Origin IGS: ttaatatccctcctatatattttttttgcaaaactattatactaaattttttgaattattaaaagcattttaaaaattttaaataaattttacttgcttttttttgatttactgtgtaggataagttaatatatataaaaaataatttattagtagataaactttttttgttggctacttgccagccattagtgtttcgagagctccaaaatgctctctcaacattaatggacgtcgcagtagcttgttaaaaaaactttaataaaatttatttattttttatatattctgattttgataatagaggaaataata .........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 tattatttcctctattatcaaaatcagaatatataaaaaataaataaattttattaaagtttttttaacaagctactgcgacgtccattaatgttgagagagcattttggagctctcgaaacactaatggctggcaagtagccaacaaaaaaagtttatctactaataaattattttttatatatattaacttatcctacacagtaaatcaaaaaaaagcaagtaaaatttatttaaaatttttaaaatgcttttaataattcaaaaaatttagtataatagttttgcaaaaaaaatatataggagggatattaa Mask Tandem Repeat Region ================================================ ttaatatccctcctatatattttttttgcaaaactattatactaaattttttgaattattaaaagcattttaaaaattttaaataaattttacttgcttttttttgatttactgtgtaggataagttaatatatataaaaaataatttattagtagataaactttttttgttggctacttgccagccattagtgtttcgagagctccaaaatgctctctcaacattaatggacgtcgcagtagcttgttaaaaaaactttaataaaatttatttattttttatatattctgattttgataatagaggaaataata Find is-nt database================================================ Query_seq: FN1141:FN1142|FN1141:FN1142:Formate transporter:Oxygen-independent coproporphyrinogen III oxidase:<-->:1791354..1791668 315 ttaatatccctcctatatattttttttgcaaaactattatactaaattttttgaattattaaaagcattttaaaaattttaaataaattttacttgcttttttttgatttactgtgtaggataagttaatatatataaaaaataatttattagtagataaactttttttgttggctacttgccagccattagtgtttcgagagctccaaaatgctctctcaacattaatggacgtcgcagtagcttgttaaaaaaactttaataaaatttatttattttttatatattctgattttgataatagaggaaataata Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: FN1141:FN1142|FN1141:FN1142:Formate transporter:Oxygen-independent coproporphyrinogen III oxidase:<-->:1791354..1791668 315 ttaatatccctcctatatattttttttgcaaaactattatactaaattttttgaattattaaaagcattttaaaaattttaaataaattttacttgcttttttttgatttactgtgtaggataagttaatatatataaaaaataatttattagtagataaactttttttgttggctacttgccagccattagtgtttcgagagctccaaaatgctctctcaacattaatggacgtcgcagtagcttgttaaaaaaactttaataaaatttatttattttttatatattctgattttgataatagaggaaataata Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: FN1141:FN1142|FN1141:FN1142:Formate transporter:Oxygen-independent coproporphyrinogen III oxidase:<-->:1791354..1791668 315 ttaatatccctcctatatattttttttgcaaaactattatactaaattttttgaattattaaaagcattttaaaaattttaaataaattttacttgcttttttttgatttactgtgtaggataagttaatatatataaaaaataatttattagtagataaactttttttgttggctacttgccagccattagtgtttcgagagctccaaaatgctctctcaacattaatggacgtcgcagtagcttgttaaaaaaactttaataaaatttatttattttttatatattctgattttgataatagaggaaataata Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ttaatatccctcctatatattttttttgcaaaactattatactaaattttttgaattattaaaagcattttaaaaattttaaataaattttacttgcttttttttgatttactgtgtaggataagttaatatatataaaaaataatttattagtagataaactttttttgttggctacttgccagccattagtgtttcgagagctccaaaatgctctctcaacattaatggacgtcgcagtagcttgttaaaaaaactttaataaaatttatttattttttatatattctgattttgataatagaggaaataata Predict ORF larger than 30AA ================================================ Protein_Len: 40 Strand: + Start: 129 End: 248 ................................................................................................................................ M Y I K N N L L V D K L F L L A T C Q P L V F R E L Q N A L S T L M D V A V A C ................................................................... Protein_Len: 56 Strand: - Start: 62 End: 229 ............................................................. F C K L F K L Y I K S A K K Q N V T Y S L N I Y I F F L K N T S L S K K N A V Q W G N T N R S S W F A R E V N M ...................................................................................... ttaatatccctcctatatattttttttgcaaaactattatactaaattttttgaattattaaaagcattttaaaaattttaaataaattttacttgcttttttttgatttactgtgtaggataagttaatatatataaaaaataatttattagtagataaactttttttgttggctacttgccagccattagtgtttcgagagctccaaaatgctctctcaacattaatggacgtcgcagtagcttgttaaaaaaactttaataaaatttatttattttttatatattctgattttgataatagaggaaataata 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: 83 Start: 103 End: 132 ......................................................................................................TTTGATTTACTGTGTAGGATAAGTTAATAT....................................................................................................................................................................................... PromScan Matrix: RpoD-17 Strand: - Score: 81 Start: 36 End: 65 ...................................CTTTTAATAATTCAAAAAATTTAGTATAAT.......................................................................................................................................................................................................................................................... PromScan Matrix: RpoD-17 Strand: - Score: 81 Start: 55 End: 84 ......................................................ATTTAAAATTTTTAAAATGCTTTTAATAAT....................................................................................................................................................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ ttaatatccctcctatatattttttttgcaaaactattatactaaattttttgaattattaaaagcattttaaaaattttaaataaattttacttgcttttttttgatttactgtgtaggataagttaatatatataaaaaataatttattagtagataaactttttttgttggctacttgccagccattagtgtttcgagagctccaaaatgctctctcaacattaatggacgtcgcagtagcttgttaaaaaaactttaataaaatttatttattttttatatattctgattttgataatagaggaaataata Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 43 HP_score: -3.0 Tail_Score: -3.15544 Start: 193 End: 224 Full_Region: CTTGCCAGCCATTAG TGTTTCGAGAGC TCCAAAAT GCTCTCTCAACA TTAATGGACGTCGCA ................................................................................................................................................................................................TGTTTCGAGAGCTCCAAAATGCTCTCTCAACA........................................................................................... TransTerm Strand: + Conf: 38 HP_score: -2.0 Tail_Score: -2.70228 Start: 245 End: 265 Full_Region: GGACGTCGCAGTAGC TTGTTAAA AAAAC TTTAATAA AATTTATTTATTTTT ....................................................................................................................................................................................................................................................TTGTTAAAAAAACTTTAATAA.................................................. Find igs database================================================ Query_seq: FN1141:FN1142|FN1141:FN1142:Formate transporter:Oxygen-independent coproporphyrinogen III oxidase:<-->:1791354..1791668 315 ttaatatccctcctatatattttttttgcaaaactattatactaaattttttgaattattaaaagcattttaaaaattttaaataaattttacttgcttttttttgatttactgtgtaggataagttaatatatataaaaaataatttattagtagataaactttttttgttggctacttgccagccattagtgtttcgagagctccaaaatgctctctcaacattaatggacgtcgcagtagcttgttaaaaaaactttaataaaatttatttattttttatatattctgattttgataatagaggaaataata Intra-Species Hit: Count: 1 Min: 112 Max: 315 Len: 204 Subject: NC_003454_FN1141_FN1142|Formate transporter:Oxygen-independent coproporphyrinogen III oxidase|NEGATIVE:POSITIVE|[1791354,1791668]|315 HSP 1 e-value: 8.0E-87 bit: 321.0 Len: 204 Query Start:112 Query End:315 Subject Strand: POSITIVE Subject Start: 112 Subject End: 315 ...............................................................................................................ctgtgtaggataagttaatatatataaaaaataatttattagtagataaacnnnnnnngttggctacttgccagccattagtgtttcgagagctccaaaatgctctctcaacattaatggacgtcgcagtagcttgttnnnnnnnctttaataaaatttatttattttttatatattctgattttgataatagaggaaataata ...............................................................................................................ctgtgtaggataagttaatatatataaaaaataatttattagtagataaactttttttgttggctacttgccagccattagtgtttcgagagctccaaaatgctctctcaacattaatggacgtcgcagtagcttgttaaaaaaactttaataaaatttatttattttttatatattctgattttgataatagaggaaataata Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUGUGUAGGAUAAGUUAAUAUAUAUAAAAAAUAAUUUAUUAGUAGAUAAACUUUUUUUGUUGGCUACUUGCCAGCCAUUAGUGUUUCGAGAGCUCCAAAAUGCUCUCUCAACAUUAAUGGACGUCGCAGUAGCUUGUUAAAAAAACUUUAAUAAAAUUUAUUUAUUUUUUAUAUAUUCUGAUUUUGAUAAUAGAGGAAAUAAUA ((.(((.....((((((..(((((((((((((((........((..((((.((((((((..(((((((.((..((((((((((((..((((((........))))))..))))))))))).)...)))))))))...)))))))).)))).))........)))))))))))))))..)))))).....))).))