Origin IGS: ctctattgcatgattaaactatttgcgatgcaaatttaaaagataattgattgaataacgaaagaatcttattaagattattaaaaaaaatgctttttgtctgcatgccacaatatcatacagaatatcatccgattatcacattcttcaataaggcagtgcccacttttaaggggtactgaagaatattgaacatattcttgcattttttcacagcaaaacatttgtccattgttgaaaaacccgtaaattagcgtgtttttttcaaatatacagttgaagaattcttaacaacataataa .........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.........1.........2.........3.........4.........5.........6.........7.........8.........9 ttattatgttgttaagaattcttcaactgtatatttgaaaaaaacacgctaatttacgggtttttcaacaatggacaaatgttttgctgtgaaaaaatgcaagaatatgttcaatattcttcagtaccccttaaaagtgggcactgccttattgaagaatgtgataatcggatgatattctgtatgatattgtggcatgcagacaaaaagcattttttttaataatcttaataagattctttcgttattcaatcaattatcttttaaatttgcatcgcaaatagtttaatcatgcaatagag Mask Tandem Repeat Region ================================================ ctctattgcatgattaaactatttgcgatgcaaatttaaaagataattgattgaataacgaaagaatcttattaagattattaaaaaaaatgctttttgtctgcatgccacaatatcatacagaatatcatccgattatcacattcttcaataaggcagtgcccacttttaaggggtactgaagaatattgaacatattcttgcattttttcacagcaaaacatttgtccattgttgaaaaacccgtaaattagcgtgtttttttcaaatatacagttgaagaattcttaacaacataataa Find is-nt database================================================ Query_seq: TF0546:TF0547|TF0546:TF0547:conserved hypothetical protein:DNA gyrase subunit A (topoisomerase):->->:577366..577667 302 ctctattgcatgattaaactatttgcgatgcaaatttaaaagataattgattgaataacgaaagaatcttattaagattattaaaaaaaatgctttttgtctgcatgccacaatatcatacagaatatcatccgattatcacattcttcaataaggcagtgcccacttttaaggggtactgaagaatattgaacatattcttgcattttttcacagcaaaacatttgtccattgttgaaaaacccgtaaattagcgtgtttttttcaaatatacagttgaagaattcttaacaacataataa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF0546:TF0547|TF0546:TF0547:conserved hypothetical protein:DNA gyrase subunit A (topoisomerase):->->:577366..577667 302 ctctattgcatgattaaactatttgcgatgcaaatttaaaagataattgattgaataacgaaagaatcttattaagattattaaaaaaaatgctttttgtctgcatgccacaatatcatacagaatatcatccgattatcacattcttcaataaggcagtgcccacttttaaggggtactgaagaatattgaacatattcttgcattttttcacagcaaaacatttgtccattgttgaaaaacccgtaaattagcgtgtttttttcaaatatacagttgaagaattcttaacaacataataa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF0546:TF0547|TF0546:TF0547:conserved hypothetical protein:DNA gyrase subunit A (topoisomerase):->->:577366..577667 302 ctctattgcatgattaaactatttgcgatgcaaatttaaaagataattgattgaataacgaaagaatcttattaagattattaaaaaaaatgctttttgtctgcatgccacaatatcatacagaatatcatccgattatcacattcttcaataaggcagtgcccacttttaaggggtactgaagaatattgaacatattcttgcattttttcacagcaaaacatttgtccattgttgaaaaacccgtaaattagcgtgtttttttcaaatatacagttgaagaattcttaacaacataataa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ctctattgcatgattaaactatttgcgatgcaaatttaaaagataattgattgaataacgaaagaatcttattaagattattaaaaaaaatgctttttgtctgcatgccacaatatcatacagaatatcatccgattatcacattcttcaataaggcagtgcccacttttaaggggtactgaagaatattgaacatattcttgcattttttcacagcaaaacatttgtccattgttgaaaaacccgtaaattagcgtgtttttttcaaatatacagttgaagaattcttaacaacataataa Predict ORF larger than 30AA ================================================ Protein_Len: 43 Strand: + Start: 51 End: 179 .................................................. M N N E R I L L R L L K K M L F V C M P Q Y H T E Y H P I I T F F N K A V P T F K G Y ........................................................................................................................... Protein_Len: 31 Strand: + Start: 97 End: 189 ................................................................................................ M S A C H N I I Q N I I R L S H S S I R Q C P L L R G T E E Y ................................................................................................................. Protein_Len: 34 Strand: - Start: 131 End: 232 .................................................................................................................................. G I I V N K L L A T G V K L P Y Q L I N F M N K C K K V A F C K D M ...................................................................... Protein_Len: 60 Strand: - Start: 84 End: 272 ................................................................................... K K D A H W L I M C F I M R N D C E E I L C H G S K L P V S S Y Q V Y E Q M K E C C F M Q G N N F F G Y I L T N K E F M .............................. Protein_Len: 35 Strand: - Start: 22 End: 126 ..................... K R H L N L L Y N I S Y R F F R I L I I L F F A K Q R C A V I D Y L M ................................................................................................................................................................................ Protein_Len: 30 Strand: - Start: 17 End: 106 ................ V I Q S A F K F S L Q N F L S L I K N L N N F F I S K T Q M .................................................................................................................................................................................................... ctctattgcatgattaaactatttgcgatgcaaatttaaaagataattgattgaataacgaaagaatcttattaagattattaaaaaaaatgctttttgtctgcatgccacaatatcatacagaatatcatccgattatcacattcttcaataaggcagtgcccacttttaaggggtactgaagaatattgaacatattcttgcattttttcacagcaaaacatttgtccattgttgaaaaacccgtaaattagcgtgtttttttcaaatatacagttgaagaattcttaacaacataataa 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================================================ ctctattgcatgattaaactatttgcgatgcaaatttaaaagataattgattgaataacgaaagaatcttattaagattattaaaaaaaatgctttttgtctgcatgccacaatatcatacagaatatcatccgattatcacattcttcaataaggcagtgcccacttttaaggggtactgaagaatattgaacatattcttgcattttttcacagcaaaacatttgtccattgttgaaaaacccgtaaattagcgtgtttttttcaaatatacagttgaagaattcttaacaacataataa Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 64 HP_score: -2.8 Tail_Score: -5.00616 Start: 180 End: 205 Full_Region: ACTTTTAAGGGGTAC TGAAGAATAT TGAAC ATATTCTTGCA TTTTTTCACAGCAAA ...................................................................................................................................................................................TGAAGAATATTGAACATATTCTTGCA................................................................................................. TransTerm Strand: + Conf: 50 HP_score: -3.8 Tail_Score: -3.52177 Start: 184 End: 200 Full_Region: TTAAGGGGTACTGAA GAATAT TGAAC ATATTC TTGCATTTTTTCACA .......................................................................................................................................................................................GAATATTGAACATATTC...................................................................................................... TransTerm Strand: - Conf: 47 HP_score: -3.8 Tail_Score: -3.06831 Start: 184 End: 200 Full_Region: tgtgaaaaaatgcaa gaatat gttca atattc ttcagtaccccttaa .......................................................................................................................................................................................gaatatgttcaatattc...................................................................................................... Find igs database================================================ Query_seq: TF0546:TF0547|TF0546:TF0547:conserved hypothetical protein:DNA gyrase subunit A (topoisomerase):->->:577366..577667 302 ctctattgcatgattaaactatttgcgatgcaaatttaaaagataattgattgaataacgaaagaatcttattaagattattaaaaaaaatgctttttgtctgcatgccacaatatcatacagaatatcatccgattatcacattcttcaataaggcagtgcccacttttaaggggtactgaagaatattgaacatattcttgcattttttcacagcaaaacatttgtccattgttgaaaaacccgtaaattagcgtgtttttttcaaatatacagttgaagaattcttaacaacataataa Intra-Species Hit: Count: 1 Min: 1 Max: 302 Len: 302 Subject: tfor_TF0546_TF0547|conserved hypothetical protein:DNA gyrase subunit A (topoisomerase)|POSITIVE:POSITIVE|[577366,577667]|302 HSP 1 e-value: 1.0E-143 bit: 509.0 Len: 302 Query Start:1 Query End:302 Subject Strand: POSITIVE Subject Start: 1 Subject End: 302 ctctattgcatgattaaactatttgcgatgcaaatttaaaagataattgattgaataacgaaagaatcttattaagattattnnnnnnnntgctttttgtctgcatgccacaatatcatacagaatatcatccgattatcacattcttcaataaggcagtgcccacttttaaggggtactgaagaatattgaacatattcttgcattttttcacagcaaaacatttgtccattgttgaaaaacccgtaaattagcgtgnnnnnnncaaatatacagttgaagaattcttaacaacataataa ctctattgcatgattaaactatttgcgatgcaaatttaaaagataattgattgaataacgaaagaatcttattaagattattaaaaaaaatgctttttgtctgcatgccacaatatcatacagaatatcatccgattatcacattcttcaataaggcagtgcccacttttaaggggtactgaagaatattgaacatattcttgcattttttcacagcaaaacatttgtccattgttgaaaaacccgtaaattagcgtgtttttttcaaatatacagttgaagaattcttaacaacataataa Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUCUAUUGCAUGAUUAAACUAUUUGCGAUGCAAAUUUAAAAGAUAAUUGAUUGAAUAACGAAAGAAUCUUAUUAAGAUUAUUAAAAAAAAUGCUUUUUGUCUGCAUGCCACAAUAUCAUACAGAAUAUCAUCCGAUUAUCACAUUCUUCAAUAAGGCAGUGCCCACUUUUAAGGGGUACUGAAGAAUAUUGAACAUAUUCUUGCAUUUUUUCACAGCAAAACAUUUGUCCAUUGUUGAAAAACCCGUAAAUUAGCGUGUUUUUUUCAAAUAUACAGUUGAAGAAUUCUUAACAACAUAAUAA ...(((((((.(((......))))))))))...........((((((((..(((..........(((((.....)))))....................((((.(((.........))).))))...)))..))))))))..((((((((((..((((((((((.((....))))))))))((((((((.....))))))))..........................)).(((..(((((((.(((......))).))))))).))).......))))))))))................. (-57.20) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUAUUAUGUUGUUAAGAAUUCUUCAACUGUAUAUUUGAAAAAAACACGCUAAUUUACGGGUUUUUCAACAAUGGACAAAUGUUUUGCUGUGAAAAAAUGCAAGAAUAUGUUCAAUAUUCUUCAGUACCCCUUAAAAGUGGGCACUGCCUUAUUGAAGAAUGUGAUAAUCGGAUGAUAUUCUGUAUGAUAUUGUGGCAUGCAGACAAAAAGCAUUUUUUUUAAUAAUCUUAAUAAGAUUCUUUCGUUAUUCAAUCAAUUAUCUUUUAAAUUUGCAUCGCAAAUAGUUUAAUCAUGCAAUAGAG (((((..(((((((...(((((((((........((((((((....((........))..))))))))...((((((....((((((..(....)...))))))...))))))........((((.(((((....)).))).)))).....))))))))).)))))))..))))).....(((((((((((((.(((((((((..(((((.............(((((.....))))).....(.....)..........)))))...))))))).))..)))))...))))))))