Origin IGS: taaagtgatgtcgactgtcacaaaaaaatcacacttccccgggaggcaaatgtgacgtttttgtgacgtttttttcttgttgagagaatgatgcaggattaaatttgcagaaaattgatcaatcattaaaagtaaaaag .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 ctttttacttttaatgattgatcaattttctgcaaatttaatcctgcatcattctctcaacaagaaaaaaacgtcacaaaaacgtcacatttgcctcccggggaagtgtgatttttttgtgacagtcgacatcacttta Mask Tandem Repeat Region ================================================ taaagtgatgtcgactgtcacaaaaaaatcacacttccccgggaggcaaatgtgacgtttttgtgacgtttttttcttgttgagagaatgatgcaggattaaatttgcagaaaattgatcaatcattaaaagtaaaaag Find is-nt database================================================ Query_seq: TF2856:TF2857|TF2856:TF2857:conserved hypothetical protein; possible TPR-repeat-containing protein:conserved hypothetical protein:->->:3043083..3043221 139 taaagtgatgtcgactgtcacaaaaaaatcacacttccccgggaggcaaatgtgacgtttttgtgacgtttttttcttgttgagagaatgatgcaggattaaatttgcagaaaattgatcaatcattaaaagtaaaaag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF2856:TF2857|TF2856:TF2857:conserved hypothetical protein; possible TPR-repeat-containing protein:conserved hypothetical protein:->->:3043083..3043221 139 taaagtgatgtcgactgtcacaaaaaaatcacacttccccgggaggcaaatgtgacgtttttgtgacgtttttttcttgttgagagaatgatgcaggattaaatttgcagaaaattgatcaatcattaaaagtaaaaag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF2856:TF2857|TF2856:TF2857:conserved hypothetical protein; possible TPR-repeat-containing protein:conserved hypothetical protein:->->:3043083..3043221 139 taaagtgatgtcgactgtcacaaaaaaatcacacttccccgggaggcaaatgtgacgtttttgtgacgtttttttcttgttgagagaatgatgcaggattaaatttgcagaaaattgatcaatcattaaaagtaaaaag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taaagtgatgtcgactgtcacaaaaaaatcacacttccccgggaggcaaatgtgacgtttttgtgacgtttttttcttgttgagagaatgatgcaggattaaatttgcagaaaattgatcaatcattaaaagtaaaaag Predict ORF larger than 30AA ================================================ Protein_Len: 42 Strand: - Start: 1 End: 126 L T I D V T V F F D C K G P L C I H R K Q S T K K K N L S H H L I L N A S F Q D I M ............. taaagtgatgtcgactgtcacaaaaaaatcacacttccccgggaggcaaatgtgacgtttttgtgacgtttttttcttgttgagagaatgatgcaggattaaatttgcagaaaattgatcaatcattaaaagtaaaaag 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================================================ taaagtgatgtcgactgtcacaaaaaaatcacacttccccgggaggcaaatgtgacgtttttgtgacgtttttttcttgttgagagaatgatgcaggattaaatttgcagaaaattgatcaatcattaaaagtaaaaag Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 65 HP_score: -7.6 Tail_Score: -3.06636 Start: 18 End: 66 Full_Region: AAGTGATGTCGACTG TCACAAAAAAATCACACTTCCC CGGGA GGCAAATGTGACGTTTTTGTGA CGTTTTTTTCTTGTT .................TCACAAAAAAATCACACTTCCCCGGGAGGCAAATGTGACGTTTTTGTGA......................................................................... TransTerm Strand: - Conf: 90 HP_score: -6.6 Tail_Score: -5.61596 Start: 29 End: 55 Full_Region: aacgtcacaaaaacg tcacatttgcct ccc ggggaagtgtga tttttttgtgacagt ............................tcacatttgcctcccggggaagtgtga.................................................................................... Find igs database================================================ Query_seq: TF2856:TF2857|TF2856:TF2857:conserved hypothetical protein; possible TPR-repeat-containing protein:conserved hypothetical protein:->->:3043083..3043221 139 taaagtgatgtcgactgtcacaaaaaaatcacacttccccgggaggcaaatgtgacgtttttgtgacgtttttttcttgttgagagaatgatgcaggattaaatttgcagaaaattgatcaatcattaaaagtaaaaag Intra-Species Hit: Count: 1 Min: 1 Max: 139 Len: 139 Subject: tfor_TF2856_TF2857|conserved hypothetical protein; possible TPR-repeat-containing protein:conserved hypothetical protein|POSITIVE:POSITIVE|[3043083,3043221]|139 HSP 1 e-value: 2.0E-48 bit: 192.0 Len: 139 Query Start:1 Query End:139 Subject Strand: POSITIVE Subject Start: 1 Subject End: 139 taaagtgatgtcgactgtcacnnnnnnntcacacttccccgggaggcaaatgtgacgtttttgtgacgnnnnnnncttgttgagagaatgatgcaggattaaatttgcagaaaattgatcaatcattaaaagtaaaaag taaagtgatgtcgactgtcacaaaaaaatcacacttccccgggaggcaaatgtgacgtttttgtgacgtttttttcttgttgagagaatgatgcaggattaaatttgcagaaaattgatcaatcattaaaagtaaaaag Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAAGUGAUGUCGACUGUCACAAAAAAAUCACACUUCCCCGGGAGGCAAAUGUGACGUUUUUGUGACGUUUUUUUCUUGUUGAGAGAAUGAUGCAGGAUUAAAUUUGCAGAAAAUUGAUCAAUCAUUAAAAGUAAAAAG ...