Origin IGS: aaaaccacagactctcaccgtgattttgctgggactcagattgtttcctgatctattgtgtagctcacacaaaatgaagcagcatattaaaaatatataactttgtacccaattatataatactttctatttatttgtcaattcctttattattatttacgatatctttatttttataactaaaaataaacattttattatatatattatttttagttatactaaaatttttataaatttccagataaaatgctataattaggttaatattttaacttttatggaggtttttatatgaatattctaattagagaagcaactgaaattgattatcctgcaataaataaa .........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 tttatttattgcaggataatcaatttcagttgcttctctaattagaatattcatataaaaacctccataaaagttaaaatattaacctaattatagcattttatctggaaatttataaaaattttagtataactaaaaataatatatataataaaatgtttatttttagttataaaaataaagatatcgtaaataataataaaggaattgacaaataaatagaaagtattatataattgggtacaaagttatatatttttaatatgctgcttcattttgtgtgagctacacaatagatcaggaaacaatctgagtcccagcaaaatcacggtgagagtctgtggtttt Mask Tandem Repeat Region ================================================ aaaaccacagactctcaccgtgattttgctgggactcagattgtttcctgatctattgtgtagctcacacaaaatgaagcagcatattaaaaatatataactttgtacccaattatataatactttctatttatttgtcaattcctttattattatttacgatatctttatttttataactaaaaataaacattttattatatatattatttttagttatactaaaatttttataaatttccagataaaatgctataattaggttaatattttaacttttatggaggtttttatatgaatattctaattagagaagcaactgaaattgattatcctgcaataaataaa Find is-nt database================================================ Query_seq: FN1586:FN1587|FN1586:FN1587:O-succinylbenzoate-CoA synthase:Acetyltransferase:<-->:98633..98980 348 aaaaccacagactctcaccgtgattttgctgggactcagattgtttcctgatctattgtgtagctcacacaaaatgaagcagcatattaaaaatatataactttgtacccaattatataatactttctatttatttgtcaattcctttattattatttacgatatctttatttttataactaaaaataaacattttattatatatattatttttagttatactaaaatttttataaatttccagataaaatgctataattaggttaatattttaacttttatggaggtttttatatgaatattctaattagagaagcaactgaaattgattatcctgcaataaataaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: FN1586:FN1587|FN1586:FN1587:O-succinylbenzoate-CoA synthase:Acetyltransferase:<-->:98633..98980 348 aaaaccacagactctcaccgtgattttgctgggactcagattgtttcctgatctattgtgtagctcacacaaaatgaagcagcatattaaaaatatataactttgtacccaattatataatactttctatttatttgtcaattcctttattattatttacgatatctttatttttataactaaaaataaacattttattatatatattatttttagttatactaaaatttttataaatttccagataaaatgctataattaggttaatattttaacttttatggaggtttttatatgaatattctaattagagaagcaactgaaattgattatcctgcaataaataaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: FN1586:FN1587|FN1586:FN1587:O-succinylbenzoate-CoA synthase:Acetyltransferase:<-->:98633..98980 348 aaaaccacagactctcaccgtgattttgctgggactcagattgtttcctgatctattgtgtagctcacacaaaatgaagcagcatattaaaaatatataactttgtacccaattatataatactttctatttatttgtcaattcctttattattatttacgatatctttatttttataactaaaaataaacattttattatatatattatttttagttatactaaaatttttataaatttccagataaaatgctataattaggttaatattttaacttttatggaggtttttatatgaatattctaattagagaagcaactgaaattgattatcctgcaataaataaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aaaaccacagactctcaccgtgattttgctgggactcagattgtttcctgatctattgtgtagctcacacaaaatgaagcagcatattaaaaatatataactttgtacccaattatataatactttctatttatttgtcaattcctttattattatttacgatatctttatttttataactaaaaataaacattttattatatatattatttttagttatactaaaatttttataaatttccagataaaatgctataattaggttaatattttaacttttatggaggtttttatatgaatattctaattagagaagcaactgaaattgattatcctgcaataaataaa Predict ORF larger than 30AA ================================================ Protein_Len: 31 Strand: + Start: 84 End: 176 ................................................................................... M L K I Y N F V P N Y I I L S I Y L S I P L L L F T I S L F L ............................................................................................................................................................................ Protein_Len: 37 Strand: + Start: 149 End: 259 .................................................................................................................................................... M