Origin IGS: cgattctccttctgcaccctttcctatcggtgcgatataataaaatttagggttcattatatcgaaaataaaaaaaatagtcaaggctaggacgacgaaaaactatattgacaaagttgtaattttcggttaatatgtcgcccatgtctaacaatacggtatgcttaaattcggaaataaaaagcggaatcttttataccgaaaaatcaaacgagtttacagctctggcagagcaaataagagtctacacttcaaaaaaacggactatc .........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 gatagtccgtttttttgaagtgtagactcttatttgctctgccagagctgtaaactcgtttgatttttcggtataaaagattccgctttttatttccgaatttaagcataccgtattgttagacatgggcgacatattaaccgaaaattacaactttgtcaatatagtttttcgtcgtcctagccttgactattttttttattttcgatataatgaaccctaaattttattatatcgcaccgataggaaagggtgcagaaggagaatcg Mask Tandem Repeat Region ================================================ cgattctccttctgcaccctttcctatcggtgcgatataataaaatttagggttcattatatcgaaaataaaaaaaatagtcaaggctaggacgacgaaaaactatattgacaaagttgtaattttcggttaatatgtcgcccatgtctaacaatacggtatgcttaaattcggaaataaaaagcggaatcttttataccgaaaaatcaaacgagtttacagctctggcagagcaaataagagtctacacttcaaaaaaacggactatc Find is-nt database================================================ Query_seq: TDE2156:TDE2157|TDE2156:TDE2157:translation initiation factor IF-3:ABC transporter, permease protein, putative:<-->:2190810..2191078 269 cgattctccttctgcaccctttcctatcggtgcgatataataaaatttagggttcattatatcgaaaataaaaaaaatagtcaaggctaggacgacgaaaaactatattgacaaagttgtaattttcggttaatatgtcgcccatgtctaacaatacggtatgcttaaattcggaaataaaaagcggaatcttttataccgaaaaatcaaacgagtttacagctctggcagagcaaataagagtctacacttcaaaaaaacggactatc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE2156:TDE2157|TDE2156:TDE2157:translation initiation factor IF-3:ABC transporter, permease protein, putative:<-->:2190810..2191078 269 cgattctccttctgcaccctttcctatcggtgcgatataataaaatttagggttcattatatcgaaaataaaaaaaatagtcaaggctaggacgacgaaaaactatattgacaaagttgtaattttcggttaatatgtcgcccatgtctaacaatacggtatgcttaaattcggaaataaaaagcggaatcttttataccgaaaaatcaaacgagtttacagctctggcagagcaaataagagtctacacttcaaaaaaacggactatc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE2156:TDE2157|TDE2156:TDE2157:translation initiation factor IF-3:ABC transporter, permease protein, putative:<-->:2190810..2191078 269 cgattctccttctgcaccctttcctatcggtgcgatataataaaatttagggttcattatatcgaaaataaaaaaaatagtcaaggctaggacgacgaaaaactatattgacaaagttgtaattttcggttaatatgtcgcccatgtctaacaatacggtatgcttaaattcggaaataaaaagcggaatcttttataccgaaaaatcaaacgagtttacagctctggcagagcaaataagagtctacacttcaaaaaaacggactatc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 cgattctccttctgcaccctttcctatcggtgcgatataataaaatttagggttcattatatcgaaaataaaaaaaatagtcaaggctaggacgacgaaaaactatattgacaaagttgtaattttcggttaatatgtcgcccatgtctaacaatacggtatgcttaaattcggaaataaaaagcggaatcttttataccgaaaaatcaaacgagtttacagctctggcagagcaaataagagtctacacttcaaaaaaacggactatc Predict ORF larger than 30AA ================================================ Protein_Len: 36 Strand: + Start: 161 End: 268 ................................................................................................................................................................ M L K F G N K K R N L L Y R K I K R V Y S S G R A N K S L H F K K T D Y . Protein_Len: 45 Strand: + Start: 135 End: 269 ...................................................................................................................................... M S P M S N N T V C L N S E I K S G I F Y T E K S N E F T A L A E Q I R V Y T S K K R T I Protein_Len: 47 Strand: - Start: 50 End: 190 ................................................. P E N Y R F Y F F Y D L S P R R F V I N V F N Y N E T L I D G M D L L V T H K F E S I F L P M ............................................................................... cgattctccttctgcaccctttcctatcggtgcgatataataaaatttagggttcattatatcgaaaataaaaaaaatagtcaaggctaggacgacgaaaaactatattgacaaagttgtaattttcggttaatatgtcgcccatgtctaacaatacggtatgcttaaattcggaaataaaaagcggaatcttttataccgaaaaatcaaacgagtttacagctctggcagagcaaataagagtctacacttcaaaaaaacggactatc 