Origin IGS: cctcaatttgaaaaaaactccgccttgaggacagtttttttgtgtgcactaaccgataaaaatttgatttccccaaggatttgcgagatttcttgccggatcttctcttgatttttgtttataaaatatgtattatctttatg .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 cataaagataatacatattttataaacaaaaatcaagagaagatccggcaagaaatctcgcaaatccttggggaaatcaaatttttatcggttagtgcacacaaaaaaactgtcctcaaggcggagtttttttcaaattgagg Mask Tandem Repeat Region ================================================ cctcaatttgaaaaaaactccgccttgaggacagtttttttgtgtgcactaaccgataaaaatttgatttccccaaggatttgcgagatttcttgccggatcttctcttgatttttgtttataaaatatgtattatctttatg Find is-nt database================================================ Query_seq: TDE1924:TDE1925|TDE1924:TDE1925:hypothetical protein:peptidyl-prolyl cis-trans isomerase, FKBP-type:<-->:1941977..1942119 143 cctcaatttgaaaaaaactccgccttgaggacagtttttttgtgtgcactaaccgataaaaatttgatttccccaaggatttgcgagatttcttgccggatcttctcttgatttttgtttataaaatatgtattatctttatg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE1924:TDE1925|TDE1924:TDE1925:hypothetical protein:peptidyl-prolyl cis-trans isomerase, FKBP-type:<-->:1941977..1942119 143 cctcaatttgaaaaaaactccgccttgaggacagtttttttgtgtgcactaaccgataaaaatttgatttccccaaggatttgcgagatttcttgccggatcttctcttgatttttgtttataaaatatgtattatctttatg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE1924:TDE1925|TDE1924:TDE1925:hypothetical protein:peptidyl-prolyl cis-trans isomerase, FKBP-type:<-->:1941977..1942119 143 cctcaatttgaaaaaaactccgccttgaggacagtttttttgtgtgcactaaccgataaaaatttgatttccccaaggatttgcgagatttcttgccggatcttctcttgatttttgtttataaaatatgtattatctttatg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 cctcaatttgaaaaaaactccgccttgaggacagtttttttgtgtgcactaaccgataaaaatttgatttccccaaggatttgcgagatttcttgccggatcttctcttgatttttgtttataaaatatgtattatctttatg Predict ORF larger than 30AA ================================================ Protein_Len: 40 Strand: - Start: 6 End: 122 ..... * N S F F E A K L V T K K H A S V S L F K I E G L I Q S I E Q R I K E Q N K N M ..................... Protein_Len: 37 Strand: - Start: 2 End: 112 . E I Q F F S R R S S L K K T H V L R Y F N S K G L S K R S K K G S R R K M ............................... cctcaatttgaaaaaaactccgccttgaggacagtttttttgtgtgcactaaccgataaaaatttgatttccccaaggatttgcgagatttcttgccggatcttctcttgatttttgtttataaaatatgtattatctttatg 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: 107 End: 136 ..........................................................................................................CTTGATTTTTGTTTATAAAATATGTATTAT....... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ cctcaatttgaaaaaaactccgccttgaggacagtttttttgtgtgcactaaccgataaaaatttgatttccccaaggatttgcgagatttcttgccggatcttctcttgatttttgtttataaaatatgtattatctttatg Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE1924:TDE1925|TDE1924:TDE1925:hypothetical protein:peptidyl-prolyl cis-trans isomerase, FKBP-type:<-->:1941977..1942119 143 cctcaatttgaaaaaaactccgccttgaggacagtttttttgtgtgcactaaccgataaaaatttgatttccccaaggatttgcgagatttcttgccggatcttctcttgatttttgtttataaaatatgtattatctttatg Intra-Species Hit: Count: 1 Min: 18 Max: 143 Len: 126 Subject: NC_002967_TDE1924_TDE1925|hypothetical protein:peptidyl-prolyl cis-trans isomerase, FKBP-type|NEGATIVE:POSITIVE|[1941977,1942119]|143 HSP 1 e-value: 4.0E-53 bit: 208.0 Len: 126 Query Start:18 Query End:143 Subject Strand: POSITIVE Subject Start: 18 Subject End: 143 .................ctccgccttgaggacagnnnnnnngtgtgcactaaccgataaaaatttgatttccccaaggatttgcgagatttcttgccggatcttctcttgatttttgtttataaaatatgtattatctttatg .................ctccgccttgaggacagtttttttgtgtgcactaaccgataaaaatttgatttccccaaggatttgcgagatttcttgccggatcttctcttgatttttgtttataaaatatgtattatctttatg Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUCCGCCUUGAGGACAGUUUUUUUGUGUGCACUAACCGAUAAAAAUUUGAUUUCCCCAAGGAUUUGCGAGAUUUCUUGCCGGAUCUUCUCUUGAUUUUUGUUUAUAAAAUAUGUAUUAUCUUUAUG .(((.(((((.((((((((((((((.((......))))).))))).)))...))).)))))....(((((....))))).)))........................................... (-21.10) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CAUAAAGAUAAUACAUAUUUUAUAAACAAAAAUCAAGAGAAGAUCCGGCAAGAAAUCUCGCAAAUCCUUGGGGAAAUCAAAUUUUUAUCGGUUAGUGCACACAAAAAAACUGUCCUCAAGGCGGAG ....