Origin IGS: taaaggcatcacttcgtagttcgtaagaaggatgaaaaaatagcggtggcttgataagcagaaaagaaatctgcctgtcaagccgccatcctattccgtatagagggtgtta .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 taacaccctctatacggaataggatggcggcttgacaggcagatttcttttctgcttatcaagccaccgctattttttcatccttcttacgaactacgaagtgatgccttta Mask Tandem Repeat Region ================================================ taaaggcatcacttcgtagttcgtaagaaggatgaaaaaatagcggtggcttgataagcagaaaagaaatctgcctgtcaagccgccatcctattccgtatagagggtgtta Find is-nt database================================================ Query_seq: TF2308:TF2309|TF2308:TF2309:conserved hypothetical protein:cysteinyl-tRNA synthetase:->->:2468920..2469031 112 taaaggcatcacttcgtagttcgtaagaaggatgaaaaaatagcggtggcttgataagcagaaaagaaatctgcctgtcaagccgccatcctattccgtatagagggtgtta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF2308:TF2309|TF2308:TF2309:conserved hypothetical protein:cysteinyl-tRNA synthetase:->->:2468920..2469031 112 taaaggcatcacttcgtagttcgtaagaaggatgaaaaaatagcggtggcttgataagcagaaaagaaatctgcctgtcaagccgccatcctattccgtatagagggtgtta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF2308:TF2309|TF2308:TF2309:conserved hypothetical protein:cysteinyl-tRNA synthetase:->->:2468920..2469031 112 taaaggcatcacttcgtagttcgtaagaaggatgaaaaaatagcggtggcttgataagcagaaaagaaatctgcctgtcaagccgccatcctattccgtatagagggtgtta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taaaggcatcacttcgtagttcgtaagaaggatgaaaaaatagcggtggcttgataagcagaaaagaaatctgcctgtcaagccgccatcctattccgtatagagggtgtta Predict ORF larger than 30AA ================================================ Protein_Len: 31 Strand: - Start: 2 End: 94 . F A D S R L E Y S P H F F L P P K I L L F S I Q R D L R W G M .................. taaaggcatcacttcgtagttcgtaagaaggatgaaaaaatagcggtggcttgataagcagaaaagaaatctgcctgtcaagccgccatcctattccgtatagagggtgtta 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================================================ taaaggcatcacttcgtagttcgtaagaaggatgaaaaaatagcggtggcttgataagcagaaaagaaatctgcctgtcaagccgccatcctattccgtatagagggtgtta Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 77 HP_score: -3.6 Tail_Score: -5.22794 Start: 41 End: 93 Full_Region: accctctatacggaa taggatggcggcttgacaggcaga tttcttt tctgcttatcaagccaccgcta ttttttcatccttct ........................................taggatggcggcttgacaggcagatttcttttctgcttatcaagccaccgcta................... TransTerm Strand: + Conf: 49 HP_score: -4.3 Tail_Score: -3.12327 Start: 42 End: 91 Full_Region: GAAGGATGAAAAAAT AGCGGTGGCTTGATAAGCAGA AAAGAAA TCTGCCTGTCAAGCCGCCATCC TATTCCGTATAGAGG .........................................AGCGGTGGCTTGATAAGCAGAAAAGAAATCTGCCTGTCAAGCCGCCATCC..................... TransTerm Strand: - Conf: 76 HP_score: -8.0 Tail_Score: -4.23218 Start: 43 End: 89 Full_Region: tctatacggaatagg atggcggcttgacaggcaga tttcttt tctgcttatcaagccaccgc tattttttcatcctt ..........................................atggcggcttgacaggcagatttcttttctgcttatcaagccaccgc....................... TransTerm Strand: - Conf: 79 HP_score: -11.5 Tail_Score: -3.12304 Start: 44 End: 88 Full_Region: ctatacggaatagga tggcggcttgacaggcaga tttcttt tctgcttatcaagccaccg ctattttttcatcct ...........................................tggcggcttgacaggcagatttcttttctgcttatcaagccaccg........................ Find igs database================================================ Query_seq: TF2308:TF2309|TF2308:TF2309:conserved hypothetical protein:cysteinyl-tRNA synthetase:->->:2468920..2469031 112 taaaggcatcacttcgtagttcgtaagaaggatgaaaaaatagcggtggcttgataagcagaaaagaaatctgcctgtcaagccgccatcctattccgtatagagggtgtta Intra-Species Hit: Count: 1 Min: 1 Max: 112 Len: 112 Subject: tfor_TF2308_TF2309|conserved hypothetical protein:cysteinyl-tRNA synthetase|POSITIVE:POSITIVE|[2468920,2469031]|112 HSP 1 e-value: 2.0E-57 bit: 222.0 Len: 112 Query Start:1 Query End:112 Subject Strand: POSITIVE Subject Start: 1 Subject End: 112 taaaggcatcacttcgtagttcgtaagaaggatgaaaaaatagcggtggcttgataagcagaaaagaaatctgcctgtcaagccgccatcctattccgtatagagggtgtta taaaggcatcacttcgtagttcgtaagaaggatgaaaaaatagcggtggcttgataagcagaaaagaaatctgcctgtcaagccgccatcctattccgtatagagggtgtta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAAGGCAUCACUUCGUAGUUCGUAAGAAGGAUGAAAAAAUAGCGGUGGCUUGAUAAGCAGAAAAGAAAUCUGCCUGUCAAGCCGCCAUCCUAUUCCGUAUAGAGGGUGUUA ....