Origin IGS: cctttagctctttatatgccgctgacacctcgctccccataattgacggttccggtgtgctctatgtcaaatagcccccccccgtactgtccgattgatgtatgttcccagtttgaaattttctacaagacttgtttctcttactttttgccacacaaaatacaactacaactatatttctttcaggtataacactttgcacaaccta .........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 taggttgtgcaaagtgttatacctgaaagaaatatagttgtagttgtattttgtgtggcaaaaagtaagagaaacaagtcttgtagaaaatttcaaactgggaacatacatcaatcggacagtacgggggggggctatttgacatagagcacaccggaaccgtcaattatggggagcgaggtgtcagcggcatataaagagctaaagg Mask Tandem Repeat Region ================================================ cctttagctctttatatgccgctgacacctcgctccccataattgacggttccggtgtgctctatgtcaaatagcccccccccgtactgtccgattgatgtatgttcccagtttgaaattttctacaagacttgtttctcttactttttgccacacaaaatacaactacaactatatttctttcaggtataacactttgcacaaccta Find is-nt database================================================ Query_seq: TF2058:TF2059|TF2058:TF2059:possible ATP-dependent DNA helicase:asparagine synthase, glutamine-hydrolyzing:->->:2223859..2224066 208 cctttagctctttatatgccgctgacacctcgctccccataattgacggttccggtgtgctctatgtcaaatagcccccccccgtactgtccgattgatgtatgttcccagtttgaaattttctacaagacttgtttctcttactttttgccacacaaaatacaactacaactatatttctttcaggtataacactttgcacaaccta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF2058:TF2059|TF2058:TF2059:possible ATP-dependent DNA helicase:asparagine synthase, glutamine-hydrolyzing:->->:2223859..2224066 208 cctttagctctttatatgccgctgacacctcgctccccataattgacggttccggtgtgctctatgtcaaatagcccccccccgtactgtccgattgatgtatgttcccagtttgaaattttctacaagacttgtttctcttactttttgccacacaaaatacaactacaactatatttctttcaggtataacactttgcacaaccta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF2058:TF2059|TF2058:TF2059:possible ATP-dependent DNA helicase:asparagine synthase, glutamine-hydrolyzing:->->:2223859..2224066 208 cctttagctctttatatgccgctgacacctcgctccccataattgacggttccggtgtgctctatgtcaaatagcccccccccgtactgtccgattgatgtatgttcccagtttgaaattttctacaagacttgtttctcttactttttgccacacaaaatacaactacaactatatttctttcaggtataacactttgcacaaccta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 cctttagctctttatatgccgctgacacctcgctccccataattgacggttccggtgtgctctatgtcaaatagcccccccccgtactgtccgattgatgtatgttcccagtttgaaattttctacaagacttgtttctcttactttttgccacacaaaatacaactacaactatatttctttcaggtataacactttgcacaaccta Predict ORF larger than 30AA ================================================ Protein_Len: 49 Strand: + Start: 43 End: 189 .......................................... M T V P V C S M S N S P P P Y C P I D V C S Q F E I F Y K T C F S Y F L P H K I Q L Q L Y F F Q V ................... Protein_Len: 46 Strand: + Start: 71 End: 208 ...................................................................... M A P P R T V R L M Y V P S L K F S T R L V S L T F C H T K Y N Y N Y I S F R Y N T L H N L Protein_Len: 32 Strand: - Start: 70 End: 165 ..................................................................... I A G G R V T R N I Y T G L K F N E V L S T E R V K Q W V F Y M ........................................... Protein_Len: 46 Strand: - Start: 65 End: 202 ................................................................ T L Y G G G T S D S Q H I N G T Q F K R C S K N R K S K A V C F V V V V I N R E P I V S Q M ...... Protein_Len: 35 Strand: - Start: 15 End: 119 .............. I G S V G R E G Y N V T G T H E I D F L G G G Y Q G I S T H E W N S M ......................................................................................... cctttagctctttatatgccgctgacacctcgctccccataattgacggttccggtgtgctctatgtcaaatagcccccccccgtactgtccgattgatgtatgttcccagtttgaaattttctacaagacttgtttctcttactttttgccacacaaaatacaactacaactatatttctttcaggtataacactttgcacaaccta 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================================================ cctttagctctttatatgccgctgacacctcgctccccataattgacggttccggtgtgctctatgtcaaatagcccccccccgtactgtccgattgatgtatgttcccagtttgaaattttctacaagacttgtttctcttactttttgccacacaaaatacaactacaactatatttctttcaggtataacactttgcacaaccta Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TF2058:TF2059|TF2058:TF2059:possible ATP-dependent DNA helicase:asparagine synthase, glutamine-hydrolyzing:->->:2223859..2224066 208 cctttagctctttatatgccgctgacacctcgctccccataattgacggttccggtgtgctctatgtcaaatagcccccccccgtactgtccgattgatgtatgttcccagtttgaaattttctacaagacttgtttctcttactttttgccacacaaaatacaactacaactatatttctttcaggtataacactttgcacaaccta Intra-Species Hit: Count: 1 Min: 1 Max: 208 Len: 208 Subject: tfor_TF2058_TF2059|possible ATP-dependent DNA helicase:asparagine synthase, glutamine-hydrolyzing|POSITIVE:POSITIVE|[2223859, 2224066]|208 HSP 1 e-value: 2.0E-98 bit: 359.0 Len: 208 Query Start:1 Query End:208 Subject Strand: POSITIVE Subject Start: 1 Subject End: 208 cctttagctctttatatgccgctgacacctcgctccccataattgacggttccggtgtgctctatgtcaaatagnnnnnnnnngtactgtccgattgatgtatgttcccagtttgaaattttctacaagacttgtttctcttactttttgccacacaaaatacaactacaactatatttctttcaggtataacactttgcacaaccta cctttagctctttatatgccgctgacacctcgctccccataattgacggttccggtgtgctctatgtcaaatagcccccccccgtactgtccgattgatgtatgttcccagtttgaaattttctacaagacttgtttctcttactttttgccacacaaaatacaactacaactatatttctttcaggtataacactttgcacaaccta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CCUUUAGCUCUUUAUAUGCCGCUGACACCUCGCUCCCCAUAAUUGACGGUUCCGGUGUGCUCUAUGUCAAAUAGCCCCCCCCCGUACUGUCCGAUUGAUGUAUGUUCCCAGUUUGAAAUUUUCUACAAGACUUGUUUCUCUUACUUUUUGCCACACAAAAUACAACUACAACUAUAUUUCUUUCAGGUAUAACACUUUGCACAACCUA ......((......((((((........................((((((..(((......((((.....)))).......))).)))))).((..((.(((((((...((((.(((((..((.....))...))))).......(((((.....)))))...))))..))).)))).))..)).)))))).......))........ (-29.24) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAGGUUGUGCAAAGUGUUAUACCUGAAAGAAAUAUAGUUGUAGUUGUAUUUUGUGUGGCAAAAAGUAAGAGAAACAAGUCUUGUAGAAAAUUUCAAACUGGGAACAUACAUCAAUCGGACAGUACGGGGGGGGGCUAUUUGACAUAGAGCACACCGGAACCGUCAAUUAUGGGGAGCGAGGUGUCAGCGGCAUAUAAAGAGCUAAAGG ..(((.((((....((((((((......(((((((((......))))))))))))))))).................(((..((((....(..(..((((...................))))...)..)....))))..))).....)))))))....((((.....))))..(((...((((.....)))).......)))