Origin IGS: cttgccacctctctttcacacactagccattatctgactctgattatcttttaaaacttctaataaatgaaagacgaaatttaccgctttggtaaaggaaaatgggggaatcttctagtttaaatataataaaaagccctcgcaaaaaaactttgcaaggacgttgacacgcggttccacctttattcggacctcagtcgcctgaggaccctctgggagtacgggactccagattgataacggcaatcagccgtcggacactagtctcagactgctgactgatttcgcatccgcactcaagaatgtgtcgtctaaggattgcatgccgtctcaccattaggcactctctgtttcttgtctcagactttttctctcatcgctttcaatttattgttgaatattctacatgaatttttattaaaaagcaagaggaaatttgaaaaaaattaaatatttttttctttctaaatgaa .........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.........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 ttcatttagaaagaaaaaaatatttaatttttttcaaatttcctcttgctttttaataaaaattcatgtagaatattcaacaataaattgaaagcgatgagagaaaaagtctgagacaagaaacagagagtgcctaatggtgagacggcatgcaatccttagacgacacattcttgagtgcggatgcgaaatcagtcagcagtctgagactagtgtccgacggctgattgccgttatcaatctggagtcccgtactcccagagggtcctcaggcgactgaggtccgaataaaggtggaaccgcgtgtcaacgtccttgcaaagtttttttgcgagggctttttattatatttaaactagaagattcccccattttcctttaccaaagcggtaaatttcgtctttcatttattagaagttttaaaagataatcagagtcagataatggctagtgtgtgaaagagaggtggcaag Mask Tandem Repeat Region ================================================ cttgccacctctctttcacacactagccattatctgactctgattatcttttaaaacttctaataaatgaaagacgaaatttaccgctttggtaaaggaaaatgggggaatcttctagtttaaatataataaaaagccctcgcaaaaaaactttgcaaggacgttgacacgcggttccacctttattcggacctcagtcgcctgaggaccctctgggagtacgggactccagattgataacggcaatcagccgtcggacactagtctcagactgctgactgatttcgcatccgcactcaagaatgtgtcgtctaaggattgcatgccgtctcaccattaggcactctctgtttcttgtctcagactttttctctcatcgctttcaatttattgttgaatattctacatgaatttttattaaaaagcaagaggaaatttgaaaaaaattaaatatttttttctttctaaatgaa Find is-nt database================================================ Query_seq: SSA_1449:SSA_1450|SSA_1449:SSA_1450:Histidinol-phosphate/aromatic aminotransferase and cobyric acid decarboxylase, putative:hypothetical protein:<-<-:1452022..1452494 473 cttgccacctctctttcacacactagccattatctgactctgattatcttttaaaacttctaataaatgaaagacgaaatttaccgctttggtaaaggaaaatgggggaatcttctagtttaaatataataaaaagccctcgcaaaaaaactttgcaaggacgttgacacgcggttccacctttattcggacctcagtcgcctgaggaccctctgggagtacgggactccagattgataacggcaatcagccgtcggacactagtctcagactgctgactgatttcgcatccgcactcaagaatgtgtcgtctaaggattgcatgccgtctcaccattaggcactctctgtttcttgtctcagactttttctctcatcgctttcaatttattgttgaatattctacatgaatttttattaaaaagcaagaggaaatttgaaaaaaattaaatatttttttctttctaaatgaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1449:SSA_1450|SSA_1449:SSA_1450:Histidinol-phosphate/aromatic aminotransferase and cobyric acid decarboxylase, putative:hypothetical protein:<-<-:1452022..1452494 473 cttgccacctctctttcacacactagccattatctgactctgattatcttttaaaacttctaataaatgaaagacgaaatttaccgctttggtaaaggaaaatgggggaatcttctagtttaaatataataaaaagccctcgcaaaaaaactttgcaaggacgttgacacgcggttccacctttattcggacctcagtcgcctgaggaccctctgggagtacgggactccagattgataacggcaatcagccgtcggacactagtctcagactgctgactgatttcgcatccgcactcaagaatgtgtcgtctaaggattgcatgccgtctcaccattaggcactctctgtttcttgtctcagactttttctctcatcgctttcaatttattgttgaatattctacatgaatttttattaaaaagcaagaggaaatttgaaaaaaattaaatatttttttctttctaaatgaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1449:SSA_1450|SSA_1449:SSA_1450:Histidinol-phosphate/aromatic aminotransferase and cobyric acid decarboxylase, putative:hypothetical protein:<-<-:1452022..1452494 473 cttgccacctctctttcacacactagccattatctgactctgattatcttttaaaacttctaataaatgaaagacgaaatttaccgctttggtaaaggaaaatgggggaatcttctagtttaaatataataaaaagccctcgcaaaaaaactttgcaaggacgttgacacgcggttccacctttattcggacctcagtcgcctgaggaccctctgggagtacgggactccagattgataacggcaatcagccgtcggacactagtctcagactgctgactgatttcgcatccgcactcaagaatgtgtcgtctaaggattgcatgccgtctcaccattaggcactctctgtttcttgtctcagactttttctctcatcgctttcaatttattgttgaatattctacatgaatttttattaaaaagcaagaggaaatttgaaaaaaattaaatatttttttctttctaaatgaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 