Origin IGS: ggaaagctattataataaaaaaatgattttatgcaagagtatcatagagagcatcccaatagcataggtctttatgtctcaatgacttatgaaaaacattgtaaaaactattcaggcataatctcaaaaaagtaaaaaatgtattttttttaatttacgtcttgacaaattaatatatgtatgataagtttacgaataggccgtttttgtgtgcgtatcattttctccctttaatttgacggcttaatacttttatttttaggaaaattgttttt .........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.........1.........2.........3.........4.........5.........6.........7.........8.........9 aaaaacaattttcctaaaaataaaagtattaagccgtcaaattaaagggagaaaatgatacgcacacaaaaacggcctattcgtaaacttatcatacatatattaatttgtcaagacgtaaattaaaaaaaatacattttttacttttttgagattatgcctgaatagtttttacaatgtttttcataagtcattgagacataaagacctatgctattgggatgctctctatgatactcttgcataaaatcatttttttattataatagctttcc Mask Tandem Repeat Region ================================================ ggaaagctattataataaaaaaatgattttatgcaagagtatcatagagagcatcccaatagcataggtctttatgtctcaatgacttatgaaaaacattgtaaaaactattcaggcataatctcaaaaaagtaaaaaatgtattttttttaatttacgtcttgacaaattaatatatgtatgataagtttacgaataggccgtttttgtgtgcgtatcattttctccctttaatttgacggcttaatacttttatttttaggaaaattgttttt Find is-nt database================================================ Query_seq: TDE1551:TDE1552|TDE1551:TDE1552:lipoyltransferase and lipoate-protein ligase family protein:hypothetical protein:<-->:1595624..1595898 275 ggaaagctattataataaaaaaatgattttatgcaagagtatcatagagagcatcccaatagcataggtctttatgtctcaatgacttatgaaaaacattgtaaaaactattcaggcataatctcaaaaaagtaaaaaatgtattttttttaatttacgtcttgacaaattaatatatgtatgataagtttacgaataggccgtttttgtgtgcgtatcattttctccctttaatttgacggcttaatacttttatttttaggaaaattgttttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE1551:TDE1552|TDE1551:TDE1552:lipoyltransferase and lipoate-protein ligase family protein:hypothetical protein:<-->:1595624..1595898 275 ggaaagctattataataaaaaaatgattttatgcaagagtatcatagagagcatcccaatagcataggtctttatgtctcaatgacttatgaaaaacattgtaaaaactattcaggcataatctcaaaaaagtaaaaaatgtattttttttaatttacgtcttgacaaattaatatatgtatgataagtttacgaataggccgtttttgtgtgcgtatcattttctccctttaatttgacggcttaatacttttatttttaggaaaattgttttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE1551:TDE1552|TDE1551:TDE1552:lipoyltransferase and lipoate-protein ligase family protein:hypothetical protein:<-->:1595624..1595898 275 ggaaagctattataataaaaaaatgattttatgcaagagtatcatagagagcatcccaatagcataggtctttatgtctcaatgacttatgaaaaacattgtaaaaactattcaggcataatctcaaaaaagtaaaaaatgtattttttttaatttacgtcttgacaaattaatatatgtatgataagtttacgaataggccgtttttgtgtgcgtatcattttctccctttaatttgacggcttaatacttttatttttaggaaaattgttttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ggaaagctattataataaaaaaatgattttatgcaagagtatcatagagagcatcccaatagcataggtctttatgtctcaatgacttatgaaaaacattgtaaaaactattcaggcataatctcaaaaaagtaaaaaatgtattttttttaatttacgtcttgacaaattaatatatgtatgataagtttacgaataggccgtttttgtgtgcgtatcattttctccctttaatttgacggcttaatacttttatttttaggaaaattgttttt Predict ORF larger than 30AA ================================================ Protein_Len: 34 Strand: + Start: 31 End: 132 .............................. M Q E Y H R E H P N S I G L Y V S M T Y E K H C K N Y S G I I S K K ............................................................................................................................................... Protein_Len: 41 Strand: - Start: 32 End: 154 ............................... A L T D Y L A D W Y C L D K H R L S K H F V N Y F S N L C L R L F T F F T N K K M ......................................................................................................................... ggaaagctattataataaaaaaatgattttatgcaagagtatcatagagagcatcccaatagcataggtctttatgtctcaatgacttatgaaaaacattgtaaaaactattcaggcataatctcaaaaaagtaaaaaatgtattttttttaatttacgtcttgacaaattaatatatgtatgataagtttacgaataggccgtttttgtgtgcgtatcattttctccctttaatttgacggcttaatacttttatttttaggaaaattgttttt 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: 161 End: 190 ................................................................................................................................................................CTTGACAAATTAATATATGTATGATAAGTT..................