Origin IGS: tacctattctgcaaatattctcatttgagctatttttcctgcattcatattaaaatcaattttcttataaatacggggtatatggtaaatttaaagccgttgcagtaaataaatttttaggtttttcttcaggtattaagaatgaaaccgtcataggttgaatataagagctttcaagaggatatagttcttccagacgaaagtcatcgattttaaaaccatattcatcacgtaattattgttcaactatgggtaagatgtttttttacacaatctcctaattgtaaagacaattatatcataaaaagatggataagtctatgtgttggatggagagcttgtaaagttttataagtatttggatgcttcaaattgtaatttatacctcttttgaagagtgataaaatacaaaaattaaataattatttcactaaataccttgacctctataaaatatattcgtattttgaaatgtaaaaggagcatgtct .........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.........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 agacatgctccttttacatttcaaaatacgaatatattttatagaggtcaaggtatttagtgaaataattatttaatttttgtattttatcactcttcaaaagaggtataaattacaatttgaagcatccaaatacttataaaactttacaagctctccatccaacacatagacttatccatctttttatgatataattgtctttacaattaggagattgtgtaaaaaaacatcttacccatagttgaacaataattacgtgatgaatatggttttaaaatcgatgactttcgtctggaagaactatatcctcttgaaagctcttatattcaacctatgacggtttcattcttaatacctgaagaaaaacctaaaaatttatttactgcaacggctttaaatttaccatataccccgtatttataagaaaattgattttaatatgaatgcaggaaaaatagctcaaatgagaatatttgcagaataggta Mask Tandem Repeat Region ================================================ tacctattctgcaaatattctcatttgagctatttttcctgcattcatattaaaatcaattttcttataaatacggggtatatggtaaatttaaagccgttgcagtaaataaatttttaggtttttcttcaggtattaagaatgaaaccgtcataggttgaatataagagctttcaagaggatatagttcttccagacgaaagtcatcgattttaaaaccatattcatcacgtaattattgttcaactatgggtaagatgtttttttacacaatctcctaattgtaaagacaattatatcataaaaagatggataagtctatgtgttggatggagagcttgtaaagttttataagtatttggatgcttcaaattgtaatttatacctcttttgaagagtgataaaatacaaaaattaaataattatttcactaaataccttgacctctataaaatatattcgtattttgaaatgtaaaaggagcatgtct Find is-nt database================================================ Query_seq: TDE1617:TDE1618|TDE1617:TDE1618:hypothetical protein:hypothetical protein:<-->:1664950..1665439 490 tacctattctgcaaatattctcatttgagctatttttcctgcattcatattaaaatcaattttcttataaatacggggtatatggtaaatttaaagccgttgcagtaaataaatttttaggtttttcttcaggtattaagaatgaaaccgtcataggttgaatataagagctttcaagaggatatagttcttccagacgaaagtcatcgattttaaaaccatattcatcacgtaattattgttcaactatgggtaagatgtttttttacacaatctcctaattgtaaagacaattatatcataaaaagatggataagtctatgtgttggatggagagcttgtaaagttttataagtatttggatgcttcaaattgtaatttatacctcttttgaagagtgataaaatacaaaaattaaataattatttcactaaataccttgacctctataaaatatattcgtattttgaaatgtaaaaggagcatgtct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE1617:TDE1618|TDE1617:TDE1618:hypothetical protein:hypothetical protein:<-->:1664950..1665439 490 tacctattctgcaaatattctcatttgagctatttttcctgcattcatattaaaatcaattttcttataaatacggggtatatggtaaatttaaagccgttgcagtaaataaatttttaggtttttcttcaggtattaagaatgaaaccgtcataggttgaatataagagctttcaagaggatatagttcttccagacgaaagtcatcgattttaaaaccatattcatcacgtaattattgttcaactatgggtaagatgtttttttacacaatctcctaattgtaaagacaattatatcataaaaagatggataagtctatgtgttggatggagagcttgtaaagttttataagtatttggatgcttcaaattgtaatttatacctcttttgaagagtgataaaatacaaaaattaaataattatttcactaaataccttgacctctataaaatatattcgtattttgaaatgtaaaaggagcatgtct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE1617:TDE1618|TDE1617:TDE1618:hypothetical protein:hypothetical protein:<-->:1664950..1665439 490 