Origin IGS: ttttaattttgtttttatagttaagtaatatgtttcccaaaatcaacgatgattttgagcgtacaaaaatacagaaatttaccgtactacccatgcatcgttcaagaatcctgtaaaattattccgaaaaaaaaagaaaaagcttttttttatacatgcgttgaagaaattcggaaaaacacacatca .........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 tgatgtgtgtttttccgaatttcttcaacgcatgtataaaaaaaagctttttctttttttttcggaataattttacaggattcttgaacgatgcatgggtagtacggtaaatttctgtatttttgtacgctcaaaatcatcgttgattttgggaaacatattacttaactataaaaacaaaattaaaa Mask Tandem Repeat Region ================================================ ttttaattttgtttttatagttaagtaatatgtttcccaaaatcaacgatgattttgagcgtacaaaaatacagaaatttaccgtactacccatgcatcgttcaagaatcctgtaaaattattccgaaaaaaaaagaaaaagcttttttttatacatgcgttgaagaaattcggaaaaacacacatca Find is-nt database================================================ Query_seq: TF0515:TF0516|TF0515:TF0516:conserved hypothetical protein:conserved hypothetical protein; possible membrane protein:->->:539636..539823 188 ttttaattttgtttttatagttaagtaatatgtttcccaaaatcaacgatgattttgagcgtacaaaaatacagaaatttaccgtactacccatgcatcgttcaagaatcctgtaaaattattccgaaaaaaaaagaaaaagcttttttttatacatgcgttgaagaaattcggaaaaacacacatca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF0515:TF0516|TF0515:TF0516:conserved hypothetical protein:conserved hypothetical protein; possible membrane protein:->->:539636..539823 188 ttttaattttgtttttatagttaagtaatatgtttcccaaaatcaacgatgattttgagcgtacaaaaatacagaaatttaccgtactacccatgcatcgttcaagaatcctgtaaaattattccgaaaaaaaaagaaaaagcttttttttatacatgcgttgaagaaattcggaaaaacacacatca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF0515:TF0516|TF0515:TF0516:conserved hypothetical protein:conserved hypothetical protein; possible membrane protein:->->:539636..539823 188 ttttaattttgtttttatagttaagtaatatgtttcccaaaatcaacgatgattttgagcgtacaaaaatacagaaatttaccgtactacccatgcatcgttcaagaatcctgtaaaattattccgaaaaaaaaagaaaaagcttttttttatacatgcgttgaagaaattcggaaaaacacacatca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ttttaattttgtttttatagttaagtaatatgtttcccaaaatcaacgatgattttgagcgtacaaaaatacagaaatttaccgtactacccatgcatcgttcaagaatcctgtaaaattattccgaaaaaaaaagaaaaagcttttttttatacatgcgttgaagaaattcggaaaaacacacatca Predict ORF larger than 30AA ================================================ Protein_Len: 53 Strand: + Start: 28 End: 186 ........................... M C F P K S T M I L S V Q K Y R N L P Y Y P C I V Q E S C K I I P K K K E K A F F Y T C V E E I R K N T H .. Protein_Len: 37 Strand: + Start: 77 End: 187 ............................................................................ M Y R T T H A S F K N P V K L F R K K K K K L F F I H A L K K F G K T H I . Protein_Len: 35 Strand: - Start: 82 End: 186 ................................................................................. R V V W A D N L F G T F N N R F F F F F S K K I C A N F F N P F V C M .. Protein_Len: 36 Strand: - Start: 2 End: 109 . K I K N K Y N L L I N G L I L S S K S R V F I C F N V T S G M C R E L M ............................................................................... ttttaattttgtttttatagttaagtaatatgtttcccaaaatcaacgatgattttgagcgtacaaaaatacagaaatttaccgtactacccatgcatcgttcaagaatcctgtaaaattattccgaaaaaaaaagaaaaagcttttttttatacatgcgttgaagaaattcggaaaaacacacatca 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================================================ ttttaattttgtttttatagttaagtaatatgtttcccaaaatcaacgatgattttgagcgtacaaaaatacagaaatttaccgtactacccatgcatcgttcaagaatcctgtaaaattattccgaaaaaaaaagaaaaagcttttttttatacatgcgttgaagaaattcggaaaaacacacatca Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TF0515:TF0516|TF0515:TF0516:conserved hypothetical protein:conserved hypothetical protein; possible membrane protein:->->:539636..539823 188 ttttaattttgtttttatagttaagtaatatgtttcccaaaatcaacgatgattttgagcgtacaaaaatacagaaatttaccgtactacccatgcatcgttcaagaatcctgtaaaattattccgaaaaaaaaagaaaaagcttttttttatacatgcgttgaagaaattcggaaaaacacacatca Intra-Species Hit: Count: 1 Min: 1 Max: 188 Len: 188 Subject: tfor_TF0515_TF0516|conserved hypothetical protein:conserved hypothetical protein; possible membrane protein|POSITIVE:POSITIVE|[539636,539823]|188 HSP 1 e-value: 1.0E-65 bit: 250.0 Len: 126 Query Start:1 Query End:126 Subject Strand: POSITIVE Subject Start: 1 Subject End: 126 ttttaattttgtttttatagttaagtaatatgtttcccaaaatcaacgatgattttgagcgtacaaaaatacagaaatttaccgtactacccatgcatcgttcaagaatcctgtaaaattattccg.............................................................. ttttaattttgtttttatagttaagtaatatgtttcccaaaatcaacgatgattttgagcgtacaaaaatacagaaatttaccgtactacccatgcatcgttcaagaatcctgtaaaattattccg.............................................................. HSP 2 e-value: 2.0E-12 bit: 73.8 Len: 37 Query Start:152 Query End:188 Subject Strand: POSITIVE Subject Start: 152 Subject End: 188 .......................................................................................................................................................atacatgcgttgaagaaattcggaaaaacacacatca .......................................................................................................................................................atacatgcgttgaagaaattcggaaaaacacacatca Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUUAAUUUUGUUUUUAUAGUUAAGUAAUAUGUUUCCCAAAAUCAACGAUGAUUUUGAGCGUACAAAAAUACAGAAAUUUACCGUACUACCCAUGCAUCGUUCAAGAAUCCUGUAAAAUUAUUCCGAAAAAAAAAGAAAAAGCUUUUUUUUAUACAUGCGUUGAAGAAAUUCGGAAAAACACACAUCA .........(((((((.((((...((((...(((((.((((((((....))))))))...(((......))).)))))))))...))))...((((((.((....((((..(.....)..))))...(((((((((......)))))))))..)))))))).(((....)))..)))))))....... (-27.00) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGAUGUGUGUUUUUCCGAAUUUCUUCAACGCAUGUAUAAAAAAAAGCUUUUUCUUUUUUUUUCGGAAUAAUUUUACAGGAUUCUUGAACGAUGCAUGGGUAGUACGGUAAAUUUCUGUAUUUUUGUACGCUCAAAAUCAUCGUUGAUUUUGGGAAACAUAUUACUUAACUAUAAAAACAAAAUUAAAA ((((((((...((((((((.....((((((..((((.(((((((((......)))))))))............)))).((((.((((.((.((((.....(((((((.......)))))))..)))))).))))))))..)))))).))))))))))))))))......................... (-37.12) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 307 128 82 182 129 tfor:TF2487|5end_transposase_2663010..2663240_POSITIVE 298 90 43 59 15 tfor:TF0292|5end_conserved_hypothetical_protein_320087..320317_POSITIVE 290 102 77 157 122 tfor:TF0330|5end_excinuclease_ABC,_subunit_A_356196..356426_POSITIVE 246 116 71 43 3 tfor:TF2511|5end_RNA_binding_protein_2689910..2690140_POSITIVE 246 75 34 77 36 tfor:TF0312|5end_outer_membrane_protein_336473..336703_POSITIVE 243 127 83 144 110 tfor:TF2712|5end_glycosyltransferase_2885918..2886148_POSITIVE 242 117 71 166 107 tfor:TF1538|5end_conserved_hypothetical_protein_1643531..1643761_POSITIVE 