...... (-59.70) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 288 170 121 64 11 tfor:TF2283|5end_hypothetical_protein_2440266..2440496_POSITIVE 272 193 154 225 186 tfor:TF2714|5end_hypothetical_protein_2887839..2888069_POSITIVE 272 232 194 71 28 tfor:TF1714|5end_hypothetical_protein_1834125..1834355_POSITIVE 270 187 142 206 167 tfor:TF2208|5end_conserved_hypothetical_protein_2382349..2382579_POSITIVE 263 194 151 62 4 tfor:TF2668|5end_hypothetical_protein_2842471..2842701_POSITIVE 259 170 123 80 35 tfor:TF1548|5end_thiophene_and_furan_oxidation_protein_1652501..1652731_POSITIVE 257 176 132 133 97 tfor:TF0340|5end_hypothetical_protein_363893..364123_POSITIVE 256 196 155 91 47 tfor:TF2534|5end_conserved_hypothetical_protein_2717044..2717274_POSITIVE 255 135 93 136 87 tfor:TF0864|5end_O-succinylbenzoate--CoA_ligase_914570..914800_POSITIVE 253 149 101 214 155 tfor:TF2332|5end_signal_peptidase_I_2491694..2491924_POSITIVE 249 159 113 171 127 tfor:TF2290|5end_ABC_transporter,_ATP-binding/permease_component_2443942..2444172_POSITIVE 248 240 203 179 133 tfor:TF2131|5end_conserved_hypothetical_protein_2306867..2307097_POSITIVE 245 197 155 230 182 tfor:TF2745|5end_hypothetical_protein_2927562..2927792_POSITIVE 243 178 133 42 2 tfor:TF2394|5end_integrase/recombinase_XerD_2565608..2565838_POSITIVE 243 200 154 71 29 tfor:TF1955|5end_amino_acid_exporter,_possible_threonine_efflux_protein_2106952..2107182_POSITIVE 243 140 93 77 32 tfor:TF1813|5end_peptide_methionine_sulfoxide_reductase_1954170..1954400_POSITIVE 243 238 213 155 127 tfor:TF1128|5end_possible_lantibiotic_biosynthesis_protein_(modification)_1202297..1202527_POSITIVE 242 204 170 227 185 tfor:TF3049|5end_conserved_hypothetical_protein_3276517..3276747_POSITIVE 242 167 128 151 105 tfor:TF1111|5end_glycosyltransferase_1180757..1180987_POSITIVE 242 200 154 216 164 tfor:TF0263|5end_ISPg3_(IS195)_transposase_292179..292409_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 281 200 154 132 86 tfor:TF2713|3end_glycosyltransferase_2887819..2887969_POSITIVE 270 185 141 62 17 tfor:TF1592|3end_hypothetical_protein_1708557..1708707_POSITIVE 258 181 151 100 57 tfor:TF3006|3end_response_regulator,_transcriptional_regulator_RprY_3227162..3227312_POSITIVE 248 240 203 148 102 tfor:TF2130|3end_conserved_hypothetical_protein;_possible_permease_2306916..2307066_POSITIVE 242 189 141 58 1 tfor:TF2172|3end_hypothetical_protein_2346135..2346285_POSITIVE 242 167 128 151 105 tfor:TF1110|3end_conserved_hypothetical_protein_1180837..1180987_POSITIVE 242 200 154 75 23 tfor:TF0261|3end_conserved_hypothetical_protein_292118..292268_POSITIVE 238 192 153 61 12 tfor:TF2169|3end_hypothetical_protein_2345354..2345504_POSITIVE 238 133 91 141 100 tfor:TF1362|3end_hypothetical_protein_1444059..1444209_POSITIVE 238 192 153 50 1 tfor:TF0361|3end_hypothetical_protein_379810..379960_POSITIVE 238 192 153 50 1 tfor:TF0349|3end_hypothetical_protein_370719..370869_POSITIVE 235 133 91 61 5 tfor:TF1698|3end_mobilization_protein_1819782..1819932_POSITIVE 234 183 153 46 17 tfor:TF0018|3end_hypothetical_protein_12091..12241_POSITIVE 233 185 141 46 8 tfor:TF1169|3end_lipoprotein_ABC_transporter,_permease_component_1251573..1251723_POSITIVE 233 195 154 108 64 tfor:TF0323|3end_NAD-dependent_epimerase/dehydratase_family_protein_351053..351203_POSITIVE 230 179 134 78 34 tfor:TF2340|3end_hypothetical_protein_2500915..2501065_POSITIVE 230 177 131 143 106 tfor:TF1518|3end_peroxiredoxin_1627724..1627874_POSITIVE 230 174 131 122 56 tfor:TF0287|3end_peptidase,_M23_family_317467..317617_POSITIVE 228 198 156 138 103 tfor:TF2914|3end_hypothetical_protein_3109643..3109793_POSITIVE 227 183 155 41 15 tfor:TF2560|3end_30S_ribosomal_protein_S3_2738747..2738897_POSITIVE