Origin IGS: ttttcctcttccggcaatagtttgtttttctactaaaatgtctatatttcaaaatttcaaacaagcagctcaccgagctgttcatataactatatttatatcatgctatttttcttgtgtcaacattatatttaattaaaatataatgaaattttactcaatgagccttttatagcctccattgaataagatataattttgtgttatactcaagccgattaaaataaagtgatttaatcggccgatatggaaacgaggaatgat .........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 atcattcctcgtttccatatcggccgattaaatcactttattttaatcggcttgagtataacacaaaattatatcttattcaatggaggctataaaaggctcattgagtaaaatttcattatattttaattaaatataatgttgacacaagaaaaatagcatgatataaatatagttatatgaacagctcggtgagctgcttgtttgaaattttgaaatatagacattttagtagaaaaacaaactattgccggaagaggaaaa Mask Tandem Repeat Region ================================================ ttttcctcttccggcaatagtttgtttttctactaaaatgtctatatttcaaaatttcaaacaagcagctcaccgagctgttcatataactatatttatatcatgctatttttcttgtgtcaacattatatttaattaaaatataatgaaattttactcaatgagccttttatagcctccattgaataagatataattttgtgttatactcaagccgattaaaataaagtgatttaatcggccgatatggaaacgaggaatgat Find is-nt database================================================ Query_seq: TDE0442:TDE0443|TDE0442:TDE0443:hypothetical protein:hypothetical protein:<-->:497814..498077 264 ttttcctcttccggcaatagtttgtttttctactaaaatgtctatatttcaaaatttcaaacaagcagctcaccgagctgttcatataactatatttatatcatgctatttttcttgtgtcaacattatatttaattaaaatataatgaaattttactcaatgagccttttatagcctccattgaataagatataattttgtgttatactcaagccgattaaaataaagtgatttaatcggccgatatggaaacgaggaatgat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE0442:TDE0443|TDE0442:TDE0443:hypothetical protein:hypothetical protein:<-->:497814..498077 264 ttttcctcttccggcaatagtttgtttttctactaaaatgtctatatttcaaaatttcaaacaagcagctcaccgagctgttcatataactatatttatatcatgctatttttcttgtgtcaacattatatttaattaaaatataatgaaattttactcaatgagccttttatagcctccattgaataagatataattttgtgttatactcaagccgattaaaataaagtgatttaatcggccgatatggaaacgaggaatgat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE0442:TDE0443|TDE0442:TDE0443:hypothetical protein:hypothetical protein:<-->:497814..498077 264 ttttcctcttccggcaatagtttgtttttctactaaaatgtctatatttcaaaatttcaaacaagcagctcaccgagctgttcatataactatatttatatcatgctatttttcttgtgtcaacattatatttaattaaaatataatgaaattttactcaatgagccttttatagcctccattgaataagatataattttgtgttatactcaagccgattaaaataaagtgatttaatcggccgatatggaaacgaggaatgat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ttttcctcttccggcaatagtttgtttttctactaaaatgtctatatttcaaaatttcaaacaagcagctcaccgagctgttcatataactatatttatatcatgctatttttcttgtgtcaacattatatttaattaaaatataatgaaattttactcaatgagccttttatagcctccattgaataagatataattttgtgttatactcaagccgattaaaataaagtgatttaatcggccgatatggaaacgaggaatgat Predict ORF larger than 30AA ================================================ Protein_Len: 40 Strand: + Start: 17 End: 136 ................ M V C F S T K M S I F Q N F K Q A A H R A V H I T I F I S C Y F S C V N I I F N ................................................................................................................................ Protein_Len: 36 Strand: - Start: 157 End: 264 ............................................................................................................................................................ E I L R K Y G G N F L I Y N Q T I S L G I L I F H N L R G I H F R P I M ttttcctcttccggcaatagtttgtttttctactaaaatgtctatatttcaaaatttcaaacaagcagctcaccgagctgttcatataactatatttatatcatgctatttttcttgtgtcaacattatatttaattaaaatataatgaaattttactcaatgagccttttatagcctccattgaataagatataattttgtgttatactcaagccgattaaaataaagtgatttaatcggccgatatggaaacgaggaatgat 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: 86 Start: 181 End: 210 ....................................................................................................................................................................................ATTGAATAAGATATAATTTTGTGTTATACT...................................................... PromScan Matrix: RpoD-17 Strand: - Score: 84 Start: 95 End: 124 ..............................................................................................GTTGACACAAGAAAAATAGCATGATATAAA............................................................................................................................................ PromScan Matrix: RpoD-17 Strand: + Score: 83 Start: 168 End: 197 .......................................................................................................................................................................TTTTATAGCCTCCATTGAATAAGATATAAT................