Origin IGS: taaacaatcatctgatcaaacgaataagagcaggagcagggctgtccgaaggtcgaagatcgaacggatagccttgtttgtccggataggttttcaagaagcatggtcaatgtgtgaaataaagaaaactctatgaatgaagatggagacgtcgaaaaatattcccggacggaagttgcacgggaaaagaaaaatacgtatctttgtgtcgaaattgtaatgatttca .........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 tgaaatcattacaatttcgacacaaagatacgtatttttcttttcccgtgcaacttccgtccgggaatatttttcgacgtctccatcttcattcatagagttttctttatttcacacattgaccatgcttcttgaaaacctatccggacaaacaaggctatccgttcgatcttcgaccttcggacagccctgctcctgctcttattcgtttgatcagatgattgttta Mask Tandem Repeat Region ================================================ taaacaatcatctgatcaaacgaataagagcaggagcagggctgtccgaaggtcgaagatcgaacggatagccttgtttgtccggataggttttcaagaagcatggtcaatgtgtgaaataaagaaaactctatgaatgaagatggagacgtcgaaaaatattcccggacggaagttgcacgggaaaagaaaaatacgtatctttgtgtcgaaattgtaatgatttca Find is-nt database================================================ Query_seq: TF0382:TF0384|TF0382:TF0384:transcription termination factor:conserved hypothetical protein:->->:405289..405516 228 taaacaatcatctgatcaaacgaataagagcaggagcagggctgtccgaaggtcgaagatcgaacggatagccttgtttgtccggataggttttcaagaagcatggtcaatgtgtgaaataaagaaaactctatgaatgaagatggagacgtcgaaaaatattcccggacggaagttgcacgggaaaagaaaaatacgtatctttgtgtcgaaattgtaatgatttca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF0382:TF0384|TF0382:TF0384:transcription termination factor:conserved hypothetical protein:->->:405289..405516 228 taaacaatcatctgatcaaacgaataagagcaggagcagggctgtccgaaggtcgaagatcgaacggatagccttgtttgtccggataggttttcaagaagcatggtcaatgtgtgaaataaagaaaactctatgaatgaagatggagacgtcgaaaaatattcccggacggaagttgcacgggaaaagaaaaatacgtatctttgtgtcgaaattgtaatgatttca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF0382:TF0384|TF0382:TF0384:transcription termination factor:conserved hypothetical protein:->->:405289..405516 228 taaacaatcatctgatcaaacgaataagagcaggagcagggctgtccgaaggtcgaagatcgaacggatagccttgtttgtccggataggttttcaagaagcatggtcaatgtgtgaaataaagaaaactctatgaatgaagatggagacgtcgaaaaatattcccggacggaagttgcacgggaaaagaaaaatacgtatctttgtgtcgaaattgtaatgatttca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taaacaatcatctgatcaaacgaataagagcaggagcagggctgtccgaaggtcgaagatcgaacggatagccttgtttgtccggataggttttcaagaagcatggtcaatgtgtgaaataaagaaaactctatgaatgaagatggagacgtcgaaaaatattcccggacggaagttgcacgggaaaagaaaaatacgtatctttgtgtcgaaattgtaatgatttca Predict ORF larger than 30AA ================================================ Protein_Len: 32 Strand: + Start: 133 End: 228 .................................................................................................................................... M N E D G D V E K Y S R T E V A R E K K N T Y L C V E I V M I S Protein_Len: 35 Strand: - Start: 97 End: 201 ................................................................................................ S A H D I H S I F F V R H I F I S V D F F I G P R F N C P F L F I R M ........................... Protein_Len: 60 Strand: - Start: 3 End: 224 .. G F T S S R V S L R T Q G S L N E L L M T L T H F L S F E I F S S P S T S F Y E R V S T A R S F F F V Y R Q T S I T I M .... taaacaatcatctgatcaaacgaataagagcaggagcagggctgtccgaaggtcgaagatcgaacggatagccttgtttgtccggataggttttcaagaagcatggtcaatgtgtgaaataaagaaaactctatgaatgaagatggagacgtcgaaaaatattcccggacggaagttgcacgggaaaagaaaaatacgtatctttgtgtcgaaattgtaatgatttca 