaacgctatgtttgggcacaccctcttttagatgtgtaaattcctccggactttatttagcctgcttggtgctgttcgaacagactgttgtgaccggatttaatacggttgctctgaagattatttgcagagcaggcttcttttaagatttattttctacctttgtccccgaaaaagtcagtagc Subject: tfor_TF2535_TF2536|histidyl-tRNA synthetase:subtilisin-like serine protease|POSITIVE:POSITIVE|[2719239,2719425]|187 HSP 1 e-value: 8.0E-77 bit: 287.0 Len: 149 Query Start:6 Query End:154 Subject Strand: NEGATIVE Subject Start: 35 Subject End: 183 .....aaaggagataacaggaactcgtgttcggagaattttgagggtgtgtcaaaacgctatgtttgggcacaccctcttttagatgtgtaaattcctccggactttatttagcctgcttggtgctgttcgaacagactgttgtgaccggattt.................................................................................... .....aaaggagataacaggaactcgtgtccggagaattttgagggtgtgtcaaaacgctatgtttgggcacaccctcttttagatgtgtaaattcctccggactttatttagcctgcttggtgctgttcgaacagactgttgtgaccggattt.................................................................................... Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAUAAAAGGAGAUAACAGGAACUCGUGUUCGGAGAAUUUUGAGGGUGUGUCAAAACGCUAUGUUUGGGCACACCCUCUUUUAGAUGUGUAAAUUCCUCCGGACUUUAUUUAGCCUGCUUGGUGCUGUUCGAACAGACUGUUGUGACCGGAUUUAAUACGGUUGCUCUGAAGAUUAUUUGCAGAGCAGGCUUCUUUUAAGAUUUAUUUUCUACCUUUGUCCCCGAAAAAGUCAGUAGC ........((.(((((.(((.......(((((((((((((.(((((((((((.((((.....)))).)))))))))))............))))).)))))))).......(((((((((..(((...((...((((.....(..((((.........))))..)))))..))......)))))))))))).....................)))))))).))............... (-75.12) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GCUACUGACUUUUUCGGGGACAAAGGUAGAAAAUAAAUCUUAAAAGAAGCCUGCUCUGCAAAUAAUCUUCAGAGCAACCGUAUUAAAUCCGGUCACAACAGUCUGUUCGAACAGCACCAAGCAGGCUAAAUAAAGUCCGGAGGAAUUUACACAUCUAAAAGAGGGUGUGCCCAAACAUAGCGUUUUGACACACCCUCAAAAUUCUCCGAACACGAGUUCCUGUUAUCUCCUUUUAUUA ......(((((.((((((((......((((.....................(((((((.((......)))))))))...(((.....(((((.(.....((((((((.(........).)))))))).......).)))))......)))...))))...(((((((((.(.((((.....)))).).))))))))).....))))))))...))))).................... (-63.40) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 955 80 31 170 121 tfor:TF2536|5end_subtilisin-like_serine_protease_2719286..2719516_POSITIVE 721 90 44 171 126 tfor:TF0476|5end_conserved_hypothetical_protein_494944..495174_POSITIVE 557 90 42 174 123 tfor:TF0792|5end_pyruvate_ferredoxin;_flavodoxin_oxidoreductase_846454..846684_POSITIVE 553 90 42 163 118 tfor:TF1284|5end_glyceraldehyde_3-phosphate_dehydrogenase_1367939..1368169_POSITIVE 513 90 42 221 163 tfor:TF2320|5end_hypothetical_protein_2476654..2476884_POSITIVE 509 81 42 228 189 tfor:TF0184|5end_dihydroneopterin_aldolase_195629..195859_POSITIVE 507 87 41 200 154 tfor:TF3007|5end_conserved_hypothetical_protein_3227256..3227486_POSITIVE 492 90 42 171 126 tfor:TF0702|5end_possible_peptidyl-prolyl_isomerase_744977..745207_POSITIVE 492 90 41 182 135 tfor:TF0146|5end_glutamine-dependent_NAD(+)_synthetase_154855..155085_POSITIVE 