Origin IGS: taaaaaagaattacgtgtctaagcggatcacttcccttttgtttttccattcgtcgcaaagcgcggggtatacggaagagaagaatcttcaccccgacgtcgagcagcagcgaaatcctttgtatca .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tgatacaaaggatttcgctgctgctcgacgtcggggtgaagattcttctcttccgtataccccgcgctttgcgacgaatggaaaaacaaaagggaagtgatccgcttagacacgtaattctttttta Mask Tandem Repeat Region ================================================ taaaaaagaattacgtgtctaagcggatcacttcccttttgtttttccattcgtcgcaaagcgcggggtatacggaagagaagaatcttcaccccgacgtcgagcagcagcgaaatcctttgtatca Find is-nt database================================================ Query_seq: TF0228:TF0229|TF0228:TF0229:probable integral outer membrane protein:beta-galactosidase:->->:254870..254996 127 taaaaaagaattacgtgtctaagcggatcacttcccttttgtttttccattcgtcgcaaagcgcggggtatacggaagagaagaatcttcaccccgacgtcgagcagcagcgaaatcctttgtatca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF0228:TF0229|TF0228:TF0229:probable integral outer membrane protein:beta-galactosidase:->->:254870..254996 127 taaaaaagaattacgtgtctaagcggatcacttcccttttgtttttccattcgtcgcaaagcgcggggtatacggaagagaagaatcttcaccccgacgtcgagcagcagcgaaatcctttgtatca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF0228:TF0229|TF0228:TF0229:probable integral outer membrane protein:beta-galactosidase:->->:254870..254996 127 taaaaaagaattacgtgtctaagcggatcacttcccttttgtttttccattcgtcgcaaagcgcggggtatacggaagagaagaatcttcaccccgacgtcgagcagcagcgaaatcctttgtatca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taaaaaagaattacgtgtctaagcggatcacttcccttttgtttttccattcgtcgcaaagcgcggggtatacggaagagaagaatcttcaccccgacgtcgagcagcagcgaaatcctttgtatca Predict ORF larger than 30AA ================================================ Protein_Len: 37 Strand: + Start: 15 End: 125 .............. M S K R I T S L L F F H S S Q S A G Y T E E K N L H P D V E Q Q R N P L Y .. Protein_Len: 39 Strand: + Start: 10 End: 126 ......... M T C L S G S L P F C F S I R R K A R G I R K R R I F T P T S S S S E I L C I . Protein_Len: 41 Strand: - Start: 3 End: 125 .. F L I V H R L P D S G K Q K E M R R L A R P I R F L L I K V G V D L L L S I R Q M .. taaaaaagaattacgtgtctaagcggatcacttcccttttgtttttccattcgtcgcaaagcgcggggtatacggaagagaagaatcttcaccccgacgtcgagcagcagcgaaatcctttgtatca 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================================================ taaaaaagaattacgtgtctaagcggatcacttcccttttgtttttccattcgtcgcaaagcgcggggtatacggaagagaagaatcttcaccccgacgtcgagcagcagcgaaatcctttgtatca Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TF0228:TF0229|TF0228:TF0229:probable integral outer membrane protein:beta-galactosidase:->->:254870..254996 127 taaaaaagaattacgtgtctaagcggatcacttcccttttgtttttccattcgtcgcaaagcgcggggtatacggaagagaagaatcttcaccccgacgtcgagcagcagcgaaatcctttgtatca Intra-Species Hit: Count: 1 Min: 1 Max: 127 Len: 127 Subject: tfor_TF0228_TF0229|probable integral outer membrane protein:beta-galactosidase|POSITIVE:POSITIVE|[254870, 254996]|127 HSP 1 e-value: 2.0E-66 bit: 252.0 Len: 127 Query Start:1 Query End:127 Subject Strand: POSITIVE Subject Start: 1 Subject End: 127 taaaaaagaattacgtgtctaagcggatcacttcccttttgtttttccattcgtcgcaaagcgcggggtatacggaagagaagaatcttcaccccgacgtcgagcagcagcgaaatcctttgtatca taaaaaagaattacgtgtctaagcggatcacttcccttttgtttttccattcgtcgcaaagcgcggggtatacggaagagaagaatcttcaccccgacgtcgagcagcagcgaaatcctttgtatca Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAAAAAGAAUUACGUGUCUAAGCGGAUCACUUCCCUUUUGUUUUUCCAUUCGUCGCAAAGCGCGGGGUAUACGGAAGAGAAGAAUCUUCACCCCGACGUCGAGCAGCAGCGAAAUCCUUUGUAUCA .......(((..(((.....(((.(((.....)))))).)))..)))..(((((.((...(((((((((.....(((((......))))))))))).)))......)).)))))............. (-31.30) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGAUACAAAGGAUUUCGCUGCUGCUCGACGUCGGGGUGAAGAUUCUUCUCUUCCGUAUACCCCGCGCUUUGCGACGAAUGGAAAAACAAAAGGGAAGUGAUCCGCUUAGACACGUAAUUCUUUUUUA ......((((((((.((.(((((..((....(((((((((((......))))).....))))))