tacctattctgcaaatattctcatttgagctatttttcctgcattcatattaaaatcaattttcttataaatacggggtatatggtaaatttaaagccgttgcagtaaataaatttttaggtttttcttcaggtattaagaatgaaaccgtcataggttgaatataagagctttcaagaggatatagttcttccagacgaaagtcatcgattttaaaaccatattcatcacgtaattattgttcaactatgggtaagatgtttttttacacaatctcctaattgtaaagacaattatatcataaaaagatggataagtctatgtgttggatggagagcttgtaaagttttataagtatttggatgcttcaaattgtaatttatacctcttttgaagagtgataaaatacaaaaattaaataattatttcactaaataccttgacctctataaaatatattcgtattttgaaatgtaaaaggagcatgtct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tacctattctgcaaatattctcatttgagctatttttcctgcattcatattaaaatcaattttcttataaatacggggtatatggtaaatttaaagccgttgcagtaaataaatttttaggtttttcttcaggtattaagaatgaaaccgtcataggttgaatataagagctttcaagaggatatagttcttccagacgaaagtcatcgattttaaaaccatattcatcacgtaattattgttcaactatgggtaagatgtttttttacacaatctcctaattgtaaagacaattatatcataaaaagatggataagtctatgtgttggatggagagcttgtaaagttttataagtatttggatgcttcaaattgtaatttatacctcttttgaagagtgataaaatacaaaaattaaataattatttcactaaataccttgacctctataaaatatattcgtattttgaaatgtaaaaggagcatgtct Predict ORF larger than 30AA ================================================ Protein_Len: 43 Strand: + Start: 223 End: 351 .............................................................................................................................................................................................................................. M H H V I I V Q L W V R C F F T Q S P N C K D N Y I I K R W I S L C V G W R A C K V L ........................................................................................................................................... Protein_Len: 31 Strand: + Start: 382 End: 474 ............................................................................................................................................................................................................................................................................................................................................................................................. M P L L K S D K I Q K L N N Y F T K Y L D L Y K I Y S Y F E M ................ Protein_Len: 37 Strand: - Start: 297 End: 407 ........................................................................................................................................................................................................................................................................................................ I M F L H I L R H T P H L A Q L T K Y T N P H K L N Y N I G R K F L S L M ................................................................................... Protein_Len: 31 Strand: - Start: 154 End: 246 ......................................................................................................................................................... L N F I L A K L L I Y N K W V F T M S K L V M N M V Y N N N M .................................................................................................................................................................................................................................................... Protein_Len: 48 Strand: - Start: 68 End: 211 ................................................................... L Y P T Y P L N L A T A T F L N K P K E E P I L F S V T M P Q I Y S S E L P Y L E E L R F D D M ....................................................................................................................................................................................................................................................................................... tacctattctgcaaatattctcatttgagctatttttcctgcattcatattaaaatcaattttcttataaatacggggtatatggtaaatttaaagccgttgcagtaaataaatttttaggtttttcttcaggtattaagaatgaaaccgtcataggttgaatataagagctttcaagaggatatagttcttccagacgaaagtcatcgattttaaaaccatattcatcacgtaattattgttcaactatgggtaagatgtttttttacacaatctcctaattgtaaagacaattatatcataaaaagatggataagtctatgtgttggatggagagcttgtaaagttttataagtatttggatgcttcaaattgtaatttatacctcttttgaagagtgataaaatacaaaaattaaataattatttcactaaataccttgacctctataaaatatattcgtattttgaaatgtaaaaggagcatgtct 