Origin IGS: tgcctacaacactataatatgcgcaattttattatgcatattagccaagtcggtacatattccacaataaaattacatttgcaaacatactatctttccgcataacagccaaaaatattgtatttattattattgagtaagaaaggagatagctaacaactttcgaggtattttccactgtgtttttgtagtgttttctccgtgttttgaatcacagagaaaacactttattcatttgtgccatgttaaactcaaaatagtatagac .........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 gtctatactattttgagtttaacatggcacaaatgaataaagtgttttctctgtgattcaaaacacggagaaaacactacaaaaacacagtggaaaatacctcgaaagttgttagctatctcctttcttactcaataataataaatacaatatttttggctgttatgcggaaagatagtatgtttgcaaatgtaattttattgtggaatatgtaccgacttggctaatatgcataataaaattgcgcatattatagtgttgtaggca Mask Tandem Repeat Region ================================================ tgcctacaacactataatatgcgcaattttattatgcatattagccaagtcggtacatattccacaataaaattacatttgcaaacatactatctttccgcataacagccaaaaatattgtatttattattattgagtaagaaaggagatagctaacaactttcgaggtattttccactgtgtttttgtagtgttttctccgtgttttgaatcacagagaaaacactttattcatttgtgccatgttaaactcaaaatagtatagac Find is-nt database================================================ Query_seq: TF1694:TF1695|TF1694:TF1695:conserved hypothetical protein:excisionase:->->:1816395..1816661 267 tgcctacaacactataatatgcgcaattttattatgcatattagccaagtcggtacatattccacaataaaattacatttgcaaacatactatctttccgcataacagccaaaaatattgtatttattattattgagtaagaaaggagatagctaacaactttcgaggtattttccactgtgtttttgtagtgttttctccgtgttttgaatcacagagaaaacactttattcatttgtgccatgttaaactcaaaatagtatagac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF1694:TF1695|TF1694:TF1695:conserved hypothetical protein:excisionase:->->:1816395..1816661 267 tgcctacaacactataatatgcgcaattttattatgcatattagccaagtcggtacatattccacaataaaattacatttgcaaacatactatctttccgcataacagccaaaaatattgtatttattattattgagtaagaaaggagatagctaacaactttcgaggtattttccactgtgtttttgtagtgttttctccgtgttttgaatcacagagaaaacactttattcatttgtgccatgttaaactcaaaatagtatagac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF1694:TF1695|TF1694:TF1695:conserved hypothetical protein:excisionase:->->:1816395..1816661 267 tgcctacaacactataatatgcgcaattttattatgcatattagccaagtcggtacatattccacaataaaattacatttgcaaacatactatctttccgcataacagccaaaaatattgtatttattattattgagtaagaaaggagatagctaacaactttcgaggtattttccactgtgtttttgtagtgttttctccgtgttttgaatcacagagaaaacactttattcatttgtgccatgttaaactcaaaatagtatagac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tgcctacaacactataatatgcgcaattttattatgcatattagccaagtcggtacatattccacaataaaattacatttgcaaacatactatctttccgcataacagccaaaaatattgtatttattattattgagtaagaaaggagatagctaacaactttcgaggtattttccactgtgtttttgtagtgttttctccgtgttttgaatcacagagaaaacactttattcatttgtgccatgttaaactcaaaatagtatagac Predict ORF larger than 30AA ================================================ Protein_Len: 39 Strand: + Start: 149 End: 262 .................................................................................................................................................... M A N N F R G I F H C V F V V F S P C F E S Q R K H F I H L C H V K L K I V * ..... Protein_Len: 33 Strand: - Start: 133 End: 231 .................................................................................................................................... Q T L F S I A L L K R P I K W Q T K T T N E G H K S D C L F C K M .................................... Protein_Len: 45 Strand: - Start: 44 End: 178 ........................................... G L R Y M N W L L I V N A F M S D K R M V A L F I T N I I I S Y S L L Y S V V K S T N E M ......................................................................................... tgcctacaacactataatatgcgcaattttattatgcatattagccaagtcggtacatattccacaataaaattacatttgcaaacatactatctttccgcataacagccaaaaatattgtatttattattattgagtaagaaaggagatagctaacaactttcgaggtattttccactgtgtttttgtagtgttttctccgtgttttgaatcacagagaaaacactttattcatttgtgccatgttaaactcaaaatagtatagac 