Origin IGS: aaatgaagattttccagtactagatgctcctataaatactaaaaaatccttacattctaaacttacatcagtaaaggtttgccaatttttaatttgaacttttaataattgcatagttcctcctagaattaattatattctatatattaaagtataaataaaaatataattaaattcaagttttttataaatagattctattatatttgtaaaaaaaataaaatataatgtggatacttaaagatagttcgttactatccaaatttattattaactacttgatgcctctaatatttcctaaactccaaaatacttttttaacattagggggcatcatagtagcttcatttaaaagttatttaaatattttttaagaaaaatttgtgatgtaacttacttatctttaaaatattaagaaataggagtataagaa .........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 ttcttatactcctatttcttaatattttaaagataagtaagttacatcacaaatttttcttaaaaaatatttaaataacttttaaatgaagctactatgatgccccctaatgttaaaaaagtattttggagtttaggaaatattagaggcatcaagtagttaataataaatttggatagtaacgaactatctttaagtatccacattatattttattttttttacaaatataatagaatctatttataaaaaacttgaatttaattatatttttatttatactttaatatatagaatataattaattctaggaggaactatgcaattattaaaagttcaaattaaaaattggcaaacctttactgatgtaagtttagaatgtaaggattttttagtatttataggagcatctagtactggaaaatcttcattt Mask Tandem Repeat Region ================================================ aaatgaagattttccagtactagatgctcctataaatactaaaaaatccttacattctaaacttacatcagtaaaggtttgccaatttttaatttgaacttttaataattgcatagttcctcctagaattaattatattctatatattaaagtataaataaaaatataattaaattcaagttttttataaatagattctattatatttgtaaaaaaaataaaatataatgtggatacttaaagatagttcgttactatccaaatttattattaactacttgatgcctctaatatttcctaaactccaaaatacttttttaacattagggggcatcatagtagcttcatttaaaagttatttaaatattttttaagaaaaatttgtgatgtaacttacttatctttaaaatattaagaaataggagtataagaa Find is-nt database================================================ Query_seq: FN0185:FN0186|FN0185:FN0186:hypothetical protein:Cytochrome c-type biogenesis protein ccdA:<-->:810560..810992 433 aaatgaagattttccagtactagatgctcctataaatactaaaaaatccttacattctaaacttacatcagtaaaggtttgccaatttttaatttgaacttttaataattgcatagttcctcctagaattaattatattctatatattaaagtataaataaaaatataattaaattcaagttttttataaatagattctattatatttgtaaaaaaaataaaatataatgtggatacttaaagatagttcgttactatccaaatttattattaactacttgatgcctctaatatttcctaaactccaaaatacttttttaacattagggggcatcatagtagcttcatttaaaagttatttaaatattttttaagaaaaatttgtgatgtaacttacttatctttaaaatattaagaaataggagtataagaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: FN0185:FN0186|FN0185:FN0186:hypothetical protein:Cytochrome c-type biogenesis protein ccdA:<-->:810560..810992 433 aaatgaagattttccagtactagatgctcctataaatactaaaaaatccttacattctaaacttacatcagtaaaggtttgccaatttttaatttgaacttttaataattgcatagttcctcctagaattaattatattctatatattaaagtataaataaaaatataattaaattcaagttttttataaatagattctattatatttgtaaaaaaaataaaatataatgtggatacttaaagatagttcgttactatccaaatttattattaactacttgatgcctctaatatttcctaaactccaaaatacttttttaacattagggggcatcatagtagcttcatttaaaagttatttaaatattttttaagaaaaatttgtgatgtaacttacttatctttaaaatattaagaaataggagtataagaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: FN0185:FN0186|FN0185:FN0186:hypothetical protein:Cytochrome c-type biogenesis protein ccdA:<-->:810560..810992 433 aaatgaagattttccagtactagatgctcctataaatactaaaaaatccttacattctaaacttacatcagtaaaggtttgccaatttttaatttgaacttttaataattgcatagttcctcctagaattaattatattctatatattaaagtataaataaaaatataattaaattcaagttttttataaatagattctattatatttgtaaaaaaaataaaatataatgtggatacttaaagatagttcgttactatccaaatttattattaactacttgatgcctctaatatttcctaaactccaaaatacttttttaacattagggggcatcatagtagcttcatttaaaagttatttaaatattttttaagaaaaatttgtgatgtaacttacttatctttaaaatattaagaaataggagtataagaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aaatgaagattttccagtactagatgctcctataaatactaaaaaatccttacattctaaacttacatcagtaaaggtttgccaatttttaatttgaacttttaataattgcatagttcctcctagaattaattatattctatatattaaagtataaataaaaatataattaaattcaagttttttataaatagattctattatatttgtaaaaaaaataaaatataatgtggatacttaaagatagttcgttactatccaaatttattattaactacttgatgcctctaatatttcctaaactccaaaatacttttttaacattagggggcatcatagtagcttcatttaaaagttatttaaatattttttaagaaaaatttgtgatgtaacttacttatctttaaaatattaagaaataggagtataagaa