Origin IGS: taggtacaatacgtgctttgaatgctatgattttgactgacttatcacggcaagcatttttccttgcattgcacttcgtaaaaaaatctatatgacaagtccgtgaaacctcattaggcaatacaacataccaattaaaccaaaaagggtgtataaaaacattacgttttgatacaccctcttcttattacaaaatagactaagagtaatgtcacatgtta .........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 taacatgtgacattactcttagtctattttgtaataagaagagggtgtatcaaaacgtaatgtttttatacaccctttttggtttaattggtatgttgtattgcctaatgaggtttcacggacttgtcatatagatttttttacgaagtgcaatgcaaggaaaaatgcttgccgtgataagtcagtcaaaatcatagcattcaaagcacgtattgtaccta Mask Tandem Repeat Region ================================================ taggtacaatacgtgctttgaatgctatgattttgactgacttatcacggcaagcatttttccttgcattgcacttcgtaaaaaaatctatatgacaagtccgtgaaacctcattaggcaatacaacataccaattaaaccaaaaagggtgtataaaaacattacgttttgatacaccctcttcttattacaaaatagactaagagtaatgtcacatgtta Find is-nt database================================================ Query_seq: TF0215:TF0216|TF0215:TF0216:tRNA/rRNA methyltransferase, TrmH family:50S ribosomal protein L20:->->:242395..242615 221 taggtacaatacgtgctttgaatgctatgattttgactgacttatcacggcaagcatttttccttgcattgcacttcgtaaaaaaatctatatgacaagtccgtgaaacctcattaggcaatacaacataccaattaaaccaaaaagggtgtataaaaacattacgttttgatacaccctcttcttattacaaaatagactaagagtaatgtcacatgtta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF0215:TF0216|TF0215:TF0216:tRNA/rRNA methyltransferase, TrmH family:50S ribosomal protein L20:->->:242395..242615 221 taggtacaatacgtgctttgaatgctatgattttgactgacttatcacggcaagcatttttccttgcattgcacttcgtaaaaaaatctatatgacaagtccgtgaaacctcattaggcaatacaacataccaattaaaccaaaaagggtgtataaaaacattacgttttgatacaccctcttcttattacaaaatagactaagagtaatgtcacatgtta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF0215:TF0216|TF0215:TF0216:tRNA/rRNA methyltransferase, TrmH family:50S ribosomal protein L20:->->:242395..242615 221 taggtacaatacgtgctttgaatgctatgattttgactgacttatcacggcaagcatttttccttgcattgcacttcgtaaaaaaatctatatgacaagtccgtgaaacctcattaggcaatacaacataccaattaaaccaaaaagggtgtataaaaacattacgttttgatacaccctcttcttattacaaaatagactaagagtaatgtcacatgtta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taggtacaatacgtgctttgaatgctatgattttgactgacttatcacggcaagcatttttccttgcattgcacttcgtaaaaaaatctatatgacaagtccgtgaaacctcattaggcaatacaacataccaattaaaccaaaaagggtgtataaaaacattacgttttgatacaccctcttcttattacaaaatagactaagagtaatgtcacatgtta Predict ORF larger than 30AA ================================================ Protein_Len: 40 Strand: - Start: 91 End: 210 .......................................................................................... I V L G H F R M L C Y L M G I L G F L T Y L F M V N Q Y V R K K N C F L S L T M ........... Protein_Len: 51 Strand: - Start: 2 End: 154 . P V I R A K F A I I K V S K D R C A N K R A N C K T F F D I H C T R S V E N P L V V Y W N F W F P H M ................................................................... taggtacaatacgtgctttgaatgctatgattttgactgacttatcacggcaagcatttttccttgcattgcacttcgtaaaaaaatctatatgacaagtccgtgaaacctcattaggcaatacaacataccaattaaaccaaaaagggtgtataaaaacattacgttttgatacaccctcttcttattacaaaatagactaagagtaatgtcacatgtta Predict Promoter with matrix: RpoD-15 score > 80================================================ Predict Promoter with matrix: RpoD-16 score > 80================================================ Predict Promoter with matrix: RpoD-17 score > 80================================================ PromScan Matrix: RpoD-17 Strand: - Score: 82 Start: 187 End: 216 ..........................................................................................................................................................................................TGTGACATTACTCTTAGTCTATTTTGTAAT..... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ taggtacaatacgtgctttgaatgctatgattttgactgacttatcacggcaagcatttttccttgcattgcacttcgtaaaaaaatctatatgacaagtccgtgaaacctcattaggcaatacaacataccaattaaaccaaaaagggtgtataaaaacattacgttttgatacaccctcttcttattacaaaatagactaagagtaatgtcacatgtta Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 87 HP_score: -9.6 Tail_Score: -3.94877 Start: 145 End: 181 Full_Region: ACCAATTAAACCAAA AAGGGTGTATAAAAAC ATTAC GTTTTGATACACCCTC TTCTTATTACAAAAT ................................................................................................................................................AAGGGTGTATAAAAACATTACGTTTTGATACACCCTC........................................ TransTerm Strand: - Conf: 100 HP_score: -12.9 Tail_Score: -5.04222 Start: 147 End: 179 Full_Region: tttgtaataagaaga gggtgtatcaaaacg taa tgtttttatacaccc tttttggtttaattg ..................................................................................................................................................gggtgtatcaaaacgtaatgtttttatacaccc.......................................... Find igs database================================================ Query_seq: TF0215:TF0216|TF0215:TF0216:tRNA/rRNA methyltransferase, TrmH family:50S ribosomal protein L20:->->:242395..242615 221 taggtacaatacgtgctttgaatgctatgattttgactgacttatcacggcaagcatttttccttgcattgcacttcgtaaaaaaatctatatgacaagtccgtgaaacctcattaggcaatacaacataccaattaaaccaaaaagggtgtataaaaacattacgttttgatacaccctcttcttattacaaaatagactaagagtaatgtcacatgtta Intra-Species Hit: Count: 1 Min: 1 Max: 221 Len: 221 Subject: tfor_TF0215_TF0216|tRNA/rRNA methyltransferase, TrmH family:50S ribosomal protein L20|POSITIVE:POSITIVE|[242395,242615]|221 HSP 1 e-value: 1.0E-109 bit: 396.0 Len: 221 Query Start:1 Query End:221 Subject Strand: POSITIVE Subject Start: 1 Subject End: 221 taggtacaatacgtgctttgaatgctatgattttgactgacttatcacggcaagcatttttccttgcattgcacttcgtnnnnnnntctatatgacaagtccgtgaaacctcattaggcaatacaacataccaattaaaccaaaaagggtgtataaaaacattacgttttgatacaccctcttcttattacaaaatagactaagagtaatgtcacatgtta taggtacaatacgtgctttgaatgctatgattttgactgacttatcacggcaagcatttttccttgcattgcacttcgtaaaaaaatctatatgacaagtccgtgaaacctcattaggcaatacaacataccaattaaaccaaaaagggtgtataaaaacattacgttttgatacaccctcttcttattacaaaatagactaagagtaatgtcacatgtta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAGGUACAAUACGUGCUUUGAAUGCUAUGAUUUUGACUGACUUAUCACGGCAAGCAUUUUUCCUUGCAUUGCACUUCGUAAAAAAAUCUAUAUGACAAGUCCGUGAAACCUCAUUAGGCAAUACAACAUACCAAUUAAACCAAAAAGGGUGUAUAAAAACAUUACGUUUUGAUACACCCUCUUCUUAUUACAAAAUAGACUAAGAGUAAUGUCACAUGUUA .((((((.....))))))....((((((((.(((.((.(((((.(((..(((((........))))).((((.....))))...........))).))))).)).)))..))))..))))....(((((................(((((((((.(((((.....))))).))))))))).................(((..........)))..))))). (-47.70) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAACAUGUGACAUUACUCUUAGUCUAUUUUGUAAUAAGAAGAGGGUGUAUCAAAACGUAAUGUUUUUAUACACCCUUUUUGGUUUAAUUGGUAUGUUGUAUUGCCUAAUGAGGUUUCACGGACUUGUCAUAUAGAUUUUUUUACGAAGUGCAAUGCAAGGAAAAAUGCUUGCCGUGAUAAGUCAGUCAAAAUCAUAGCAUUCAAAGCACGUAUUGUACCUA ....((((((((........(((((......(((...(((((((((((((.(((((.....))))).)))))))))))))...)))...((((........))))..............)))))))))))))...............(((((((((...(...((((((((...((((......))))....)).)))))).....)..)))))))))