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================================================ tgcctacaacactataatatgcgcaattttattatgcatattagccaagtcggtacatattccacaataaaattacatttgcaaacatactatctttccgcataacagccaaaaatattgtatttattattattgagtaagaaaggagatagctaacaactttcgaggtattttccactgtgtttttgtagtgttttctccgtgttttgaatcacagagaaaacactttattcatttgtgccatgttaaactcaaaatagtatagac Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 100 HP_score: -12.0 Tail_Score: -4.42976 Start: 191 End: 226 Full_Region: CACTGTGTTTTTGTA GTGTTTTCTCCGTGTT TTGA ATCACAGAGAAAACAC TTTATTCATTTGTGC ..............................................................................................................................................................................................GTGTTTTCTCCGTGTTTTGAATCACAGAGAAAACAC......................................... Find igs database================================================ Query_seq: TF1694:TF1695|TF1694:TF1695:conserved hypothetical protein:excisionase:->->:1816395..1816661 267 tgcctacaacactataatatgcgcaattttattatgcatattagccaagtcggtacatattccacaataaaattacatttgcaaacatactatctttccgcataacagccaaaaatattgtatttattattattgagtaagaaaggagatagctaacaactttcgaggtattttccactgtgtttttgtagtgttttctccgtgttttgaatcacagagaaaacactttattcatttgtgccatgttaaactcaaaatagtatagac Intra-Species Hit: Count: 1 Min: 1 Max: 267 Len: 267 Subject: tfor_TF1694_TF1695|conserved hypothetical protein:excisionase|POSITIVE:POSITIVE|[1816395, 1816661]|267 HSP 1 e-value: 1.0E-149 bit: 529.0 Len: 267 Query Start:1 Query End:267 Subject Strand: POSITIVE Subject Start: 1 Subject End: 267 tgcctacaacactataatatgcgcaattttattatgcatattagccaagtcggtacatattccacaataaaattacatttgcaaacatactatctttccgcataacagccaaaaatattgtatttattattattgagtaagaaaggagatagctaacaactttcgaggtattttccactgtgtttttgtagtgttttctccgtgttttgaatcacagagaaaacactttattcatttgtgccatgttaaactcaaaatagtatagac tgcctacaacactataatatgcgcaattttattatgcatattagccaagtcggtacatattccacaataaaattacatttgcaaacatactatctttccgcataacagccaaaaatattgtatttattattattgagtaagaaaggagatagctaacaactttcgaggtattttccactgtgtttttgtagtgttttctccgtgttttgaatcacagagaaaacactttattcatttgtgccatgttaaactcaaaatagtatagac Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGCCUACAACACUAUAAUAUGCGCAAUUUUAUUAUGCAUAUUAGCCAAGUCGGUACAUAUUCCACAAUAAAAUUACAUUUGCAAACAUACUAUCUUUCCGCAUAACAGCCAAAAAUAUUGUAUUUAUUAUUAUUGAGUAAGAAAGGAGAUAGCUAACAACUUUCGAGGUAUUUUCCACUGUGUUUUUGUAGUGUUUUCUCCGUGUUUUGAAUCACAGAGAAAACACUUUAUUCAUUUGUGCCAUGUUAAACUCAAAAUAGUAUAGAC ((((.((.......(((((((((.(((...))).))))))))).....)).))))........((((((..........((....))............((......))......))))))...(((((((.((((((..(((((..(........)..)))))..(((((........(((..(....(((((((((((.(((........))).)))))))))))..)..)))..))))).......)))))))))))))..... (-50.60) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GUCUAUACUAUUUUGAGUUUAACAUGGCACAAAUGAAUAAAGUGUUUUCUCUGUGAUUCAAAACACGGAGAAAACACUACAAAAACACAGUGGAAAAUACCUCGAAAGUUGUUAGCUAUCUCCUUUCUUACUCAAUAAUAAUAAAUACAAUAUUUUUGGCUGUUAUGCGGAAAGAUAGUAUGUUUGCAAAUGUAAUUUUAUUGUGGAAUAUGUACCGACUUGGCUAAUAUGCAUAAUAAAAUUGCGCAUAUUAUAGUGUUGUAGGCA ((((((..((((((((((.......((.............(((((((((((((((........)))))))))))))))...........((((..((((...(....).))))..))))..))......)))))).))))...(((((.....((((.((......)).)))).(((((((((........((((((((((((((..((((...((.....))