Origin IGS: tgaacaacagacgctattccccgtgcaccgtcattctttccatttacgatcacaaagatagcccgcccgtcagggccgtttgattttaagatataaataccctccctgctgcgacggataaagctctttcgtataccaaatttaatctctaactttgtcggacgaaaacaggaataacc .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 ggttattcctgttttcgtccgacaaagttagagattaaatttggtatacgaaagagctttatccgtcgcagcagggagggtatttatatcttaaaatcaaacggccctgacgggcgggctatctttgtgatcgtaaatggaaagaatgacggtgcacggggaatagcgtctgttgttca Mask Tandem Repeat Region ================================================ tgaacaacagacgctattccccgtgcaccgtcattctttccatttacgatcacaaagatagcccgcccgtcagggccgtttgattttaagatataaataccctccctgctgcgacggataaagctctttcgtataccaaatttaatctctaactttgtcggacgaaaacaggaataacc Find is-nt database================================================ Query_seq: TF1788:TF1789|TF1788:TF1789:conserved hypothetical protein:conserved hypothetical protein:->->:1930180..1930358 179 tgaacaacagacgctattccccgtgcaccgtcattctttccatttacgatcacaaagatagcccgcccgtcagggccgtttgattttaagatataaataccctccctgctgcgacggataaagctctttcgtataccaaatttaatctctaactttgtcggacgaaaacaggaataacc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF1788:TF1789|TF1788:TF1789:conserved hypothetical protein:conserved hypothetical protein:->->:1930180..1930358 179 tgaacaacagacgctattccccgtgcaccgtcattctttccatttacgatcacaaagatagcccgcccgtcagggccgtttgattttaagatataaataccctccctgctgcgacggataaagctctttcgtataccaaatttaatctctaactttgtcggacgaaaacaggaataacc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF1788:TF1789|TF1788:TF1789:conserved hypothetical protein:conserved hypothetical protein:->->:1930180..1930358 179 tgaacaacagacgctattccccgtgcaccgtcattctttccatttacgatcacaaagatagcccgcccgtcagggccgtttgattttaagatataaataccctccctgctgcgacggataaagctctttcgtataccaaatttaatctctaactttgtcggacgaaaacaggaataacc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tgaacaacagacgctattccccgtgcaccgtcattctttccatttacgatcacaaagatagcccgcccgtcagggccgtttgattttaagatataaataccctccctgctgcgacggataaagctctttcgtataccaaatttaatctctaactttgtcggacgaaaacaggaataacc Predict ORF larger than 30AA ================================================ Protein_Len: 48 Strand: - Start: 3 End: 146 .. V V S A I G R A G D N K G N V I V F I A R G D P G N S K L I Y I G E R S R R I F S K R I G F K M ................................. tgaacaacagacgctattccccgtgcaccgtcattctttccatttacgatcacaaagatagcccgcccgtcagggccgtttgattttaagatataaataccctccctgctgcgacggataaagctctttcgtataccaaatttaatctctaactttgtcggacgaaaacaggaataacc 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================================================ tgaacaacagacgctattccccgtgcaccgtcattctttccatttacgatcacaaagatagcccgcccgtcagggccgtttgattttaagatataaataccctccctgctgcgacggataaagctctttcgtataccaaatttaatctctaactttgtcggacgaaaacaggaataacc Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 70 HP_score: -6.0 Tail_Score: -4.20806 Start: 63 End: 78 Full_Region: GATCACAAAGATAGC CCGCCC GTCA GGGCCG TTTGATTTTAAGATA ..............................................................CCGCCCGTCAGGGCCG..................................................................................................... Find igs database================================================ Query_seq: TF1788:TF1789|TF1788:TF1789:conserved hypothetical protein:conserved hypothetical protein:->->:1930180..1930358 179 tgaacaacagacgctattccccgtgcaccgtcattctttccatttacgatcacaaagatagcccgcccgtcagggccgtttgattttaagatataaataccctccctgctgcgacggataaagctctttcgtataccaaatttaatctctaactttgtcggacgaaaacaggaataacc Intra-Species Hit: Count: 1 Min: 1 Max: 179 Len: 179 Subject: tfor_TF1788_TF1789|conserved hypothetical protein:conserved hypothetical protein|POSITIVE:POSITIVE|[1930180,1930358]|179 HSP 1 e-value: 3.0E-97 bit: 355.0 Len: 179 Query Start:1 Query End:179 Subject Strand: POSITIVE Subject Start: 1 Subject End: 179 tgaacaacagacgctattccccgtgcaccgtcattctttccatttacgatcacaaagatagcccgcccgtcagggccgtttgattttaagatataaataccctccctgctgcgacggataaagctctttcgtataccaaatttaatctctaactttgtcggacgaaaacaggaataacc tgaacaacagacgctattccccgtgcaccgtcattctttccatttacgatcacaaagatagcccgcccgtcagggccgtttgattttaagatataaataccctccctgctgcgacggataaagctctttcgtataccaaatttaatctctaactttgtcggacgaaaacaggaataacc Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGAACAACAGACGCUAUUCCCCGUGCACCGUCAUUCUUUCCAUUUACGAUCACAAAGAUAGCCCGCCCGUCAGGGCCGUUUGAUUUUAAGAUAUAAAUACCCUCCCUGCUGCGACGGAUAAAGCUCUUUCGUAUACCAAAUUUAAUCUCUAACUUUGUCGGACGAAAACAGGAAUAACC ..............((((((.......(((((..........((((.(((((....((..((((........))))..))))))).))))...........(.....)....))))).........((((((....((((.(((.....))).))))....))))))...))))))... (-31.20) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GGUUAUUCCUGUUUUCGUCCGACAAAGUUAGAGAUUAAAUUUGGUAUACGAAAGAGCUUUAUCCGUCGCAGCAGGGAGGGUAUUUAUAUCUUAAAAUCAAACGGCCCUGACGGGCGGGCUAUCUUUGUGAUCGUAAAUGGAAAGAAUGACGGUGCACGGGGAAUAGCGUCUGUUGUUCA .....((((.((((.((..(.((((((.(((.((((......(((((((....).....(((((.((.(....).)))))))..))))))....))))...(.((((....)))).).))).)))))))..)).)))))))).(((..(((((((..........))).))))..))). (-46.30) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 385 79 32 45 1 tfor:TF1589|5end_surface_antigen_BspA_1703189..1703419_POSITIVE 375 131 99 226 188 tfor:TF2729|5end_possible_outer_membrane_protein_2908216..2908446_POSITIVE 366 86 41 60 7 tfor:TF1010|5end_penicillin_binding_protein_2_1064795..1065025_POSITIVE 352 67 21 199 150 tfor:TF3022|5end_chorismate_synthase_3246136..3246366_POSITIVE 349 87 41 188 143 tfor:TF1329|5end_glucose-1-phosphate_thymidyltransferase_1408578..1408808_POSITIVE 348 138 101 66 28 tfor:TF0959|5end_periplasmic_protease_1005218..1005448_POSITIVE 344 79 34 106 44 tfor:TF0841|5end_NADH_dehydrogenase/NAD(P)H_nitroreductase_892165..892395_POSITIVE 341 137 91 152 94 tfor:TF0229|5end_beta-galactosidase_254857..255087_POSITIVE 330 86 46 64 18 tfor:TF1011|5end_cell_division_protein;_rod_shape-determining_protein_1066647..1066877_POSITIVE 329 69 22 230 150 tfor:TF2193|5end_outer_membrane_protein,_TonB_dependent_receptor_2368432..2368662_POSITIVE 