(((((((((((..((((((((((..((((((((((...)))))....)))))..))))))))))..(((((((.....)))))))...((((((......)))))).....)))))..))))))............ (-36.00) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUUUUUACUUUUAAUGAUUGAUCAAUUUUCUGCAAAUUUAAUCCUGCAUCAUUCUCUCAACAAGAAAAAAACGUCACAAAAACGUCACAUUUGCCUCCCGGGGAAGUGUGAUUUUUUUGUGACAGUCGACAUCACUUUA .............(((.(((((........((((..........))))........................((((((((((.(((((((((.((.....)).))))))))).)))))))))).))))))))....... (-33.30) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 337 76 36 64 22 tfor:TF1948|5end_conserved_hypothetical_protein_2095942..2096172_POSITIVE 328 80 36 157 112 tfor:TF1680|5end_peptide_chain_release_factor_3_1793315..1793545_POSITIVE 324 89 41 64 11 tfor:TF0534|5end_hypothetical_protein_559509..559739_POSITIVE 318 80 34 72 19 tfor:TF2945|5end_DNA-directed_RNA_polymerase_beta'_subunit_3147448..3147678_POSITIVE 310 78 34 78 31 tfor:TF2399|5end_precorrin-2_methyltransferase_2571250..2571480_POSITIVE 304 98 51 185 137 tfor:TF1959|5end_conserved_hypothetical_protein_2109377..2109607_POSITIVE 299 67 32 230 203 tfor:TF3098|5end_conserved_hypothetical_protein_3329913..3330143_POSITIVE 298 87 43 220 166 tfor:TF0780|5end_alpha-L-arabinofuranosidase,_precursor_A_831944..832174_POSITIVE 293 90 41 68 25 tfor:TF2708|5end_DNA_gyrase_subunit_B_2880164..2880394_POSITIVE 290 80 34 64 21 tfor:TF1002|5end_replicative_DNA_helicase_1056620..1056850_POSITIVE 287 70 37 231 187 tfor:TF1660|5end_hypothetical_protein_1775269..1775499_POSITIVE 285 72 38 72 36 tfor:TF0674|5end_transposase_fragment_717199..717429_POSITIVE 284 79 33 230 177 tfor:TF0617|5end_alpha-1,2-mannosidase_650862..651092_POSITIVE 282 69 31 63 25 tfor:TF2218|5end_two-component_system_response_regulator_2390162..2390392_POSITIVE 281 80 38 152 121 tfor:TF2888|5end_50S_ribosomal_protein_L21_3077995..3078225_POSITIVE 281 97 51 143 99 tfor:TF1845|5end_hypothetical_protein_1996620..1996850_POSITIVE 281 67 31 72 30 tfor:TF0091|5end_outer_membrane_protein_97701..97931_POSITIVE 278 55 34 128 103 tfor:TF1763|5end_K+-dependent_Na+/Ca+_exchanger_related-protein_1900406..1900636_POSITIVE 276 86 41 231 189 tfor:TF1200|5end_conserved_hypothetical_protein_1282717..1282947_POSITIVE 275 79 40 98 52 tfor:TF0281|5end_hypothetical_protein_308909..309139_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 371 69 21 77 28 tfor:TF2856|3end_conserved_hypothetical_protein;_possible_TPR-repeat-containing_protein_3043022..3043172_POSITIVE 337 76 36 65 23 tfor:TF1947|3end_conserved_hypothetical_protein_2096023..2096173_POSITIVE 328 80 36 81 36 tfor:TF1679|3end_conserved_hypothetical_protein_1793319..1793469_POSITIVE 323 79 34 48 2 tfor:TF3153|3end_conserved_hypothetical_protein_3389324..3389474_POSITIVE 298 87 43 70 16 tfor:TF0779|3end_possible_outer_membrane_protein_831874..832024_POSITIVE 296 71 37 92 47 tfor:TF1659|3end_hypothetical_protein_1775209..1775359_POSITIVE 285 72 38 148 112 tfor:TF0673|3end_conserved_hypothetical_protein_717355..717505_POSITIVE 281 97 51 136 92 tfor:TF1844|3end_hypothetical_protein_1996693..1996843_POSITIVE 277 79 34 106 64 tfor:TF0596|3end_conserved_hypothetical_protein_628652..628802_POSITIVE 275 79 40 145 99 tfor:TF0280|3end_hypothetical_protein_309036..309186_POSITIVE 273 97 51 92 48 tfor:TF2745|3end_hypothetical_protein_2927947..2928097_POSITIVE 273 68 34 110 61 tfor:TF2480|3end_hypothetical_protein_2657708..2657858_POSITIVE 273 79 34 86 31 tfor:TF2263|3end_transfer_region-related_protein,_TraN_2432964..2433114_POSITIVE 273 78 40 85 39 tfor:TF0287|3end_peptidase,_M23_family_317467..317617_POSITIVE 271 78 35 112 57 tfor:TF0885|3end_conjugative_transposon_protein_fragment_938055..938205_POSITIVE 269 79 39 127 73 tfor:TF3105|3end_hypothetical_protein_3338342..3338492_POSITIVE 266 98 56 110 60 tfor:TF0795|3end_hypothetical_protein_853199..853349_POSITIVE 263 97 51 136 92 tfor:TF1846|3end_hypothetical_protein_1997015..1997165_POSITIVE 263 97 51 126 82 tfor:TF1845|3end_hypothetical_protein_1997005..1997155_POSITIVE 257 79 37 52 7 tfor:TF2498|3end_electron_transfer_flavoprotein,_alpha_subunit_2673885..2674035_POSITIVE