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ ggaaagctattataataaaaaaatgattttatgcaagagtatcatagagagcatcccaatagcataggtctttatgtctcaatgacttatgaaaaacattgtaaaaactattcaggcataatctcaaaaaagtaaaaaatgtattttttttaatttacgtcttgacaaattaatatatgtatgataagtttacgaataggccgtttttgtgtgcgtatcattttctccctttaatttgacggcttaatacttttatttttaggaaaattgttttt Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 46 HP_score: -2.3 Tail_Score: -3.65535 Start: 133 End: 152 Full_Region: tgtcaagacgtaaat taaaaaa aataca tttttta cttttttgagattat ....................................................................................................................................taaaaaaaatacatttttta........................................................................................................................... Find igs database================================================ Query_seq: TDE1551:TDE1552|TDE1551:TDE1552:lipoyltransferase and lipoate-protein ligase family protein:hypothetical protein:<-->:1595624..1595898 275 ggaaagctattataataaaaaaatgattttatgcaagagtatcatagagagcatcccaatagcataggtctttatgtctcaatgacttatgaaaaacattgtaaaaactattcaggcataatctcaaaaaagtaaaaaatgtattttttttaatttacgtcttgacaaattaatatatgtatgataagtttacgaataggccgtttttgtgtgcgtatcattttctccctttaatttgacggcttaatacttttatttttaggaaaattgttttt Intra-Species Hit: Count: 1 Min: 1 Max: 275 Len: 275 Subject: NC_002967_TDE1551_TDE1552|lipoyltransferase and lipoate-protein ligase family protein:hypothetical protein|NEGATIVE:POSITIVE|[1595624,1595898]|275 HSP 1 e-value: 3.0E-64 bit: 246.0 Len: 124 Query Start:152 Query End:275 Subject Strand: POSITIVE Subject Start: 152 Subject End: 275 .......................................................................................................................................................aatttacgtcttgacaaattaatatatgtatgataagtttacgaataggccgtttttgtgtgcgtatcattttctccctttaatttgacggcttaatacttttatttttaggaaaattgttttt .......................................................................................................................................................aatttacgtcttgacaaattaatatatgtatgataagtttacgaataggccgtttttgtgtgcgtatcattttctccctttaatttgacggcttaatacttttatttttaggaaaattgttttt HSP 2 e-value: 3.0E-52 bit: 206.0 Len: 125 Query Start:1 Query End:125 Subject Strand: POSITIVE Subject Start: 1 Subject End: 125 ggaaagctattataatnnnnnnntgattttatgcaagagtatcatagagagcatcccaatagcataggtctttatgtctcaatgacttatgaaaaacattgtaaaaactattcaggcataatctc...................................................................................................................................................... ggaaagctattataataaaaaaatgattttatgcaagagtatcatagagagcatcccaatagcataggtctttatgtctcaatgacttatgaaaaacattgtaaaaactattcaggcataatctc...................................................................................................................................................... Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GGAAAGCUAUUAUAAUAAAAAAAUGAUUUUAUGCAAGAGUAUCAUAGAGAGCAUCCCAAUAGCAUAGGUCUUUAUGUCUCAAUGACUUAUGAAAAACAUUGUAAAAACUAUUCAGGCAUAAUCUCAAAAAAGUAAAAAAUGUAUUUUUUUUAAUUUACGUCUUGACAAAUUAAUAUAUGUAUGAUAAGUUUACGAAUAGGCCGUUUUUGUGUGCGUAUCAUUUUCUCCCUUUAAUUUGACGGCUUAAUACUUUUAUUUUUAGGAAAAUUGUUUUU .((((((.(((.(..((((((..(((..((((((..(((((.((((((((.(..............).))))))))...(((((............))))).......)))))..))))))..))).(((((((....(((((..((....))..))))).....((((((((.....(.((((((.((.((((((.........)))))).)).))))))...).....)))))))).........))))))).))))))..).))).)))))) (-48.64) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAAACAAUUUUCCUAAAAAUAAAAGUAUUAAGCCGUCAAAUUAAAGGGAGAAAAUGAUACGCACACAAAAACGGCCUAUUCGUAAACUUAUCAUACAUAUAUUAAUUUGUCAAGACGUAAAUUAAAAAAAAUACAUUUUUUACUUUUUUGAGAUUAUGCCUGAAUAGUUUUUACAAUGUUUUUCAUAAGUCAUUGAGACAUAAAGACCUAUGCUAUUGGGAUGCUCUCUAUGAUACUCUUGCAUAAAAUCAUUUUUUUAUUAUAAUAGCUUUCC ......................(((((((((..((...........))(((((((((((............((((.....))))......................((((((((((.(((...(((((((......))))))).......((((.(((.(((.((((((........(((.