((((((..(((((..(((....)))..)))))........((((((((((((.(((((.......))))).))))))))))))...((((.....))))..)))))). (-42.80) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAACACCCUCUAUACGGAAUAGGAUGGCGGCUUGACAGGCAGAUUUCUUUUCUGCUUAUCAAGCCACCGCUAUUUUUUCAUCCUUCUUACGAACUACGAAGUGAUGCCUUUA ...............(((((((..(((.(((((((.(((((((.......))))))).))))))).))))))))))..((((((((...........)))).))))...... (-35.10) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 354 90 43 224 151 tfor:TF1694|5end_conserved_hypothetical_protein_1812493..1812723_POSITIVE 325 100 58 189 138 tfor:TF1836|5end_hypothetical_protein_1984534..1984764_POSITIVE 321 100 67 49 18 tfor:TF1221|5end_conserved_hypothetical_protein_1307723..1307953_POSITIVE 311 106 66 70 30 tfor:TF2322|5end_conserved_hypothetical_protein;_possible_lipoprotein_2482743..2482973_POSITIVE 311 109 68 212 171 tfor:TF0497|5end_conserved_hypothetical_protein_524058..524288_POSITIVE 308 110 70 79 32 tfor:TF2035|5end_conserved_hypothetical_protein_2194665..2194895_POSITIVE 306 107 73 163 130 tfor:TF1343|5end_hypothetical_protein_1424630..1424860_POSITIVE 305 78 31 103 47 tfor:TF3039|5end_ABC_transporter,_ATP-binding_protein_3265731..3265961_POSITIVE 304 108 73 46 12 tfor:TF2654|5end_arginyl-tRNA_synthetase_2822692..2822922_POSITIVE 304 90 42 227 172 tfor:TF0890|5end_transfer_region-related_protein,_TraQ_940014..940244_POSITIVE 303 110 78 225 195 tfor:TF2951|5end_O-succinylbenzoic_acid--CoA_ligase_3158496..3158726_POSITIVE 303 110 70 92 43 tfor:TF2108|5end_hypothetical_protein_2277385..2277615_POSITIVE 303 53 11 56 17 tfor:TF0500|5end_hypothetical_protein_526688..526918_POSITIVE 302 109 70 70 40 tfor:TF0168|5end_hypothetical_protein_178160..178390_POSITIVE 300 110 65 72 24 tfor:TF0644|5end_pyruvate_phosphate_dikinase_685784..686014_POSITIVE 298 110 70 62 13 tfor:TF2165|5end_hypothetical_protein_2341654..2341884_POSITIVE 298 99 61 63 9 tfor:TF1415|5end_outer_membrane_protein,_TonB_dependent_receptor_1494268..1494498_POSITIVE 297 85 42 143 93 tfor:TF2129|5end_possible_3-oxoacyl-(acyl-carrier-protein)_synthase_2305464..2305694_POSITIVE 296 85 43 220 182 tfor:TF1901|5end_conserved_hypothetical_protein_2056467..2056697_POSITIVE 295 108 71 163 112 tfor:TF2880|5end_phenylalanyl-tRNA_synthetase,_beta_subunit_3069052..3069282_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 418 87 45 46 4 tfor:TF2308|3end_conserved_hypothetical_protein_2468859..2469009_POSITIVE 321 100 67 43 12 tfor:TF1220|3end_conserved_hypothetical_protein_1307797..1307947_POSITIVE 309 109 67 105 61 tfor:TF0673|3end_conserved_hypothetical_protein_717355..717505_POSITIVE 308 110 70 72 25 tfor:TF2034|3end_arabinose-proton_symporter_2194738..2194888_POSITIVE 306 107 73 73 40 tfor:TF1342|3end_possible_lipoprotein_1424620..1424770_POSITIVE 305 78 31 91 35 tfor:TF3038|3end_conserved_hypothetical_protein_3265799..3265949_POSITIVE 303 110 70 63 14 tfor:TF2107|3end_hypothetical_protein_2277436..2277586_POSITIVE 302 109 70 64 34 tfor:TF0167|3end_conserved_hypothetical_protein_178234..178384_POSITIVE 300 90 42 61 1 tfor:TF2666|3end_hypothetical_protein_2842263..2842413_POSITIVE 297 85 42 133 83 tfor:TF2128|3end_3-oxoacyl-(acyl-carrier_protein)_synthase_2305534..2305684_POSITIVE 294 110 71 149 100 tfor:TF1186|3end_hypothetical_protein_1269815..1269965_POSITIVE 292 88 50 58 22 tfor:TF1983|3end_conserved_hypothetical_protein_2135000..2135150_POSITIVE 288 98 71 97 64 tfor:TF1944|3end_conserved_hypothetical_protein_2093309..2093459_POSITIVE 287 99 57 96 62 tfor:TF3053|3end_conserved_hypothetical_protein_3278889..3279039_POSITIVE 287 90 42 129 77 tfor:TF2979|3end_possible_outer_membrane__protein_3193164..3193314_POSITIVE 284 99 60 146 106 tfor:TF0816|3end_hypothetical_protein_874467..874617_POSITIVE 281 99 58 72 37 tfor:TF2662|3end_hypothetical_protein_2837131..2837281_POSITIVE 281 90 43 72 19 tfor:TF1575|3end_DNA-binding_response_regulator_1685895..1686045_POSITIVE 280 90 42 61 1 tfor:TF2668|3end_hypothetical_protein_2842733..2842883_POSITIVE 277 87 42 102 48 tfor:TF0407|3end_lipoate-protein_ligase_B_(lipoyltransferase)_425844..425994_POSITIVE