Origin IGS: taaaatcctctcctttttgttcttacctctatttttattctaatcttactttcatttttatatctcttattataaatcataattatgaattaagaatgaattttatgtttaaattttgacacttatctctatattttataacaattttcttttataaattaaagataaacatttgttatatattttatgggaaaaaaatttaataagctttcttaatctctcgtacatttagtatatataattaaaatgaatacctaatgaatacactttattacttaatattatatcatatttctaagaatacaaaaaaccacaagaaatgaggggagagacttgtggtttttctatctacatattcattttattagggaggggtttatctatgttcccttatatgccttaagtatatagtagaaaaatgaatgtaaaatgaatttaccatattttttttttaaattttt .........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.........1.........2.........3.........4.........5.........6.........7.........8.........9 aaaaatttaaaaaaaaaatatggtaaattcattttacattcatttttctactatatacttaaggcatataagggaacatagataaacccctccctaataaaatgaatatgtagatagaaaaaccacaagtctctcccctcatttcttgtggttttttgtattcttagaaatatgatataatattaagtaataaagtgtattcattaggtattcattttaattatatatactaaatgtacgagagattaagaaagcttattaaatttttttcccataaaatatataacaaatgtttatctttaatttataaaagaaaattgttataaaatatagagataagtgtcaaaatttaaacataaaattcattcttaattcataattatgatttataataagagatataaaaatgaaagtaagattagaataaaaatagaggtaagaacaaaaaggagaggatttta Mask Tandem Repeat Region ================================================ taaaatcctctcctttttgttcttacctctatttttattctaatcttactttcatttttatatctcttattataaatcataattatgaattaagaatgaattttatgtttaaattttgacacttatctctatattttataacaattttcttttataaattaaagataaacatttgttatatattttatgggaaaaaaatttaataagctttcttaatctctcgtacatttagtatatataattaaaatgaatacctaatgaatacactttattacttaatattatatcatatttctaagaatacaaaaaaccacaagaaatgaggggagagacttgtggtttttctatctacatattcattttattagggaggggtttatctatgttcccttatatgccttaagtatatagtagaaaaatgaatgtaaaatgaatttaccatattttttttttaaattttt Find is-nt database================================================ Query_seq: FN2085:FN2086|FN2085:FN2086:hypothetical protein:General secretion pathway protein D:<-<-:597136..597596 461 taaaatcctctcctttttgttcttacctctatttttattctaatcttactttcatttttatatctcttattataaatcataattatgaattaagaatgaattttatgtttaaattttgacacttatctctatattttataacaattttcttttataaattaaagataaacatttgttatatattttatgggaaaaaaatttaataagctttcttaatctctcgtacatttagtatatataattaaaatgaatacctaatgaatacactttattacttaatattatatcatatttctaagaatacaaaaaaccacaagaaatgaggggagagacttgtggtttttctatctacatattcattttattagggaggggtttatctatgttcccttatatgccttaagtatatagtagaaaaatgaatgtaaaatgaatttaccatattttttttttaaattttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: FN2085:FN2086|FN2085:FN2086:hypothetical protein:General secretion pathway protein D:<-<-:597136..597596 461 taaaatcctctcctttttgttcttacctctatttttattctaatcttactttcatttttatatctcttattataaatcataattatgaattaagaatgaattttatgtttaaattttgacacttatctctatattttataacaattttcttttataaattaaagataaacatttgttatatattttatgggaaaaaaatttaataagctttcttaatctctcgtacatttagtatatataattaaaatgaatacctaatgaatacactttattacttaatattatatcatatttctaagaatacaaaaaaccacaagaaatgaggggagagacttgtggtttttctatctacatattcattttattagggaggggtttatctatgttcccttatatgccttaagtatatagtagaaaaatgaatgtaaaatgaatttaccatattttttttttaaattttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: FN2085:FN2086|FN2085:FN2086:hypothetical protein:General secretion pathway protein D:<-<-:597136..597596 461 taaaatcctctcctttttgttcttacctctatttttattctaatcttactttcatttttatatctcttattataaatcataattatgaattaagaatgaattttatgtttaaattttgacacttatctctatattttataacaattttcttttataaattaaagataaacatttgttatatattttatgggaaaaaaatttaataagctttcttaatctctcgtacatttagtatatataattaaaatgaatacctaatgaatacactttattacttaatattatatcatatttctaagaatacaaaaaaccacaagaaatgaggggagagacttgtggtttttctatctacatattcattttattagggaggggtttatctatgttcccttatatgccttaagtatatagtagaaaaatgaatgtaaaatgaatttaccatattttttttttaaattttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taaaatcctctcctttttgttcttacctctatttttattctaatcttactttcatttttatatctcttattataaatcataattatgaattaagaatgaattttatgtttaaattttgacacttatctctatattttataacaattttcttttataaattaaagataaacatttgttatatattttatgggaaaaaaatttaataagctttcttaatctctcgtacatttagtatatataattaaaatgaatacctaatgaatacactttattacttaatattatatcatatttctaagaatacaaaaaaccacaagaaatgaggggagagacttgtggtttttctatctacatattcattttattagggaggggtttatctatgttcccttatatgccttaagtatatagtagaaaaatgaatgtaaaatgaatttaccatattttttttttaaattttt