I I Y D I F I F I T K N K H F I I Y I I F S Y T K I F I N F Q I K C Y N ......................................................................................... Protein_Len: 45 Strand: - Start: 134 End: 268 ..................................................................................................................................... K D I G K N N N V I D K N K Y S F I F M K N Y I N N K T I S F N K Y I E L Y F A I I L N M ................................................................................ Protein_Len: 32 Strand: - Start: 1 End: 96 F G C V R V T I K S P S L N N G S R N H L E C L I F C C I L F M ............................................................................................................................................................................................................................................................ aaaaccacagactctcaccgtgattttgctgggactcagattgtttcctgatctattgtgtagctcacacaaaatgaagcagcatattaaaaatatataactttgtacccaattatataatactttctatttatttgtcaattcctttattattatttacgatatctttatttttataactaaaaataaacattttattatatatattatttttagttatactaaaatttttataaatttccagataaaatgctataattaggttaatattttaacttttatggaggtttttatatgaatattctaattagagaagcaactgaaattgattatcctgcaataaataaa 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: 86 Start: 134 End: 163 .....................................................................................................................................TTTGTCAATTCCTTTATTATTATTTACGAT......................................................................................................................................................................................... PromScan Matrix: RpoD-17 Strand: + Score: 82 Start: 230 End: 259 .....................................................................................................................................................................................................................................TTTATAAATTTCCAGATAAAATGCTATAAT......................................................................................... PromScan Matrix: RpoD-17 Strand: + Score: 81 Start: 172 End: 201 ...........................................................................................................................................................................TTTTATAACTAAAAATAAACATTTTATTAT................................................................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aaaaccacagactctcaccgtgattttgctgggactcagattgtttcctgatctattgtgtagctcacacaaaatgaagcagcatattaaaaatatataactttgtacccaattatataatactttctatttatttgtcaattcctttattattatttacgatatctttatttttataactaaaaataaacattttattatatatattatttttagttatactaaaatttttataaatttccagataaaatgctataattaggttaatattttaacttttatggaggtttttatatgaatattctaattagagaagcaactgaaattgattatcctgcaataaataaa Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 83 HP_score: -6.7 Tail_Score: -4.94992 Start: 211 End: 227 Full_Region: TATTATATATATTAT TTTTAGT TAT ACTAAAA TTTTTATAAATTTCC ..................................................................................................................................................................................................................TTTTAGTTATACTAAAA......................................................................................................................... Find igs database================================================ Query_seq: FN1586:FN1587|FN1586:FN1587:O-succinylbenzoate-CoA synthase:Acetyltransferase:<-->:98633..98980 348 