Origin IGS: aaaataaatagaatttattaaggatttagggtttctaaaaaactttaaatccttttttataagagagaacattactccaaaaggtgacagaaactcattctattgacaaaaaatcaatatatttttataataatagtataagaaaataggattctgaagaaagatagaaaaggttaaaaatataataatattccaatattcaattaagaatttctcacaattgaaatttttatagaaaaaaataaaaactatttaaggaggaattttatgaaaaaaacactattttctatattacttataggaatttgt .........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 acaaattcctataagtaatatagaaaatagtgtttttttcataaaattcctccttaaatagtttttatttttttctataaaaatttcaattgtgagaaattcttaattgaatattggaatattattatatttttaaccttttctatctttcttcagaatcctattttcttatactattattataaaaatatattgattttttgtcaatagaatgagtttctgtcaccttttggagtaatgttctctcttataaaaaaggatttaaagttttttagaaaccctaaatccttaataaattctatttatttt Mask Tandem Repeat Region ================================================ aaaataaatagaatttattaaggatttagggtttctaaaaaactttaaatccttttttataagagagaacattactccaaaaggtgacagaaactcattctattgacaaaaaatcaatatatttttataataatagtataagaaaataggattctgaagaaagatagaaaaggttaaaaatataataatattccaatattcaattaagaatttctcacaattgaaatttttatagaaaaaaataaaaactatttaaggaggaattttatgaaaaaaacactattttctatattacttataggaatttgt Find is-nt database================================================ Query_seq: FN0549:FN0550|FN0549:FN0550:O-sialoglycoprotein endopeptidase:Mannose-1-phosphate guanylyl transferase (GDP):->->:1202492..1202800 309 aaaataaatagaatttattaaggatttagggtttctaaaaaactttaaatccttttttataagagagaacattactccaaaaggtgacagaaactcattctattgacaaaaaatcaatatatttttataataatagtataagaaaataggattctgaagaaagatagaaaaggttaaaaatataataatattccaatattcaattaagaatttctcacaattgaaatttttatagaaaaaaataaaaactatttaaggaggaattttatgaaaaaaacactattttctatattacttataggaatttgt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: FN0549:FN0550|FN0549:FN0550:O-sialoglycoprotein endopeptidase:Mannose-1-phosphate guanylyl transferase (GDP):->->:1202492..1202800 309 aaaataaatagaatttattaaggatttagggtttctaaaaaactttaaatccttttttataagagagaacattactccaaaaggtgacagaaactcattctattgacaaaaaatcaatatatttttataataatagtataagaaaataggattctgaagaaagatagaaaaggttaaaaatataataatattccaatattcaattaagaatttctcacaattgaaatttttatagaaaaaaataaaaactatttaaggaggaattttatgaaaaaaacactattttctatattacttataggaatttgt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: FN0549:FN0550|FN0549:FN0550:O-sialoglycoprotein endopeptidase:Mannose-1-phosphate guanylyl transferase (GDP):->->:1202492..1202800 309 aaaataaatagaatttattaaggatttagggtttctaaaaaactttaaatccttttttataagagagaacattactccaaaaggtgacagaaactcattctattgacaaaaaatcaatatatttttataataatagtataagaaaataggattctgaagaaagatagaaaaggttaaaaatataataatattccaatattcaattaagaatttctcacaattgaaatttttatagaaaaaaataaaaactatttaaggaggaattttatgaaaaaaacactattttctatattacttataggaatttgt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aaaataaatagaatttattaaggatttagggtttctaaaaaactttaaatccttttttataagagagaacattactccaaaaggtgacagaaactcattctattgacaaaaaatcaatatatttttataataatagtataagaaaataggattctgaagaaagatagaaaaggttaaaaatataataatattccaatattcaattaagaatttctcacaattgaaatttttatagaaaaaaataaaaactatttaaggaggaattttatgaaaaaaacactattttctatattacttataggaatttgt Predict ORF larger than 30AA ================================================ Protein_Len: 32 Strand: + Start: 8 End: 103 ....... M E F I K D L G F L K N F K S F F I R E N I T P K G D R N S F Y .............................................................................................................................................................................................................. Protein_Len: 