......... (-58.99) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAUUAUUUCCUCUAUUAUCAAAAUCAGAAUAUAUAAAAAAUAAAUAAAUUUUAUUAAAGUUUUUUUAACAAGCUACUGCGACGUCCAUUAAUGUUGAGAGAGCAUUUUGGAGCUCUCGAAACACUAAUGGCUGGCAAGUAGCCAACAAAAAAAGUUUAUCUACUAAUAAAUUAUUUUUUAUAUAUAUUAACUUAUCCUACACAG ............................(((((((((((((((...........((((.(((((((.....((((((((.(.(.((((((.((((..((((((........))))))..)))).)))))))).)).))))))....))))))).))))............)))))))))))))))................... (-48.40) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 696 120 72 171 123 NC_003454:FN0695|5end_ABC_transporter_ATP-binding_protein_1352886..1353116_POSITIVE 585 130 84 215 171 NC_003454:FN2091|5end_hypothetical_protein_602481..602711_NEGATIVE 342 29 1 231 203 NC_003454:FN1141|5end_Formate_transporter_1791263..1791493_NEGATIVE 341 106 62 187 142 NC_003454:FN1439|5end_Transcriptional_regulator,_DeoR_family_2106428..2106658_POSITIVE 341 106 62 83 38 NC_003454:FN1438|5end_hypothetical_protein_2106324..2106554_POSITIVE 284 119 72 210 162 NC_003454:FN1995|5end_hypothetical_protein_498245..498475_POSITIVE 272 98 52 45 2 NC_003454:FN0299|5end_Aspartyl-tRNA_synthetase_932393..932623_POSITIVE 268 106 62 186 141 NC_003454:FN1351|5end_15_kDa_lipoprotein_precursor_2003372..2003602_NEGATIVE 257 106 62 213 168 NC_003454:FN1740|5end_ATP_synthase_subunit_K_238400..238630_NEGATIVE 254 110 64 64 13 NC_003454:FN1431|5end_Branched-chain_amino_acid_transport_system_permease_protein_livH_2100252..2100482_NEGATIVE 253 125 82 56 23 NC_003454:FN0187|5end_Thiol:disulfide_interchange_protein_tlpA_811590..811820_POSITIVE 247 96 53 101 46 NC_003454:FN1164|5end_Glucokinase_1821754..1821984_POSITIVE 241 111 71 231 195 NC_003454:FN1584|5end_Beta-lactamase_96158..96388_NEGATIVE 237 109 61 72 7 NC_003454:FN0216|5end_3-oxoacyl-[acyl-carrier_protein]_reductase_840864..841094_NEGATIVE 227 108 64 83 24 NC_003454:FN1355|5end_Integral_membrane_protein_2007575..2007805_NEGATIVE 225 98 72 69 43 NC_003454:FN0947|5end_hypothetical_protein_1600457..1600687_POSITIVE 223 125 84 188 147 NC_003454:FN1862|5end_L-beta-lysine_5,6-aminomutase_beta_subunit_353122..353352_NEGATIVE 220 108 71 38 3 NC_003454:FN1925|5end_Arsenical_pump_membrane_protein_424335..424565_NEGATIVE 219 118 72 61 13 NC_003454:FN0490|5end_Integral_membrane_protein_1136234..1136464_NEGATIVE 219 98 52 69 10 NC_003454:FN0465|5end_hypothetical_protein_1110046..1110276_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 696 120 72 69 21 NC_003454:FN0694|3end_S-layer_protein_1352864..1353014_POSITIVE 589 130 81 65 18 NC_003454:FN0829|3end_hypothetical_protein_1489580..1489730_NEGATIVE 585 130 84 82 38 NC_003454:FN2092|3end_Integral_membrane_protein_602614..602764_NEGATIVE 429 132 91 49 7 NC_003454:FN1260|3end_Sensory_Transduction_Protein_Kinase_1915863..1916013_NEGATIVE 335 134 98 71 35 NC_003454:FN1076|3end_hypothetical_protein_1723677..1723827_POSITIVE 268 106 62 52 7 NC_003454:FN1352|3end_ABC_transporter_ATP-binding_protein_2003506..2003656_NEGATIVE 257 106 62 52 7 NC_003454:FN1741|3end_ATP_synthase_subunit_I_238561..238711_NEGATIVE 247 96 53 77 22 NC_003454:FN1163|3end_Thioredoxin_reductase_1821810..1821960_POSITIVE 244 130 82 66 12 NC_003454:FN1259|3end_Uracil-DNA_glycosylase_1915756..1915906_POSITIVE 235 108 74 78 43 NC_003454:FN0535|3end_hypothetical_protein_1190009..1190159_POSITIVE 226 96 53 135 98 NC_003454:FN1253|3end_hypothetical_protein_1910229..1910379_NEGATIVE 219 118 72 56 8 NC_003454:FN0491|3end_Alanine_racemase_1136239..1136389_NEGATIVE 218 108 73 141 115 NC_003454:FN1628|3end_LSU_ribosomal_protein_L18P_133580..133730_NEGATIVE 213 104 63 75 28 NC_003454:FN0081|3end_Ethanolamine_utilization_protein_eutL_720768..720918_POSITIVE 212 138 92 80 41 NC_003454:FN1199|3end_DNA_polymerase_IV_1860193..1860343_POSITIVE 211 100 62 48 6 NC_003454:FN0439|3end_hypothetical_protein_1080837..1080987_NEGATIVE 210 87 51 135 99 NC_003454:FN2032|3end_DNA-directed_RNA_polymerase_omega_chain_537121..537271_NEGATIVE 208 113 71 50 9 NC_003454:FN0659|3end_ABC_transporter_permease_protein_1315690..1315840_NEGATIVE 207 109 69 119 70 NC_003454:FN1428|3end_Branched-chain_amino_acid_transport_ATP-binding_protein_livF_2096860..2097010_NEGATIVE 207 134 92 135 89 NC_003454:FN0103|3end_Ribonucleoside-diphosphate_reductase_beta_chain_739607..739757_POSITIVE