(((((........))))).))).........)))))))))))).)))).....)))))))).))))))))))))))))....)))).))))).. (-36.23) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 897 80 31 171 122 NC_002967:TDE1551|5end_lipoyltransferase_and_lipoate-protein_ligase_family_protein_1595533..1595763_NEGATIVE 423 104 63 227 186 NC_002967:TDE1507|5end_L-serine_dehydratase,_iron-sulfur-dependent,_beta_subunit_1555724..1555954_NEGATIVE 303 245 201 181 141 NC_002967:TDE1168|5end_hypothetical_protein_1199482..1199712_NEGATIVE 288 240 193 60 7 NC_002967:TDE2305|5end_hypothetical_protein_2343652..2343882_POSITIVE 278 90 42 118 66 NC_002967:TDE2329|5end_hypothetical_protein_2366493..2366723_NEGATIVE 272 228 193 102 59 NC_002967:TDE0408|5end_oxidoreductase,_NAD-binding_461372..461602_NEGATIVE 271 230 181 104 65 NC_002967:TDE0352|5end_ribose_5-phosphate_isomerase_B_396207..396437_POSITIVE 256 233 196 196 157 NC_002967:TDE1252|5end_lipoprotein,_putative_1286400..1286630_POSITIVE 256 238 196 118 59 NC_002967:TDE0572|5end_hypothetical_protein_603494..603724_POSITIVE 256 240 193 113 66 NC_002967:TDE0259|5end_transcriptional_regulator,_MarR_family_293257..293487_POSITIVE 254 229 182 102 56 NC_002967:TDE1357|5end_aldose_1-epimerase_1396695..1396925_POSITIVE 251 229 188 180 130 NC_002967:TDE1527|5end_hypothetical_protein_1570804..1571034_POSITIVE 250 237 194 114 69 NC_002967:TDE1455|5end_prevent-host-death_family_protein_1502865..1503095_POSITIVE 243 216 192 76 50 NC_002967:TDE2586|5end_DNA_polymerase_III_subunits_gamma_and_tau_2622089..2622319_NEGATIVE 241 240 198 157 107 NC_002967:TDE2459|5end_hypothetical_protein_2485934..2486164_NEGATIVE 241 68 32 225 178 NC_002967:TDE1549|5end_recombination_protein_RecR_1592140..1592370_POSITIVE 240 80 32 100 53 NC_002967:TDE0472|5end_hypothetical_protein_528376..528606_POSITIVE 238 79 39 231 194 NC_002967:TDE0118|5end_hypothetical_protein_137047..137277_NEGATIVE 237 243 206 111 78 NC_002967:TDE1277|5end_Fe-hydrogenase_large_subunit_family_protein_1310681..1310911_POSITIVE 237 229 199 207 183 NC_002967:TDE0026|5end_TraB_family_protein_33016..33246_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 492 105 63 134 92 NC_002967:TDE2464|3end_hypothetical_protein_2489369..2489519_POSITIVE 366 110 68 42 1 NC_002967:TDE1629|3end_dihydrolipoamide_dehydrogenase_1677153..1677303_NEGATIVE 288 240 193 63 10 NC_002967:TDE2304|3end_hypothetical_protein_2343735..2343885_POSITIVE 282 228 183 139 83 NC_002967:TDE2086|3end_DnaJ_domain_protein_2115475..2115625_POSITIVE 281 243 201 114 74 NC_002967:TDE1907|3end_holo-(acyl-carrier-protein)_synthase_1924726..1924876_NEGATIVE 281 217 172 147 103 NC_002967:TDE0523|3end_hypothetical_protein_569238..569388_NEGATIVE 250 237 194 51 6 NC_002967:TDE1454|3end_sugar_transporter_1502882..1503032_POSITIVE 239 105 63 134 92 NC_002967:TDE1853|3end_hypothetical_protein_1881966..1882116_NEGATIVE 239 245 201 54 10 NC_002967:TDE1789|3end_hypothetical_protein_1827338..1827488_NEGATIVE 239 244 202 85 30 NC_002967:TDE0975|3end_hypothetical_protein_999879..1000029_POSITIVE 239 226 185 118 70 NC_002967:TDE0626|3end_hypothetical_protein_659684..659834_POSITIVE 235 79 31 109 66 NC_002967:TDE0600|3end_hypothetical_protein_638562..638712_NEGATIVE 234 230 184 92 54 NC_002967:TDE1243|3end_hemolysin_C_1275891..1276041_POSITIVE 233 239 194 101 36 NC_002967:TDE0394|3end_oligopeptide/dipeptide_ABC_transporter,_permease_protein_445023..445173_POSITIVE 230 215 182 63 29 NC_002967:TDE1735|3end_hypothetical_protein_1789998..1790148_POSITIVE 228 224 184 92 46 NC_002967:TDE1958|3end_surface_protein,_putative_1972309..1972459_NEGATIVE 226 98 51 86 32 NC_002967:TDE2668|3end_serine_hydroxymethyltransferase_2704546..2704696_NEGATIVE 224 80 37 114 77 NC_002967:TDE0875|3end_ribosomal_large_subunit_pseudouridine_synthase_B_898273..898423_POSITIVE 223 244 202 57 2 NC_002967:TDE1806|3end_hypothetical_protein_1843190..1843340_NEGATIVE 222 79 36 71 19 NC_002967:TDE2000|3end_ABC_transporter,_ATP-binding/permease_protein,_HlyB_family_2019639..2019789_POSITIVE