Origin IGS: gtttttattgtataaggtgggaataggttccctaaagcatttcttccgattccgcccaaaaaagtaaagaggatatcgaatagaatctgctcatcatataaaagagaggcgacacccatattgttcgcctctctttgtattcttagtttatttttggactctctc .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 gagagagtccaaaaataaactaagaatacaaagagaggcgaacaatatgggtgtcgcctctcttttatatgatgagcagattctattcgatatcctctttacttttttgggcggaatcggaagaaatgctttagggaacctattcccaccttatacaataaaaac Mask Tandem Repeat Region ================================================ gtttttattgtataaggtgggaataggttccctaaagcatttcttccgattccgcccaaaaaagtaaagaggatatcgaatagaatctgctcatcatataaaagagaggcgacacccatattgttcgcctctctttgtattcttagtttatttttggactctctc Find is-nt database================================================ Query_seq: PG0707:PG0708|PG0707:PG0708:TonB-dependent receptor, putative:peptidyl-prolyl cis-trans isomerase, FKBP-type:<-<-:763723..763887 165 gtttttattgtataaggtgggaataggttccctaaagcatttcttccgattccgcccaaaaaagtaaagaggatatcgaatagaatctgctcatcatataaaagagaggcgacacccatattgttcgcctctctttgtattcttagtttatttttggactctctc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG0707:PG0708|PG0707:PG0708:TonB-dependent receptor, putative:peptidyl-prolyl cis-trans isomerase, FKBP-type:<-<-:763723..763887 165 gtttttattgtataaggtgggaataggttccctaaagcatttcttccgattccgcccaaaaaagtaaagaggatatcgaatagaatctgctcatcatataaaagagaggcgacacccatattgttcgcctctctttgtattcttagtttatttttggactctctc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG0707:PG0708|PG0707:PG0708:TonB-dependent receptor, putative:peptidyl-prolyl cis-trans isomerase, FKBP-type:<-<-:763723..763887 165 gtttttattgtataaggtgggaataggttccctaaagcatttcttccgattccgcccaaaaaagtaaagaggatatcgaatagaatctgctcatcatataaaagagaggcgacacccatattgttcgcctctctttgtattcttagtttatttttggactctctc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gtttttattgtataaggtgggaataggttccctaaagcatttcttccgattccgcccaaaaaagtaaagaggatatcgaatagaatctgctcatcatataaaagagaggcgacacccatattgttcgcctctctttgtattcttagtttatttttggactctctc Predict ORF larger than 30AA ================================================ Protein_Len: 39 Strand: + Start: 49 End: 165 ................................................ M P P K K V K R I S N R I C S S Y K R E A T P I L F A S L C I L S L F L D S L Protein_Len: 46 Strand: - Start: 3 End: 140 .. K I T Y P P F L N G L A N R G I G G L F T F L I D F L I Q E D Y L L S A V G M N N A E R Q M ......................... gtttttattgtataaggtgggaataggttccctaaagcatttcttccgattccgcccaaaaaagtaaagaggatatcgaatagaatctgctcatcatataaaagagaggcgacacccatattgttcgcctctctttgtattcttagtttatttttggactctctc Predict Promoter with matrix: RpoD-15 score > 80================================================ Predict Promoter with matrix: RpoD-16 score > 80================================================ Predict Promoter with matrix: RpoD-17 score > 80================================================ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ gtttttattgtataaggtgggaataggttccctaaagcatttcttccgattccgcccaaaaaagtaaagaggatatcgaatagaatctgctcatcatataaaagagaggcgacacccatattgttcgcctctctttgtattcttagtttatttttggactctctc Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 86 HP_score: -8.7 Tail_Score: -4.57353 Start: 104 End: 133 Full_Region: aactaagaatacaaa gagaggcgaaca atatggg tgtcgcctctc ttttatatgatgagc .......................................................................................................gagaggcgaacaatatgggtgtcgcctctc................................ Find igs database================================================ Query_seq: PG0707:PG0708|PG0707:PG0708:TonB-dependent receptor, putative:peptidyl-prolyl cis-trans isomerase, FKBP-type:<-<-:763723..763887 165 gtttttattgtataaggtgggaataggttccctaaagcatttcttccgattccgcccaaaaaagtaaagaggatatcgaatagaatctgctcatcatataaaagagaggcgacacccatattgttcgcctctctttgtattcttagtttatttttggactctctc Intra-Species Hit: Count: 1 Min: 1 Max: 165 Len: 165 Subject: NC_002950_PG0707_PG0708|TonB-dependent receptor, putative:peptidyl-prolyl cis-trans isomerase, FKBP-type|NEGATIVE:NEGATIVE|[763723,763887]|165 HSP 1 e-value: 7.0E-89 bit: 327.0 Len: 165 Query Start:1 Query End:165 Subject Strand: POSITIVE Subject Start: 1 Subject End: 165 gtttttattgtataaggtgggaataggttccctaaagcatttcttccgattccgcccaaaaaagtaaagaggatatcgaatagaatctgctcatcatataaaagagaggcgacacccatattgttcgcctctctttgtattcttagtttatttttggactctctc gtttttattgtataaggtgggaataggttccctaaagcatttcttccgattccgcccaaaaaagtaaagaggatatcgaatagaatctgctcatcatataaaagagaggcgacacccatattgttcgcctctctttgtattcttagtttatttttggactctctc Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GUUUUUAUUGUAUAAGGUGGGAAUAGGUUCCCUAAAGCAUUUCUUCCGAUUCCGCCCAAAAAAGUAAAGAGGAUAUCGAAUAGAAUCUGCUCAUCAUAUAAAAGAGAGGCGACACCCAUAUUGUUCGCCUCUCUUUGUAUUCUUAGUUUAUUUUUGGACUCUCUC ((((.......(((((.((((((((..........((((.((((..(((((((.................))).))))...))))..)))).........((((((((((((((.......)).)))))))))))).)))))))).)))))....))))...... (-41.33) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAGAGAGUCCAAAAAUAAACUAAGAAUACAAAGAGAGGCGAACAAUAUGGGUGUCGCCUCUCUUUUAUAUGAUGAGCAGAUUCUAUUCGAUAUCCUCUUUACUUUUUUGGGCGGAAUCGGAAGAAAUGCUUUAGGGAACCUAUUCCCACCUUAUACAAUAAAAAC ....................((((.....((((((((((((.((.......))))))))))))))........(((((..((((.((((((.(((.(((.........))).))))))))))))).)))))..(((((....)))))..))))............ (-43.60) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 923 60 11 151 102 NC_002950:PG0707|5end_TonB-dependent_receptor,_putative_763632..763862_NEGATIVE 354 148 111 71 29 NC_002950:PG0230|5end_transaldolase_265372..265602_POSITIVE 298 140 91 91 34 NC_002950:PG0092|5end_transporter,_putative_108598..108828_NEGATIVE 292 143 105 124 78 NC_002950:PG2052|5end_dihydrodipicolinate_synthase_2149636..2149866_POSITIVE 284 130 85 51 10 NC_002950:PG1660|5end_RNA_polymerase_sigma-70_factor,_ECF_subfamily_1744268..1744498_NEGATIVE 284 99 51 93 32 NC_002950:PG0180|5end_lipoprotein,_putative_203055..203285_POSITIVE 283 58 16 162 124 NC_002950:PG0841|5end_mobilizable_transposon,_excision_protein,_putative_903674..903904_NEGATIVE 280 129 85 46 6 NC_002950:PG0701|5end_cobinamide_kinase/cobinamide_phosphate_guanylyltransferase_756511..756741_POSITIVE 279 78 32 108 60 