Origin IGS: acctttgcaagaaaacaaaccggatttcacggcagatacaaaacaccgtcagggggtgtgcatacatactcgccccatcgctgtccggcaacacaagaaa .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tttcttgtgttgccggacagcgatggggcgagtatgtatgcacaccccctgacggtgttttgtatctgccgtgaaatccggtttgttttcttgcaaaggt Mask Tandem Repeat Region ================================================ acctttgcaagaaaacaaaccggatttcacggcagatacaaaacaccgtcagggggtgtgcatacatactcgccccatcgctgtccggcaacacaagaaa Find is-nt database================================================ Query_seq: TF0745:TF0744|TF0745:TF0744:conserved hypothetical protein:DNA polymerase III subunit, gamma/tau:->->:791135..791234 100 acctttgcaagaaaacaaaccggatttcacggcagatacaaaacaccgtcagggggtgtgcatacatactcgccccatcgctgtccggcaacacaagaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF0745:TF0744|TF0745:TF0744:conserved hypothetical protein:DNA polymerase III subunit, gamma/tau:->->:791135..791234 100 acctttgcaagaaaacaaaccggatttcacggcagatacaaaacaccgtcagggggtgtgcatacatactcgccccatcgctgtccggcaacacaagaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF0745:TF0744|TF0745:TF0744:conserved hypothetical protein:DNA polymerase III subunit, gamma/tau:->->:791135..791234 100 acctttgcaagaaaacaaaccggatttcacggcagatacaaaacaccgtcagggggtgtgcatacatactcgccccatcgctgtccggcaacacaagaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 acctttgcaagaaaacaaaccggatttcacggcagatacaaaacaccgtcagggggtgtgcatacatactcgccccatcgctgtccggcaacacaagaaa Predict ORF larger than 30AA ================================================ Protein_Len: 32 Strand: + Start: 5 End: 100 .... M Q E N K P D F T A D T K H R Q G V C I H T R P I A V R Q H K K Protein_Len: 31 Strand: - Start: 2 End: 94 . R Q L F V F R I E R C I C F V T L P H A Y M S A G D S D P L M ...... acctttgcaagaaaacaaaccggatttcacggcagatacaaaacaccgtcagggggtgtgcatacatactcgccccatcgctgtccggcaacacaagaaa 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================================================ acctttgcaagaaaacaaaccggatttcacggcagatacaaaacaccgtcagggggtgtgcatacatactcgccccatcgctgtccggcaacacaagaaa Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TF0745:TF0744|TF0745:TF0744:conserved hypothetical protein:DNA polymerase III subunit, gamma/tau:->->:791135..791234 100 acctttgcaagaaaacaaaccggatttcacggcagatacaaaacaccgtcagggggtgtgcatacatactcgccccatcgctgtccggcaacacaagaaa Intra-Species Hit: Count: 1 Min: 1 Max: 100 Len: 100 Subject: tfor_TF0745_TF0744|conserved hypothetical protein:DNA polymerase III subunit, gamma/tau|POSITIVE:POSITIVE|[791135,791234]|100 HSP 1 e-value: 2.0E-50 bit: 198.0 Len: 100 Query Start:1 Query End:100 Subject Strand: POSITIVE Subject Start: 1 Subject End: 100 acctttgcaagaaaacaaaccggatttcacggcagatacaaaacaccgtcagggggtgtgcatacatactcgccccatcgctgtccggcaacacaagaaa acctttgcaagaaaacaaaccggatttcacggcagatacaaaacaccgtcagggggtgtgcatacatactcgccccatcgctgtccggcaacacaagaaa Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACCUUUGCAAGAAAACAAACCGGAUUUCACGGCAGAUACAAAACACCGUCAGGGGGUGUGCAUACAUACUCGCCCCAUCGCUGUCCGGCAACACAAGAAA ...................(((((.....((((.(((..........)))..((((((.(........).))))))...)))))))))............ (-22.70) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUCUUGUGUUGCCGGACAGCGAUGGGGCGAGUAUGUAUGCACACCCCCUGACGGUGUUUUGUAUCUGCCGUGAAAUCCGGUUUGUUUUCUUGCAAAGGU ...........((((((.......((((.(.(((....))).).)))).(.(((((...........))))).)..))))))