Origin IGS: cagcataaatgaagccccagcctatcgccgcatttgatgttaagtaacacagctttcaaagcaacggttgaaactaaagtgcaccggaacaaatgggaaaggagtaaaatgcttttgttgacataagacaatgaaaatattatcctatttatacagctttttgaattggaggcagtaaa .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tttactgcctccaattcaaaaagctgtataaataggataatattttcattgtcttatgtcaacaaaagcattttactcctttcccatttgttccggtgcactttagtttcaaccgttgctttgaaagctgtgttacttaacatcaaatgcggcgataggctggggcttcatttatgctg Mask Tandem Repeat Region ================================================ cagcataaatgaagccccagcctatcgccgcatttgatgttaagtaacacagctttcaaagcaacggttgaaactaaagtgcaccggaacaaatgggaaaggagtaaaatgcttttgttgacataagacaatgaaaatattatcctatttatacagctttttgaattggaggcagtaaa Find is-nt database================================================ Query_seq: TDE2738:TDE2739|TDE2738:TDE2739:oligoendopeptidase F, putative:hypothetical protein:->->:2794634..2794812 179 cagcataaatgaagccccagcctatcgccgcatttgatgttaagtaacacagctttcaaagcaacggttgaaactaaagtgcaccggaacaaatgggaaaggagtaaaatgcttttgttgacataagacaatgaaaatattatcctatttatacagctttttgaattggaggcagtaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE2738:TDE2739|TDE2738:TDE2739:oligoendopeptidase F, putative:hypothetical protein:->->:2794634..2794812 179 cagcataaatgaagccccagcctatcgccgcatttgatgttaagtaacacagctttcaaagcaacggttgaaactaaagtgcaccggaacaaatgggaaaggagtaaaatgcttttgttgacataagacaatgaaaatattatcctatttatacagctttttgaattggaggcagtaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE2738:TDE2739|TDE2738:TDE2739:oligoendopeptidase F, putative:hypothetical protein:->->:2794634..2794812 179 cagcataaatgaagccccagcctatcgccgcatttgatgttaagtaacacagctttcaaagcaacggttgaaactaaagtgcaccggaacaaatgggaaaggagtaaaatgcttttgttgacataagacaatgaaaatattatcctatttatacagctttttgaattggaggcagtaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 cagcataaatgaagccccagcctatcgccgcatttgatgttaagtaacacagctttcaaagcaacggttgaaactaaagtgcaccggaacaaatgggaaaggagtaaaatgcttttgttgacataagacaatgaaaatattatcctatttatacagctttttgaattggaggcagtaaa Predict ORF larger than 30AA ================================================ Protein_Len: 30 Strand: + Start: 34 End: 123 ................................. M M L S N T A F K A T V E T K V H R N K W E R S K M L L L T ........................................................ Protein_Len: 32 Strand: - Start: 43 End: 138 .......................................... T V C S E F C R N F S F H V P V F P F P T F H K Q Q C L V I F M ......................................... Protein_Len: 50 Strand: - Start: 3 End: 152 .. C L H L G L R D G C K I N L L V A K L A V T S V L T C R F L H S L L L I S K N V Y S L S F I I R N M ........................... cagcataaatgaagccccagcctatcgccgcatttgatgttaagtaacacagctttcaaagcaacggttgaaactaaagtgcaccggaacaaatgggaaaggagtaaaatgcttttgttgacataagacaatgaaaatattatcctatttatacagctttttgaattggaggcagtaaa 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: 84 Start: 117 End: 146 ....................................................................................................................GTTGACATAAGACAATGAAAATATTATCCT................................