30 Strand: + Start: 220 End: 309 ........................................................................................................................................................................................................................... M E I F I E K N K N Y L R R N F M K K T L F S I L L I G I C Protein_Len: 50 Strand: - Start: 103 End: 252 ...................................................................................................... Q C F I L I N K Y Y Y Y L F I P N Q L F I S F T L F I I I N W Y E I L F K E C N F N K Y F F I F V M ......................................................... Protein_Len: 30 Strand: - Start: 1 End: 90 F Y I S N I L S K P N R F F K L D K K I L S F M V G F P S M ........................................................................................................................................................................................................................... aaaataaatagaatttattaaggatttagggtttctaaaaaactttaaatccttttttataagagagaacattactccaaaaggtgacagaaactcattctattgacaaaaaatcaatatatttttataataatagtataagaaaataggattctgaagaaagatagaaaaggttaaaaatataataatattccaatattcaattaagaatttctcacaattgaaatttttatagaaaaaaataaaaactatttaaggaggaattttatgaaaaaaacactattttctatattacttataggaatttgt 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: 93 Start: 102 End: 131 .....................................................................................................ATTGACAAAAAATCAATATATTTTTATAAT.................................................................................................................................................................................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aaaataaatagaatttattaaggatttagggtttctaaaaaactttaaatccttttttataagagagaacattactccaaaaggtgacagaaactcattctattgacaaaaaatcaatatatttttataataatagtataagaaaataggattctgaagaaagatagaaaaggttaaaaatataataatattccaatattcaattaagaatttctcacaattgaaatttttatagaaaaaaataaaaactatttaaggaggaattttatgaaaaaaacactattttctatattacttataggaatttgt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: FN0549:FN0550|FN0549:FN0550:O-sialoglycoprotein endopeptidase:Mannose-1-phosphate guanylyl transferase (GDP):->->:1202492..1202800 309 aaaataaatagaatttattaaggatttagggtttctaaaaaactttaaatccttttttataagagagaacattactccaaaaggtgacagaaactcattctattgacaaaaaatcaatatatttttataataatagtataagaaaataggattctgaagaaagatagaaaaggttaaaaatataataatattccaatattcaattaagaatttctcacaattgaaatttttatagaaaaaaataaaaactatttaaggaggaattttatgaaaaaaacactattttctatattacttataggaatttgt Intra-Species Hit: Count: 1 Min: 1 Max: 309 Len: 309 Subject: NC_003454_FN0549_FN0550|O-sialoglycoprotein endopeptidase:Mannose-1-phosphate guanylyl transferase (GDP)|POSITIVE:POSITIVE|[1202492,1202800]|309 HSP 1 e-value: 2.0E-65 bit: 250.0 Len: 126 Query Start:1 Query End:126 Subject Strand: POSITIVE Subject Start: 1 Subject End: 126 aaaataaatagaatttattaaggatttagggtttctaaaaaactttaaatccttttttataagagagaacattactccaaaaggtgacagaaactcattctattgacaaaaaatcaatatattttt....................................................................................................................................................................................... aaaataaatagaatttattaaggatttagggtttctaaaaaactttaaatccttttttataagagagaacattactccaaaaggtgacagaaactcattctattgacaaaaaatcaatatattttt....................................................................................................................................................................................... HSP 