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================================================ taaacaatcatctgatcaaacgaataagagcaggagcagggctgtccgaaggtcgaagatcgaacggatagccttgtttgtccggataggttttcaagaagcatggtcaatgtgtgaaataaagaaaactctatgaatgaagatggagacgtcgaaaaatattcccggacggaagttgcacgggaaaagaaaaatacgtatctttgtgtcgaaattgtaatgatttca Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TF0382:TF0384|TF0382:TF0384:transcription termination factor:conserved hypothetical protein:->->:405289..405516 228 taaacaatcatctgatcaaacgaataagagcaggagcagggctgtccgaaggtcgaagatcgaacggatagccttgtttgtccggataggttttcaagaagcatggtcaatgtgtgaaataaagaaaactctatgaatgaagatggagacgtcgaaaaatattcccggacggaagttgcacgggaaaagaaaaatacgtatctttgtgtcgaaattgtaatgatttca Intra-Species Hit: Count: 1 Min: 1 Max: 228 Len: 228 Subject: tfor_TF0382_TF0384|transcription termination factor:conserved hypothetical protein|POSITIVE:POSITIVE|[405289,405516]|228 HSP 1 e-value: 1.0E-126 bit: 452.0 Len: 228 Query Start:1 Query End:228 Subject Strand: POSITIVE Subject Start: 1 Subject End: 228 taaacaatcatctgatcaaacgaataagagcaggagcagggctgtccgaaggtcgaagatcgaacggatagccttgtttgtccggataggttttcaagaagcatggtcaatgtgtgaaataaagaaaactctatgaatgaagatggagacgtcgaaaaatattcccggacggaagttgcacgggaaaagaaaaatacgtatctttgtgtcgaaattgtaatgatttca taaacaatcatctgatcaaacgaataagagcaggagcagggctgtccgaaggtcgaagatcgaacggatagccttgtttgtccggataggttttcaagaagcatggtcaatgtgtgaaataaagaaaactctatgaatgaagatggagacgtcgaaaaatattcccggacggaagttgcacgggaaaagaaaaatacgtatctttgtgtcgaaattgtaatgatttca Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAACAAUCAUCUGAUCAAACGAAUAAGAGCAGGAGCAGGGCUGUCCGAAGGUCGAAGAUCGAACGGAUAGCCUUGUUUGUCCGGAUAGGUUUUCAAGAAGCAUGGUCAAUGUGUGAAAUAAAGAAAACUCUAUGAAUGAAGAUGGAGACGUCGAAAAAUAUUCCCGGACGGAAGUUGCACGGGAAAAGAAAAAUACGUAUCUUUGUGUCGAAAUUGUAAUGAUUUCA .....(((((((((..(((((........((....)).((((((((((..((((...))))...)))))))))).)))))..))))).)))).....(((((((...((((...(((.(((((((................((((....))))........(((((((((....)))...))))))..............))))))).)))..))))..))).)))). (-67.70) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGAAAUCAUUACAAUUUCGACACAAAGAUACGUAUUUUUCUUUUCCCGUGCAACUUCCGUCCGGGAAUAUUUUUCGACGUCUCCAUCUUCAUUCAUAGAGUUUUCUUUAUUUCACACAUUGACCAUGCUUCUUGAAAACCUAUCCGGACAAACAAGGCUAUCCGUUCGAUCUUCGACCUUCGGACAGCCCUGCUCCUGCUCUUAUUCGUUUGAUCAGAUGAUUGUUUA ...(((((((.....((((.....(((((((((.........((((((..(.......)..)))))).........))))....))))).....((((.((((((............................)))))))))).))))(((((..((((.((((.(((.....)))....)))).))))..((....))........)))))....)))))))..... (-47.96) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 444 89 41 118 63 tfor:TF3039|5end_ABC_transporter,_ATP-binding_protein_3265731..3265961_POSITIVE 429 74 33 163 122 tfor:TF1027|5end_hypothetical_protein_1085641..1085871_POSITIVE 427 189 144 213 154 tfor:TF2886|5end_RNA_methylase_SpoU_family_3075651..3075881_POSITIVE 402 70 31 76 29 tfor:TF2378|5end_peptide_chain_release_factor_1_2542682..2542912_POSITIVE 402 78 34 88 40 tfor:TF0080|5end_phosphate_ABC_transporter,_periplasmic_phosphate-binding_protein_86325..86555_POSITIVE 396 80 35 