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: 87 Start: 293 End: 322 ....................................................................................................................................................................................................................................................................................................ATAGACTTATCCATCTTTTTATGATATAAT........................................................................................................................................................................ PromScan Matrix: RpoD-17 Strand: + Score: 83 Start: 426 End: 455 .........................................................................................................................................................................................................................................................................................................................................................................................................................................TTTCACTAAATACCTTGACCTCTATAAAAT................................... PromScan Matrix: RpoD-17 Strand: + Score: 81 Start: 378 End: 407 .........................................................................................................................................................................................................................................................................................................................................................................................ATTTATACCTCTTTTGAAGAGTGATAAAAT................................................................................... PromScan Matrix: RpoD-17 Strand: + Score: 81 Start: 439 End: 468 ......................................................................................................................................................................................................................................................................................................................................................................................................................................................CTTGACCTCTATAAAATATATTCGTATTTT...................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tacctattctgcaaatattctcatttgagctatttttcctgcattcatattaaaatcaattttcttataaatacggggtatatggtaaatttaaagccgttgcagtaaataaatttttaggtttttcttcaggtattaagaatgaaaccgtcataggttgaatataagagctttcaagaggatatagttcttccagacgaaagtcatcgattttaaaaccatattcatcacgtaattattgttcaactatgggtaagatgtttttttacacaatctcctaattgtaaagacaattatatcataaaaagatggataagtctatgtgttggatggagagcttgtaaagttttataagtatttggatgcttcaaattgtaatttatacctcttttgaagagtgataaaatacaaaaattaaataattatttcactaaataccttgacctctataaaatatattcgtattttgaaatgtaaaaggagcatgtct Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE1617:TDE1618|TDE1617:TDE1618:hypothetical protein:hypothetical protein:<-->:1664950..1665439 490 tacctattctgcaaatattctcatttgagctatttttcctgcattcatattaaaatcaattttcttataaatacggggtatatggtaaatttaaagccgttgcagtaaataaatttttaggtttttcttcaggtattaagaatgaaaccgtcataggttgaatataagagctttcaagaggatatagttcttccagacgaaagtcatcgattttaaaaccatattcatcacgtaattattgttcaactatgggtaagatgtttttttacacaatctcctaattgtaaagacaattatatcataaaaagatggataagtctatgtgttggatggagagcttgtaaagttttataagtatttggatgcttcaaattgtaatttatacctcttttgaagagtgataaaatacaaaaattaaataattatttcactaaataccttgacctctataaaatatattcgtattttgaaatgtaaaaggagcatgtct