Predict ORF larger than 30AA ================================================ Protein_Len: 49 Strand: + Start: 225 End: 371 ................................................................................................................................................................................................................................ M M W I L K D S S L L S K F I I N Y L M P L I F P K L Q N T F L T L G G I I V A S F K S Y L N I F .............................................................. Protein_Len: 43 Strand: - Start: 1 End: 129 F S S K G T S S A G I F V L F D K C E L S V D T F T Q W N K I Q V K L L Q M T G G L M ................................................................................................................................................................................................................................................................................................................ aaatgaagattttccagtactagatgctcctataaatactaaaaaatccttacattctaaacttacatcagtaaaggtttgccaatttttaatttgaacttttaataattgcatagttcctcctagaattaattatattctatatattaaagtataaataaaaatataattaaattcaagttttttataaatagattctattatatttgtaaaaaaaataaaatataatgtggatacttaaagatagttcgttactatccaaatttattattaactacttgatgcctctaatatttcctaaactccaaaatacttttttaacattagggggcatcatagtagcttcatttaaaagttatttaaatattttttaagaaaaatttgtgatgtaacttacttatctttaaaatattaagaaataggagtataagaa 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: 85 Start: 381 End: 410 ............................................................................................................................................................................................................................................................................................................................................................................................TTTGTGATGTAACTTACTTATCTTTAAAAT....................... PromScan Matrix: RpoD-17 Strand: + Score: 84 Start: 100 End: 129 ...................................................................................................TTTTAATAATTGCATAGTTCCTCCTAGAAT................................................................................................................................................................................................................................................................................................................ PromScan Matrix: RpoD-17 Strand: - Score: 83 Start: 151 End: 180 ......................................................................................................................................................CTTGAATTTAATTATATTTTTATTTATACT............................................................................................................................................................................................................................................................