Origin IGS: tagtgtctatggcctgataaacaggtgatatggttaagtctccccgtacgtcggggattcttaacctttttgcgtctatttcattacaagttcaaaaacaattcctaactactaactaa .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 ttagttagtagttaggaattgtttttgaacttgtaatgaaatagacgcaaaaaggttaagaatccccgacgtacggggagacttaaccatatcacctgtttatcaggccatagacacta Mask Tandem Repeat Region ================================================ tagtgtctatggcctgataaacaggtgatatggttaagtctccccgtacgtcggggattcttaacctttttgcgtctatttcattacaagttcaaaaacaattcctaactactaactaa Find is-nt database================================================ Query_seq: TF2943:TF2944|TF2943:TF2944:50S ribosomal protein L7/L12:DNA-directed RNA polymerase, beta subunit:->->:3143628..3143746 119 tagtgtctatggcctgataaacaggtgatatggttaagtctccccgtacgtcggggattcttaacctttttgcgtctatttcattacaagttcaaaaacaattcctaactactaactaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF2943:TF2944|TF2943:TF2944:50S ribosomal protein L7/L12:DNA-directed RNA polymerase, beta subunit:->->:3143628..3143746 119 tagtgtctatggcctgataaacaggtgatatggttaagtctccccgtacgtcggggattcttaacctttttgcgtctatttcattacaagttcaaaaacaattcctaactactaactaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF2943:TF2944|TF2943:TF2944:50S ribosomal protein L7/L12:DNA-directed RNA polymerase, beta subunit:->->:3143628..3143746 119 tagtgtctatggcctgataaacaggtgatatggttaagtctccccgtacgtcggggattcttaacctttttgcgtctatttcattacaagttcaaaaacaattcctaactactaactaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tagtgtctatggcctgataaacaggtgatatggttaagtctccccgtacgtcggggattcttaacctttttgcgtctatttcattacaagttcaaaaacaattcctaactactaactaa Predict ORF larger than 30AA ================================================ Protein_Len: 30 Strand: + Start: 30 End: 116 ............................. M V K S P R T S G I L N L F A S I S L Q V Q K Q F L T T N * ... tagtgtctatggcctgataaacaggtgatatggttaagtctccccgtacgtcggggattcttaacctttttgcgtctatttcattacaagttcaaaaacaattcctaactactaactaa 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================================================ tagtgtctatggcctgataaacaggtgatatggttaagtctccccgtacgtcggggattcttaacctttttgcgtctatttcattacaagttcaaaaacaattcctaactactaactaa Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 100 HP_score: -12.9 Tail_Score: -4.75356 Start: 32 End: 66 Full_Region: ATAAACAGGTGATAT GGTTAAGTCTCCCCG TACGT CGGGGATTCTTAACC TTTTTGCGTCTATTT ...............................GGTTAAGTCTCCCCGTACGTCGGGGATTCTTAACC..................................................... Find igs database================================================ Query_seq: TF2943:TF2944|TF2943:TF2944:50S ribosomal protein L7/L12:DNA-directed RNA polymerase, beta subunit:->->:3143628..3143746 119 tagtgtctatggcctgataaacaggtgatatggttaagtctccccgtacgtcggggattcttaacctttttgcgtctatttcattacaagttcaaaaacaattcctaactactaactaa Intra-Species Hit: Count: 1 Min: 1 Max: 119 Len: 119 Subject: tfor_TF2943_TF2944|50S ribosomal protein L7/L12:DNA-directed RNA polymerase, beta subunit|POSITIVE:POSITIVE|[3143628,3143746]|119 HSP 1 e-value: 1.0E-61 bit: 236.0 Len: 119 Query Start:1 Query End:119 Subject Strand: POSITIVE Subject Start: 1 Subject End: 119 tagtgtctatggcctgataaacaggtgatatggttaagtctccccgtacgtcggggattcttaacctttttgcgtctatttcattacaagttcaaaaacaattcctaactactaactaa tagtgtctatggcctgataaacaggtgatatggttaagtctccccgtacgtcggggattcttaacctttttgcgtctatttcattacaagttcaaaaacaattcctaactactaactaa Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAGUGUCUAUGGCCUGAUAAACAGGUGAUAUGGUUAAGUCUCCCCGUACGUCGGGGAUUCUUAACCUUUUUGCGUCUAUUUCAUUACAAGUUCAAAAACAAUUCCUAACUACUAACUAA (((((..(((.(((((.....))))).))).(((((((..((((((.....))))))..)))))))...........................................)))))..... (-32.70) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUAGUUAGUAGUUAGGAAUUGUUUUUGAACUUGUAAUGAAAUAGACGCAAAAAGGUUAAGAAUCCCCGACGUACGGGGAGACUUAACCAUAUCACCUGUUUAUCAGGCCAUAGACACUA .....((((..(((((.....((((((...