Origin IGS: tgttttattgttatggatgaatttgtctgtatggattgggtacaaagatagataaaaagaacggaagttgtttattcggttaaaaatatatcggaatgttttgtaagtaataaaactatccgtacttttgtgcccgatttttacggatgaaataaaataagcattaaaataagagttt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aaactcttattttaatgcttattttatttcatccgtaaaaatcgggcacaaaagtacggatagttttattacttacaaaacattccgatatatttttaaccgaataaacaacttccgttctttttatctatctttgtacccaatccatacagacaaattcatccataacaataaaaca Mask Tandem Repeat Region ================================================ tgttttattgttatggatgaatttgtctgtatggattgggtacaaagatagataaaaagaacggaagttgtttattcggttaaaaatatatcggaatgttttgtaagtaataaaactatccgtacttttgtgcccgatttttacggatgaaataaaataagcattaaaataagagttt Find is-nt database================================================ Query_seq: TF2934:TF2933|TF2934:TF2933:acetyltransferase/carbonic anhydrase:30S ribosomal protein S21:->->:3137306..3137483 178 tgttttattgttatggatgaatttgtctgtatggattgggtacaaagatagataaaaagaacggaagttgtttattcggttaaaaatatatcggaatgttttgtaagtaataaaactatccgtacttttgtgcccgatttttacggatgaaataaaataagcattaaaataagagttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF2934:TF2933|TF2934:TF2933:acetyltransferase/carbonic anhydrase:30S ribosomal protein S21:->->:3137306..3137483 178 tgttttattgttatggatgaatttgtctgtatggattgggtacaaagatagataaaaagaacggaagttgtttattcggttaaaaatatatcggaatgttttgtaagtaataaaactatccgtacttttgtgcccgatttttacggatgaaataaaataagcattaaaataagagttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF2934:TF2933|TF2934:TF2933:acetyltransferase/carbonic anhydrase:30S ribosomal protein S21:->->:3137306..3137483 178 tgttttattgttatggatgaatttgtctgtatggattgggtacaaagatagataaaaagaacggaagttgtttattcggttaaaaatatatcggaatgttttgtaagtaataaaactatccgtacttttgtgcccgatttttacggatgaaataaaataagcattaaaataagagttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tgttttattgttatggatgaatttgtctgtatggattgggtacaaagatagataaaaagaacggaagttgtttattcggttaaaaatatatcggaatgttttgtaagtaataaaactatccgtacttttgtgcccgatttttacggatgaaataaaataagcattaaaataagagttt Predict ORF larger than 30AA ================================================ Protein_Len: 32 Strand: + Start: 52 End: 147 ................................................... M K R T E V V Y S V K N I S E C F V S N K T I R T F V P D F Y G ............................... Protein_Len: 51 Strand: - Start: 1 End: 153 T K N N H I F K D T H I P Y L S L Y F S R F N N I R N F I Y R F T K Y T I F S D T S K H G I K V S S M ......................... tgttttattgttatggatgaatttgtctgtatggattgggtacaaagatagataaaaagaacggaagttgtttattcggttaaaaatatatcggaatgttttgtaagtaataaaactatccgtacttttgtgcccgatttttacggatgaaataaaataagcattaaaataagagttt 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================================================ tgttttattgttatggatgaatttgtctgtatggattgggtacaaagatagataaaaagaacggaagttgtttattcggttaaaaatatatcggaatgttttgtaagtaataaaactatccgtacttttgtgcccgatttttacggatgaaataaaataagcattaaaataagagttt Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 45 HP_score: -3.3 Tail_Score: -3.1733 Start: 92 End: 122 Full_Region: CGGTTAAAAATATAT CGGAATGTTTTGT AAGTA ATAAAACTATCCG TACTTTTGTGCCCGA ...........................................................................................CGGAATGTTTTGTAAGTAATAAAACTATCCG........................................................ Find igs database================================================ Query_seq: TF2934:TF2933|TF2934:TF2933:acetyltransferase/carbonic anhydrase:30S ribosomal protein S21:->->:3137306..3137483 178 tgttttattgttatggatgaatttgtctgtatggattgggtacaaagatagataaaaagaacggaagttgtttattcggttaaaaatatatcggaatgttttgtaagtaataaaactatccgtacttttgtgcccgatttttacggatgaaataaaataagcattaaaataagagttt Intra-Species Hit: Count: 1 Min: 1 Max: 178 Len: 178 Subject: tfor_TF2934_TF2933|acetyltransferase/carbonic anhydrase:30S ribosomal protein S21|POSITIVE:POSITIVE|[3137306,3137483]|178 HSP 1 e-value: 1.0E-96 bit: 353.0 Len: 178 Query Start:1 Query End:178 Subject Strand: POSITIVE Subject Start: 1 Subject End: 178 tgttttattgttatggatgaatttgtctgtatggattgggtacaaagatagataaaaagaacggaagttgtttattcggttaaaaatatatcggaatgttttgtaagtaataaaactatccgtacttttgtgcccgatttttacggatgaaataaaataagcattaaaataagagttt tgttttattgttatggatgaatttgtctgtatggattgggtacaaagatagataaaaagaacggaagttgtttattcggttaaaaatatatcggaatgttttgtaagtaataaaactatccgtacttttgtgcccgatttttacggatgaaataaaataagcattaaaataagagttt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGUUUUAUUGUUAUGGAUGAAUUUGUCUGUAUGGAUUGGGUACAAAGAUAGAUAAAAAGAACGGAAGUUGUUUAUUCGGUUAAAAAUAUAUCGGAAUGUUUUGUAAGUAAUAAAACUAUCCGUACUUUUGUGCCCGAUUUUUACGGAUGAAAUAAAAUAAGCAUUAAAAUAAGAGUUU (((((((.((((.((......((..((((((..((((((((((((((...((...(((.(((....))).)))..))..............((((..(((((((.....)))))))..))))...))))))))))))))..))))))..))......)))))).)))))))....... (-50.60) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAACUCUUAUUUUAAUGCUUAUUUUAUUUCAUCCGUAAAAAUCGGGCACAAAAGUACGGAUAGUUUUAUUACUUACAAAACAUUCCGAUAUAUUUUUAACCGAAUAAACAACUUCCGUUCUUUUUAUCUAUCUUUGUACCCAAUCCAUACAGACAAAUUCAUCCAUAACAAUAAAACA .........(((((.((....((((((.......))))))...(((.(((((....((((..(((((.........)))))..))))..........(((.(((........))).))).............))))).)))...........................)).))))).. (-17.70) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 279 70 21 168 123 tfor:TF1960|5end_TonB_protein_2110631..2110861_POSITIVE 272 51 26 32 9 tfor:TF2241|5end_ATP-dependent_DNA_helicase_2415401..2415631_POSITIVE 268 67 22 155 105 tfor:TF1656|5end_possible_2-methylthioadenine_synthetase_1771115..1771345_POSITIVE 267 70 21 210 151 tfor:TF0239|5end_conserved_hypothetical_protein_268894..269124_POSITIVE 261 99 61 175 127 tfor:TF1897|5end_conserved_hypothetical_protein;_possible_aminopeptidase_2049259..2049489_POSITIVE 260 141 121 204 183 tfor:TF0207|5end_conserved_hypothetical_protein_233105..233335_POSITIVE 257 43 3 103 72 tfor:TF0565|5end_hypothetical_protein_597765..597995_POSITIVE 255 147 101 155 110 tfor:TF2804|5end_conserved_hypothetical_protein_2993494..2993724_POSITIVE 254 149 116 75 35 tfor:TF1059|5end_possible_xanthan_lyase_1127181..1127411_POSITIVE 