((((((.(......((......))...).))))))...))..))).)))).)))))))).... (-29.40) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 426 78 35 230 180 tfor:TF0751|5end_dipeptidyl_peptidase_IV_798663..798893_POSITIVE 423 99 53 223 180 tfor:TF3027|5end_zinc_metalloprotease_3250223..3250453_POSITIVE 401 99 51 112 55 tfor:TF2246|5end_hypothetical_protein_2421288..2421518_POSITIVE 397 70 24 64 15 tfor:TF0470|5end_hypothetical_protein_487253..487483_POSITIVE 389 70 24 159 110 tfor:TF1579|5end_hypothetical_protein_1686889..1687119_POSITIVE 373 78 35 214 170 tfor:TF0098|5end_permease_108103..108333_POSITIVE 361 99 52 166 127 tfor:TF1681|5end_dTDP-4-keto-L-rhamnose_reductase_1794904..1795134_POSITIVE 352 117 91 34 2 tfor:TF2913|5end_conserved_hypothetical_protein_3107910..3108140_POSITIVE 350 110 61 82 24 tfor:TF1201|5end_possible_preprotein_translocase_1283732..1283962_POSITIVE 350 118 71 212 151 tfor:TF0763|5end_chromate_transport_protein_809675..809905_POSITIVE 347 96 52 88 30 tfor:TF1436|5end_phosphoglycolate_phosphatase_1521128..1521358_POSITIVE 347 109 63 213 159 tfor:TF0923|5end_tetracycline_resistance_element_mobilization_regulatory_protein_961256..961486_POSITIVE 347 107 61 175 131 tfor:TF0692|5end_conserved_hypothetical_protein_736379..736609_POSITIVE 346 80 35 103 51 tfor:TF2653|5end_hypothetical_protein_2822093..2822323_POSITIVE 345 108 61 149 102 tfor:TF2809|5end_conserved_hypothetical_protein;_possible_translation_factor_(SUA5)_2999832..3000062_POSITIVE 345 117 72 194 144 tfor:TF2712|5end_glycosyltransferase_2885918..2886148_POSITIVE 345 80 31 177 118 tfor:TF1886|5end_auxin-regulated_protein_2038720..2038950_POSITIVE 342 110 61 175 117 tfor:TF2252|5end_transfer_region-related_protein,_TraF_2424621..2424851_POSITIVE 341 70 22 196 137 tfor:TF1049|5end_cobyrinic_acid_a,c-diamide_synthase_1110140..1110370_POSITIVE 340 110 61 53 7 tfor:TF2039|5end_possible_cell-cycle_regulation_histidine_triad_(HIT)_protein_2199318..2199548_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 433 117 85 44 3 tfor:TF2912|3end_hypothetical_protein_3108000..3108150_POSITIVE 419 100 52 81 25 tfor:TF1730|3end_diaminopimelate_decarboxylase_1855907..1856057_POSITIVE 369 98 52 151 97 tfor:TF1732|3end_conserved_hypothetical_protein_1855979..1856129_POSITIVE 361 99 52 151 112 tfor:TF1680|3end_peptide_chain_release_factor_3_1794969..1795119_POSITIVE 350 110 61 68 10 tfor:TF1200|3end_conserved_hypothetical_protein_1283798..1283948_POSITIVE 348 110 61 138 63 tfor:TF1181|3end_methylated-DNA--[protein]-cysteine_S-methyltransferase_1267991..1268141_POSITIVE 346 80 31 52 1 tfor:TF2652|3end_hypothetical_protein_2822122..2822272_POSITIVE 346 99 51 119 62 tfor:TF2336|3end_conserved_hypothetical_protein_2498159..2498309_POSITIVE 345 108 61 146 99 tfor:TF2808|3end_bacterial_sugar_transferase_2999909..3000059_POSITIVE 345 80 31 128 69 tfor:TF1885|3end_conserved_hypothetical_protein_2038751..2038901_POSITIVE 339 110 72 108 54 tfor:TF2991|3end_conserved_hypothetical_protein_3209107..3209257_POSITIVE 336 99 51 148 106 tfor:TF0889|3end_conjugative_transposon_protein,_TraO_940078..940228_POSITIVE 335 106 64 61 11 tfor:TF0425|3end_outer_membrane_protein_444705..444855_POSITIVE 334 69 23 61 23 tfor:TF0583|3end_possible_gliding_motility-related_protein_613829..613979_POSITIVE 332 113 73 123 71 tfor:TF2654|3end_arginyl-tRNA_synthetase_2824559..2824709_POSITIVE 325 110 61 114 40 tfor:TF0064|3end_conserved_hypothetical_protein_70412..70562_POSITIVE 322 96 59 71 31 tfor:TF0234|3end_5,10-methylenetetrahydrofolate_reductase_261512..261662_POSITIVE 320 108 61 117 52 tfor:TF0141|3end_exodeoxyribonuclease_VII,_large_subunit_149830..149980_POSITIVE 319 70 21 135 81 tfor:TF0350|3end_hypothetical_protein_371101..371251_POSITIVE 315 108 61 74 44 tfor:TF0472|3end_multidrug_resistance_protein,_AcrB/AcrD/AcrF_family_(cation_efflux_pump)_491057..491207_POSITIVE