((((((.....))))))......................((((((.((....)).))....(((((((((.......(((((....((....))....))))).....))))))))))))). (-20.30) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 889 100 51 208 159 NC_002967:TDE1924|5end_hypothetical_protein_1941886..1942116_NEGATIVE 315 87 41 171 123 NC_002967:TDE0535|5end_ABC_transporter,_ATP-binding_protein_577323..577553_POSITIVE 296 99 51 63 6 NC_002967:TDE2320|5end_RNA_polymerase_sigma-24_factor,_putative_2356951..2357181_NEGATIVE 285 100 51 82 25 NC_002967:TDE2162|5end_NOL1/NOP2/sun_family_protein_2194689..2194919_POSITIVE 269 41 2 223 180 NC_002967:TDE1376|5end_hypothetical_protein_1418586..1418816_POSITIVE 267 99 54 76 34 NC_002967:TDE0793|5end_hypothetical_protein_818910..819140_POSITIVE 265 100 51 186 145 NC_002967:TDE1975|5end_hypothetical_protein_1988869..1989099_POSITIVE 263 93 65 149 123 NC_002967:TDE0687|5end_phosphoribosylaminoimidazole_carboxylase,_PurE_protein_723674..723904_POSITIVE 258 100 60 109 59 NC_002967:TDE1082|5end_ribosomal_large_subunit_pseudouridine_synthase,_RluD_subfamily_1113135..1113365_POSITIVE 257 83 42 198 152 NC_002967:TDE0575|5end_aspartyl/glutamyl-tRNA_amidotransferase_subunit_B_607733..607963_NEGATIVE 255 31 1 56 22 NC_002967:TDE2408|5end_hypothetical_protein_2435387..2435617_NEGATIVE 255 80 34 173 123 NC_002967:TDE1961|5end_PIN_domain_protein_1974975..1975205_NEGATIVE 254 43 3 179 143 NC_002967:TDE2009|5end_hypothetical_protein_2030382..2030612_POSITIVE 253 102 63 85 49 NC_002967:TDE2636|5end_hypothetical_protein_2676070..2676300_POSITIVE 250 50 1 57 5 NC_002967:TDE1308|5end_transketolase_1342463..1342693_POSITIVE 249 103 63 171 129 NC_002967:TDE2341|5end_membrane-associated_zinc_metalloprotease,_putative_2379218..2379448_NEGATIVE 248 100 52 113 70 NC_002967:TDE1644|5end_methionyl-tRNA_formyltransferase_1695546..1695776_NEGATIVE 248 88 49 70 37 NC_002967:TDE0949|5end_enolase_972010..972240_POSITIVE 246 101 63 60 18 NC_002967:TDE2651|5end_ABC_transporter,_ATP-binding_protein_2689149..2689379_POSITIVE 246 92 53 178 141 NC_002967:TDE0771|5end_ribosomal_protein_S19_808795..809025_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 306 86 41 151 104 NC_002967:TDE0534|3end_hypothetical_protein_577384..577534_POSITIVE 296 99 51 66 9 NC_002967:TDE2321|3end_hypothetical_protein_2356948..2357098_NEGATIVE 267 99 54 92 50 NC_002967:TDE0792|3end_ribosomal_protein_L17_819006..819156_POSITIVE 264 79 32 130 84 NC_002967:TDE0118|3end_hypothetical_protein_136574..136724_NEGATIVE 258 100 60 122 72 NC_002967:TDE1081|3end_hypothetical_protein_1113228..1113378_POSITIVE 254 43 3 132 96 NC_002967:TDE2008|3end_ABC_transporter,_ATP-binding/permease_protein_2030415..2030565_POSITIVE 252 117 77 116 70 NC_002967:TDE0481|3end_hypothetical_protein_538197..538347_NEGATIVE 250 89 52 118 79 NC_002967:TDE1263|3end_hypothetical_protein_1298136..1298286_POSITIVE 249 103 63 151 109 NC_002967:TDE2342|3end_1-deoxy-D-xylulose_5-phosphate_reductoisomerase_2379238..2379388_NEGATIVE 248 100 52 116 73 NC_002967:TDE1645|3end_polypeptide_deformylase_1695543..1695693_NEGATIVE 245 102 65 36 4 NC_002967:TDE0326|3end_ATP-dependent_DNA_helicase_RecQ_358748..358898_NEGATIVE 241 97 55 56 12 NC_002967:TDE2404|3end_RNA_polymerase_sigma-54_factor,_putative_2429313..2429463_NEGATIVE 240 88 46 122 90 NC_002967:TDE0974|3end_hypothetical_protein_998875..999025_POSITIVE 240 100 56 151 110 NC_002967:TDE0779|3end_ribosomal_protein_L5_812432..812582_POSITIVE 237 38 3 63 33 NC_002967:TDE2736|3end_hypothetical_protein_2791702..2791852_NEGATIVE 237 91 55 117 75 NC_002967:TDE0923|3end_ABC_transporter,_ATP-binding/permease_protein_943920..944070_NEGATIVE 236 80 42 84 41 NC_002967:TDE2735|3end_surface_antigen,_putative_2791616..2791766_POSITIVE 235 80 44 61 25 NC_002967:TDE1811|3end_hypothetical_protein_1846773..1846923_NEGATIVE 235 39 2 129 86 NC_002967:TDE1235|3end_hypothetical_protein_1269557..1269707_POSITIVE 229 89 46 110 57 NC_002967:TDE1720|3end_radical_SAM_domain_protein_1775232..1775382_POSITIVE