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ ttttcctcttccggcaatagtttgtttttctactaaaatgtctatatttcaaaatttcaaacaagcagctcaccgagctgttcatataactatatttatatcatgctatttttcttgtgtcaacattatatttaattaaaatataatgaaattttactcaatgagccttttatagcctccattgaataagatataattttgtgttatactcaagccgattaaaataaagtgatttaatcggccgatatggaaacgaggaatgat Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 81 HP_score: -10.0 Tail_Score: -3.2918 Start: 66 End: 80 Full_Region: AAAATTTCAAACAAG CAGCTC ACC GAGCTG TTCATATAACTATAT .................................................................CAGCTCACCGAGCTG........................................................................................................................................................................................ TransTerm Strand: - Conf: 79 HP_score: -10.0 Tail_Score: -2.99162 Start: 66 End: 80 Full_Region: atatagttatatgaa cagctc ggt gagctg cttgtttgaaatttt .................................................................cagctcggtgagctg........................................................................................................................................................................................ TransTerm Strand: - Conf: 50 HP_score: -4.2 Tail_Score: -3.01712 Start: 126 End: 146 Full_Region: ttgagtaaaatttca ttatattt taatt aaatataa tgttgacacaagaaa .............................................................................................................................ttatattttaattaaatataa...................................................................................................................... Find igs database================================================ Query_seq: TDE0442:TDE0443|TDE0442:TDE0443:hypothetical protein:hypothetical protein:<-->:497814..498077 264 ttttcctcttccggcaatagtttgtttttctactaaaatgtctatatttcaaaatttcaaacaagcagctcaccgagctgttcatataactatatttatatcatgctatttttcttgtgtcaacattatatttaattaaaatataatgaaattttactcaatgagccttttatagcctccattgaataagatataattttgtgttatactcaagccgattaaaataaagtgatttaatcggccgatatggaaacgaggaatgat Intra-Species Hit: Count: 1 Min: 1 Max: 264 Len: 264 Subject: NC_002967_TDE0442_TDE0443|hypothetical protein:hypothetical protein|NEGATIVE:POSITIVE|[497814,498077]|264 HSP 1 e-value: 1.0E-148 bit: 523.0 Len: 264 Query Start:1 Query End:264 Subject Strand: POSITIVE Subject Start: 1 Subject End: 264 ttttcctcttccggcaatagtttgtttttctactaaaatgtctatatttcaaaatttcaaacaagcagctcaccgagctgttcatataactatatttatatcatgctatttttcttgtgtcaacattatatttaattaaaatataatgaaattttactcaatgagccttttatagcctccattgaataagatataattttgtgttatactcaagccgattaaaataaagtgatttaatcggccgatatggaaacgaggaatgat ttttcctcttccggcaatagtttgtttttctactaaaatgtctatatttcaaaatttcaaacaagcagctcaccgagctgttcatataactatatttatatcatgctatttttcttgtgtcaacattatatttaattaaaatataatgaaattttactcaatgagccttttatagcctccattgaataagatataattttgtgttatactcaagccgattaaaataaagtgatttaatcggccgatatggaaacgaggaatgat Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUUCCUCUUCCGGCAAUAGUUUGUUUUUCUACUAAAAUGUCUAUAUUUCAAAAUUUCAAACAAGCAGCUCACCGAGCUGUUCAUAUAACUAUAUUUAUAUCAUGCUAUUUUUCUUGUGUCAACAUUAUAUUUAAUUAAAAUAUAAUGAAAUUUUACUCAAUGAGCCUUUUAUAGCCUCCAUUGAAUAAGAUAUAAUUUUGUGUUAUACUCAAGCCGAUUAAAAUAAAGUGAUUUAAUCGGCCGAUAUGGAAACGAGGAAUGAU ..((((((....(((((....)))))..............((((((((...............((((((((...))))))))..((((((.(((.(((((((.....................((((((((((.....)))))))))).........((((((((.((.....)).)).))))))....)))))))...))))))))).....((((((((((.........)))))))))).))))))))...)))))).... (-60.30) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUCAUUCCUCGUUUCCAUAUCGGCCGAUUAAAUCACUUUAUUUUAAUCGGCUUGAGUAUAACACAAAAUUAUAUCUUAUUCAAUGGAGGCUAUAAAAGGCUCAUUGAGUAAAAUUUCAUUAUAUUUUAAUUAAAUAUAAUGUUGACACAAGAAAAAUAGCAUGAUAUAAAUAUAGUUAUAUGAACAGCUCGGUGAGCUGCUUGUUUGAAAUUUUGAAAUAUAGACAUUUUAGUAGAAAAACAAACUAUUGCCGGAAGAGGAAAA ....((((((...(((((...(((((((((((.........)))))))))))(((((((((.......))))).))))....)))))