2 e-value: 5.0E-17 bit: 89.7 Len: 45 Query Start:191 Query End:235 Subject Strand: POSITIVE Subject Start: 191 Subject End: 235 ..............................................................................................................................................................................................ttccaatattcaattaagaatttctcacaattgaaatttttatag.......................................................................... ..............................................................................................................................................................................................ttccaatattcaattaagaatttctcacaattgaaatttttatag.......................................................................... HSP 3 e-value: 5.0E-14 bit: 79.8 Len: 61 Query Start:249 Query End:309 Subject Strand: POSITIVE Subject Start: 249 Subject End: 309 ........................................................................................................................................................................................................................................................ctatttaaggaggaattttatgnnnnnnncactattttctatattacttataggaatttgt ........................................................................................................................................................................................................................................................ctatttaaggaggaattttatgaaaaaaacactattttctatattacttataggaatttgt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAAUAAAUAGAAUUUAUUAAGGAUUUAGGGUUUCUAAAAAACUUUAAAUCCUUUUUUAUAAGAGAGAACAUUACUCCAAAAGGUGACAGAAACUCAUUCUAUUGACAAAAAAUCAAUAUAUUUUUAUAAUAAUAGUAUAAGAAAAUAGGAUUCUGAAGAAAGAUAGAAAAGGUUAAAAAUAUAAUAAUAUUCCAAUAUUCAAUUAAGAAUUUCUCACAAUUGAAAUUUUUAUAGAAAAAAAUAAAAACUAUUUAAGGAGGAAUUUUAUGAAAAAAACACUAUUUUCUAUAUUACUUAUAGGAAUUUGU ......(((((((......(((((((((((((((.....)))))))))))))))........(((......(((((......)))))......))).)))))))............(((.((((((((((...(((((((.((((((((..(((((........)))))...............((((.(((((....(((...((((((((((........))))))))))..)))..(((((.....))))).....))))).))))..........))))))))))))))).)))))))))).))) (-57.70) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACAAAUUCCUAUAAGUAAUAUAGAAAAUAGUGUUUUUUUCAUAAAAUUCCUCCUUAAAUAGUUUUUAUUUUUUUCUAUAAAAAUUUCAAUUGUGAGAAAUUCUUAAUUGAAUAUUGGAAUAUUAUUAUAUUUUUAACCUUUUCUAUCUUUCUUCAGAAUCCUAUUUUCUUAUACUAUUAUUAUAAAAAUAUAUUGAUUUUUUGUCAAUAGAAUGAGUUUCUGUCACCUUUUGGAGUAAUGUUCUCUCUUAUAAAAAAGGAUUUAAAGUUUUUUAGAAACCCUAAAUCCUUAAUAAAUUCUAUUUAUUUU ......................(((((........)))))..............(((((((..((((((....................((((((((.((((......))))...(((((((((((...........................(((((.........(((((.(((((...(((((((.........))))))).))))).))))).)))))...((....))))))))))))).))))))))..(((((((((..(((((...)))))..)))))))))))))))