..... (-41.41) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 405 59 17 47 4 tfor:TF0038|5end_conserved_hypothetical_protein_39907..40137_POSITIVE 399 79 32 220 171 tfor:TF2772|5end_tRNA_pseudouridine_synthase_B_2957383..2957613_POSITIVE 392 83 44 231 185 tfor:TF2322|5end_conserved_hypothetical_protein;_possible_lipoprotein_2482743..2482973_POSITIVE 390 60 15 67 23 tfor:TF2853|5end_2-C-methyl-D-erythritol_2,4-cyclodiphosphate_synthase_3040172..3040402_POSITIVE 384 100 52 68 19 tfor:TF0462|5end_possible_cobalamin_biosynthesis_precorrin-3_methylase_477600..477830_POSITIVE 376 96 52 147 83 tfor:TF2487|5end_transposase_2663010..2663240_POSITIVE 376 80 31 220 178 tfor:TF1064|5end_ampG_permease_1134004..1134234_POSITIVE 374 59 17 108 67 tfor:TF2159|5end_conserved_hypothetical_protein_2334446..2334676_POSITIVE 368 98 51 223 165 tfor:TF2561|5end_50S_ribosomal_protein_L16_2738693..2738923_POSITIVE 365 60 20 65 18 tfor:TF1293|5end_ATPase,_possible_AAA_superfamily_1374579..1374809_POSITIVE 354 100 53 68 28 tfor:TF0970|5end_2-keto-3-deoxygluconate_kinase_1020396..1020626_POSITIVE 352 89 42 224 168 tfor:TF2307|5end_two-component_system_sensor_histidine_kinase/response_2462618..2462848_POSITIVE 348 66 21 86 24 tfor:TF2898|5end_conserved_hypothetical_protein_3087061..3087291_POSITIVE 348 67 21 199 148 tfor:TF1531|5end_potassium_uptake_protein_1636534..1636764_POSITIVE 343 59 17 60 28 tfor:TF3046|5end_hypothetical_protein_3274948..3275178_POSITIVE 343 80 31 101 32 tfor:TF1010|5end_penicillin_binding_protein_2_1064795..1065025_POSITIVE 340 68 21 220 169 tfor:TF1831|5end_conserved_hypothetical_protein_1980365..1980595_POSITIVE 338 60 17 66 13 tfor:TF0491|5end_conserved_hypothetical_protein_513827..514057_POSITIVE 334 97 52 160 118 tfor:TF2043|5end_fructokinase_2202267..2202497_POSITIVE 334 60 17 61 3 tfor:TF0538|5end_hypothetical_protein_566891..567121_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 433 86 44 68 19 tfor:TF2321|3end_hypothetical_protein_2482657..2482807_POSITIVE 405 59 17 51 8 tfor:TF0037|3end_sialic_acid-specific_9-O-acetylesterase_39991..40141_POSITIVE 343 80 31 111 42 tfor:TF1009|3end_conserved_hypothetical_protein;_posible_rod-shape_determining_protein,_MreD_1064885..1065035_POSITIVE 338 60 17 63 10 tfor:TF0490|3end_conserved_hypothetical_protein_513904..514054_POSITIVE 333 56 18 48 1 tfor:TF2407|3end_glycosyltransferase_2582595..2582745_POSITIVE 331 57 16 147 106 tfor:TF0002|3end_hypothetical_protein_647..797_POSITIVE 327 77 31 58 17 tfor:TF2272|3end_conserved_hypothetical_protein_2436514..2436664_POSITIVE 326 60 19 94 51 tfor:TF0629|3end_hypothetical_protein_666710..666860_POSITIVE 326 47 1 132 85 tfor:TF0533|3end_hypothetical_protein_559519..559669_POSITIVE 325 100 51 58 12 tfor:TF2411|3end_outer_membrane_protein_2587072..2587222_POSITIVE 323 66 23 138 98 tfor:TF3021|3end_FKBP-type_peptidyl-prolyl_cis-trans_isomerase_3246194..3246344_POSITIVE 322 60 17 101 59 tfor:TF2347|3end_outer_membrane_protein,_TonB_dependent_receptor_2511092..2511242_POSITIVE 322 56 19 88 44 tfor:TF0599|3end_hypothetical_protein_630130..630280_POSITIVE 321 65 25 138 99 tfor:TF0402|3end_conserved_hypothetical_protein_422609..422759_POSITIVE 320 38 2 135 86 tfor:TF1168|3end_hypothetical_protein_1249092..1249242_POSITIVE 319 113 73 102 66 tfor:TF2950|3end_chloromuconate_cycloisomerase_3158549..3158699_POSITIVE 319 62 30 69 27 tfor:TF1794|3end_possible_glucose-1-phosphatase_1935816..1935966_POSITIVE 316 93 54 133 80 tfor:TF1443|3end_hypothetical_protein_1528203..1528353_POSITIVE 312 60 19 40 4 tfor:TF2874|3end_conserved_hypothetical_protein_3065224..3065374_POSITIVE 312 116 78 87 52 tfor:TF1732|3end_conserved_hypothetical_protein_1855979..1856129_POSITIVE