...)))).))))))))))))))))))))))).))))))))))). (-67.62) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 335 180 132 184 119 tfor:TF2299|5end_hypothetical_protein_2449994..2450224_POSITIVE 303 210 165 98 46 tfor:TF1134|5end_hypothetical_protein_1210376..1210606_POSITIVE 298 72 44 36 6 tfor:TF0442|5end_Na+-transporting_NADH:ubiquinone_oxidoreductase,_subunit_4_465270..465500_POSITIVE 290 117 76 200 147 tfor:TF2661|5end_hypothetical_protein_2833509..2833739_POSITIVE 287 209 165 164 123 tfor:TF1496|5end_tyrosyl-tRNA_synthetase_1594700..1594930_POSITIVE 277 210 179 135 98 tfor:TF0577|5end_possible_endo-1,4-beta-xylanase_B_606975..607205_POSITIVE 268 177 131 110 51 tfor:TF2015|5end_N6-adenine-specific_DNA_methylase_2171606..2171836_POSITIVE 261 188 142 193 149 tfor:TF2948|5end_2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxy_late_synthase_3154823..3155053_POSITIVE 259 67 21 203 164 tfor:TF0107|5end_ion_channel_protein_113913..114143_POSITIVE 255 210 161 216 164 tfor:TF2561|5end_50S_ribosomal_protein_L16_2738693..2738923_POSITIVE 253 219 179 205 161 tfor:TF3131|5end_uracil-DNA_glycosylase_3364467..3364697_POSITIVE 252 110 62 39 1 tfor:TF0424|5end_outer_membrane_receptor,_TonB-linked_440028..440258_POSITIVE 245 110 62 206 155 tfor:TF3149|5end_conserved_hypothetical_protein_3384424..3384654_POSITIVE 244 211 171 223 180 tfor:TF2549|5end_30S_ribosomal_protein_S7_2731711..2731941_POSITIVE 243 246 201 133 89 tfor:TF1538|5end_conserved_hypothetical_protein_1643531..1643761_POSITIVE 242 215 174 150 109 tfor:TF1707|5end_conserved_hypothetical_protein_1828433..1828663_POSITIVE 242 213 173 52 9 tfor:TF0592|5end_epimerase/reductase_625418..625648_POSITIVE 242 208 161 160 100 tfor:TF0205|5end_exsB_protein_231523..231753_POSITIVE 240 204 162 162 110 tfor:TF1034|5end_conserved_hypothetical_protein_1095063..1095293_POSITIVE 239 209 168 220 172 tfor:TF1874|5end_conserved_hypothetical_protein_2028060..2028290_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 303 210 165 107 55 tfor:TF1133|3end_conserved_hypothetical_protein_1210465..1210615_POSITIVE 290 117 76 151 98 tfor:TF2660|3end_hypothetical_protein_2833540..2833690_POSITIVE 268 177 131 76 17 tfor:TF2014|3end_dipeptidyl_aminopeptidase_IV_2171652..2171802_POSITIVE 267 199 154 52 3 tfor:TF2298|3end_hypothetical_protein_2449928..2450078_POSITIVE 259 67 21 117 78 tfor:TF0105|3end_DNA-binding_stress_protein,_Dps_family_113907..114057_POSITIVE 257 222 183 129 83 tfor:TF2680|3end_conserved_hypothetical_protein_2855716..2855866_POSITIVE 247 194 151 150 101 tfor:TF0287|3end_peptidase,_M23_family_317467..317617_POSITIVE 244 211 171 136 93 tfor:TF2548|3end_30S_ribosomal_protein_S12_2731704..2731854_POSITIVE 242 215 174 143 102 tfor:TF1706|3end_conserved_hypothetical_protein_1828506..1828656_POSITIVE 242 215 174 49 8 tfor:TF1705|3end_conserved_hypothetical_protein;_possible_DNA_helicase_1828412..1828562_POSITIVE 236 199 151 52 3 tfor:TF2405|3end_RNA_polymerase_ECF-type_sigma_factor_2580566..2580716_POSITIVE 235 178 144 133 95 tfor:TF1907|3end_ADP-heptose:LPS_heptosyltransferase_II_2062717..2062867_POSITIVE 235 209 167 113 65 tfor:TF1151|3end_conserved_hypothetical_protein_1233262..1233412_POSITIVE 233 209 161 138 100 tfor:TF2940|3end_50S_ribosomal_protein_L11_3141890..3142040_POSITIVE 228 75 40 145 105 tfor:TF1750|3end_hypothetical_protein_1886566..1886716_POSITIVE 227 250 201 70 25 tfor:TF0910|3end_Tn5520-like_integrase_(transfer_factor)_953778..953928_POSITIVE 227 219 174 58 16 tfor:TF0500|3end_hypothetical_protein_526923..527073_POSITIVE 226 176 134 57 6 tfor:TF2803|3end_dehydrogenase,_possible_NADH-dependent_dehydrogenase_2993467..2993617_POSITIVE 226 198 157 90 51 tfor:TF2491|3end_hypothetical_protein_2665299..2665449_POSITIVE 226 200 152 140 94 tfor:TF2118|3end_conserved_hypothetical_protein_2291693..2291843_POSITIVE