Origin IGS: tttttacctctcctatcagttttttatataggaaaatagtgaatacttttaaataaaaattaatttttcttgaaaattccattcaagtaaatttaaatgagcttactgcgacgtcctataatgttgaaagagcattttggagctcgagaaacattataggctgtcaagtaagtgatatataaaaatataaagttataaaaagcaaattttcaagaaaaatgattgatactaactagcaatgag .........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 ctcattgctagttagtatcaatcatttttcttgaaaatttgctttttataactttatatttttatatatcacttacttgacagcctataatgtttctcgagctccaaaatgctctttcaacattataggacgtcgcagtaagctcatttaaatttacttgaatggaattttcaagaaaaattaatttttatttaaaagtattcactattttcctatataaaaaactgataggagaggtaaaaa Mask Tandem Repeat Region ================================================ tttttacctctcctatcagttttttatataggaaaatagtgaatacttttaaataaaaattaatttttcttgaaaattccattcaagtaaatttaaatgagcttactgcgacgtcctataatgttgaaagagcattttggagctcgagaaacattataggctgtcaagtaagtgatatataaaaatataaagttataaaaagcaaattttcaagaaaaatgattgatactaactagcaatgag Find is-nt database================================================ Query_seq: FN1731:FN1732|FN1731:FN1732:Anthranilate synthase component II:hypothetical protein:<-<-:231128..231370 243 tttttacctctcctatcagttttttatataggaaaatagtgaatacttttaaataaaaattaatttttcttgaaaattccattcaagtaaatttaaatgagcttactgcgacgtcctataatgttgaaagagcattttggagctcgagaaacattataggctgtcaagtaagtgatatataaaaatataaagttataaaaagcaaattttcaagaaaaatgattgatactaactagcaatgag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: FN1731:FN1732|FN1731:FN1732:Anthranilate synthase component II:hypothetical protein:<-<-:231128..231370 243 tttttacctctcctatcagttttttatataggaaaatagtgaatacttttaaataaaaattaatttttcttgaaaattccattcaagtaaatttaaatgagcttactgcgacgtcctataatgttgaaagagcattttggagctcgagaaacattataggctgtcaagtaagtgatatataaaaatataaagttataaaaagcaaattttcaagaaaaatgattgatactaactagcaatgag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: FN1731:FN1732|FN1731:FN1732:Anthranilate synthase component II:hypothetical protein:<-<-:231128..231370 243 tttttacctctcctatcagttttttatataggaaaatagtgaatacttttaaataaaaattaatttttcttgaaaattccattcaagtaaatttaaatgagcttactgcgacgtcctataatgttgaaagagcattttggagctcgagaaacattataggctgtcaagtaagtgatatataaaaatataaagttataaaaagcaaattttcaagaaaaatgattgatactaactagcaatgag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tttttacctctcctatcagttttttatataggaaaatagtgaatacttttaaataaaaattaatttttcttgaaaattccattcaagtaaatttaaatgagcttactgcgacgtcctataatgttgaaagagcattttggagctcgagaaacattataggctgtcaagtaagtgatatataaaaatataaagttataaaaagcaaattttcaagaaaaatgattgatactaactagcaatgag Predict ORF larger than 30AA ================================================ Protein_Len: 39 Strand: + Start: 63 End: 179 .............................................................. M F L E N S I Q V N L N E L T A T S Y N V E R A F W S S R N I I G C Q V S D I ................................................................ Protein_Len: 31 Strand: - Start: 96 End: 188 ............................................................................................... I L K S R R G I I N F S C K P A R S V N Y A T L Y T I Y L F M ....................................................... tttttacctctcctatcagttttttatataggaaaatagtgaatacttttaaataaaaattaatttttcttgaaaattccattcaagtaaatttaaatgagcttactgcgacgtcctataatgttgaaagagcattttggagctcgagaaacattataggctgtcaagtaagtgatatataaaaatataaagttataaaaagcaaattttcaagaaaaatgattgatactaactagcaatgag 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================================================ tttttacctctcctatcagttttttatataggaaaatagtgaatacttttaaataaaaattaatttttcttgaaaattccattcaagtaaatttaaatgagcttactgcgacgtcctataatgttgaaagagcattttggagctcgagaaacattataggctgtcaagtaagtgatatataaaaatataaagttataaaaagcaaattttcaagaaaaatgattgatactaactagcaatgag Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 69 HP_score: -2.5 Tail_Score: -5.27938 Start: 60 End: 96 Full_Region: tcgcagtaagctcat ttaaatttacttgaa tggaatt ttcaagaaaaattaa tttttatttaaaagt ...........................................................ttaaatttacttgaatggaattttcaagaaaaattaa................................................................................................................................................... Find igs database================================================ Query_seq: FN1731:FN1732|FN1731:FN1732:Anthranilate synthase component II:hypothetical protein:<-<-:231128..231370 243 tttttacctctcctatcagttttttatataggaaaatagtgaatacttttaaataaaaattaatttttcttgaaaattccattcaagtaaatttaaatgagcttactgcgacgtcctataatgttgaaagagcattttggagctcgagaaacattataggctgtcaagtaagtgatatataaaaatataaagttataaaaagcaaattttcaagaaaaatgattgatactaactagcaatgag Intra-Species Hit: Count: 1 Min: 1 Max: 174 Len: 174 Subject: NC_003454_FN1731_FN1732|Anthranilate synthase component II:hypothetical protein|NEGATIVE:NEGATIVE|[231128,231370]|243 HSP 1 e-value: 4.0E-94 bit: 345.0 Len: 174 Query Start:1 Query End:174 Subject Strand: POSITIVE Subject Start: 1 Subject End: 174 tttttacctctcctatcagttttttatataggaaaatagtgaatacttttaaataaaaattaatttttcttgaaaattccattcaagtaaatttaaatgagcttactgcgacgtcctataatgttgaaagagcattttggagctcgagaaacattataggctgtcaagtaagtg..................................................................... tttttacctctcctatcagttttttatataggaaaatagtgaatacttttaaataaaaattaatttttcttgaaaattccattcaagtaaatttaaatgagcttactgcgacgtcctataatgttgaaagagcattttggagctcgagaaacattataggctgtcaagtaagtg..................................................................... Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUUUACCUCUCCUAUCAGUUUUUUAUAUAGGAAAAUAGUGAAUACUUUUAAAUAAAAAUUAAUUUUUCUUGAAAAUUCCAUUCAAGUAAAUUUAAAUGAGCUUACUGCGACGUCCUAUAAUGUUGAAAGAGCAUUUUGGAGCUCGAGAAACAUUAUAGGCUGUCAAGUAAGUG ..(((((...((((((...........)))))).....)))))................((((.(((.((((((.......)))))).))).))))....(((((((..((((.(((((((((((....((((........))))....))))))))))).)))).))))))). (-45.70) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CACUUACUUGACAGCCUAUAAUGUUUCUCGAGCUCCAAAAUGCUCUUUCAACAUUAUAGGACGUCGCAGUAAGCUCAUUUAAAUUUACUUGAAUGGAAUUUUCAAGAAAAAUUAAUUUUUAUUUAAAAGUAUUCACUAUUUUCCUAUAUAAAAAACUGAUAGGAGAGGUAAAAA ..((((((((((..(((((((((((....((((........))))....)))))))))))..)))).)))))).....((((.(((.((((((.......)))))).))).)))).......................(((((((((...........)))))))))....... (-43.40) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 831 140 91 231 182 NC_003454:FN1731|5end_Anthranilate_synthase_component_II_231037..231267_NEGATIVE 672 149 101 212 163 NC_003454:FN1142|5end_Oxygen-independent_coproporphyrinogen_III_oxidase_1791529..1791759_POSITIVE 647 149 101 192 143 NC_003454:FN1439|5end_Transcriptional_regulator,_DeoR_family_2106428..2106658_POSITIVE 647 149 101 88 39 NC_003454:FN1438|5end_hypothetical_protein_2106324..2106554_POSITIVE 614 149 101 218 169 NC_003454:FN1740|5end_ATP_synthase_subunit_K_238400..238630_NEGATIVE 594 170 