Origin IGS: tatcccccccattaaaagtatacaatctcatctataaaaaatgcggatagttatacctgtttactatttatttccaagcaacaaaatcacttacacattttctgaatcggccaattggctgtgagcataacagccgctcaatctgcaattggacataactccatttgtcggctttgaaaacgatagtatatg .........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 catatactatcgttttcaaagccgacaaatggagttatgtccaattgcagattgagcggctgttatgctcacagccaattggccgattcagaaaatgtgtaagtgattttgttgcttggaaataaatagtaaacaggtataactatccgcattttttatagatgagattgtatacttttaatgggggggata Mask Tandem Repeat Region ================================================ tatcccccccattaaaagtatacaatctcatctataaaaaatgcggatagttatacctgtttactatttatttccaagcaacaaaatcacttacacattttctgaatcggccaattggctgtgagcataacagccgctcaatctgcaattggacataactccatttgtcggctttgaaaacgatagtatatg Find is-nt database================================================ Query_seq: TDE1766:TDE1767|TDE1766:TDE1767:hypothetical protein:hypothetical protein:<-<-:1812824..1813015 192 tatcccccccattaaaagtatacaatctcatctataaaaaatgcggatagttatacctgtttactatttatttccaagcaacaaaatcacttacacattttctgaatcggccaattggctgtgagcataacagccgctcaatctgcaattggacataactccatttgtcggctttgaaaacgatagtatatg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE1766:TDE1767|TDE1766:TDE1767:hypothetical protein:hypothetical protein:<-<-:1812824..1813015 192 tatcccccccattaaaagtatacaatctcatctataaaaaatgcggatagttatacctgtttactatttatttccaagcaacaaaatcacttacacattttctgaatcggccaattggctgtgagcataacagccgctcaatctgcaattggacataactccatttgtcggctttgaaaacgatagtatatg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE1766:TDE1767|TDE1766:TDE1767:hypothetical protein:hypothetical protein:<-<-:1812824..1813015 192 tatcccccccattaaaagtatacaatctcatctataaaaaatgcggatagttatacctgtttactatttatttccaagcaacaaaatcacttacacattttctgaatcggccaattggctgtgagcataacagccgctcaatctgcaattggacataactccatttgtcggctttgaaaacgatagtatatg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tatcccccccattaaaagtatacaatctcatctataaaaaatgcggatagttatacctgtttactatttatttccaagcaacaaaatcacttacacattttctgaatcggccaattggctgtgagcataacagccgctcaatctgcaattggacataactccatttgtcggctttgaaaacgatagtatatg Predict ORF larger than 30AA ================================================ Protein_Len: 33 Strand: + Start: 57 End: 155 ........................................................ M F T I Y F Q A T K S L T H F L N R P I G C E H N S R S I C N W T ..................................... Protein_Len: 32 Strand: - Start: 94 End: 189 ............................................................................................. V N E S D A L Q S H A Y C G S L R C N S M V G N T P K S F S L M ... Protein_Len: 38 Strand: - Start: 71 End: 184 ...................................................................... K W A V F D S V C K R F R G I P Q S C L L R E I Q L Q V Y S W K D A K F V M ........ tatcccccccattaaaagtatacaatctcatctataaaaaatgcggatagttatacctgtttactatttatttccaagcaacaaaatcacttacacattttctgaatcggccaattggctgtgagcataacagccgctcaatctgcaattggacataactccatttgtcggctttgaaaacgatagtatatg 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================================================ tatcccccccattaaaagtatacaatctcatctataaaaaatgcggatagttatacctgtttactatttatttccaagcaacaaaatcacttacacattttctgaatcggccaattggctgtgagcataacagccgctcaatctgcaattggacataactccatttgtcggctttgaaaacgatagtatatg Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE1766:TDE1767|TDE1766:TDE1767:hypothetical protein:hypothetical protein:<-<-:1812824..1813015 192 tatcccccccattaaaagtatacaatctcatctataaaaaatgcggatagttatacctgtttactatttatttccaagcaacaaaatcacttacacattttctgaatcggccaattggctgtgagcataacagccgctcaatctgcaattggacataactccatttgtcggctttgaaaacgatagtatatg Intra-Species Hit: Count: 1 Min: 11 Max: 192 Len: 182 Subject: NC_002967_TDE1766_TDE1767|hypothetical protein:hypothetical protein|NEGATIVE:NEGATIVE|[1812824,1813015]|192 HSP 1 e-value: 6.0E-99 bit: 361.0 Len: 182 Query Start:11 Query End:192 Subject Strand: POSITIVE Subject Start: 11 Subject End: 192 ..........attaaaagtatacaatctcatctataaaaaatgcggatagttatacctgtttactatttatttccaagcaacaaaatcacttacacattttctgaatcggccaattggctgtgagcataacagccgctcaatctgcaattggacataactccatttgtcggctttgaaaacgatagtatatg ..........attaaaagtatacaatctcatctataaaaaatgcggatagttatacctgtttactatttatttccaagcaacaaaatcacttacacattttctgaatcggccaattggctgtgagcataacagccgctcaatctgcaattggacataactccatttgtcggctttgaaaacgatagtatatg Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUUAAAAGUAUACAAUCUCAUCUAUAAAAAAUGCGGAUAGUUAUACCUGUUUACUAUUUAUUUCCAAGCAACAAAAUCACUUACACAUUUUCUGAAUCGGCCAAUUGGCUGUGAGCAUAACAGCCGCUCAAUCUGCAAUUGGACAUAACUCCAUUUGUCGGCUUUGAAAACGAUAGUAUAUG .......((((((.(((...........(((((..(((((......)))))..).)))).((((.((((............................(((((....)))))(((((.........)))))....((((.((((......)))).))))..)))).))))..))).)))))). (-36.20) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CAUAUACUAUCGUUUUCAAAGCCGACAAAUGGAGUUAUGUCCAAUUGCAGAUUGAGCGGCUGUUAUGCUCACAGCCAAUUGGCCGAUUCAGAAAAUGUGUAAGUGAUUUUGUUGCUUGGAAAUAAAUAGUAAACAGGUAUAACUAUCCGCAUUUUUUAUAGAUGAGAUUGUAUACUUUUAAU ....((((((.((((((((.((.((((((.(((......)))..(((((.((((((((((((....((.....))....)))))).))))....)).))))).....))))))))))))))))..))))))...(((((((...(((..(((((.....))))).)))..)))))))..... (-43.10) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 953 130 81 231 182 NC_002967:TDE1766|5end_hypothetical_protein_1812733..1812963_NEGATIVE 463 137 91 144 96 NC_002967:TDE1817|5end_hypothetical_protein_1852599..1852829_NEGATIVE 350 137 101 71 34 NC_002967:TDE1006|5end_flagellar_basal-body_rod_protein_FlgG_1030427..1030657_POSITIVE 347 138 92 51 3 NC_002967:TDE0239|5end_glycine_reductase_complex_protein_GrdD_272982..273212_NEGATIVE 346 138 91 200 140 NC_002967:TDE0987|5end_oligopeptide/dipeptide_ABC_transporter,_ATP-binding_protein_1014041..1014271_POSITIVE 339 137 91 149 99 NC_002967:TDE1791|5end_hypothetical_protein_1828775..1829005_NEGATIVE 335 136 97 64 30 NC_002967:TDE2485|5end_hypothetical_protein_2509123..2509353_NEGATIVE 332 141 103 224 177 NC_002967:TDE2056|5end_outer_membrane_hemin-binding_protein_A_2085070..2085300_NEGATIVE 331 168 121 182 135 