cttgccacctctctttcacacactagccattatctgactctgattatcttttaaaacttctaataaatgaaagacgaaatttaccgctttggtaaaggaaaatgggggaatcttctagtttaaatataataaaaagccctcgcaaaaaaactttgcaaggacgttgacacgcggttccacctttattcggacctcagtcgcctgaggaccctctgggagtacgggactccagattgataacggcaatcagccgtcggacactagtctcagactgctgactgatttcgcatccgcactcaagaatgtgtcgtctaaggattgcatgccgtctcaccattaggcactctctgtttcttgtctcagactttttctctcatcgctttcaatttattgttgaatattctacatgaatttttattaaaaagcaagaggaaatttgaaaaaaattaaatatttttttctttctaaatgaa Predict ORF larger than 30AA ================================================ Protein_Len: 35 Strand: + Start: 233 End: 337 ........................................................................................................................................................................................................................................ M D N G N Q P S D T S L R L L T D F A S A L K N V S S K D C M P S H H ........................................................................................................................................ Protein_Len: 43 Strand: + Start: 279 End: 407 ...................................................................................................................................................................................................................................................................................... M I S H P H S R M C R L R I A C R L T I R H S L F L V S D F F S H R F Q F I V E Y S T .................................................................. Protein_Len: 43 Strand: + Start: 319 End: 447 .............................................................................................................................................................................................................................................................................................................................. M H A V S P L G T L C F L S Q T F S L I A F N L L L N I L H E F L L K S K R K F E K N .......................... Protein_Len: 47 Strand: - Start: 197 End: 337 .................................................................................................................................................................................................... D G S S G R P T R S E L N I V A I L R R V S T E S Q Q S I E C G C E L I H R R L I A H R R V M ........................................................................................................................................ Protein_Len: 43 Strand: - Start: 118 End: 246 ..................................................................................................................... N L Y L L F G E C F F K A L V N V R P E V K I R V E T A Q P G E P L V P S W I S L P M ................................................................................................................................................................................................................................... Protein_Len: 33 Strand: - Start: 47 End: 145 .............................................. R K F S R I F S L R F K G S Q Y L F I P S D E L K F I I F L G R M ........................................................................................................................................................................................................................................................................................................................................ Protein_Len: 31 Strand: - Start: 19 End: 111 .................. V S A M I Q S Q N D K L V E L L H F V F N V A K T F S F P P M .......................................................................................................................................................................................................................................................................................................................................................................... cttgccacctctctttcacacactagccattatctgactctgattatcttttaaaacttctaataaatgaaagacgaaatttaccgctttggtaaaggaaaatgggggaatcttctagtttaaatataataaaaagccctcgcaaaaaaactttgcaaggacgttgacacgcggttccacctttattcggacctcagtcgcctgaggaccctctgggagtacgggactccagattgataacggcaatcagccgtcggacactagtctcagactgctgactgatttcgcatccgcactcaagaatgtgtcgtctaaggattgcatgccgtctcaccattaggcactctctgtttcttgtctcagactttttctctcatcgctttcaatttattgttgaatattctacatgaatttttattaaaaagcaagaggaaatttgaaaaaaattaaatatttttttctttctaaatgaa 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: 82 Start: 400 End: 429 ...............................................................................................................................................................................................................................................................................................................................................................................................................CTTGCTTTTTAATAAAAATTCATGTAGAAT............................................ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ cttgccacctctctttcacacactagccattatctgactctgattatcttttaaaacttctaataaatgaaagacgaaatttaccgctttggtaaaggaaaatgggggaatcttctagtttaaatataataaaaagccctcgcaaaaaaactttgcaaggacgttgacacgcggttccacctttattcggacctcagtcgcctgaggaccctctgggagtacgggactccagattgataacggcaatcagccgtcggacactagtctcagactgctgactgatttcgcatccgcactcaagaatgtgtcgtctaaggattgcatgccgtctcaccattaggcactctctgtttcttgtctcagactttttctctcatcgctttcaatttattgttgaatattctacatgaatttttattaaaaagcaagaggaaatttgaaaaaaattaaatatttttttctttctaaatgaa Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 100 HP_score: -10.2 Tail_Score: -5.33331 Start: 136 End: 162 Full_Region: gaaccgcgtgtcaac gtccttgcaaag ttt ttttgcgagggc tttttattatattta .......................................................................................................................................gtccttgcaaagtttttttgcgagggc....................................................................................................................................................................................................................................................................................................................... Find igs database================================================ Query_seq: SSA_1449:SSA_1450|SSA_1449:SSA_1450:Histidinol-phosphate/aromatic aminotransferase and cobyric acid decarboxylase, putative:hypothetical protein:<-<-:1452022..1452494 473 cttgccacctctctttcacacactagccattatctgactctgattatcttttaaaacttctaataaatgaaagacgaaatttaccgctttggtaaaggaaaatgggggaatcttctagtttaaatataataaaaagccctcgcaaaaaaactttgcaaggacgttgacacgcggttccacctttattcggacctcagtcgcctgaggaccctctgggagtacgggactccagattgataacggcaatcagccgtcggacactagtctcagactgctgactgatttcgcatccgcactcaagaatgtgtcgtctaaggattgcatgccgtctcaccattaggcactctctgtttcttgtctcagactttttctctcatcgctttcaatttattgttgaatattctacatgaatttttattaaaaagcaagaggaaatttgaaaaaaattaaatatttttttctttctaaatgaa Intra-Species Hit: Count: 1 Min: 1 Max: 439 Len: 439 Subject: NC_009009_SSA_1449_SSA_1450|Histidinol-phosphate/aromatic aminotransferase and cobyric acid decarboxylase, putative:hypothetical protein|NEGATIVE:NEGATIVE|[1452022,1452494]|473 