121 198 148 NC_003454:FN0053|5end_Branched-chain_amino_acid_transport_system_carrier_protein_689340..689570_POSITIVE 539 170 122 221 175 NC_003454:FN1995|5end_hypothetical_protein_498245..498475_POSITIVE 475 150 103 227 179 NC_003454:FN1328|5end_Exodeoxyribonuclease_VII_small_subunit_1983129..1983359_NEGATIVE 454 149 106 221 176 NC_003454:FN1581|5end_DNA_mismatch_repair_protein_mutS_93231..93461_NEGATIVE 399 149 106 191 146 NC_003454:FN1351|5end_15_kDa_lipoprotein_precursor_2003372..2003602_NEGATIVE 388 149 106 219 173 NC_003454:FN0054|5end_tyrosyl-tRNA_synthetase_690836..691066_POSITIVE 328 140 92 220 172 NC_003454:FN0186|5end_Cytochrome_c-type_biogenesis_protein_ccdA_810853..811083_POSITIVE 265 149 105 224 176 NC_003454:FN0220|5end_Autolysin_sensor_kinase_844934..845164_NEGATIVE 247 170 129 191 148 NC_003454:FN0344|5end_Methyltransferase_977761..977991_NEGATIVE 246 160 116 205 161 NC_003454:FN2091|5end_hypothetical_protein_602481..602711_NEGATIVE 241 107 68 196 156 NC_003454:FN1458|5end_UDP-N-acetylmuramoylalanine--D-glutamate_ligase_2140341..2140571_NEGATIVE 227 40 8 203 170 NC_003454:FN1367|5end_Methyl-accepting_chemotaxis_protein_2018143..2018373_NEGATIVE 224 150 113 189 153 NC_003454:FN0498|5end_hypothetical_protein_1143289..1143519_NEGATIVE 209 48 4 136 93 NC_003454:FN1035|5end_Iron-sulfur_flavoprotein_1688280..1688510_POSITIVE 209 117 77 198 159 NC_003454:FN0109|5end_hypothetical_protein_744809..745039_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 678 160 113 67 20 NC_003454:FN0828|3end_ABC_transporter_permease_protein_1489505..1489655_POSITIVE 614 149 101 57 8 NC_003454:FN1741|3end_ATP_synthase_subunit_I_238561..238711_NEGATIVE 594 170 121 69 19 NC_003454:FN0052|3end_Arsenate_reductase_689291..689441_POSITIVE 552 170 121 73 24 NC_003454:FN1077|3end_hypothetical_protein_1723754..1723904_NEGATIVE 488 170 122 64 15 NC_003454:FN1259|3end_Uracil-DNA_glycosylase_1915756..1915906_POSITIVE 436 170 138 34 2 NC_003454:FN1329|3end_Methyltransferase_1983342..1983492_NEGATIVE 399 149 106 57 12 NC_003454:FN1352|3end_ABC_transporter_ATP-binding_protein_2003506..2003656_NEGATIVE 259 160 115 57 12 NC_003454:FN1076|3end_hypothetical_protein_1723677..1723827_POSITIVE 246 160 116 72 28 NC_003454:FN2092|3end_Integral_membrane_protein_602614..602764_NEGATIVE 239 160 113 55 5 NC_003454:FN0829|3end_hypothetical_protein_1489580..1489730_NEGATIVE 209 48 4 121 78 NC_003454:FN1034|3end_Transcriptional_regulator,_TetR_family_1688345..1688495_POSITIVE 209 131 95 98 59 NC_003454:FN1710|3end_Integral_membrane_protein,_YGGT_family_206347..206497_POSITIVE 202 141 107 83 45 NC_003454:FN1944|3end_Sodium-dependent_tryptophan_transporter_448026..448176_POSITIVE 196 89 43 46 6 NC_003454:FN1379|3end_Citrate_lyase_beta_chain_2027325..2027475_POSITIVE 196 124 90 51 18 NC_003454:FN0718|3end_hypothetical_protein_1376004..1376154_POSITIVE 190 147 105 143 100 NC_003454:FN1886|3end_hypothetical_protein_371754..371904_POSITIVE 187 162 121 142 93 NC_003454:FN1375|3end_Citrate-sodium_symport_2023860..2024010_POSITIVE 186 165 132 37 8 NC_003454:FN1862|3end_L-beta-lysine_5,6-aminomutase_beta_subunit_352331..352481_NEGATIVE 185 150 101 46 4 NC_003454:FN1738|3end_ATP_synthase_subunit_C_236340..236490_NEGATIVE 184 125 82 72 18 NC_003454:FN0631|3end_PTS_system,_IIB_component_1289868..1290018_NEGATIVE