Origin IGS: ttaaatagctccaaatattttattgtccttattctatcaaaaaataaaataaaaaacaagataaagttttttgccggtaaacattttttttcattttaagctctttgataaactaagctatctaacaaaaagaaaattttatatttaaagataatacaatttattaaaagattcaatcaggttttgcacacgggtattcacccgtgtgcttttttg .........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 caaaaaagcacacgggtgaatacccgtgtgcaaaacctgattgaatcttttaataaattgtattatctttaaatataaaattttctttttgttagatagcttagtttatcaaagagcttaaaatgaaaaaaaatgtttaccggcaaaaaactttatcttgttttttattttattttttgatagaataaggacaataaaatatttggagctatttaa Mask Tandem Repeat Region ================================================ ttaaatagctccaaatattttattgtccttattctatcaaaaaataaaataaaaaacaagataaagttttttgccggtaaacattttttttcattttaagctctttgataaactaagctatctaacaaaaagaaaattttatatttaaagataatacaatttattaaaagattcaatcaggttttgcacacgggtattcacccgtgtgcttttttg Find is-nt database================================================ Query_seq: TDE0489:TDE0490|TDE0489:TDE0490:hypothetical protein:hypothetical protein:<-<-:546146..546361 216 ttaaatagctccaaatattttattgtccttattctatcaaaaaataaaataaaaaacaagataaagttttttgccggtaaacattttttttcattttaagctctttgataaactaagctatctaacaaaaagaaaattttatatttaaagataatacaatttattaaaagattcaatcaggttttgcacacgggtattcacccgtgtgcttttttg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE0489:TDE0490|TDE0489:TDE0490:hypothetical protein:hypothetical protein:<-<-:546146..546361 216 ttaaatagctccaaatattttattgtccttattctatcaaaaaataaaataaaaaacaagataaagttttttgccggtaaacattttttttcattttaagctctttgataaactaagctatctaacaaaaagaaaattttatatttaaagataatacaatttattaaaagattcaatcaggttttgcacacgggtattcacccgtgtgcttttttg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE0489:TDE0490|TDE0489:TDE0490:hypothetical protein:hypothetical protein:<-<-:546146..546361 216 ttaaatagctccaaatattttattgtccttattctatcaaaaaataaaataaaaaacaagataaagttttttgccggtaaacattttttttcattttaagctctttgataaactaagctatctaacaaaaagaaaattttatatttaaagataatacaatttattaaaagattcaatcaggttttgcacacgggtattcacccgtgtgcttttttg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ttaaatagctccaaatattttattgtccttattctatcaaaaaataaaataaaaaacaagataaagttttttgccggtaaacattttttttcattttaagctctttgataaactaagctatctaacaaaaagaaaattttatatttaaagataatacaatttattaaaagattcaatcaggttttgcacacgggtattcacccgtgtgcttttttg Predict ORF larger than 30AA ================================================ ttaaatagctccaaatattttattgtccttattctatcaaaaaataaaataaaaaacaagataaagttttttgccggtaaacattttttttcattttaagctctttgataaactaagctatctaacaaaaagaaaattttatatttaaagataatacaatttattaaaagattcaatcaggttttgcacacgggtattcacccgtgtgcttttttg 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: 31 End: 60 ..............................CTTGTTTTTTATTTTATTTTTTGATAGAAT............................................................................................................................................................ PromScan Matrix: RpoD-17 Strand: - Score: 81 Start: 148 End: 177 ...................................................................................................................................................ATTGAATCTTTTAATAAATTGTATTATCTT....................