NC_002950:PG1302|5end_hypothetical_protein_1380637..1380867_NEGATIVE 278 59 28 34 5 NC_002950:PG1030|5end_hypothetical_protein_1091400..1091630_POSITIVE 278 57 14 179 135 NC_002950:PG0677|5end_saccharopine_dehydrogenase_727653..727883_POSITIVE 276 137 96 81 31 NC_002950:PG1387|5end_hypothetical_protein_1470058..1470288_NEGATIVE 273 90 41 127 73 NC_002950:PG1369|5end_glycerol-3-phosphate_dehydrogenase_(NAD(P)+)_1450407..1450637_NEGATIVE 273 54 16 83 43 NC_002950:PG0733|5end_riboflavin_synthase_subunit_alpha_783174..783404_POSITIVE 272 65 26 39 5 NC_002950:PG0607|5end_hypothetical_protein_662552..662782_POSITIVE 268 86 46 53 11 NC_002950:PG1792|5end_sodium/hydrogen_antiporter_1881622..1881852_POSITIVE 266 58 15 197 149 NC_002950:PG1640|5end_DNA-damage-inducible_protein_F_1721245..1721475_NEGATIVE 265 129 85 69 27 NC_002950:PG0125|5end_hypothetical_protein_146786..147016_NEGATIVE 262 60 12 225 180 NC_002950:PG2033|5end_glutamate_synthase,_small_subunit_2134803..2135033_NEGATIVE 262 56 16 202 168 NC_002950:PG1999|5end_hypothetical_protein_2088821..2089051_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 337 138 96 62 12 NC_002950:PG1910|3end_ribosomal_protein_L17_2010282..2010432_NEGATIVE 306 57 16 63 15 NC_002950:PG0507|3end_hypothetical_protein_548190..548340_POSITIVE 284 56 11 87 45 NC_002950:PG1411|3end_potassium_uptake_protein_TrkA,_putative_1493481..1493631_NEGATIVE 275 137 103 130 93 NC_002950:PG1786|3end_hypothetical_protein_1875322..1875472_POSITIVE 270 149 106 48 11 NC_002950:PG0053|3end_hypothetical_protein_64967..65117_NEGATIVE 268 57 16 49 4 NC_002950:PG1854|3end_5-formyltetrahydrofolate_cyclo-ligase_family_protein_1953325..1953475_NEGATIVE 265 60 11 144 100 NC_002950:PG0949|3end_hypothetical_protein_1009773..1009923_POSITIVE 265 129 85 72 30 NC_002950:PG0126|3end_type_I_phosphodiesterase/nucleotide_pyrophosphatase_family_protein_146783..146933_NEGATIVE 264 54 20 140 101 NC_002950:PG0198|3end_hypothetical_protein_237501..237651_POSITIVE 262 60 12 118 73 NC_002950:PG2034|3end_oxidoreductase,_FAD-binding,_putative_2134910..2135060_NEGATIVE 260 141 104 49 7 NC_002950:PG1388|3end_hypothetical_protein_1470095..1470245_NEGATIVE 259 149 106 91 48 NC_002950:PG2044|3end_hypothetical_protein_2144165..2144315_POSITIVE 259 49 2 143 98 NC_002950:PG0389|3end_transcription_antitermination_protein_NusG_422833..422983_POSITIVE 258 57 17 76 33 NC_002950:PG2068|3end_glycerol-3-phosphate_cytidylyltransferase_2164872..2165022_POSITIVE 256 55 14 115 72 NC_002950:PG1690|3end_Sua5/YciO/YrdC/YwlC_family_protein_1775171..1775321_NEGATIVE 256 57 15 121 84 NC_002950:PG1497|3end_DNA-binding_protein,_histone-like_family_1574635..1574785_POSITIVE 253 55 16 68 21 NC_002950:PG0524|3end_hypothetical_protein_568963..569113_POSITIVE 251 146 101 72 12 NC_002950:PG0769|3end_fibronectin_type_III_domain_protein_822555..822705_NEGATIVE 251 52 21 75 34 NC_002950:PG0104|3end_DNA_topoisomerase_III_127448..127598_POSITIVE 250 59 15 65 23 NC_002950:PG1483|3end_conjugative_transposon_protein_TraE_1558783..1558933_NEGATIVE