aaaaccacagactctcaccgtgattttgctgggactcagattgtttcctgatctattgtgtagctcacacaaaatgaagcagcatattaaaaatatataactttgtacccaattatataatactttctatttatttgtcaattcctttattattatttacgatatctttatttttataactaaaaataaacattttattatatatattatttttagttatactaaaatttttataaatttccagataaaatgctataattaggttaatattttaacttttatggaggtttttatatgaatattctaattagagaagcaactgaaattgattatcctgcaataaataaa Intra-Species Hit: Count: 1 Min: 1 Max: 348 Len: 348 Subject: NC_003454_FN1586_FN1587|O-succinylbenzoate-CoA synthase:Acetyltransferase|NEGATIVE:POSITIVE|[98633, 98980]|348 HSP 1 e-value: 2.0E-56 bit: 220.0 Len: 111 Query Start:1 Query End:111 Subject Strand: POSITIVE Subject Start: 1 Subject End: 111 aaaaccacagactctcaccgtgattttgctgggactcagattgtttcctgatctattgtgtagctcacacaaaatgaagcagcatattaaaaatatataactttgtaccca............................................................................................................................................................................................................................................. aaaaccacagactctcaccgtgattttgctgggactcagattgtttcctgatctattgtgtagctcacacaaaatgaagcagcatattaaaaatatataactttgtaccca............................................................................................................................................................................................................................................. HSP 2 e-value: 2.0E-54 bit: 214.0 Len: 108 Query Start:241 Query End:348 Subject Strand: POSITIVE Subject Start: 241 Subject End: 348 ................................................................................................................................................................................................................................................ccagataaaatgctataattaggttaatattttaacttttatggaggtttttatatgaatattctaattagagaagcaactgaaattgattatcctgcaataaataaa ................................................................................................................................................................................................................................................ccagataaaatgctataattaggttaatattttaacttttatggaggtttttatatgaatattctaattagagaagcaactgaaattgattatcctgcaataaataaa Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAACCACAGACUCUCACCGUGAUUUUGCUGGGACUCAGAUUGUUUCCUGAUCUAUUGUGUAGCUCACACAAAAUGAAGCAGCAUAUUAAAAAUAUAUAACUUUGUACCCAAUUAUAUAAUACUUUCUAUUUAUUUGUCAAUUCCUUUAUUAUUAUUUACGAUAUCUUUAUUUUUAUAACUAAAAAUAAACAUUUUAUUAUAUAUAUUAUUUUUAGUUAUACUAAAAUUUUUAUAAAUUUCCAGAUAAAAUGCUAUAAUUAGGUUAAUAUUUUAACUUUUAUGGAGGUUUUUAUAUGAAUAUUCUAAUUAGAGAAGCAACUGAAAUUGAUUAUCCUGCAAUAAAUAAA ....(((((((.((.......)).)))).)))...((((.((((((((((((.((.(((((.(((((.......)).))).))))).)).......................((((((((.((((((..((((((((..((((.................((((....))))..(((((((((((((((.................)))))))))))))))..............))))..))))))))...........(((((((....)))))))....))))))..))))))))........))))).)))))))))))......................... (-57.43) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUAUUUAUUGCAGGAUAAUCAAUUUCAGUUGCUUCUCUAAUUAGAAUAUUCAUAUAAAAACCUCCAUAAAAGUUAAAAUAUUAACCUAAUUAUAGCAUUUUAUCUGGAAAUUUAUAAAAAUUUUAGUAUAACUAAAAAUAAUAUAUAUAAUAAAAUGUUUAUUUUUAGUUAUAAAAAUAAAGAUAUCGUAAAUAAUAAUAAAGGAAUUGACAAAUAAAUAGAAAGUAUUAUAUAAUUGGGUACAAAGUUAUAUAUUUUUAAUAUGCUGCUUCAUUUUGUGUGAGCUACACAAUAGAUCAGGAAACAAUCUGAGUCCCAGCAAAAUCACGGUGAGAGUCUGUGGUUUU ..........((((.(((.((((((((...((((....(((((((..(((....)))...............(((((....)))))))))))).))))...(((((.(((((((....)))))))..(((((((((((((((.((((........))))))))))))))))))).......))))).................))))))))........((((((....(((((((((........))))))))))))))).))).))))......(((((((...)))))))(((((..(....).))))).........