HSP 1 e-value: 0.0 bit: 829.0 Len: 439 Query Start:1 Query End:439 Subject Strand: POSITIVE Subject Start: 1 Subject End: 439 cttgccacctctctttcacacactagccattatctgactctgattatcttttaaaacttctaataaatgaaagacgaaatttaccgctttggtaaaggaaaatgggggaatcttctagtttaaatataataaaaagccctcgcnnnnnnnctttgcaaggacgttgacacgcggttccacctttattcggacctcagtcgcctgaggaccctctgggagtacgggactccagattgataacggcaatcagccgtcggacactagtctcagactgctgactgatttcgcatccgcactcaagaatgtgtcgtctaaggattgcatgccgtctcaccattaggcactctctgtttcttgtctcagactttttctctcatcgctttcaatttattgttgaatattctacatgaatttttattaaaaagcaagaggaaatttg.................................. cttgccacctctctttcacacactagccattatctgactctgattatcttttaaaacttctaataaatgaaagacgaaatttaccgctttggtaaaggaaaatgggggaatcttctagtttaaatataataaaaagccctcgcaaaaaaactttgcaaggacgttgacacgcggttccacctttattcggacctcagtcgcctgaggaccctctgggagtacgggactccagattgataacggcaatcagccgtcggacactagtctcagactgctgactgatttcgcatccgcactcaagaatgtgtcgtctaaggattgcatgccgtctcaccattaggcactctctgtttcttgtctcagactttttctctcatcgctttcaatttattgttgaatattctacatgaatttttattaaaaagcaagaggaaatttg.................................. Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUUGCCACCUCUCUUUCACACACUAGCCAUUAUCUGACUCUGAUUAUCUUUUAAAACUUCUAAUAAAUGAAAGACGAAAUUUACCGCUUUGGUAAAGGAAAAUGGGGGAAUCUUCUAGUUUAAAUAUAAUAAAAAGCCCUCGCAAAAAAACUUUGCAAGGACGUUGACACGCGGUUCCACCUUUAUUCGGACCUCAGUCGCCUGAGGACCCUCUGGGAGUACGGGACUCCAGAUUGAUAACGGCAAUCAGCCGUCGGACACUAGUCUCAGACUGCUGACUGAUUUCGCAUCCGCACUCAAGAAUGUGUCGUCUAAGGAUUGCAUGCCGUCUCACCAUUAGGCACUCUCUGUUUCUUGUCUCAGACUUUUUCUCUCAUCGCUUUCAAUUUAUUGUUGAAUAUUCUACAUGAAUUUUUAUUAAAAAGCAAGAGGAAAUUUG .......(((((((((............................................(((((((((((((.(((..((((((.....))))))......((((((((......(((((..............(.(((.(((((.....))))).))).)...((((...(((((...........)))))..(((.((((((((....(((((.(((.....))))))))......((((((.(((((.(((((((....))))..))).)))))........((((((((((........)))).......))).))).))))))....)).)))))))))..........))))..)))))..)))))))))))))))).)))))))).((((.((((.....)))).))))....))))..)))))....... (-103.91) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CAAAUUUCCUCUUGCUUUUUAAUAAAAAUUCAUGUAGAAUAUUCAACAAUAAAUUGAAAGCGAUGAGAGAAAAAGUCUGAGACAAGAAACAGAGAGUGCCUAAUGGUGAGACGGCAUGCAAUCCUUAGACGACACAUUCUUGAGUGCGGAUGCGAAAUCAGUCAGCAGUCUGAGACUAGUGUCCGACGGCUGAUUGCCGUUAUCAAUCUGGAGUCCCGUACUCCCAGAGGGUCCUCAGGCGACUGAGGUCCGAAUAAAGGUGGAACCGCGUGUCAACGUCCUUGCAAAGUUUUUUUGCGAGGGCUUUUUAUUAUAUUUAAACUAGAAGAUUCCCCCAUUUUCCUUUACCAAAGCGGUAAAUUUCGUCUUUCAUUUAUUAGAAGUUUUAAAAGAUAAUCAGAGUCAGAUAAUGGCUAGUGUGUGAAAGAGAGGUGGCAAG ....(((((((((((((((.......((((..(((.((....)).)))...)))))))))))).))).))))...((((..........))))...((((...(((((((..(((((((..(((......(((((..((((((.(((.(((..(....).))).))).)).))))...))))).((((((.....)))))).....((((((((.....))).))))).((.((((((....)))))).))..........)))...)))))))...((((((((((((...))))))))))))....................((((((......)))))).))))))).........(((((.((((((((.((((((..(((......(((.......)))....)))..)))))).))))))))))))))))).. (-124.01) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 908 50 1 141 92 NC_009009:SSA_1449|5end_Histidinol-phosphate/aromatic_aminotransferase_and_cobyric_acid_decarboxylase,_putative_1451931..1452161_NEGATIVE 409 200 157 75 13 NC_009009:SSA_1572|5end_hypothetical_protein_1575908..1576138_NEGATIVE 398 215 171 203 152 NC_009009:SSA_0487|5end_Delta-aminolevulinic_acid_dehydratase,_putative_487349..487579_POSITIVE 386 218 174 189 125 NC_009009:SSA_1550|5end_hypothetical_protein_1552665..1552895_NEGATIVE 379 243 201 219 172 NC_009009:SSA_1439|5end_hypothetical_protein_1444373..1444603_NEGATIVE 375 272 232 128 77 