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aaatgaagattttccagtactagatgctcctataaatactaaaaaatccttacattctaaacttacatcagtaaaggtttgccaatttttaatttgaacttttaataattgcatagttcctcctagaattaattatattctatatattaaagtataaataaaaatataattaaattcaagttttttataaatagattctattatatttgtaaaaaaaataaaatataatgtggatacttaaagatagttcgttactatccaaatttattattaactacttgatgcctctaatatttcctaaactccaaaatacttttttaacattagggggcatcatagtagcttcatttaaaagttatttaaatattttttaagaaaaatttgtgatgtaacttacttatctttaaaatattaagaaataggagtataagaa Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 57 HP_score: -5.2 Tail_Score: -3.7108 Start: 243 End: 259 Full_Region: ttaataataaatttg gatagt aacga actatc tttaagtatccacat ..................................................................................................................................................................................................................................................gatagtaacgaactatc.............................................................................................................................................................................. TransTerm Strand: + Conf: 49 HP_score: -2.4 Tail_Score: -4.13561 Start: 348 End: 364 Full_Region: ATCATAGTAGCTTCA TTTAAA AGTTA TTTAAA TATTTTTTAAGAAAA ...........................................................................................................................................................................................................................................................................................................................................................TTTAAAAGTTATTTAAA..................................................................... Find igs database================================================ Query_seq: FN0185:FN0186|FN0185:FN0186:hypothetical protein:Cytochrome c-type biogenesis protein ccdA:<-->:810560..810992 433 aaatgaagattttccagtactagatgctcctataaatactaaaaaatccttacattctaaacttacatcagtaaaggtttgccaatttttaatttgaacttttaataattgcatagttcctcctagaattaattatattctatatattaaagtataaataaaaatataattaaattcaagttttttataaatagattctattatatttgtaaaaaaaataaaatataatgtggatacttaaagatagttcgttactatccaaatttattattaactacttgatgcctctaatatttcctaaactccaaaatacttttttaacattagggggcatcatagtagcttcatttaaaagttatttaaatattttttaagaaaaatttgtgatgtaacttacttatctttaaaatattaagaaataggagtataagaa Intra-Species Hit: Count: 1 Min: 1 Max: 433 Len: 433 Subject: NC_003454_FN0185_FN0186|hypothetical protein:Cytochrome c-type biogenesis protein ccdA|NEGATIVE:POSITIVE|[810560,810992]|433 HSP 1 e-value: 1.0E-118 bit: 426.0 Len: 215 Query Start:219 Query End:433 Subject Strand: POSITIVE Subject Start: 219 Subject End: 433 ..........................................................................................................................................................................................................................taaaatataatgtggatacttaaagatagttcgttactatccaaatttattattaactacttgatgcctctaatatttcctaaactccaaaatacttttttaacattagggggcatcatagtagcttcatttaaaagttatttaaatattttttaagaaaaatttgtgatgtaacttacttatctttaaaatattaagaaataggagtataagaa ..........................................................................................................................................................................................................................taaaatataatgtggatacttaaagatagttcgttactatccaaatttattattaactacttgatgcctctaatatttcctaaactccaaaatacttttttaacattagggggcatcatagtagcttcatttaaaagttatttaaatattttttaagaaaaatttgtgatgtaacttacttatctttaaaatattaagaaataggagtataagaa HSP 2 e-value: 