(((((((((((....).)))))))))) (-62.30) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 934 50 1 141 92 NC_003454:FN1586|5end_O-succinylbenzoate-CoA_synthase_98542..98772_NEGATIVE 307 66 21 155 109 NC_003454:FN0642|5end_hypothetical_protein_1299461..1299691_NEGATIVE 271 56 12 191 135 NC_003454:FN1627|5end_SSU_ribosomal_protein_S5P_133556..133786_NEGATIVE 263 58 13 183 138 NC_003454:FN1758|5end_Thiamin-phosphate_pyrophosphorylase_253886..254116_NEGATIVE 258 61 21 109 70 NC_003454:FN1152|5end_aspartate_aminotransferase_1806617..1806847_POSITIVE 255 83 47 180 143 NC_003454:FN0780|5end_Hypothetical_membrane-spanning_protein_1437490..1437720_NEGATIVE 253 57 13 87 34 NC_003454:FN1793|5end_Phosphoenolpyruvate-protein_phosphotransferase_275273..275503_NEGATIVE 239 67 25 137 91 NC_003454:FN2044|5end_LSU_ribosomal_protein_L33P_550109..550339_NEGATIVE 235 48 8 208 168 NC_003454:FN0201|5end_Glutaconyl-COA_decarboxylase_beta_subunit_826542..826772_POSITIVE 234 280 235 143 103 NC_003454:FN1264|5end_hypothetical_protein_1920766..1920996_POSITIVE 232 147 105 104 63 NC_003454:FN0761|5end_Bvg_accessory_factor_1418869..1419099_POSITIVE 230 70 26 60 7 NC_003454:FN2099|5end_hypothetical_protein_608245..608475_POSITIVE 229 170 121 126 82 NC_003454:FN1551|5end_hypothetical_protein_66187..66417_NEGATIVE 228 66 22 204 157 NC_003454:FN0478|5end_GcpE_protein_1125883..1126113_POSITIVE 227 86 44 169 129 NC_003454:FN1148|5end_Serine/threonine_sodium_symporter_1798012..1798242_POSITIVE 220 64 26 40 7 NC_003454:FN1266|5end_UTP--glucose-1-phosphate_uridylyltransferase_1923063..1923293_NEGATIVE 220 41 5 153 121 NC_003454:FN1126|5end_Acetyltransferase_1770287..1770517_NEGATIVE 218 85 45 147 118 NC_003454:FN0088|5end_hypothetical_protein_724887..725117_POSITIVE 217 335 303 101 71 NC_003454:FN1099|5end_hypothetical_protein_1743965..1744195_POSITIVE 213 48 3 221 173 NC_003454:FN0312|5end_Anaerobic_ribonucleoside-triphosphate_reductase_activating_protein_949316..949546_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 229 48 15 142 105 NC_003454:FN1899|3end_Hypothetical_lipoprotein_386714..386864_NEGATIVE 229 170 121 112 68 NC_003454:FN1552|3end_hypothetical_protein_66201..66351_NEGATIVE 222 181 141 72 34 NC_003454:FN0023|3end_Short-chain_fatty_acids_transporter_662780..662930_POSITIVE 220 64 26 49 16 NC_003454:FN1267|3end_hypothetical_protein_1923054..1923204_NEGATIVE 220 41 5 133 101 NC_003454:FN1127|3end_Hypothetical_membrane-spanning_protein_1770307..1770457_NEGATIVE 218 85 45 134 105 NC_003454:FN0087|3end_Ethanolamine_utilization_protein_eutN_724954..725104_POSITIVE 207 178 134 150 107 NC_003454:FN0742|3end_hypothetical_protein_1400671..1400821_POSITIVE 198 148 110 114 65 NC_003454:FN1205|3end_Protease_1863879..1864029_NEGATIVE 198 50 5 146 104 NC_003454:FN1628|3end_LSU_ribosomal_protein_L18P_133580..133730_NEGATIVE 196 49 1 88 26 NC_003454:FN0632|3end_PTS_system,_IIA_component_1290342..1290492_NEGATIVE 196 70 23 112 66 NC_003454:FN0102|3end_Ribonucleoside-diphosphate_reductase_alpha_chain_738580..738730_POSITIVE 195 70 28 46 1 NC_003454:FN0325|3end_50S_ribosomal_protein_L20_960924..961074_NEGATIVE 193 69 27 58 22 NC_003454:FN1020|3end_3-hydroxybutyryl-CoA_dehydratase_1673800..1673950_NEGATIVE 193 324 284 55 11 NC_003454:FN0928|3end_O-sialoglycoprotein_endopeptidase_1582382..1582532_NEGATIVE 193 290 243 102 57 NC_003454:FN0392|3end_Oxygen-independent_coproporphyrinogen_III_oxidase_1030597..1030747_POSITIVE 192 52 12 136 99 NC_003454:FN1031|3end_Hypothetical_membrane-spanning_protein_1684721..1684871_NEGATIVE 191 56 24 135 97 NC_003454:FN0203|3end_Glutaconate_CoA-transferase_subunit_B_829631..829781_POSITIVE 190 66 22 51 7 NC_003454:FN1352|3end_ABC_transporter_ATP-binding_protein_2003506..2003656_NEGATIVE 190 319 285 149 109 NC_003454:FN1293|3end_hypothetical_protein_1950966..1951116_NEGATIVE 190 99 65 53 21 NC_003454:FN1559|3end_cell_volume_regulation_protein_CvrA_82490..82640_POSITIVE