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ ttaaatagctccaaatattttattgtccttattctatcaaaaaataaaataaaaaacaagataaagttttttgccggtaaacattttttttcattttaagctctttgataaactaagctatctaacaaaaagaaaattttatatttaaagataatacaatttattaaaagattcaatcaggttttgcacacgggtattcacccgtgtgcttttttg Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE0489:TDE0490|TDE0489:TDE0490:hypothetical protein:hypothetical protein:<-<-:546146..546361 216 ttaaatagctccaaatattttattgtccttattctatcaaaaaataaaataaaaaacaagataaagttttttgccggtaaacattttttttcattttaagctctttgataaactaagctatctaacaaaaagaaaattttatatttaaagataatacaatttattaaaagattcaatcaggttttgcacacgggtattcacccgtgtgcttttttg Intra-Species Hit: Count: 1 Min: 1 Max: 216 Len: 216 Subject: NC_002967_TDE0489_TDE0490|hypothetical protein:hypothetical protein|NEGATIVE:NEGATIVE|[546146,546361]|216 HSP 1 e-value: 2.0E-71 bit: 270.0 Len: 160 Query Start:57 Query End:216 Subject Strand: POSITIVE Subject Start: 57 Subject End: 216 ........................................................caagataaagttttttgccggtaaacannnnnnnncattttaagctctttgataaactaagctatctaacaaaaagaaaattttatatttaaagataatacaatttattaaaagattcaatcaggttttgcacacgggtattcacccgtgtgcttttttg ........................................................caagataaagttttttgccggtaaacattttttttcattttaagctctttgataaactaagctatctaacaaaaagaaaattttatatttaaagataatacaatttattaaaagattcaatcaggttttgcacacgggtattcacccgtgtgcttttttg HSP 2 e-value: 5.0E-13 bit: 75.8 Len: 38 Query Start:1 Query End:38 Subject Strand: POSITIVE Subject Start: 1 Subject End: 38 ttaaatagctccaaatattttattgtccttattctatc.................................................................................................................................................................................. ttaaatagctccaaatattttattgtccttattctatc.................................................................................................................................................................................. Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUAAAUAGCUCCAAAUAUUUUAUUGUCCUUAUUCUAUCAAAAAAUAAAAUAAAAAACAAGAUAAAGUUUUUUGCCGGUAAACAUUUUUUUUCAUUUUAAGCUCUUUGAUAAACUAAGCUAUCUAACAAAAAGAAAAUUUUAUAUUUAAAGAUAAUACAAUUUAUUAAAAGAUUCAAUCAGGUUUUGCACACGGGUAUUCACCCGUGUGCUUUUUUG ...............(((((((((..................))))))))).(((((..(((..((((((((....(((((.(((((((((.......((((.............)))).........)))))))))))))).......(((((......)))))))))))))..)))..)))))((((((((((....))))))))))....... (-35.28) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CAAAAAAGCACACGGGUGAAUACCCGUGUGCAAAACCUGAUUGAAUCUUUUAAUAAAUUGUAUUAUCUUUAAAUAUAAAAUUUUCUUUUUGUUAGAUAGCUUAGUUUAUCAAAGAGCUUAAAAUGAAAAAAAAUGUUUACCGGCAAAAAACUUUAUCUUGUUUUUUAUUUUAUUUUUUGAUAGAAUAAGGACAAUAAAAUAUUUGGAGCUAUUUAA ((((((.((((((((((....))))))))))..........................(((((((.......))))))).......)))))).((((((((((..((((((((((((..((((((((((((....((((.........)))).........)))))))))))))))))))))))).......(((........))))))))))))). (-47.52) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 733 120 71 211 162 NC_002967:TDE0489|5end_hypothetical_protein_546055..546285_NEGATIVE 289 103 64 44 13 NC_002967:TDE0578|5end_hypothetical_protein_609493..609723_POSITIVE 283 210 170 54 5 NC_002967:TDE0793|5end_hypothetical_protein_818910..819140_POSITIVE 270 110 65 159 104 NC_002967:TDE1911|5end_hypothetical_protein_1929098..1929328_NEGATIVE 270 208 170 65 26 NC_002967:TDE0708|5end_nitroreductase_family_protein_743900..744130_POSITIVE 263 106 64 104 58 