253 63 21 144 107 tfor:TF3153|5end_conserved_hypothetical_protein_3386872..3387102_POSITIVE 253 65 22 189 137 tfor:TF3028|5end_1-deoxy-d-xylulose-5-phosphate_reductoisomerase_3251642..3251872_POSITIVE 253 150 117 39 10 tfor:TF2677|5end_aspartate_transaminase_2850809..2851039_POSITIVE 252 79 31 63 8 tfor:TF0061|5end_hypothetical_protein_62833..63063_POSITIVE 244 50 1 64 13 tfor:TF3148|5end_hypoxanthine-guanine_phosphoribosyltransferase_3383652..3383882_POSITIVE 244 150 101 196 157 tfor:TF1874|5end_conserved_hypothetical_protein_2028060..2028290_POSITIVE 244 150 101 196 157 tfor:TF1132|5end_conserved_hypothetical_protein_1208926..1209156_POSITIVE 238 139 91 47 6 tfor:TF2457|5end_ABC_transporter,_permease_component,_zinc-binding_protein_2633147..2633377_POSITIVE 238 39 8 183 156 tfor:TF1430|5end_hypothetical_protein_1514867..1515097_POSITIVE 238 80 31 80 31 tfor:TF0754|5end_GDP-4-keto-6-deoxy-D-mannose-3,5-epimerase-4-redu_ctase_(GDP-L-fucose_synthetase)_801631..801861_POSITIVE 237 150 114 166 123 tfor:TF0120|5end_hexouronate_transporter_131307..131537_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 330 157 120 111 71 tfor:TF2530|3end_conserved_hypothetical_protein_2712926..2713076_POSITIVE 295 134 96 65 29 tfor:TF0391|3end_hypothetical_protein_412088..412238_POSITIVE 255 147 101 48 3 tfor:TF2803|3end_dehydrogenase,_possible_NADH-dependent_dehydrogenase_2993467..2993617_POSITIVE 253 63 21 120 83 tfor:TF3152|3end_hypothetical_protein_3386928..3387078_POSITIVE 253 65 22 86 34 tfor:TF3027|3end_zinc_metalloprotease_3251619..3251769_POSITIVE 238 137 121 19 3 tfor:TF1600|3end_uroporphyrinogen-III_synthase_1714817..1714967_POSITIVE 238 80 31 82 33 tfor:TF0752|3end_nucleotide-binding_protein;_MAF-like_protein_801713..801863_POSITIVE 237 150 114 113 70 tfor:TF0119|3end_gluconate_aldolase_131334..131484_POSITIVE 235 104 61 98 48 tfor:TF2707|3end_glutamine_amidotransferase_2880163..2880313_POSITIVE 234 70 22 93 44 tfor:TF1982|3end_1,4-alpha-glucan_branching_enzyme_2134130..2134280_POSITIVE 234 169 122 68 9 tfor:TF1835|3end_possible_dihydroxy-acid_dehydratase_1984586..1984736_POSITIVE 234 70 22 93 44 tfor:TF1826|3end_1,4-alpha-glucan_branching_enzyme,_N-terminal_region_1976812..1976962_POSITIVE 234 42 7 138 104 tfor:TF0944|3end_TonB-dependent_receptor_988399..988549_POSITIVE 231 150 119 142 110 tfor:TF2889|3end_50S_ribosomal_protein_L27_3078688..3078838_POSITIVE 230 68 24 49 8 tfor:TF2240|3end__tetracycline_resistance_element_mobilization_regulatory_protein_2415417..2415567_POSITIVE 226 136 121 146 131 tfor:TF1285|3end_hypothetical_protein_1369245..1369395_POSITIVE 226 80 32 150 101 tfor:TF0517|3end_TPR-repeat-containing_protein_541807..541957_POSITIVE 224 151 115 150 95 tfor:TF1813|3end_peptide_methionine_sulfoxide_reductase_1955293..1955443_POSITIVE 223 92 56 105 70 tfor:TF1237|3end_possible_L-fuculose_kinase_1323599..1323749_POSITIVE 222 149 104 51 10 tfor:TF2503|3end_conserved_hypothetical_protein_2680111..2680261_POSITIVE