241 127 83 190 147 tfor:TF2900|5end_conserved_hypothetical_protein_3088252..3088482_POSITIVE 239 126 87 200 160 tfor:TF3055|5end_hypothetical_protein_3278775..3279005_POSITIVE 237 120 82 98 60 tfor:TF0070|5end_possible_regulatory_element_76942..77172_POSITIVE 236 114 83 113 85 tfor:TF2986|5end_conserved_hypothetical_protein;_possible_glycosyltransferase_3201818..3202048_POSITIVE 236 103 82 230 205 tfor:TF2373|5end_UDP-3-O-acyl-GlcNAc_deacetylase_2538344..2538574_POSITIVE 236 125 82 64 27 tfor:TF2186|5end_outer_membrane_protein_2360291..2360521_POSITIVE 235 100 54 153 115 tfor:TF2375|5end_conserved_hypothetical_protein_2540953..2541183_POSITIVE 234 126 82 61 15 tfor:TF2120|5end_holliday_junction_endonuclease_2292108..2292338_POSITIVE 233 70 30 56 19 tfor:TF3039|5end_ABC_transporter,_ATP-binding_protein_3265731..3265961_POSITIVE 232 99 57 217 163 tfor:TF2649|5end_fumarate_reductase/succinate_dehydrogenase,_flavoprotein_subunit_2819002..2819232_POSITIVE 232 128 83 201 153 tfor:TF2403|5end_outer_membrane_protein,_TonB_dependent_receptor_2576159..2576389_POSITIVE 232 127 81 134 94 tfor:TF0816|5end_hypothetical_protein_874217..874447_POSITIVE 231 100 52 230 190 tfor:TF0302|5end_FKBP-type_peptidyl-prolyl_cis-trans_isomerase_328641..328871_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 290 102 77 121 86 tfor:TF0329|3end_membrane-bound_lytic_murein_transglycosylase_D_356240..356390_POSITIVE 243 127 83 151 117 tfor:TF2711|3end_hemolysis_secretion_protein_2886005..2886155_POSITIVE 236 125 82 49 12 tfor:TF2185|3end_outer_membrane_protein,_TonB_dependent_receptor_2360356..2360506_POSITIVE 234 126 82 61 15 tfor:TF2119|3end_conserved_hypothetical_protein_2292188..2292338_POSITIVE 233 70 30 44 7 tfor:TF3038|3end_conserved_hypothetical_protein_3265799..3265949_POSITIVE 227 126 81 109 65 tfor:TF2789|3end_enoyl-[acyl-carrier-protein]_reductase_2973365..2973515_POSITIVE 226 111 72 113 81 tfor:TF2891|3end_lipoprotein_3079381..3079531_POSITIVE 226 112 73 103 59 tfor:TF2447|3end_lipoprotein_2624990..2625140_POSITIVE 225 126 83 66 18 tfor:TF0635|3end_glucosylceramidase_precursor_670758..670908_POSITIVE 222 162 124 79 34 tfor:TF1753|3end_topoisomerase_IV_subunit_A_1890993..1891143_POSITIVE 221 112 72 134 89 tfor:TF3150|3end_conserved_hypothetical_protein_3386245..3386395_POSITIVE 219 85 43 150 101 tfor:TF2772|3end_tRNA_pseudouridine_synthase_B_2958179..2958329_POSITIVE 216 126 82 144 100 tfor:TF0041|3end_outer_membrane_protein,_TonB_dependent_receptor_45942..46092_POSITIVE 214 128 81 83 41 tfor:TF2879|3end_tRNA_(guanine-N-1)-methyltransferase_3069008..3069158_POSITIVE 213 126 82 119 78 tfor:TF1697|3end_mobilizable_transposon,_excision_protein_1819293..1819443_POSITIVE 212 92 55 67 28 tfor:TF2156|3end_conserved_hypothetical_protein;_possible_protease_2333005..2333155_POSITIVE 212 128 81 64 3 tfor:TF1236|3end_L-rhamnose_isomerase_1322106..1322256_POSITIVE 211 175 156 53 34 tfor:TF2077|3end_conserved_hypothetical_protein;_possible_chromosome_segregation_ATPase_2244363..2244513_POSITIVE 211 77 32 76 17 tfor:TF1921|3end_hypothetical_protein_2072051..2072201_POSITIVE 211 113 82 143 112 tfor:TF0193|3end_conserved_hypothetical_protein;_possible_internalin-like_protein_(LPXTG_motif)_215240..215390_POSITIVE