485 90 42 165 118 tfor:TF1024|5end_50S_ribosomal_protein_L19_1081948..1082178_POSITIVE 474 89 42 173 125 tfor:TF0811|5end_conserved_hypothetical_protein;_posible_sugar_phosphate_isomerase_869787..870017_POSITIVE 456 82 42 201 160 tfor:TF0662|5end_hypothetical_protein_708316..708546_POSITIVE 442 69 26 147 96 tfor:TF0797|5end_conserved_hypothetical_protein_853296..853526_POSITIVE 438 81 42 204 164 tfor:TF2593|5end_amino_acid_transport_protein_2762882..2763112_POSITIVE 423 89 42 84 38 tfor:TF1046|5end_hypothetical_protein_1108178..1108408_POSITIVE 417 89 42 166 110 tfor:TF0107|5end_ion_channel_protein_113913..114143_POSITIVE 395 77 42 167 132 tfor:TF0216|5end_50S_ribosomal_protein_L20_242476..242706_POSITIVE 394 80 31 149 98 tfor:TF2947|5end_isochorismate_synthase_3153633..3153863_POSITIVE 390 189 143 109 65 tfor:TF2304|5end_OmpA_family_protein_2459320..2459550_POSITIVE 386 79 34 229 181 tfor:TF1454|5end_sugar_phosphate_epimerase/isomerase_1539696..1539926_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 977 150 101 52 3 tfor:TF2535|3end_histidyl-tRNA_synthetase_2719178..2719328_POSITIVE 522 90 41 125 73 tfor:TF2413|3end_hypothetical_protein_2590680..2590830_POSITIVE 513 90 42 75 17 tfor:TF2319|3end_acyl_carrier_protein_2476588..2476738_POSITIVE 509 81 42 47 8 tfor:TF0182|3end_DNA-binding_protein,_HU-related_195528..195678_POSITIVE 456 82 42 62 21 tfor:TF0661|3end_hypothetical_protein_708257..708407_POSITIVE 438 81 42 49 9 tfor:TF2592|3end_conserved_hypothetical_protein_2762807..2762957_POSITIVE 423 89 42 71 25 tfor:TF1045|3end_conserved_hypothetical_protein_1108245..1108395_POSITIVE 417 89 42 80 24 tfor:TF0105|3end_DNA-binding_stress_protein,_Dps_family_113907..114057_POSITIVE 406 78 42 49 13 tfor:TF2765|3end_subtilisin-like_serine_protease_2951460..2951610_POSITIVE 398 88 42 77 28 tfor:TF1997|3end_ROK_family_transcriptional_regulator_2152686..2152836_POSITIVE 386 79 34 110 62 tfor:TF1452|3end_conserved_hypothetical_protein;_possible_transglutaminase-like_enzyme_1539657..1539807_POSITIVE 373 79 40 60 19 tfor:TF1354|3end_TonB_protein_1435216..1435366_POSITIVE 368 80 33 56 10 tfor:TF1416|3end_outer_membrane_protein_1499413..1499563_POSITIVE 349 153 112 146 93 tfor:TF2188|3end_conserved_hypothetical_protein_2363535..2363685_POSITIVE 329 149 114 42 4 tfor:TF1237|3end_possible_L-fuculose_kinase_1323599..1323749_POSITIVE 326 70 23 88 40 tfor:TF2256|3end_transfer_region-related_protein,_TraI_2428614..2428764_POSITIVE 326 190 141 141 95 tfor:TF0462|3end_possible_cobalamin_biosynthesis_precorrin-3_methylase_479095..479245_POSITIVE 322 149 101 68 16 tfor:TF2846|3end_cobyric_acid_synthase_3036469..3036619_POSITIVE 319 78 31 64 18 tfor:TF1897|3end_conserved_hypothetical_protein;_possible_aminopeptidase_2052107..2052257_POSITIVE 316 140 96 143 98 tfor:TF2953|3end_possible_TonB-dependent_outer_membrane_receptor_3161501..3161651_POSITIVE