NC_002967:TDE2439|5end_hypothetical_protein_2470361..2470591_NEGATIVE 259 210 171 200 156 NC_002967:TDE1689|5end_ABC_transporter,_ATP-binding_protein_1746565..1746795_NEGATIVE 253 207 178 39 7 NC_002967:TDE0311|5end_thymidylate_synthase_342816..343046_POSITIVE 252 205 163 147 96 NC_002967:TDE0875|5end_ribosomal_large_subunit_pseudouridine_synthase_B_897489..897719_POSITIVE 243 94 57 67 34 NC_002967:TDE0965|5end_conserved_hypothetical_protein_TIGR00282_991367..991597_NEGATIVE 242 101 63 182 146 NC_002967:TDE2057|5end_hypothetical_protein_2085343..2085573_NEGATIVE 237 209 178 55 28 NC_002967:TDE0938|5end_hypothetical_protein_962174..962404_NEGATIVE 236 106 68 105 60 NC_002967:TDE1746|5end_hypothetical_protein_1800715..1800945_NEGATIVE 233 210 178 100 61 NC_002967:TDE0827|5end_hypothetical_protein_848053..848283_NEGATIVE 231 107 65 105 54 NC_002967:TDE2542|5end_antigen,_putative_2570826..2571056_NEGATIVE 231 118 71 155 117 NC_002967:TDE1872|5end_hypothetical_protein_1894691..1894921_NEGATIVE 231 125 83 122 80 NC_002967:TDE0724|5end_hypothetical_protein_761853..762083_POSITIVE 228 79 31 121 82 NC_002967:TDE2306|5end_hypothetical_protein_2344251..2344481_NEGATIVE 228 208 179 219 183 NC_002967:TDE2030|5end_lipoprotein,_RlpA_family_2058254..2058484_POSITIVE 228 209 169 121 83 NC_002967:TDE1918|5end_hypothetical_protein_1938344..1938574_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 297 99 58 67 26 NC_002967:TDE1670|3end_transcriptional_regulator,_MarR_family_1723913..1724063_NEGATIVE 289 103 64 148 117 NC_002967:TDE0578|3end_hypothetical_protein_609677..609827_POSITIVE 283 210 170 70 21 NC_002967:TDE0792|3end_ribosomal_protein_L17_819006..819156_POSITIVE 252 205 163 112 61 NC_002967:TDE0874|3end_transcriptional_regulator,_putative_897534..897684_POSITIVE 243 94 57 34 1 NC_002967:TDE0966|3end_hydrolase,_TatD_family_991400..991550_NEGATIVE 236 106 68 108 63 NC_002967:TDE1747|3end_nicotinate_(nicotinamide)_nucleotide_adenylyltransferase_1800712..1800862_NEGATIVE 231 118 71 117 79 NC_002967:TDE1873|3end_hypothetical_protein_1894729..1894879_NEGATIVE 228 79 31 137 98 NC_002967:TDE2307|3end_seryl-tRNA_synthetase_2344235..2344385_NEGATIVE 228 209 169 146 108 NC_002967:TDE1919|3end_hypothetical_protein_1938319..1938469_NEGATIVE 227 203 167 99 61 NC_002967:TDE2459|3end_hypothetical_protein_2485764..2485914_NEGATIVE 226 209 176 143 112 NC_002967:TDE0826|3end_hypothetical_protein_847860..848010_POSITIVE 226 208 178 129 104 NC_002967:TDE0573|3end_hypothetical_protein_604910..605060_POSITIVE 225 210 181 44 15 NC_002967:TDE1935|3end_hypothetical_protein_1953166..1953316_POSITIVE 223 208 190 25 7 NC_002967:TDE0707|3end_hypothetical_protein_743940..744090_POSITIVE 221 107 65 116 62 NC_002967:TDE1909|3end_conserved_hypothetical_protein_TIGR00159_1926048..1926198_NEGATIVE 220 108 64 105 64 NC_002967:TDE2473|3end_30S_ribosomal_protein_S21_2496587..2496737_POSITIVE 220 210 171 66 21 NC_002967:TDE0383|3end_hypothetical_protein_435159..435309_POSITIVE 213 106 63 86 33 NC_002967:TDE1788|3end_hypothetical_protein_1826628..1826778_NEGATIVE 213 106 64 92 41 NC_002967:TDE0852|3end_50S_ribosomal_protein_L13_875527..875677_POSITIVE 212 208 190 125 108 NC_002967:TDE1141|3end_tail_fiber_domain_protein_1169860..1170010_NEGATIVE