3.0E-65 bit: 250.0 Len: 126 Query Start:1 Query End:126 Subject Strand: POSITIVE Subject Start: 1 Subject End: 126 aaatgaagattttccagtactagatgctcctataaatactaaaaaatccttacattctaaacttacatcagtaaaggtttgccaatttttaatttgaacttttaataattgcatagttcctcctag................................................................................................................................................................................................................................................................................................................... aaatgaagattttccagtactagatgctcctataaatactaaaaaatccttacattctaaacttacatcagtaaaggtttgccaatttttaatttgaacttttaataattgcatagttcctcctag................................................................................................................................................................................................................................................................................................................... Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAUGAAGAUUUUCCAGUACUAGAUGCUCCUAUAAAUACUAAAAAAUCCUUACAUUCUAAACUUACAUCAGUAAAGGUUUGCCAAUUUUUAAUUUGAACUUUUAAUAAUUGCAUAGUUCCUCCUAGAAUUAAUUAUAUUCUAUAUAUUAAAGUAUAAAUAAAAAUAUAAUUAAAUUCAAGUUUUUUAUAAAUAGAUUCUAUUAUAUUUGUAAAAAAAAUAAAAUAUAAUGUGGAUACUUAAAGAUAGUUCGUUACUAUCCAAAUUUAUUAUUAACUACUUGAUGCCUCUAAUAUUUCCUAAACUCCAAAAUACUUUUUUAACAUUAGGGGGCAUCAUAGUAGCUUCAUUUAAAAGUUAUUUAAAUAUUUUUUAAGAAAAAUUUGUGAUGUAACUUACUUAUCUUUAAAAUAUUAAGAAAUAGGAGUAUAAGAA .......................((((((((((............((((..(((((...((((..((....(((((((((...............))))))))).....))...)))).......((((((((((((((...(((((....)))))......))))))))).)))))...(((((((((((((..........)))))))))))))..........)))))))))..(((((((((((..(((((.((((((((((........(((((((((((((.........(((((.....((((....)))).....))))))))))))).))))).....((((((((.(((....))).))))))))..))))))).))))))))..)).)))))))))...........))))))))))..... (-82.56) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUCUUAUACUCCUAUUUCUUAAUAUUUUAAAGAUAAGUAAGUUACAUCACAAAUUUUUCUUAAAAAAUAUUUAAAUAACUUUUAAAUGAAGCUACUAUGAUGCCCCCUAAUGUUAAAAAAGUAUUUUGGAGUUUAGGAAAUAUUAGAGGCAUCAAGUAGUUAAUAAUAAAUUUGGAUAGUAACGAACUAUCUUUAAGUAUCCACAUUAUAUUUUAUUUUUUUUACAAAUAUAAUAGAAUCUAUUUAUAAAAAACUUGAAUUUAAUUAUAUUUUUAUUUAUACUUUAAUAUAUAGAAUAUAAUUAAUUCUAGGAGGAACUAUGCAAUUAUUAAAAGUUCAAAUUAAAAAUUGGCAAACCUUUACUGAUGUAAGUUUAGAAUGUAAGGAUUUUUUAGUAUUUAUAGGAGCAUCUAGUACUGGAAAAUCUUCAUUU ........((((((...........((((((((((.((..((((((((.(((((((...........((((((((.....)))))))).(((((((.(((((((..((((((((........................)))))))).))))))))))))))......)))))))))).)))))..))))))))))))..............((((..(((((((.(((((..........))))).)))))))..)))).(((((((((((((....((((......)))).)))))))))))))...))))))(((((.((((.(((.((((.((((((........))))...)).)))).)))))))))))).(((((..(((((((((((((((...(((......))))))))))))))))))))))) (-87.66) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 749 50 1 141 92 NC_003454:FN0185|5end_hypothetical_protein_810469..810699_NEGATIVE 299 130 86 107 67 NC_003454:FN1379|5end_Citrate_lyase_beta_chain_2026355..2026585_POSITIVE 291 266 221 157 109 NC_003454:FN0367|5end_Integral_membrane_protein_996901..997131_NEGATIVE 286 141 101 116 77 NC_003454:FN1423|5end_Flavoprotein_2090070..2090300_NEGATIVE 276 350 303 225 178 NC_003454:FN2091|5end_hypothetical_protein_602481..602711_NEGATIVE 260 344 301 187 142 NC_003454:FN0695|5end_ABC_transporter_ATP-binding_protein_1352886..1353116_POSITIVE 