Predict ORF larger than 30AA ================================================ Protein_Len: 41 Strand: + Start: 286 End: 408 ............................................................................................................................................................................................................................................................................................. M I F L R I Q K T T R N E G R D L W F F Y L H I H F I R E G F I Y V P L Y A L S I ..................................................... Protein_Len: 30 Strand: - Start: 139 End: 228 .......................................................................................................................................... L L K R K Y I L S L C K N Y I K H S F F K I L K R L R E Y M ......................................................................................................................................................................................................................................... taaaatcctctcctttttgttcttacctctatttttattctaatcttactttcatttttatatctcttattataaatcataattatgaattaagaatgaattttatgtttaaattttgacacttatctctatattttataacaattttcttttataaattaaagataaacatttgttatatattttatgggaaaaaaatttaataagctttcttaatctctcgtacatttagtatatataattaaaatgaatacctaatgaatacactttattacttaatattatatcatatttctaagaatacaaaaaaccacaagaaatgaggggagagacttgtggtttttctatctacatattcattttattagggaggggtttatctatgttcccttatatgccttaagtatatagtagaaaaatgaatgtaaaatgaatttaccatattttttttttaaattttt 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: 82 Start: 115 End: 144 ..................................................................................................................TTTGACACTTATCTCTATATTTTATAACAA............................................................................................................................................................................................................................................................................................................................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ taaaatcctctcctttttgttcttacctctatttttattctaatcttactttcatttttatatctcttattataaatcataattatgaattaagaatgaattttatgtttaaattttgacacttatctctatattttataacaattttcttttataaattaaagataaacatttgttatatattttatgggaaaaaaatttaataagctttcttaatctctcgtacatttagtatatataattaaaatgaatacctaatgaatacactttattacttaatattatatcatatttctaagaatacaaaaaaccacaagaaatgaggggagagacttgtggtttttctatctacatattcattttattagggaggggtttatctatgttcccttatatgccttaagtatatagtagaaaaatgaatgtaaaatgaatttaccatattttttttttaaattttt Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 41 HP_score: -2.9 Tail_Score: -2.65862 Start: 425 End: 439 Full_Region: AGTAGAAAAATGAAT GTAAA ATGAA TTTAC CATATTTTTTTTTTA ........................................................................................................................................................................................................................................................................................................................................................................................................................................GTAAAATGAATTTAC...................... Find igs database================================================ Query_seq: FN2085:FN2086|FN2085:FN2086:hypothetical protein:General secretion pathway protein D:<-<-:597136..597596 461 