229 177 tfor:TF0377|5end_FtsK/SpoIIIE_family_cell_division_protein_394944..395174_POSITIVE 389 66 21 66 15 tfor:TF1578|5end_hypothetical_protein_1686187..1686417_POSITIVE 388 68 21 88 33 tfor:TF2039|5end_possible_cell-cycle_regulation_histidine_triad_(HIT)_protein_2199318..2199548_POSITIVE 386 73 32 179 134 tfor:TF1253|5end_hypothetical_protein_1335982..1336212_POSITIVE 386 73 32 148 94 tfor:TF0995|5end_conserved_hypothetical_protein_1049695..1049925_POSITIVE 384 210 162 178 134 tfor:TF1286|5end_hypothetical_protein_1369199..1369429_POSITIVE 381 63 28 67 27 tfor:TF2997|5end_hypothetical_protein_3211408..3211638_POSITIVE 380 68 21 84 21 tfor:TF2822|5end_arginine_repressor_3011793..3012023_POSITIVE 378 85 41 70 27 tfor:TF0371|5end_beta-mannosidase_precursor_386763..386993_POSITIVE 374 77 33 49 1 tfor:TF3143|5end_conserved_hypothetical_protein;_possible_membrane_protein_3377465..3377695_POSITIVE 373 79 37 78 29 tfor:TF1149|5end_conserved_hypothetical_protein;_possible_branched-chain_amino_acid_aminotransferase_1229218..1229448_POSITIVE 371 68 21 65 2 tfor:TF2101|5end_hypothetical_protein_2273702..2273932_POSITIVE 371 70 21 86 36 tfor:TF1677|5end_ATP_synthase,_beta_subunit_1789321..1789551_POSITIVE 371 90 47 230 188 tfor:TF1237|5end_possible_L-fuculose_kinase_1322041..1322271_POSITIVE 363 67 21 61 6 tfor:TF2050|5end_possible_glycosyltransferase_2213919..2214149_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 500 78 33 56 8 tfor:TF0382|3end_transcription_termination_factor_405228..405378_POSITIVE 444 89 41 106 51 tfor:TF3038|3end_conserved_hypothetical_protein_3265799..3265949_POSITIVE 429 74 33 81 40 tfor:TF1026|3end_beta-N-acetylglucosaminidase;_beta_lactamase_1085639..1085789_POSITIVE 384 210 162 144 100 tfor:TF1285|3end_hypothetical_protein_1369245..1369395_POSITIVE 380 68 21 84 21 tfor:TF2821|3end_conserved_hypothetical_protein_3011873..3012023_POSITIVE 377 63 22 148 102 tfor:TF2640|3end_hypothetical_protein_2809533..2809683_POSITIVE 377 67 28 146 96 tfor:TF0994|3end_maltose_O-acetyltransferase_1049782..1049932_POSITIVE 372 78 31 122 76 tfor:TF2013|3end_polysaccharide_deacetylase_2169341..2169491_POSITIVE 371 70 21 78 28 tfor:TF1676|3end_ATP_synthase,__epsilon_subunit_1789393..1789543_POSITIVE 359 67 21 54 7 tfor:TF2049|3end_glycosyltransferase_2213992..2214142_POSITIVE 354 63 28 148 109 tfor:TF2921|3end_hypothetical_protein_3118790..3118940_POSITIVE 354 63 28 148 109 tfor:TF2438|3end_hypothetical_protein_2616157..2616307_POSITIVE 346 90 44 60 10 tfor:TF1262|3end_PDZ_domain_protein_1348831..1348981_POSITIVE 345 79 40 47 3 tfor:TF1148|3end_para-aminobenzoate_synthase_component_I_1229267..1229417_POSITIVE 341 67 21 61 15 tfor:TF2808|3end_bacterial_sugar_transferase_2999909..3000059_POSITIVE 340 90 48 150 93 tfor:TF0982|3end_conserved_hypothetical_protein_1039474..1039624_POSITIVE 340 66 26 71 28 tfor:TF0234|3end_5,10-methylenetetrahydrofolate_reductase_261512..261662_POSITIVE 337 78 35 61 15 tfor:TF0199|3end_conserved_hypothetical_protein_224064..224214_POSITIVE 335 72 32 75 35 tfor:TF0332|3end_conserved_hypothetical_protein_360045..360195_POSITIVE 334 68 33 104 62 tfor:TF2746|3end_hypothetical_protein_2928246..2928396_POSITIVE