326 79 32 45 1 tfor:TF1591|5end_surface_antigen_BspA_1706387..1706617_POSITIVE 323 82 41 69 13 tfor:TF2833|5end_lipid_A_disaccharide_synthase_3023973..3024203_POSITIVE 321 70 21 206 156 tfor:TF2789|5end_enoyl-[acyl-carrier-protein]_reductase_2972431..2972661_POSITIVE 320 137 107 49 14 tfor:TF1289|5end_ribosomal_protein_L11_methyltransferase_1370302..1370532_POSITIVE 318 126 101 40 13 tfor:TF2747|5end_heat_shock_protein,_HSP90_family_2928279..2928509_POSITIVE 318 80 32 215 155 tfor:TF2655|5end_DNA_topoisomerase_I_2824543..2824773_POSITIVE 318 120 71 65 8 tfor:TF2529|5end_nucleotidyl_transferase_family;_possible_mannose-1-phosphate_guanyltransferase_2710670..2710900_POSITIVE 318 69 21 153 106 tfor:TF1891|5end_hypothetical_protein_2043389..2043619_POSITIVE 317 109 61 217 175 tfor:TF2048|5end_conserved_hypothetical_protein_2210643..2210873_POSITIVE 317 79 36 206 154 tfor:TF0955|5end_conserved_hypothetical_protein_999215..999445_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 366 86 41 70 17 tfor:TF1009|3end_conserved_hypothetical_protein;_posible_rod-shape_determining_protein,_MreD_1064885..1065035_POSITIVE 330 86 46 71 25 tfor:TF1010|3end_penicillin_binding_protein_2_1066734..1066884_POSITIVE 327 40 1 137 92 tfor:TF1292|3end_sensor_histidine_protein_kinase_1374554..1374704_POSITIVE 318 80 32 151 91 tfor:TF2654|3end_arginyl-tRNA_synthetase_2824559..2824709_POSITIVE 318 120 71 64 7 tfor:TF2527|3end_RNA_polymerase_ECF-type_sigma_factor_2710749..2710899_POSITIVE 312 78 34 142 80 tfor:TF3021|3end_FKBP-type_peptidyl-prolyl_cis-trans_isomerase_3246194..3246344_POSITIVE 312 149 101 97 42 tfor:TF1558|3end_possible_heme_biosynthesis_protein_1665959..1666109_POSITIVE 304 76 31 150 88 tfor:TF2635|3end_ABC_transporter,_ATP-binding_protein/permease_component_2806101..2806251_POSITIVE 303 41 12 63 24 tfor:TF2311|3end_conserved_hypothetical_protein_2471612..2471762_POSITIVE 301 83 46 98 58 tfor:TF2152|3end_uronate_isomerase_2328061..2328211_POSITIVE 295 129 90 97 48 tfor:TF1190|3end_conserved_hypothetical_protein;_possible_membrane_protein_1273707..1273857_POSITIVE 291 110 63 62 6 tfor:TF0382|3end_transcription_termination_factor_405228..405378_POSITIVE 288 76 31 104 47 tfor:TF1295|3end_conserved_hypothetical_protein_1377256..1377406_POSITIVE 288 133 100 149 110 tfor:TF1273|3end_hypothetical_protein_1357462..1357612_POSITIVE 287 132 98 77 41 tfor:TF2515|3end_outer_membrane_protein,_TonB_dependent_receptor_2694865..2695015_POSITIVE 285 119 72 92 53 tfor:TF2547|3end_hypothetical_protein_2730947..2731097_POSITIVE 285 80 32 86 34 tfor:TF1326|3end_hypothetical_protein_1404100..1404250_POSITIVE 284 78 40 47 1 tfor:TF2160|3end_magnesium_chelatase,_subunit_I_2337049..2337199_POSITIVE 284 109 64 53 18 tfor:TF1588|3end_hypothetical_protein_1702560..1702710_POSITIVE 283 78 33 146 94 tfor:TF2878|3end_conserved_hypothetical_protein;_possible_CAAX_amino_terminal_protease_family_3068283..3068433_POSITIVE