taaaatcctctcctttttgttcttacctctatttttattctaatcttactttcatttttatatctcttattataaatcataattatgaattaagaatgaattttatgtttaaattttgacacttatctctatattttataacaattttcttttataaattaaagataaacatttgttatatattttatgggaaaaaaatttaataagctttcttaatctctcgtacatttagtatatataattaaaatgaatacctaatgaatacactttattacttaatattatatcatatttctaagaatacaaaaaaccacaagaaatgaggggagagacttgtggtttttctatctacatattcattttattagggaggggtttatctatgttcccttatatgccttaagtatatagtagaaaaatgaatgtaaaatgaatttaccatattttttttttaaattttt Intra-Species Hit: Count: 1 Min: 1 Max: 443 Len: 443 Subject: NC_003454_FN2085_FN2086|hypothetical protein:General secretion pathway protein D|NEGATIVE:NEGATIVE|[597136,597596]|461 HSP 1 e-value: 0.0 bit: 837.0 Len: 443 Query Start:1 Query End:443 Subject Strand: POSITIVE Subject Start: 1 Subject End: 443 taaaatcctctcctttttgttcttacctctatttttattctaatcttactttcatttttatatctcttattataaatcataattatgaattaagaatgaattttatgtttaaattttgacacttatctctatattttataacaattttcttttataaattaaagataaacatttgttatatattttatgggnnnnnnntttaataagctttcttaatctctcgtacatttagtatatataattaaaatgaatacctaatgaatacactttattacttaatattatatcatatttctaagaatacaaaaaaccacaagaaatgaggggagagacttgtggtttttctatctacatattcattttattagggaggggtttatctatgttcccttatatgccttaagtatatagtagaaaaatgaatgtaaaatgaatttaccata.................. taaaatcctctcctttttgttcttacctctatttttattctaatcttactttcatttttatatctcttattataaatcataattatgaattaagaatgaattttatgtttaaattttgacacttatctctatattttataacaattttcttttataaattaaagataaacatttgttatatattttatgggaaaaaaatttaataagctttcttaatctctcgtacatttagtatatataattaaaatgaatacctaatgaatacactttattacttaatattatatcatatttctaagaatacaaaaaaccacaagaaatgaggggagagacttgtggtttttctatctacatattcattttattagggaggggtttatctatgttcccttatatgccttaagtatatagtagaaaaatgaatgtaaaatgaatttaccata.................. Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAAAUCCUCUCCUUUUUGUUCUUACCUCUAUUUUUAUUCUAAUCUUACUUUCAUUUUUAUAUCUCUUAUUAUAAAUCAUAAUUAUGAAUUAAGAAUGAAUUUUAUGUUUAAAUUUUGACACUUAUCUCUAUAUUUUAUAACAAUUUUCUUUUAUAAAUUAAAGAUAAACAUUUGUUAUAUAUUUUAUGGGAAAAAAAUUUAAUAAGCUUUCUUAAUCUCUCGUACAUUUAGUAUAUAUAAUUAAAAUGAAUACCUAAUGAAUACACUUUAUUACUUAAUAUUAUAUCAUAUUUCUAAGAAUACAAAAAACCACAAGAAAUGAGGGGAGAGACUUGUGGUUUUUCUAUCUACAUAUUCAUUUUAUUAGGGAGGGGUUUAUCUAUGUUCCCUUAUAUGCCUUAAGUAUAUAGUAGAAAAAUGAAUGUAAAAUGAAUUUACCAUA .......((((((((((..(((((.......(((.((((((.........((((((((((((........))))))...((((((((.((((((((((((((((.((((........))))....((.(((((...((((((((...(((((........))))).......)))))))).....)))))))..)))))))).......)))))))).....((((.....)))).)))))))).))))))....(((((((.....))))))).......................)))))).))).......)))))..))))))))))...((((((..(((.......(((((((((((...((((((.((.....))...))))))(((((((.....))))))).....))))))))))).....)))...)))))) (-76.55) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAUGGUAAAUUCAUUUUACAUUCAUUUUUCUACUAUAUACUUAAGGCAUAUAAGGGAACAUAGAUAAACCCCUCCCUAAUAAAAUGAAUAUGUAGAUAGAAAAACCACAAGUCUCUCCCCUCAUUUCUUGUGGUUUUUUGUAUUCUUAGAAAUAUGAUAUAAUAUUAAGUAAUAAAGUGUAUUCAUUAGGUAUUCAUUUUAAUUAUAUAUACUAAAUGUACGAGAGAUUAAGAAAGCUUAUUAAAUUUUUUUCCCAUAAAAUAUAUAACAAAUGUUUAUCUUUAAUUUAUAAAAGAAAAUUGUUAUAAAAUAUAGAGAUAAGUGUCAAAAUUUAAACAUAAAAUUCAUUCUUAAUUCAUAAUUAUGAUUUAUAAUAAGAGAUAUAAAAAUGAAAGUAAGAUUAGAAUAAAAAUAGAGGUAAGAACAAAAAGGAGAGGAUUUUA ....(((((.....))))).....(((((((((((((((.(((.....(((.(((((...............))))).)))...))).))))))).)))))))).......(((((((((((.(((((((..(((((((((((..((((.(((((......)))))..(((((((((((...((....))....)))))).))))).....))))..)))))))))))))))))).....(((((((((......(((.....))).....(..((((((((((.(((((((..........)))))))...))))))))))..).))))))))).......((((..(((((.(((((..(((((.(((.......))).)))))..)))))..)))))...)))).......))))............)))))))