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: 56 End: 85 .......................................................CTTGACTATTTTTTTTATTTTCGATATAAT........................................................................................................................................................................................ PromScan Matrix: RpoD-17 Strand: + Score: 90 Start: 107 End: 136 ..........................................................................................................ATTGACAAAGTTGTAATTTTCGGTTAATAT..................................................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ cgattctccttctgcaccctttcctatcggtgcgatataataaaatttagggttcattatatcgaaaataaaaaaaatagtcaaggctaggacgacgaaaaactatattgacaaagttgtaattttcggttaatatgtcgcccatgtctaacaatacggtatgcttaaattcggaaataaaaagcggaatcttttataccgaaaaatcaaacgagtttacagctctggcagagcaaataagagtctacacttcaaaaaaacggactatc Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE2156:TDE2157|TDE2156:TDE2157:translation initiation factor IF-3:ABC transporter, permease protein, putative:<-->:2190810..2191078 269 cgattctccttctgcaccctttcctatcggtgcgatataataaaatttagggttcattatatcgaaaataaaaaaaatagtcaaggctaggacgacgaaaaactatattgacaaagttgtaattttcggttaatatgtcgcccatgtctaacaatacggtatgcttaaattcggaaataaaaagcggaatcttttataccgaaaaatcaaacgagtttacagctctggcagagcaaataagagtctacacttcaaaaaaacggactatc Intra-Species Hit: Count: 1 Min: 1 Max: 253 Len: 253 Subject: NC_002967_TDE2156_TDE2157|translation initiation factor IF-3:ABC transporter, permease protein, putative|NEGATIVE:POSITIVE|[2190810,2191078]|269 HSP 1 e-value: 1.0E-127 bit: 454.0 Len: 253 Query Start:1 Query End:253 Subject Strand: POSITIVE Subject Start: 1 Subject End: 253 cgattctccttctgcaccctttcctatcggtgcgatataataaaatttagggttcattatatcgaaaatnnnnnnnntagtcaaggctaggacgacgaaaaactatattgacaaagttgtaattttcggttaatatgtcgcccatgtctaacaatacggtatgcttaaattcggaaataaaaagcggaatcttttataccgaaaaatcaaacgagtttacagctctggcagagcaaataagagtctacacttc................ cgattctccttctgcaccctttcctatcggtgcgatataataaaatttagggttcattatatcgaaaataaaaaaaatagtcaaggctaggacgacgaaaaactatattgacaaagttgtaattttcggttaatatgtcgcccatgtctaacaatacggtatgcttaaattcggaaataaaaagcggaatcttttataccgaaaaatcaaacgagtttacagctctggcagagcaaataagagtctacacttc................ Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CGAUUCUCCUUCUGCACCCUUUCCUAUCGGUGCGAUAUAAUAAAAUUUAGGGUUCAUUAUAUCGAAAAUAAAAAAAAUAGUCAAGGCUAGGACGACGAAAAACUAUAUUGACAAAGUUGUAAUUUUCGGUUAAUAUGUCGCCCAUGUCUAACAAUACGGUAUGCUUAAAUUCGGAAAUAAAAAGCGGAAUCUUUUAUACCGAAAAAUCAAACGAGUUUACAGCUCUGGCAGAGCAAAUAAGAGUCUACACUUC .((((((.....((((((..........))))))........((((((.((((.(((...(((((((((........((((....))))..(((((...................))))).)))))))))....)))..)))).............(((((((.....((((.(..........).))))....)))))))...........))))))...((((.....)))).....))))))........ (-50.31) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAAGUGUAGACUCUUAUUUGCUCUGCCAGAGCUGUAAACUCGUUUGAUUUUUCGGUAUAAAAGAUUCCGCUUUUUAUUUCCGAAUUUAAGCAUACCGUAUUGUUAGACAUGGGCGACAUAUUAACCGAAAAUUACAACUUUGUCAAUAUAGUUUUUCGUCGUCCUAGCCUUGACUAUUUUUUUUAUUUUCGAUAUAAUGAACCCUAAAUUUUAUUAUAUCGCACCGAUAGGAAAGGGUGCAGAAGGAGAAUCG ..........(((((.(((((.((..(((.(((........(((((((....((((((...((((((..............))))))....))))))....)))))))..(((((((.....(((........(((....))).......)))....))))))).))).)))......(((((((((..((((((((((((........))))))))))))....))))))))).)).))))))))))