(((.(((...((((((((((((.......((((((((((.....))))))))))....................(.((((((......)))))).)...))))))))))))..((((((......(((((((......))))))).....))))))..))).)))....)))))).. (-66.30) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 836 110 61 201 152 NC_002967:TDE0442|5end_hypothetical_protein_497723..497953_NEGATIVE 265 100 63 80 32 NC_002967:TDE2543|5end_hypothetical_protein_2570950..2571180_NEGATIVE 265 100 63 204 156 NC_002967:TDE2542|5end_antigen,_putative_2570826..2571056_NEGATIVE 265 250 212 78 39 NC_002967:TDE0907|5end_hypothetical_protein_924644..924874_POSITIVE 252 190 141 123 66 NC_002967:TDE2119|5end_glycine_reductase_complex_selenoprotein_GrdB2_2152693..2152923_NEGATIVE 244 117 74 173 133 NC_002967:TDE2004|5end_hypothetical_protein_2023622..2023852_POSITIVE 242 250 209 54 7 NC_002967:TDE2309|5end_sigma-54_dependent_transcriptional_regulator,_putative_2348099..2348329_NEGATIVE 242 259 225 41 1 NC_002967:TDE0885|5end_50S_ribosomal_protein_L19_902945..903175_POSITIVE 238 245 201 72 31 NC_002967:TDE1664|5end_hypothetical_protein_1717862..1718092_POSITIVE 237 110 65 216 162 NC_002967:TDE2113|5end_hypothetical_protein_2139412..2139642_NEGATIVE 234 200 157 140 100 NC_002967:TDE1773|5end_hypothetical_protein_1817101..1817331_NEGATIVE 232 80 33 163 109 NC_002967:TDE2347|5end_30S_ribosomal_protein_S2_2384378..2384608_NEGATIVE 231 105 63 231 192 NC_002967:TDE2363|5end_high-affinity_branched_chain_amino_acid_ABC_transporter,_ATP-binding_protein_2398179..2398409_NEGATIVE 230 84 56 148 122 NC_002967:TDE2393|5end_hypothetical_protein_2422398..2422628_POSITIVE 230 94 65 152 115 NC_002967:TDE1325|5end_hypothetical_protein_1361721..1361951_NEGATIVE 229 230 182 79 34 NC_002967:TDE0668|5end_FeS_assembly_protein_SufD_705759..705989_POSITIVE 228 110 65 140 88 NC_002967:TDE0909|5end_type_II_DNA_modification_methyltransferase_M.TdeIII_927166..927396_POSITIVE 223 43 1 59 18 NC_002967:TDE0220|5end_hypothetical_protein_254005..254235_NEGATIVE 223 43 1 220 179 NC_002967:TDE0219|5end_hypothetical_protein_253844..254074_NEGATIVE 222 109 64 120 72 NC_002967:TDE2767|5end_flagellar_protein-related_protein_2821093..2821323_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 265 100 63 95 47 NC_002967:TDE2544|3end_hypothetical_protein_2570935..2571085_NEGATIVE 265 250 212 73 34 NC_002967:TDE0906|3end_ABC_transporter,_ATP-binding_protein_924719..924869_POSITIVE 265 259 216 48 2 NC_002967:TDE0884|3end_tRNA_(guanine-N(1)-)-methyltransferase_903032..903182_POSITIVE 262 256 214 97 54 NC_002967:TDE0073|3end_riboflavin_biosynthesis_protein_RibF,_putative_83159..83309_NEGATIVE 252 190 141 111 54 NC_002967:TDE2120|3end_glycine_reductase_complex_proprotein_GrdE2_2152705..2152855_NEGATIVE 246 182 147 130 84 NC_002967:TDE1916|3end_glycerol_kinase_1933277..1933427_NEGATIVE 244 117 74 102 62 NC_002967:TDE2003|3end_internalin-related_protein_2023631..2023781_POSITIVE 241 260 214 58 6 NC_002967:TDE0143|3end_thiamine_ABC_transporter,_thiamine-binding_protein_165103..165253_POSITIVE 240 243 208 144 96 NC_002967:TDE0467|3end_hypothetical_protein_519006..519156_NEGATIVE 238 29 7 136 110 NC_002967:TDE2577|3end_hypothetical_protein_2602490..2602640_NEGATIVE 235 259 214 76 29 NC_002967:TDE0946|3end_hypothetical_protein_968735..968885_POSITIVE 232 244 209 49 8 NC_002967:TDE0680|3end_protein-export_membrane_protein_SecF_717613..717763_NEGATIVE 230 94 65 84 47 NC_002967:TDE1327|3end_hypothetical_protein_1361789..1361939_NEGATIVE 229 230 182 76 31 NC_002967:TDE0667|3end_FeS_assembly_protein_SufB_705836..705986_POSITIVE 226 258 213 81 35 NC_002967:TDE2437|3end_cyclic_nucleotide_binding_domain_protein_2467418..2467568_NEGATIVE 224 242 212 49 18 NC_002967:TDE0138|3end_alkyldihydroxyacetonephosphate_synthase,_putative_160061..160211_POSITIVE 223 50 4 123 82 NC_002967:TDE0969|3end_hypothetical_protein_994575..994725_POSITIVE 223 50 4 123 82 NC_002967:TDE0724|3end_hypothetical_protein_763237..763387_POSITIVE 222 109 64 94 46 NC_002967:TDE2768|3end_flagellar_hook_protein_2821119..2821269_NEGATIVE 219 79 37 109 72 NC_002967:TDE0912|3end_hypothetical_protein_931528..931678_POSITIVE