...... (-75.46) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 717 50 1 141 92 NC_003454:FN2085|5end_hypothetical_protein_597045..597275_NEGATIVE 314 70 26 105 60 NC_003454:FN0508|5end_Serine_protease_1158652..1158882_NEGATIVE 266 398 353 73 34 NC_003454:FN0383|5end_Lipopolysaccharide_N-acetylglucosaminyltransferase_1014148..1014378_POSITIVE 252 400 352 134 85 NC_003454:FN1410|5end_Transporter_2069934..2070164_POSITIVE 248 350 327 197 174 NC_003454:FN0789|5end_Transporter_1445278..1445508_NEGATIVE 245 380 335 228 180 NC_003454:FN0019|5end_Transcription-repair_coupling_factor_656549..656779_POSITIVE 244 48 6 115 68 NC_003454:FN1531|5end_Negative_regulator_of_murein_hydrolase_44970..45200_NEGATIVE 239 406 365 59 21 NC_003454:FN1744|5end_Transporter_242920..243150_NEGATIVE 236 58 11 49 2 NC_003454:FN0049|5end_hypothetical_protein_686351..686581_POSITIVE 230 68 25 105 63 NC_003454:FN0889|5end_Dihydrolipoamide_acyltransferase_1551393..1551623_NEGATIVE 229 70 30 106 71 NC_003454:FN1105|5end_hypothetical_protein_1750041..1750271_POSITIVE 227 67 27 113 82 NC_003454:FN0084|5end_Acetaldehyde_dehydrogenase_[acetylating]_721572..721802_POSITIVE 222 65 21 141 93 NC_003454:FN1667|5end_dTDP-glucose_4,6-dehydratase_164472..164702_NEGATIVE 220 68 23 62 4 NC_003454:FN0970|5end_Precorrin-8X_methylmutase_1623266..1623496_NEGATIVE 219 67 21 101 56 NC_003454:FN1609|5end_hypothetical_protein_119613..119843_NEGATIVE 218 69 21 106 57 NC_003454:FN1028|5end_deoxyuridine_5'-triphosphate_nucleotidohydrolase_1682383..1682613_NEGATIVE 216 80 32 125 64 NC_003454:FN0451|5end_hypothetical_protein_1094853..1095083_POSITIVE 215 389 341 143 84 NC_003454:FN1091|5end_Sigma_factor_sigB_regulation_protein_rsbU_1735915..1736145_POSITIVE 214 69 21 124 84 NC_003454:FN1011|5end_MGPA_protein_1665660..1665890_NEGATIVE 213 348 308 91 51 NC_003454:FN0563|5end_tRNA_(5-methylaminomethyl-2-thiouridylate)_-methyltransferase_1215286..1215516_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 489 370 321 75 30 NC_003454:FN2085|3end_hypothetical_protein_596560..596710_NEGATIVE 266 398 353 69 30 NC_003454:FN0382|3end_hypothetical_protein_1014224..1014374_POSITIVE 256 47 8 146 100 NC_003454:FN0065|3end_Transcription_accessory_protein_(S1_RNA_binding_domain)_702184..702334_POSITIVE 244 48 6 149 102 NC_003454:FN1532|3end_murein_hydrolase_exporter_44936..45086_NEGATIVE 229 70 30 102 67 NC_003454:FN1104|3end_Holliday_junction_DNA_helicase_ruvA_1750117..1750267_POSITIVE 225 78 33 91 48 NC_003454:FN1287|3end_Bacterial_Protein_Translation_Initiation_Factor_1_(IF-1)_1944415..1944565_NEGATIVE 223 63 26 118 81 NC_003454:FN0637|3end_Hypothetical_exported_24-amino_acid_repeat_protein_1295636..1295786_NEGATIVE 218 69 21 104 55 NC_003454:FN1029|3end_Zinc_protease_1682385..1682535_NEGATIVE 217 411 378 104 65 NC_003454:FN1342|3end_Holo-[acyl-carrier_protein]_synthase_1996091..1996241_NEGATIVE 216 80 32 122 61 NC_003454:FN0450|3end_ABC_transporter_ATP-binding_protein_1094930..1095080_POSITIVE 214 69 21 104 64 NC_003454:FN1012|3end_HPr_kinase/phosphorylase_1665680..1665830_NEGATIVE 213 348 308 104 64 NC_003454:FN0562|3end_Hypothetical_cytosolic_protein_1215379..1215529_POSITIVE 213 350 311 65 28 NC_003454:FN1737|3end_V-type_ATP_synthase_subunit_F_236039..236189_NEGATIVE 212 65 26 129 82 NC_003454:FN0109|3end_hypothetical_protein_744333..744483_NEGATIVE 211 80 39 101 65 NC_003454:FN1203|3end_GTP-binding_protein_1862311..1862461_NEGATIVE 210 366 322 95 53 NC_003454:FN1986|3end_hypothetical_protein_490007..490157_POSITIVE 209 46 4 121 82 NC_003454:FN1491|3end_PTS_system,_IIA_component_2172302..2172452_NEGATIVE 207 65 21 112 68 NC_003454:FN0247|3end_Hypothetical_cytosolic_protein_871578..871728_POSITIVE 206 39 4 90 49 NC_003454:FN2023|3end_Hypothetical_cytosolic_protein_526172..526322_NEGATIVE 204 50 6 125 84 NC_003454:FN0416|3end_Type_III_restriction-modification_system_methylation_subunit_1055957..1056107_POSITIVE