((((......))))...))))))(((((((..((((((.....))))))..)))))))......((((.....)))))).)))..)))) (-30.90) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 400 58 12 212 158 tfor:TF0554|5end_Bacteroides_aerotolerance_protein,_BatC_586303..586533_POSITIVE 359 66 24 209 157 tfor:TF2044|5end_excinuclease_ABC,_subunit_A_2203228..2203458_POSITIVE 344 57 11 172 118 tfor:TF1681|5end_dTDP-4-keto-L-rhamnose_reductase_1794904..1795134_POSITIVE 333 53 11 221 181 tfor:TF1191|5end_possible_transcriptional_regulator_1273615..1273845_POSITIVE 329 54 11 210 165 tfor:TF2655|5end_DNA_topoisomerase_I_2824543..2824773_POSITIVE 326 66 23 208 156 tfor:TF1866|5end_conserved_hypothetical_protein;_possible_transposase_2022272..2022502_POSITIVE 323 70 23 218 169 tfor:TF0269|5end_possible_transposase_element_297060..297290_POSITIVE 317 60 11 53 5 tfor:TF2840|5end_hypothetical_protein_3031060..3031290_POSITIVE 315 55 11 222 186 tfor:TF0467|5end_acetyltransferase-related_protein_485936..486166_POSITIVE 314 72 31 85 39 tfor:TF3024|5end_periplasmic_protease_3247204..3247434_POSITIVE 312 59 12 86 28 tfor:TF2341|5end_hypothetical_protein_2505735..2505965_POSITIVE 312 58 11 200 138 tfor:TF1732|5end_conserved_hypothetical_protein_1854619..1854849_POSITIVE 306 56 11 219 169 tfor:TF0541|5end_conserved_hypothetical_protein_568473..568703_POSITIVE 302 57 12 215 172 tfor:TF1441|5end_conserved_hypothetical_protein_1525567..1525797_POSITIVE 296 49 3 40 1 tfor:TF2831|5end_ABC_transporter,_permease_component_3021317..3021547_POSITIVE 294 55 12 217 177 tfor:TF2130|5end_conserved_hypothetical_protein;_possible_permease_2306486..2306716_POSITIVE 292 70 23 183 138 tfor:TF3124|5end_dTDP-glucose_4,6-dehydratase_3358655..3358885_POSITIVE 292 56 11 154 108 tfor:TF0574|5end_AMP_nucleosidase_604787..605017_POSITIVE 291 66 23 208 156 tfor:TF1096|5end_conserved_hypothetical_protein_1165065..1165295_POSITIVE 289 53 12 93 54 tfor:TF3127|5end_acetyltransferase,_possible_GNAT_family_3361627..3361857_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 436 66 23 59 14 tfor:TF2943|3end_50S_ribosomal_protein_L7/L12_3143567..3143717_POSITIVE 329 54 11 146 101 tfor:TF2654|3end_arginyl-tRNA_synthetase_2824559..2824709_POSITIVE 323 70 23 110 61 tfor:TF0268|3end_hypothetical_protein_297032..297182_POSITIVE 321 60 12 84 32 tfor:TF2799|3end_RNA_polymerase_ECF-type_sigma_factor_2985052..2985202_POSITIVE 319 76 32 119 81 tfor:TF0886|3end_conjugative_transposon_protein_fragment_938152..938302_POSITIVE 318 80 32 92 27 tfor:TF0874|3end_transposase_926652..926802_POSITIVE 315 49 2 62 22 tfor:TF2830|3end_ABC_transporter,_ATP-binding_protein_3021419..3021569_POSITIVE 314 72 31 102 56 tfor:TF3022|3end_chorismate_synthase_3247301..3247451_POSITIVE 297 53 11 70 26 tfor:TF0862|3end_conserved_hypothetical_protein_fragment_914459..914609_POSITIVE 292 56 11 139 93 tfor:TF0573|3end_DNA_polymerase_III,_delta_subunit_604852..605002_POSITIVE 289 53 12 71 32 tfor:TF3126|3end_glycosyltransferase,_group_2_family_3361685..3361835_POSITIVE 287 59 22 54 8 tfor:TF2339|3end_hypothetical_protein_2505783..2505933_POSITIVE 281 52 11 89 42 tfor:TF2773|3end_S-adenosylmethionine_tRNA_ribosyltransferase_2959243..2959393_POSITIVE 277 56 12 59 2 tfor:TF2428|3end_conserved_hypothetical_protein_2610525..2610675_POSITIVE 277 60 11 52 2 tfor:TF1036|3end_iron(III)_ABC_transporter,_permease_component_1098274..1098424_POSITIVE 275 85 43 92 35 tfor:TF0952|3end_conserved_hypothetical_protein_998009..998159_POSITIVE 272 78 33 57 7 tfor:TF1680|3end_peptide_chain_release_factor_3_1794969..1795119_POSITIVE 270 57 11 143 108 tfor:TF1280|3end_electron_transfer_flavoprotein,_beta_subunit_1365257..1365407_POSITIVE 267 87 43 80 35 tfor:TF2556|3end_conserved_hypothetical_protein_2737095..2737245_POSITIVE 266 59 15 133 92 tfor:TF2742|3end_single-strand_DNA-specific_exonuclease_2925603..2925753_POSITIVE