Origin IGS: taatgcaatgttgtcctaactagagtttgctgaataacgcattttgccaattaaactattgattgttaagataatatgagcaatcagtcaaaattaagcgacatgtttagaaaaatttacatacagcccatttcctatatccgacaaagctttatttgtggtatagaaaagcatctcagaaactatctttgtagaattaattaaataagctttatttaaaagaataaaacatgtaagaggt .........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 acctcttacatgttttattcttttaaataaagcttatttaattaattctacaaagatagtttctgagatgcttttctataccacaaataaagctttgtcggatataggaaatgggctgtatgtaaatttttctaaacatgtcgcttaattttgactgattgctcatattatcttaacaatcaatagtttaattggcaaaatgcgttattcagcaaactctagttaggacaacattgcatta Mask Tandem Repeat Region ================================================ taatgcaatgttgtcctaactagagtttgctgaataacgcattttgccaattaaactattgattgttaagataatatgagcaatcagtcaaaattaagcgacatgtttagaaaaatttacatacagcccatttcctatatccgacaaagctttatttgtggtatagaaaagcatctcagaaactatctttgtagaattaattaaataagctttatttaaaagaataaaacatgtaagaggt Find is-nt database================================================ Query_seq: TF1116:TF1117|TF1116:TF1117:conserved hypothetical protein:conserved hypothetical protein:->->:1187003..1187243 241 taatgcaatgttgtcctaactagagtttgctgaataacgcattttgccaattaaactattgattgttaagataatatgagcaatcagtcaaaattaagcgacatgtttagaaaaatttacatacagcccatttcctatatccgacaaagctttatttgtggtatagaaaagcatctcagaaactatctttgtagaattaattaaataagctttatttaaaagaataaaacatgtaagaggt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF1116:TF1117|TF1116:TF1117:conserved hypothetical protein:conserved hypothetical protein:->->:1187003..1187243 241 taatgcaatgttgtcctaactagagtttgctgaataacgcattttgccaattaaactattgattgttaagataatatgagcaatcagtcaaaattaagcgacatgtttagaaaaatttacatacagcccatttcctatatccgacaaagctttatttgtggtatagaaaagcatctcagaaactatctttgtagaattaattaaataagctttatttaaaagaataaaacatgtaagaggt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF1116:TF1117|TF1116:TF1117:conserved hypothetical protein:conserved hypothetical protein:->->:1187003..1187243 241 taatgcaatgttgtcctaactagagtttgctgaataacgcattttgccaattaaactattgattgttaagataatatgagcaatcagtcaaaattaagcgacatgtttagaaaaatttacatacagcccatttcctatatccgacaaagctttatttgtggtatagaaaagcatctcagaaactatctttgtagaattaattaaataagctttatttaaaagaataaaacatgtaagaggt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taatgcaatgttgtcctaactagagtttgctgaataacgcattttgccaattaaactattgattgttaagataatatgagcaatcagtcaaaattaagcgacatgtttagaaaaatttacatacagcccatttcctatatccgacaaagctttatttgtggtatagaaaagcatctcagaaactatctttgtagaattaattaaataagctttatttaaaagaataaaacatgtaagaggt Predict ORF larger than 30AA ================================================ Protein_Len: 42 Strand: + Start: 76 End: 201 ........................................................................... M S N Q S K L S D M F R K I Y I Q P I S Y I R Q S F I C G I E K H L R N Y L C R I N ........................................ Protein_Len: 43 Strand: - Start: 97 End: 225 ................................................................................................ A V H K S F N V Y L G N G I D S L A K N T T Y F L M E S V I K T S N I L Y A K N L L M ................ taatgcaatgttgtcctaactagagtttgctgaataacgcattttgccaattaaactattgattgttaagataatatgagcaatcagtcaaaattaagcgacatgtttagaaaaatttacatacagcccatttcctatatccgacaaagctttatttgtggtatagaaaagcatctcagaaactatctttgtagaattaattaaataagctttatttaaaagaataaaacatgtaagaggt Predict Promoter with matrix: RpoD-15 score > 80================================================ Predict Promoter with matrix: RpoD-16 score > 80================================================ Predict Promoter with matrix: RpoD-17 score > 80================================================ PromScan Matrix: RpoD-17 Strand: + Score: 88 Start: 43 End: 72 ..........................................TTTGCCAATTAAACTATTGATTGTTAAGAT......................................................................................................................................................................... PromScan Matrix: RpoD-17 Strand: - Score: 81 Start: 41 End: 70 ........................................CTTAACAATCAATAGTTTAATTGGCAAAAT........................................................................................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ taatgcaatgttgtcctaactagagtttgctgaataacgcattttgccaattaaactattgattgttaagataatatgagcaatcagtcaaaattaagcgacatgtttagaaaaatttacatacagcccatttcctatatccgacaaagctttatttgtggtatagaaaagcatctcagaaactatctttgtagaattaattaaataagctttatttaaaagaataaaacatgtaagaggt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TF1116:TF1117|TF1116:TF1117:conserved hypothetical protein:conserved hypothetical protein:->->:1187003..1187243 241 taatgcaatgttgtcctaactagagtttgctgaataacgcattttgccaattaaactattgattgttaagataatatgagcaatcagtcaaaattaagcgacatgtttagaaaaatttacatacagcccatttcctatatccgacaaagctttatttgtggtatagaaaagcatctcagaaactatctttgtagaattaattaaataagctttatttaaaagaataaaacatgtaagaggt Intra-Species Hit: Count: 1 Min: 1 Max: 241 Len: 241 Subject: tfor_TF1116_TF1117|conserved hypothetical protein:conserved hypothetical protein|POSITIVE:POSITIVE|[1187003,1187243]|241 HSP 1 e-value: 1.0E-134 bit: 478.0 Len: 241 Query Start:1 Query End:241 Subject Strand: POSITIVE Subject Start: 1 Subject End: 241 taatgcaatgttgtcctaactagagtttgctgaataacgcattttgccaattaaactattgattgttaagataatatgagcaatcagtcaaaattaagcgacatgtttagaaaaatttacatacagcccatttcctatatccgacaaagctttatttgtggtatagaaaagcatctcagaaactatctttgtagaattaattaaataagctttatttaaaagaataaaacatgtaagaggt taatgcaatgttgtcctaactagagtttgctgaataacgcattttgccaattaaactattgattgttaagataatatgagcaatcagtcaaaattaagcgacatgtttagaaaaatttacatacagcccatttcctatatccgacaaagctttatttgtggtatagaaaagcatctcagaaactatctttgtagaattaattaaataagctttatttaaaagaataaaacatgtaagaggt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAUGCAAUGUUGUCCUAACUAGAGUUUGCUGAAUAACGCAUUUUGCCAAUUAAACUAUUGAUUGUUAAGAUAAUAUGAGCAAUCAGUCAAAAUUAAGCGACAUGUUUAGAAAAAUUUACAUACAGCCCAUUUCCUAUAUCCGACAAAGCUUUAUUUGUGGUAUAGAAAAGCAUCUCAGAAACUAUCUUUGUAGAAUUAAUUAAAUAAGCUUUAUUUAAAAGAAUAAAACAUGUAAGAGGU ...((((.((((.((.(((.((((((((((((((((.(((((((((...........((((((((((...........))))))))))))))))...)))...))))))).....((((((....((...(((.(((((.((.(((((......)))))))))))).))))).....(((.....))).))))))..........))))))))).)))...))....))))))))...... (-39.50) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACCUCUUACAUGUUUUAUUCUUUUAAAUAAAGCUUAUUUAAUUAAUUCUACAAAGAUAGUUUCUGAGAUGCUUUUCUAUACCACAAAUAAAGCUUUGUCGGAUAUAGGAAAUGGGCUGUAUGUAAAUUUUUCUAAACAUGUCGCUUAAUUUUGACUGAUUGCUCAUAUUAUCUUAACAAUCAAUAGUUUAAUUGGCAAAAUGCGUUAUUCAGCAAACUCUAGUUAGGACAACAUUGCAUUA .......((((((((......((((.(((.(((((((((.......(((....(((.....))).))).......((((((((((((......))))).)).))))).))))))))).))).)))).......)))))))).(((.((((..(((((((((...............)))))...)))).)))))))..((((((((.((((((........))).))).)))