..))))))).... (-46.60) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 269 56 20 209 174 NC_003454:FN1023|5end_5-Nitroimidazole_antibiotic_resistance_protein_1678030..1678260_NEGATIVE 238 59 14 83 38 NC_003454:FN1401|5end_urocanate_hydratase_2058592..2058822_POSITIVE 206 300 253 231 181 NC_003454:FN2085|5end_hypothetical_protein_597045..597275_NEGATIVE 194 270 226 49 11 NC_003454:FN1425|5end_hypothetical_protein_2091911..2092141_POSITIVE 193 108 70 217 177 NC_003454:FN0145|5end_hypothetical_protein_774306..774536_POSITIVE 191 180 136 70 25 NC_003454:FN1672|5end_Membrane-bound_O-acyltransferase_171293..171523_NEGATIVE 189 55 20 151 120 NC_003454:FN1103|5end_Excinuclease_ABC_subunit_A_1746559..1746789_POSITIVE 187 87 44 185 147 NC_003454:FN1864|5end_DNA_mismatch_repair_protein_mutS_356141..356371_NEGATIVE 186 89 42 50 1 NC_003454:FN2023|5end_Hypothetical_cytosolic_protein_526642..526872_NEGATIVE 183 54 11 85 48 NC_003454:FN0716|5end_Phophatidylinositol-4-phosphate_5-kinase_1373969..1374199_POSITIVE 183 276 231 208 163 NC_003454:FN0122|5end_hypothetical_protein_753401..753631_POSITIVE 181 54 20 197 161 NC_003454:FN1080|5end_Export_ABC_transporter_1725534..1725764_POSITIVE 181 237 194 51 10 NC_003454:FN0604|5end_Proton/sodium-aspartate_symport_protein_1258570..1258800_POSITIVE 181 119 75 69 25 NC_003454:FN0375|5end_Iron(III)-binding_protein_1005293..1005523_POSITIVE 179 67 23 67 12 NC_003454:FN1683|5end_Acetyltransferase_179082..179312_NEGATIVE 177 106 78 194 164 NC_003454:FN0084|5end_Acetaldehyde_dehydrogenase_[acetylating]_721572..721802_POSITIVE 177 66 21 87 43 NC_003454:FN2031|5end_Thiamine_biosynthesis_lipoprotein_apbE_537083..537313_NEGATIVE 175 52 20 49 22 NC_003454:FN0495|5end_Acetyl-CoA_acetyltransferase_1139567..1139797_POSITIVE 174 97 52 108 65 NC_003454:FN1586|5end_O-succinylbenzoate-CoA_synthase_98542..98772_NEGATIVE 172 107 70 57 14 NC_003454:FN1994|5end_hypothetical_protein_497577..497807_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 269 56 20 67 32 NC_003454:FN1024|3end_DNA-binding_protein_HU_1678172..1678322_NEGATIVE 261 54 20 71 37 NC_003454:FN0549|3end_O-sialoglycoprotein_endopeptidase_1202431..1202581_POSITIVE 221 91 57 84 42 NC_003454:FN0486|3end_Transposase_1131710..1131860_POSITIVE 216 100 52 146 101 NC_003454:FN0245|3end_Copper-exporting_ATPase_870680..870830_POSITIVE 193 108 70 65 25 NC_003454:FN0143|3end_hypothetical_protein_774234..774384_POSITIVE 189 55 20 83 52 NC_003454:FN1102|3end_tRNA_2'phosphotransferase_1746571..1746721_POSITIVE 189 101 61 75 38 NC_003454:FN1590|3end_Hypothetical_lipoprotein_100560..100710_NEGATIVE 187 91 60 84 47 NC_003454:FN0841|3end_Transposase_1502804..1502954_POSITIVE 183 54 11 92 55 NC_003454:FN0715|3end_hypothetical_protein_1374056..1374206_POSITIVE 183 164 141 45 22 NC_003454:FN0701|3end_Methyltransferase_1360894..1361044_POSITIVE 181 54 20 60 24 NC_003454:FN1079|3end_Neutrophil-activating_protein_A_1725477..1725627_POSITIVE 180 109 74 105 65 NC_003454:FN0139|3end_Transposase_771640..771790_POSITIVE 179 67 23 66 11 NC_003454:FN1684|3end_N-acetylneuraminate_synthase_179083..179233_NEGATIVE 178 166 121 77 34 NC_003454:FN1668|3end_Cholinephosphate_cytidylyltransferase_164691..164841_NEGATIVE 177 106 78 86 56 NC_003454:FN0083|3end_Ethanolamine_utilization_protein_eutM_precursor_721544..721694_POSITIVE 177 66 21 49 5 NC_003454:FN2032|3end_DNA-directed_RNA_polymerase_omega_chain_537121..537271_NEGATIVE 172 107 70 50 7 NC_003454:FN1993|3end_SUA5_protein_497650..497800_POSITIVE 170 98 53 35 3 NC_003454:FN2101|3end_Transporter_611231..611381_POSITIVE 168 176 147 59 28 NC_003454:FN0048|3end_4-nitrophenylphosphatase_685285..685435_NEGATIVE 165 91 60 85 45 NC_003454:FN1889|3end_Transposase_373027..373177_POSITIVE