((((......)))).... (-24.60) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 428 89 45 59 10 tfor:TF2878|5end_conserved_hypothetical_protein;_possible_CAAX_amino_terminal_protease_family_3067304..3067534_POSITIVE 417 89 44 160 113 tfor:TF2375|5end_conserved_hypothetical_protein_2540953..2541183_POSITIVE 412 90 50 53 3 tfor:TF2846|5end_cobyric_acid_synthase_3034896..3035126_POSITIVE 410 76 31 129 81 tfor:TF2241|5end_ATP-dependent_DNA_helicase_2415401..2415631_POSITIVE 387 89 44 155 89 tfor:TF3022|5end_chorismate_synthase_3246136..3246366_POSITIVE 372 80 31 77 24 tfor:TF1203|5end_L-asparaginase_I_1285232..1285462_POSITIVE 369 90 47 100 56 tfor:TF0600|5end_oxidoreductase/dehydrogenase_630083..630313_POSITIVE 368 90 47 45 1 tfor:TF2661|5end_hypothetical_protein_2833509..2833739_POSITIVE 367 86 46 200 159 tfor:TF1767|5end_3-dehydroquinate_synthase_1905492..1905722_POSITIVE 364 56 11 74 29 tfor:TF0882|5end_hypothetical_protein_935919..936149_POSITIVE 363 89 43 67 18 tfor:TF0307|5end_conserved_hypothetical_protein_332783..333013_POSITIVE 362 87 46 226 183 tfor:TF1191|5end_possible_transcriptional_regulator_1273615..1273845_POSITIVE 361 89 47 168 115 tfor:TF2941|5end_50S_ribosomal_protein_L1_3141828..3142058_POSITIVE 358 89 44 187 139 tfor:TF2022|5end_conserved_hypothetical_protein_2178524..2178754_POSITIVE 357 89 42 58 8 tfor:TF0090|5end_conserved_hypothetical_protein_96285..96515_POSITIVE 354 88 46 204 166 tfor:TF0369|5end_hypothetical_protein_385933..386163_POSITIVE 352 89 43 167 113 tfor:TF2357|5end_collagenase_2522561..2522791_POSITIVE 351 90 45 69 8 tfor:TF0799|5end_conserved_hypothetical_protein_855191..855421_POSITIVE 350 89 47 84 26 tfor:TF2979|5end_possible_outer_membrane__protein_3190778..3191008_POSITIVE 347 100 52 98 41 tfor:TF2424|5end_hypothetical_protein_2603032..2603262_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 466 90 46 62 8 tfor:TF2847|3end_hypothetical_protein_3034985..3035135_POSITIVE 410 76 31 65 17 tfor:TF2240|3end__tetracycline_resistance_element_mobilization_regulatory_protein_2415417..2415567_POSITIVE 404 98 51 72 16 tfor:TF3153|3end_conserved_hypothetical_protein_3389324..3389474_POSITIVE 387 89 44 133 67 tfor:TF3021|3end_FKBP-type_peptidyl-prolyl_cis-trans_isomerase_3246194..3246344_POSITIVE 369 90 47 67 23 tfor:TF0599|3end_hypothetical_protein_630130..630280_POSITIVE 364 56 11 68 23 tfor:TF0881|3end_conserved_hypothetical_protein_935993..936143_POSITIVE 361 89 47 150 97 tfor:TF2940|3end_50S_ribosomal_protein_L11_3141890..3142040_POSITIVE 353 80 31 58 10 tfor:TF2342|3end_glutathione_peroxidase_2506639..2506789_POSITIVE 350 89 47 88 30 tfor:TF2978|3end_conserved_hypothetical_protein_3190862..3191012_POSITIVE 347 90 45 50 8 tfor:TF2340|3end_hypothetical_protein_2500915..2501065_POSITIVE 347 90 45 121 72 tfor:TF1846|3end_hypothetical_protein_1997015..1997165_POSITIVE 347 90 45 111 62 tfor:TF1845|3end_hypothetical_protein_1997005..1997155_POSITIVE 343 89 47 51 15 tfor:TF0960|3end_beta-galactosidase_1010506..1010656_POSITIVE 343 89 51 81 42 tfor:TF0541|3end_conserved_hypothetical_protein_571858..572008_POSITIVE 342 90 46 68 3 tfor:TF2488|3end_hypothetical_protein_2664478..2664628_POSITIVE 337 88 46 151 85 tfor:TF0764|3end_conserved_hypothetical_protein;_possible_exopolyphosphatase-related_protein_811371..811521_POSITIVE 331 89 46 57 9 tfor:TF2840|3end_hypothetical_protein_3031289..3031439_POSITIVE 330 85 45 150 107 tfor:TF2610|3end_nitroreductase_2787241..2787391_POSITIVE 330 75 31 112 61 tfor:TF0959|3end_periplasmic_protease_1008540..1008690_POSITIVE 329 88 46 115 70 tfor:TF3022|3end_chorismate_synthase_3247301..3247451_POSITIVE