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ cagcataaatgaagccccagcctatcgccgcatttgatgttaagtaacacagctttcaaagcaacggttgaaactaaagtgcaccggaacaaatgggaaaggagtaaaatgcttttgttgacataagacaatgaaaatattatcctatttatacagctttttgaattggaggcagtaaa Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE2738:TDE2739|TDE2738:TDE2739:oligoendopeptidase F, putative:hypothetical protein:->->:2794634..2794812 179 cagcataaatgaagccccagcctatcgccgcatttgatgttaagtaacacagctttcaaagcaacggttgaaactaaagtgcaccggaacaaatgggaaaggagtaaaatgcttttgttgacataagacaatgaaaatattatcctatttatacagctttttgaattggaggcagtaaa Intra-Species Hit: Count: 1 Min: 1 Max: 179 Len: 179 Subject: NC_002967_TDE2738_TDE2739|oligoendopeptidase F, putative:hypothetical protein|POSITIVE:POSITIVE|[2794634,2794812]|179 HSP 1 e-value: 3.0E-97 bit: 355.0 Len: 179 Query Start:1 Query End:179 Subject Strand: POSITIVE Subject Start: 1 Subject End: 179 cagcataaatgaagccccagcctatcgccgcatttgatgttaagtaacacagctttcaaagcaacggttgaaactaaagtgcaccggaacaaatgggaaaggagtaaaatgcttttgttgacataagacaatgaaaatattatcctatttatacagctttttgaattggaggcagtaaa cagcataaatgaagccccagcctatcgccgcatttgatgttaagtaacacagctttcaaagcaacggttgaaactaaagtgcaccggaacaaatgggaaaggagtaaaatgcttttgttgacataagacaatgaaaatattatcctatttatacagctttttgaattggaggcagtaaa Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CAGCAUAAAUGAAGCCCCAGCCUAUCGCCGCAUUUGAUGUUAAGUAACACAGCUUUCAAAGCAACGGUUGAAACUAAAGUGCACCGGAACAAAUGGGAAAGGAGUAAAAUGCUUUUGUUGACAUAAGACAAUGAAAAUAUUAUCCUAUUUAUACAGCUUUUUGAAUUGGAGGCAGUAAA ...............((((.....(((..((((((...(((...((((...(((.....)))....)))).)))..))))))..)))......))))..((((....((((.(((..(((........)))..))).)))).)))).....(((.((((((......)))))).))).. (-34.20) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUACUGCCUCCAAUUCAAAAAGCUGUAUAAAUAGGAUAAUAUUUUCAUUGUCUUAUGUCAACAAAAGCAUUUUACUCCUUUCCCAUUUGUUCCGGUGCACUUUAGUUUCAACCGUUGCUUUGAAAGCUGUGUUACUUAACAUCAAAUGCGGCGAUAGGCUGGGGCUUCAUUUAUGCUG ......(((.(((.........(((((((..((((((((((......))))))))))................(((..(((((......((..((((..((....))....))))..))...)))))..)))..............))))))).......))))))............. (-35.59) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 322 58 14 188 148 NC_002967:TDE2251|5end_uracil_permease_2289440..2289670_POSITIVE 295 46 2 77 32 NC_002967:TDE2572|5end_CDP-diacylglycerol--glycerol-3-phosphate_3-phosphatidyltransferase_2598738..2598968_NEGATIVE 295 42 2 111 75 NC_002967:TDE2268|5end_hypothetical_protein_2304959..2305189_NEGATIVE 289 29 1 64 37 NC_002967:TDE0153|5end_coenzyme_A_disulfide_reductase,_putative_176185..176415_NEGATIVE 287 67 35 64 21 NC_002967:TDE2713|5end_RNA_methyltransferase,_TrmH_family_2770324..2770554_NEGATIVE 282 123 84 180 146 NC_002967:TDE2697|5end_3-oxo-5-alpha-steroid_4-dehydrogenase_family_protein_2740260..2740490_POSITIVE 279 35 13 230 207 NC_002967:TDE1199|5end_cell_division_protein_FtsL,_putative_1231341..1231571_POSITIVE 278 37 7 49 4 NC_002967:TDE0849|5end_hypothetical_protein_871599..871829_POSITIVE 275 86 43 59 7 NC_002967:TDE2484|5end_hypothetical_protein_2507720..2507950_NEGATIVE 