NC_002967:TDE0279|5end_hypothetical_protein_309782..310012_NEGATIVE 322 137 91 162 111 NC_002967:TDE1820|5end_hypothetical_protein_1854692..1854922_NEGATIVE 308 129 86 68 13 NC_002967:TDE0456|5end_pyridoxine_biosynthesis_protein_513384..513614_NEGATIVE 307 165 121 54 18 NC_002967:TDE2571|5end_hypothetical_protein_2598152..2598382_NEGATIVE 303 148 104 66 17 NC_002967:TDE2164|5end_hypothetical_protein_2196955..2197185_NEGATIVE 302 128 93 207 168 NC_002967:TDE1734|5end_exodeoxyribonuclease_III_1788613..1788843_POSITIVE 301 139 91 222 159 NC_002967:TDE2119|5end_glycine_reductase_complex_selenoprotein_GrdB2_2152693..2152923_NEGATIVE 301 138 93 150 103 NC_002967:TDE0637|5end_oligopeptide/dipeptide_ABC_transporter,_ATP-binding_protein_672491..672721_NEGATIVE 297 166 123 99 58 NC_002967:TDE1105|5end_ribosome-binding_factor_A_1138199..1138429_NEGATIVE 295 136 93 151 105 NC_002967:TDE2491|5end_DNA_polymerase_domain_protein_2515499..2515729_NEGATIVE 294 126 97 78 45 NC_002967:TDE2428|5end_ribosomal_protein_L33_2456292..2456522_NEGATIVE 292 168 121 174 120 NC_002967:TDE1794|5end_hypothetical_protein_1832958..1833188_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 371 144 107 72 29 NC_002967:TDE2735|3end_surface_antigen,_putative_2791616..2791766_POSITIVE 350 137 101 59 22 NC_002967:TDE1005|3end_hypothetical_protein_1030495..1030645_POSITIVE 337 137 97 48 7 NC_002967:TDE1806|3end_hypothetical_protein_1843190..1843340_NEGATIVE 336 137 96 44 4 NC_002967:TDE1789|3end_hypothetical_protein_1827338..1827488_NEGATIVE 332 141 103 136 89 NC_002967:TDE2057|3end_hypothetical_protein_2085158..2085308_NEGATIVE 331 168 121 69 22 NC_002967:TDE0280|3end_PIN_domain_protein_309895..310045_NEGATIVE 309 168 121 83 35 NC_002967:TDE1803|3end_hypothetical_protein_1838395..1838545_NEGATIVE 307 165 121 61 25 NC_002967:TDE2572|3end_CDP-diacylglycerol--glycerol-3-phosphate_3-phosphatidyltransferase_2598145..2598295_NEGATIVE 297 166 123 106 65 NC_002967:TDE1106|3end_translation_initiation_factor_IF-2_1138192..1138342_NEGATIVE 295 136 93 141 95 NC_002967:TDE2492|3end_hypothetical_protein_2515509..2515659_NEGATIVE 293 137 98 53 6 NC_002967:TDE1843|3end_hypothetical_protein_1872199..1872349_NEGATIVE 292 168 121 69 15 NC_002967:TDE1795|3end_funZ_protein,_putative_1833063..1833213_NEGATIVE 290 164 121 66 35 NC_002967:TDE0119|3end_flagellar_protein_FliS_137058..137208_NEGATIVE 288 166 123 44 3 NC_002967:TDE2643|3end_oxidoreductase,_FAD-dependent_2683734..2683884_POSITIVE 287 135 92 109 63 NC_002967:TDE2250|3end_hypothetical_protein_2289409..2289559_POSITIVE 282 173 133 87 50 NC_002967:TDE2741|3end_hypothetical_protein_2796722..2796872_POSITIVE 278 168 124 83 40 NC_002967:TDE0277|3end_hypothetical_protein_308109..308259_NEGATIVE 277 137 96 42 2 NC_002967:TDE1839|3end_hypothetical_protein_1870391..1870541_NEGATIVE 275 136 93 151 106 NC_002967:TDE0638|3end_oligopeptide/dipeptide_ABC_transporter,_permease_protein_672488..672638_NEGATIVE 273 137 97 88 40 NC_002967:TDE1770|3end_hypothetical_protein_1814468..1814618_POSITIVE