...))))). (-41.88) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 397 58 21 230 193 tfor:TF2720|5end_conserved_hypothetical_protein_2893119..2893349_POSITIVE 261 48 3 87 26 tfor:TF2043|5end_fructokinase_2202267..2202497_POSITIVE 257 184 141 104 52 tfor:TF0504|5end_Fe-S_oxidoreductase,_family_2_528433..528663_POSITIVE 256 150 123 26 2 tfor:TF2165|5end_hypothetical_protein_2341654..2341884_POSITIVE 255 70 23 231 179 tfor:TF0208|5end_transposase_element_234336..234566_POSITIVE 254 136 94 125 78 tfor:TF2218|5end_two-component_system_response_regulator_2390162..2390392_POSITIVE 250 47 8 41 9 tfor:TF1069|5end_glucokinase_regulatory_protein,_sugar_phosphate_isomerase_domain_1138884..1139114_POSITIVE 246 48 11 76 37 tfor:TF1837|5end_conserved_hypothetical_protein;_possible_outer_membrane_protein_1985480..1985710_POSITIVE 241 44 4 192 160 tfor:TF1729|5end_aspartokinase_1853310..1853540_POSITIVE 234 135 96 209 172 tfor:TF0001|5end_hypothetical_protein_-116..114_POSITIVE 233 51 14 203 161 tfor:TF1678|5end_periplasmic_protease_1791097..1791327_POSITIVE 233 160 116 96 44 tfor:TF1610|5end_peptide_chain_release_factor_RF-2_1728635..1728865_POSITIVE 230 167 126 99 53 tfor:TF0758|5end_peptidyl-tRNA_hydrolase_805307..805537_POSITIVE 228 169 121 197 150 tfor:TF2662|5end_hypothetical_protein_2835270..2835500_POSITIVE 228 48 1 101 51 tfor:TF0058|5end_conserved_hypothetical_protein_59833..60063_POSITIVE 227 68 22 117 66 tfor:TF0546|5end_conserved_hypothetical_protein_576380..576610_POSITIVE 225 197 169 37 11 tfor:TF3053|5end_conserved_hypothetical_protein_3278564..3278794_POSITIVE 225 150 102 53 6 tfor:TF2831|5end_ABC_transporter,_permease_component_3021317..3021547_POSITIVE 224 196 160 183 146 tfor:TF3042|5end_ferrous_iron_transport_protein_B_3269362..3269592_POSITIVE 224 48 7 78 31 tfor:TF1995|5end_exonuclease_2147148..2147378_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 463 62 21 109 68 tfor:TF2719|3end_hypothetical_protein_2893074..2893224_POSITIVE 261 48 3 96 35 tfor:TF2042|3end_sugar_phosphate_isomerase,_polysialic_acid_capsule_expression_protein_2202356..2202506_POSITIVE 257 184 141 55 3 tfor:TF0502|3end_acetylglutamate_kinase_528464..528614_POSITIVE 254 136 94 48 1 tfor:TF2217|3end_hypothetical_protein_2390165..2390315_POSITIVE 250 47 8 41 9 tfor:TF1068|3end_conserved_hypothetical_protein;_possible_N-acetylglucosamine_kinase_1138964..1139114_POSITIVE 241 44 4 147 115 tfor:TF1728|3end_cell_division_ABC_transporter,_ATP-binding_protein_FtsE_1853345..1853495_POSITIVE 236 166 125 114 77 tfor:TF0008|3end_hypothetical_protein_4336..4486_POSITIVE 234 135 96 45 8 tfor:TF3165|3end_thiol:disulfide_interchange_protein,_thioredoxin_family_protein_3405343..3405493_POSITIVE 228 169 121 112 65 tfor:TF2661|3end_hypothetical_protein_2835265..2835415_POSITIVE 227 68 22 110 59 tfor:TF0545|3end_glucose-inhibited_division_protein_B_576453..576603_POSITIVE 225 197 169 47 21 tfor:TF3052|3end_conserved_hypothetical_protein_3278654..3278804_POSITIVE 225 150 102 75 28 tfor:TF2830|3end_ABC_transporter,_ATP-binding_protein_3021419..3021569_POSITIVE 224 196 160 146 109 tfor:TF3041|3end_hypothetical_protein_3269405..3269555_POSITIVE 224 48 7 78 31 tfor:TF1994|3end_acyl-CoA_synthetase_2147228..2147378_POSITIVE 223 196 159 114 67 tfor:TF0919|3end_conserved_hypothetical_protein_957773..957923_POSITIVE 219 147 104 93 43 tfor:TF2950|3end_chloromuconate_cycloisomerase_3158549..3158699_POSITIVE 219 49 3 79 31 tfor:TF2777|3end_hypothetical_protein_2961902..2962052_POSITIVE 219 149 124 139 113 tfor:TF0397|3end_ferredoxin-like_protein_419064..419214_POSITIVE 218 160 113 103 54 tfor:TF2793|3end_possible_L-lysine_2,3-aminomutase_2979888..2980038_POSITIVE 218 153 119 77 24 tfor:TF1757|3end_chromosome_partitioning_protein_1894825..1894975_POSITIVE