272 70 27 60 21 NC_002967:TDE2005|5end_hypothetical_protein_2023776..2024006_POSITIVE 272 64 25 61 21 NC_002967:TDE0841|5end_hypothetical_protein_861598..861828_NEGATIVE 260 32 1 50 7 NC_002967:TDE0169|5end_methyl-accepting_chemotaxis_domain_protein_198792..199022_NEGATIVE 258 58 14 90 52 NC_002967:TDE1974|5end_UDP-N-acetylglucosamine--N-acetylmuramyl-_(pentapeptide)_pyrophosphoryl-undecaprenol_N-acetylglucosamine_transferase_1988910..1989140_NEGATIVE 255 55 13 218 177 NC_002967:TDE1636|5end_surface_antigen,_putative_1685955..1686185_NEGATIVE 252 67 25 190 152 NC_002967:TDE0137|5end_carbohydrate_kinase,_FGGY_family_156640..156870_POSITIVE 250 125 82 211 169 NC_002967:TDE2232|5end_iron_compound_ABC_transporter,_ATP-binding_protein,_putative_2271285..2271515_NEGATIVE 250 41 13 159 121 NC_002967:TDE1384|5end_cadmium-translocating_P-type_ATPase_1422765..1422995_POSITIVE 250 55 13 130 84 NC_002967:TDE0094|5end_hypothetical_protein_112219..112449_POSITIVE 247 39 2 153 115 NC_002967:TDE2660|5end_hypothetical_protein_2697517..2697747_NEGATIVE 246 54 12 53 5 NC_002967:TDE2766|5end_motility_protein_A_2820874..2821104_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 322 58 14 77 37 NC_002967:TDE2250|3end_hypothetical_protein_2289409..2289559_POSITIVE 295 42 2 139 103 NC_002967:TDE2269|3end_hypothetical_protein_2304931..2305081_NEGATIVE 293 59 11 101 56 NC_002967:TDE0166|3end_hypothetical_protein_195050..195200_NEGATIVE 289 29 1 41 14 NC_002967:TDE0154|3end_adenylate/guanylate_cyclase_catalytic_domain_protein_176208..176358_NEGATIVE 279 43 6 64 24 NC_002967:TDE2571|3end_hypothetical_protein_2597922..2598072_NEGATIVE 276 67 21 126 82 NC_002967:TDE0908|3end_ABC_transporter,_ATP-binding/permease_protein_927085..927235_POSITIVE 272 70 27 49 10 NC_002967:TDE2004|3end_hypothetical_protein_2023845..2023995_POSITIVE 271 57 14 64 7 NC_002967:TDE0919|3end_hypothetical_protein_939125..939275_POSITIVE 265 56 11 127 81 NC_002967:TDE0440|3end_DNA-binding_protein_496306..496456_POSITIVE 258 29 13 120 101 NC_002967:TDE1914|3end_Holliday_junction_DNA_helicase_RuvB_1930889..1931039_NEGATIVE 254 50 3 96 32 NC_002967:TDE1052|3end_rubredoxin_1078712..1078862_NEGATIVE 253 58 12 59 17 NC_002967:TDE2604|3end_hypothetical_protein_2644224..2644374_NEGATIVE 251 97 58 85 41 NC_002967:TDE0870|3end_phosphatase/nucleotidase_894676..894826_POSITIVE 250 55 13 139 93 NC_002967:TDE0093|3end_UDP-N-acetylenolpyruvoylglucosamine_reductase,_putative_112308..112458_POSITIVE 247 39 2 146 108 NC_002967:TDE2661|3end_hypothetical_protein_2697524..2697674_NEGATIVE 247 64 22 58 12 NC_002967:TDE0117|3end_lipoprotein,_putative_136607..136757_POSITIVE 245 88 52 60 25 NC_002967:TDE1633|3end_citrate_lyase_acyl_carrier_protein_1682428..1682578_NEGATIVE 243 70 27 122 75 NC_002967:TDE2422|3end_ribosomal_protein_L7/L12_2452911..2453061_NEGATIVE 241 105 65 83 42 NC_002967:TDE2727|3end_GTPase_YjeQ,_putative_2784251..2784401_NEGATIVE 240 45 14 60 22 NC_002967:TDE2543|3end_hypothetical_protein_2570753..2570903_NEGATIVE