257 314 277 88 47 NC_003454:FN0201|5end_Glutaconyl-COA_decarboxylase_beta_subunit_826542..826772_POSITIVE 255 346 302 88 45 NC_003454:FN1591|5end_RNFB-related_protein_103135..103365_NEGATIVE 251 300 255 66 21 NC_003454:FN1495|5end_hypothetical_protein_2174410..2174640_NEGATIVE 251 300 255 90 45 NC_003454:FN1494|5end_Rod_shape-determining_protein_mreC_2174386..2174616_NEGATIVE 240 60 12 72 22 NC_003454:FN0658|5end_ABC_transporter_substrate-binding_protein_1315675..1315905_NEGATIVE 236 148 112 126 89 NC_003454:FN1948|5end_hypothetical_protein_453524..453754_NEGATIVE 235 130 81 110 54 NC_003454:FN0093|5end_Thioredoxin_729169..729399_POSITIVE 234 160 113 205 146 NC_003454:FN0688|5end_hypothetical_protein_1344068..1344298_POSITIVE 233 86 47 195 151 NC_003454:FN1917|5end_tRNA_delta(2)-isopentenylpyrophosphate_transferase_413756..413986_NEGATIVE 232 70 21 210 150 NC_003454:FN1828|5end_LSU_ribosomal_protein_L9P_317700..317930_NEGATIVE 232 346 307 228 196 NC_003454:FN1823|5end_Transcriptional_regulator,_TetR_family_311720..311950_POSITIVE 231 157 112 131 89 NC_003454:FN2101|5end_Transporter_610246..610476_POSITIVE 230 59 11 106 54 NC_003454:FN0242|5end_Trk_system_potassium_uptake_protein_trkA_865228..865458_POSITIVE 229 33 10 46 23 NC_003454:FN0712|5end_Chromate_transport_protein_1370776..1371006_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 375 350 303 75 28 NC_003454:FN0829|3end_hypothetical_protein_1489580..1489730_NEGATIVE 312 362 329 69 36 NC_003454:FN1260|3end_Sensory_Transduction_Protein_Kinase_1915863..1916013_NEGATIVE 312 344 308 71 35 NC_003454:FN1076|3end_hypothetical_protein_1723677..1723827_POSITIVE 299 130 86 98 58 NC_003454:FN1378|3end_Citrate_lyase_acyl_carrier_protein_2026426..2026576_POSITIVE 286 141 101 91 52 NC_003454:FN1424|3end_ACYL-COA_dehydrogenase,_short-chain_specific_2090095..2090245_NEGATIVE 276 350 303 92 45 NC_003454:FN2092|3end_Integral_membrane_protein_602614..602764_NEGATIVE 260 344 301 85 40 NC_003454:FN0694|3end_S-layer_protein_1352864..1353014_POSITIVE 257 314 277 73 32 NC_003454:FN0200|3end_Biotin_carboxyl_carrier_protein_of_glutaconyl-COA_decarboxylase_826607..826757_POSITIVE 255 346 302 61 18 NC_003454:FN1592|3end_Na(+)-translocating_NADH-quinone_reductase_subunit_D_103162..103312_NEGATIVE 251 300 255 65 20 NC_003454:FN1495|3end_hypothetical_protein_-89..61_NEGATIVE 240 60 12 57 7 NC_003454:FN0659|3end_ABC_transporter_permease_protein_1315690..1315840_NEGATIVE 236 148 112 116 79 NC_003454:FN1949|3end_Xaa-Pro_dipeptidase_453534..453684_NEGATIVE 234 363 327 102 57 NC_003454:FN0777|3end_GTP-binding_protein_LepA_1433018..1433168_NEGATIVE 234 160 113 103 44 NC_003454:FN0687|3end_hypothetical_protein_1344046..1344196_POSITIVE 231 157 112 121 79 NC_003454:FN2100|3end_hypothetical_protein_610316..610466_POSITIVE 230 59 11 93 41 NC_003454:FN0241|3end_Dihydrofolate_reductase_865295..865445_POSITIVE 229 33 10 53 30 NC_003454:FN0711|3end_Phosphopantothenate--cysteine_ligase_1370863..1371013_POSITIVE 226 136 108 62 31 NC_003454:FN0982|3end_bifunctional_phosphoribosylaminoimidazolecarboxamide_formyltransferase/IMP_cyclohydrolase_1634137..1634287_NEGATIVE 225 127 84 95 51 NC_003454:FN0408|3end_Acetyl-coenzyme_A_carboxylase_carboxyl_transferase_subunit_beta_1046345..1046495_POSITIVE 220 320 277 73 26 NC_003454:FN0710|3end_hypothetical_protein_1369632..1369782_POSITIVE