NC_009009:SSA_0402|5end_Histidine_kinase,_putative_399144..399374_POSITIVE 366 179 131 152 106 NC_009009:SSA_0912|5end_Phenylalanyl-tRNA_synthetase_alpha_chain,_putative_923100..923330_POSITIVE 364 210 162 62 13 NC_009009:SSA_1848|5end_Methionyl-tRNA_formyltransferase,_putative_1843178..1843408_NEGATIVE 361 199 151 179 127 NC_009009:SSA_0755|5end_hypothetical_protein_736212..736442_POSITIVE 359 215 171 143 92 NC_009009:SSA_2044|5end_Cysteinyl-tRNA_synthetase,_putative_2048409..2048639_NEGATIVE 358 220 171 205 156 NC_009009:SSA_1821|5end_Acetyltransferase_(N-acetylase_of_ribosomal_proteins),_putative_1810610..1810840_NEGATIVE 358 180 132 179 127 NC_009009:SSA_0631|5end_Tryptophan_synthase_beta_chain,_putative_619872..620102_POSITIVE 358 229 190 61 14 NC_009009:SSA_0031|5end_Glutamine_phosphoribosylpyrophosphate_amidotransferase,_putative_36439..36669_POSITIVE 355 210 162 63 7 NC_009009:SSA_1433|5end_tRNA_delta(2)-isopentenylpyrophosphate_transferase,_putative_1440817..1441047_NEGATIVE 355 350 305 156 112 NC_009009:SSA_1254|5end_hypothetical_protein_1281484..1281714_NEGATIVE 351 219 171 154 108 NC_009009:SSA_0869|5end_Peptide_chain_release_factor_2,_putative_861914..862144_POSITIVE 350 184 141 173 130 NC_009009:SSA_0661|5end_Isoleucyl-tRNA_synthetase,_putative_644876..645106_POSITIVE 349 218 171 161 111 NC_009009:SSA_1648|5end_hypothetical_protein_1647909..1648139_NEGATIVE 349 364 321 69 22 NC_009009:SSA_1092|5end_Dihydrofolate_reductase,_putative_1109599..1109829_POSITIVE 348 231 191 140 100 NC_009009:SSA_1650|5end_3-Ketoacyl-ACP_reductase,_putative_1649594..1649824_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 386 350 306 142 92 NC_009009:SSA_2340|3end_hypothetical_protein_2341539..2341689_NEGATIVE 375 272 232 126 75 NC_009009:SSA_0401|3end_Two-component_response_transcriptional_regulator_(CheY-like_receiver_and_winged-helix_DNA-binding_domains),_putative_399222..399372_POSITIVE 363 359 311 61 20 NC_009009:SSA_0567|3end_Isochorismitase_family_protein,_putative_561442..561592_POSITIVE 359 215 171 125 74 NC_009009:SSA_2045|3end_Reductase,_putative_2048427..2048577_NEGATIVE 348 231 191 147 107 NC_009009:SSA_1651|3end_hypothetical_protein_1649587..1649737_NEGATIVE 347 310 263 137 79 NC_009009:SSA_1077|3end_N-acetyl-glucosamine_matabolism,_putative_1095829..1095979_POSITIVE 347 216 173 60 14 NC_009009:SSA_0451|3end_Conserved_uncharacterized_protein_451636..451786_POSITIVE 344 264 221 71 19 NC_009009:SSA_1899|3end_hypothetical_protein_1894443..1894593_NEGATIVE 343 367 323 117 69 NC_009009:SSA_1320|3end_hypothetical_protein_1336829..1336979_NEGATIVE 327 289 247 42 1 NC_009009:SSA_1856|3end_hypothetical_protein_1852077..1852227_NEGATIVE 327 203 163 148 110 NC_009009:SSA_1124|3end_Oxidoreductase,_putative_1148547..1148697_NEGATIVE 327 208 163 40 1 NC_009009:SSA_0590|3end_hypothetical_protein_582817..582967_POSITIVE 326 327 285 121 81 NC_009009:SSA_1416|3end_hypothetical_protein_1426520..1426670_NEGATIVE 319 215 173 143 94 NC_009009:SSA_1960|3end_hypothetical_protein_1956571..1956721_NEGATIVE 319 219 182 136 98 NC_009009:SSA_1044|3end_Homoserine_kinase,_putative_1060799..1060949_POSITIVE 317 387 344 117 69 NC_009009:SSA_1769|3end_hypothetical_protein_1756939..1757089_NEGATIVE 317 299 253 143 97 NC_009009:SSA_1478|3end_Transposase_ORF1,_putative_1483124..1483274_POSITIVE 316 286 242 89 46 NC_009009:SSA_1189|3end_GTP-binding_protein,_putative_1216806..1216956_NEGATIVE 315 290 256 46 6 NC_009009:SSA_0910|3end_ABC-type_multidrug_transporter,_ATPase_component,_putative_922161..922311_POSITIVE 315 233 193 148 103 NC_009009:SSA_0833|3end_Accessory_secretory_protein_Asp1,_putative_819600..819750_POSITIVE