..... (-54.80) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 875 50 1 141 92 NC_002967:TDE2156|5end_translation_initiation_factor_IF-3_2190719..2190949_NEGATIVE 346 235 197 109 64 NC_002967:TDE2691|5end_hypothetical_protein_2728838..2729068_POSITIVE 312 165 136 51 22 NC_002967:TDE0543|5end_hypothetical_protein_583126..583356_POSITIVE 284 37 1 47 10 NC_002967:TDE0778|5end_ribosomal_protein_L24_811487..811717_POSITIVE 279 235 206 109 74 NC_002967:TDE0830|5end_hypothetical_protein_852025..852255_NEGATIVE 274 57 13 91 53 NC_002967:TDE2529|5end_hypothetical_protein_2557238..2557468_NEGATIVE 271 228 181 219 181 NC_002967:TDE2063|5end_ferrous_iron_transport_protein_B_2091264..2091494_NEGATIVE 271 38 3 188 140 NC_002967:TDE1556|5end_hypothetical_protein_1598787..1599017_POSITIVE 267 34 10 56 26 NC_002967:TDE2535|5end_pyruvate_kinase_2560892..2561122_POSITIVE 265 175 136 88 49 NC_002967:TDE2344|5end_undecaprenyl_diphosphate_synthase_2381945..2382175_NEGATIVE 262 200 155 182 145 NC_002967:TDE2611|5end_hypothetical_protein_2651980..2652210_POSITIVE 262 173 140 229 200 NC_002967:TDE2427|5end_preprotein_translocase,_SecE_subunit_2455982..2456212_NEGATIVE 258 33 1 227 187 NC_002967:TDE1759|5end_hypothetical_protein_1809164..1809394_NEGATIVE 258 41 4 139 97 NC_002967:TDE0502|5end_ankyrin_repeat_protein_556558..556788_NEGATIVE 257 224 181 230 184 NC_002967:TDE1002|5end_hypothetical_protein_1029137..1029367_NEGATIVE 256 165 126 77 42 NC_002967:TDE2485|5end_hypothetical_protein_2509123..2509353_NEGATIVE 250 33 3 198 165 NC_002967:TDE2735|5end_surface_antigen,_putative_2790154..2790384_POSITIVE 249 163 124 197 160 NC_002967:TDE2624|5end_hypothetical_protein_2664905..2665135_NEGATIVE 248 59 16 201 157 NC_002967:TDE1497|5end_hypothetical_protein_1543208..1543438_POSITIVE 248 234 191 35 1 NC_002967:TDE0155|5end_adenylate/guanylate_cyclase_catalytic_domain_protein_180154..180384_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 279 235 206 39 4 NC_002967:TDE0831|3end_hypothetical_protein_852095..852245_NEGATIVE 275 235 206 39 4 NC_002967:TDE2689|3end_hypothetical_protein_2728848..2728998_POSITIVE 265 175 136 87 48 NC_002967:TDE2345|3end_ribosome_recycling_factor_2381946..2382096_NEGATIVE 262 173 140 89 60 NC_002967:TDE2428|3end_ribosomal_protein_L33_2456122..2456272_NEGATIVE 260 230 181 101 45 NC_002967:TDE1004|3end_flagellar_filament_core_protein_1029276..1029426_NEGATIVE 259 229 186 75 29 NC_002967:TDE2265|3end_hypothetical_protein_2302634..2302784_POSITIVE 258 41 4 117 75 NC_002967:TDE0503|3end_hypothetical_protein_556580..556730_NEGATIVE 250 37 2 37 1 NC_002967:TDE0777|3end_50S_ribosomal_protein_L14_811557..811707_POSITIVE 248 36 4 123 89 NC_002967:TDE2558|3end_ABC_transporter,_ATP-binding/permease_protein_2583729..2583879_NEGATIVE 248 54 11 47 2 NC_002967:TDE2181|3end_PAP2_family_protein_2211995..2212145_NEGATIVE 248 176 136 44 1 NC_002967:TDE1918|3end_hypothetical_protein_1937391..1937541_NEGATIVE 246 48 4 140 86 NC_002967:TDE0157|3end_KHG/KDPG_family_aldolase/carbohydrate_kinase,_PfkB_family_185711..185861_POSITIVE 242 230 182 46 2 NC_002967:TDE1323|3end_hypothetical_protein_1360968..1361118_POSITIVE 242 215 173 87 45 NC_002967:TDE1248|3end_hypothetical_protein_1283620..1283770_POSITIVE 238 38 1 45 4 NC_002967:TDE1212|3end_flagellar_basal-body_rod_protein_FlgB_1245873..1246023_POSITIVE 236 200 155 69 24 NC_002967:TDE1254|3end_Smr_domain_protein_1289003..1289153_POSITIVE 234 60 17 78 46 NC_002967:TDE2679|3end_hypothetical_protein_2720482..2720632_POSITIVE 234 104 61 45 13 NC_002967:TDE1147|3end_hypothetical_protein_1185529..1185679_NEGATIVE 231 227 185 50 15 NC_002967:TDE2644|3end_pyridine_nucleotide-disulphide_oxidoreductase_family_protein_2685059..2685209_POSITIVE 231 121 84 49 10 NC_002967:TDE2528|3end_hypothetical_protein_2556220..2556370_NEGATIVE