... (-54.50) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 456 187 146 205 161 tfor:TF0662|5end_hypothetical_protein_708316..708546_POSITIVE 405 186 147 163 123 tfor:TF0187|5end_ferredoxin_202151..202381_POSITIVE 391 185 146 78 39 tfor:TF1046|5end_hypothetical_protein_1108178..1108408_POSITIVE 388 183 146 192 156 tfor:TF3007|5end_conserved_hypothetical_protein_3227256..3227486_POSITIVE 364 188 146 153 112 tfor:TF2947|5end_isochorismate_synthase_3153633..3153863_POSITIVE 354 186 146 218 176 tfor:TF1505|5end_conserved_hypothetical_protein_1610773..1611003_POSITIVE 337 57 12 91 43 tfor:TF1966|5end_conserved_hypothetical_protein_2114989..2115219_POSITIVE 329 186 146 228 192 tfor:TF1999|5end_ArgK_protein_with_ATPase_and_kinase_domains_2152769..2152999_POSITIVE 317 183 146 227 190 tfor:TF0184|5end_dihydroneopterin_aldolase_195629..195859_POSITIVE 315 183 146 203 165 tfor:TF2593|5end_amino_acid_transport_protein_2762882..2763112_POSITIVE 301 78 37 50 6 tfor:TF2165|5end_hypothetical_protein_2341654..2341884_POSITIVE 294 75 33 123 87 tfor:TF1476|5end_outer_membrane_protein_P49_1569723..1569953_POSITIVE 293 50 3 188 133 tfor:TF0285|5end_conserved_hypothetical_protein_314465..314695_POSITIVE 292 180 138 200 157 tfor:TF2289|5end_secretion_protein,_possible_HlyD_family_2442725..2442955_POSITIVE 284 89 47 184 146 tfor:TF2371|5end_conserved_hypothetical_protein_2536974..2537204_POSITIVE 281 188 146 170 126 tfor:TF0811|5end_conserved_hypothetical_protein;_posible_sugar_phosphate_isomerase_869787..870017_POSITIVE 277 81 44 66 17 tfor:TF1760|5end_guanosine-3',5'-bis(diphosphate)_3'-pyrophosphohydrolase_1897081..1897311_POSITIVE 277 56 13 45 7 tfor:TF0279|5end_conserved_hypothetical_protein_307142..307372_POSITIVE 272 55 12 189 136 tfor:TF1852|5end_prtQ_protein_2004643..2004873_POSITIVE 271 106 61 48 7 tfor:TF2974|5end_conserved_hypothetical_protein;_possible_hydrolase_3181418..3181648_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 456 187 146 66 22 tfor:TF0661|3end_hypothetical_protein_708257..708407_POSITIVE 408 185 146 57 14 tfor:TF2765|3end_subtilisin-like_serine_protease_2951460..2951610_POSITIVE 391 185 146 65 26 tfor:TF1045|3end_conserved_hypothetical_protein_1108245..1108395_POSITIVE 360 183 146 112 75 tfor:TF2413|3end_hypothetical_protein_2590680..2590830_POSITIVE 329 186 146 65 29 tfor:TF1997|3end_ROK_family_transcriptional_regulator_2152686..2152836_POSITIVE 317 183 146 46 9 tfor:TF0182|3end_DNA-binding_protein,_HU-related_195528..195678_POSITIVE 315 183 146 48 10 tfor:TF2592|3end_conserved_hypothetical_protein_2762807..2762957_POSITIVE 298 200 163 40 1 tfor:TF0178|3end_ferritin_188223..188373_POSITIVE 274 56 12 135 89 tfor:TF2609|3end_dipeptidase,_pathogenicity_island-encoded_protein_D_2786264..2786414_POSITIVE 272 55 12 147 94 tfor:TF1851|3end_methionine_synthase_I_2004681..2004831_POSITIVE 271 81 48 49 5 tfor:TF1759|3end_membrane-bound_lytic_murein_transglycosylase_D_precursor_1897144..1897294_POSITIVE 262 78 31 136 74 tfor:TF0235|3end_hypothetical_protein_261849..261999_POSITIVE 262 186 146 49 8 tfor:TF0135|3end_hypothetical_protein_146554..146704_POSITIVE 260 65 22 47 1 tfor:TF2226|3end_CTn_excision_protein_2395956..2396106_POSITIVE 259 79 37 128 83 tfor:TF3033|3end_S1_RNA_binding_domain_protein,_S1_ribosomal_protein_3258983..3259133_POSITIVE 254 149 117 85 52 tfor:TF2364|3end_conserved_hypothetical_protein;_possible_DNA_binding_protein,_excisionase_family_2530747..2530897_POSITIVE 254 73 37 48 7 tfor:TF2107|3end_hypothetical_protein_2277436..2277586_POSITIVE 254 118 76 147 101 tfor:TF1786|3end_hypothetical_protein_1926425..1926575_POSITIVE 252 60 12 74 24 tfor:TF1575|3end_DNA-binding_response_regulator_1685895..1686045_POSITIVE 248 77 40 137 90 tfor:TF2285|3end_hypothetical_protein_2441024..2441174_POSITIVE