Intra-Species Hit: Count: 1 Min: 1 Max: 490 Len: 490 Subject: NC_002967_TDE1617_TDE1618|hypothetical protein:hypothetical protein|NEGATIVE:POSITIVE|[1664950,1665439]|490 HSP 1 e-value: 0.0 bit: 930.0 Len: 490 Query Start:1 Query End:490 Subject Strand: POSITIVE Subject Start: 1 Subject End: 490 tacctattctgcaaatattctcatttgagctatttttcctgcattcatattaaaatcaattttcttataaatacggggtatatggtaaatttaaagccgttgcagtaaataaatttttaggtttttcttcaggtattaagaatgaaaccgtcataggttgaatataagagctttcaagaggatatagttcttccagacgaaagtcatcgattttaaaaccatattcatcacgtaattattgttcaactatgggtaagatgnnnnnnnacacaatctcctaattgtaaagacaattatatcataaaaagatggataagtctatgtgttggatggagagcttgtaaagttttataagtatttggatgcttcaaattgtaatttatacctcttttgaagagtgataaaatacaaaaattaaataattatttcactaaataccttgacctctataaaatatattcgtattttgaaatgtaaaaggagcatgtct tacctattctgcaaatattctcatttgagctatttttcctgcattcatattaaaatcaattttcttataaatacggggtatatggtaaatttaaagccgttgcagtaaataaatttttaggtttttcttcaggtattaagaatgaaaccgtcataggttgaatataagagctttcaagaggatatagttcttccagacgaaagtcatcgattttaaaaccatattcatcacgtaattattgttcaactatgggtaagatgtttttttacacaatctcctaattgtaaagacaattatatcataaaaagatggataagtctatgtgttggatggagagcttgtaaagttttataagtatttggatgcttcaaattgtaatttatacctcttttgaagagtgataaaatacaaaaattaaataattatttcactaaataccttgacctctataaaatatattcgtattttgaaatgtaaaaggagcatgtct Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UACCUAUUCUGCAAAUAUUCUCAUUUGAGCUAUUUUUCCUGCAUUCAUAUUAAAAUCAAUUUUCUUAUAAAUACGGGGUAUAUGGUAAAUUUAAAGCCGUUGCAGUAAAUAAAUUUUUAGGUUUUUCUUCAGGUAUUAAGAAUGAAACCGUCAUAGGUUGAAUAUAAGAGCUUUCAAGAGGAUAUAGUUCUUCCAGACGAAAGUCAUCGAUUUUAAAACCAUAUUCAUCACGUAAUUAUUGUUCAACUAUGGGUAAGAUGUUUUUUUACACAAUCUCCUAAUUGUAAAGACAAUUAUAUCAUAAAAAGAUGGAUAAGUCUAUGUGUUGGAUGGAGAGCUUGUAAAGUUUUAUAAGUAUUUGGAUGCUUCAAAUUGUAAUUUAUACCUCUUUUGAAGAGUGAUAAAAUACAAAAAUUAAAUAAUUAUUUCACUAAAUACCUUGACCUCUAUAAAAUAUAUUCGUAUUUUGAAAUGUAAAAGGAGCAUGUCU .(((((..((((((..............(((((...(((((.(((.(((..((((....))))..))).))).)))))...))))).............))))))............)))))...(((((.(((.((((((.(((((((......))))......(((((((.((.....))...)))))))...(((....))).))).)))))).)))..(((((.((((((....(((((((.((.((.((((((.....)))))).))......(((((((....)))))))..........)).)))))))...)))))).))))))))))((((((((....))))))))......(((((((...(((((.(((((..((((.....))))..))))).)))))............(((((((..((((((.......................))))))))))))).....))))))).... (-98.87) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGACAUGCUCCUUUUACAUUUCAAAAUACGAAUAUAUUUUAUAGAGGUCAAGGUAUUUAGUGAAAUAAUUAUUUAAUUUUUGUAUUUUAUCACUCUUCAAAAGAGGUAUAAAUUACAAUUUGAAGCAUCCAAAUACUUAUAAAACUUUACAAGCUCUCCAUCCAACACAUAGACUUAUCCAUCUUUUUAUGAUAUAAUUGUCUUUACAAUUAGGAGAUUGUGUAAAAAAACAUCUUACCCAUAGUUGAACAAUAAUUACGUGAUGAAUAUGGUUUUAAAAUCGAUGACUUUCGUCUGGAAGAACUAUAUCCUCUUGAAAGCUCUUAUAUUCAACCUAUGACGGUUUCAUUCUUAAUACCUGAAGAAAAACCUAAAAAUUUAUUUACUGCAACGGCUUUAAAUUUACCAUAUACCCCGUAUUUAUAAGAAAAUUGAUUUUAAUAUGAAUGCAGGAAAAAUAGCUCAAAUGAGAAUAUUUGCAGAAUAGGUA .((.(((.........))).)).......((((((((((((.(((((...((((((((.(((.........(((((...(((((.(((((..((((.....))))..))))).))))).))))).)))..)))))))).............((.(((((...................((((...(((((.(..(((((((..((.((((((((..(..((((......))))..)..)).))))))))..)))))))..).))))).))))..........((((.....)))).)).))).))....)))))))))).....))))))).((((((...(((((..(((((........))))))))))..............((((((......................((.(((((((((..((((....))))..))))))))).))........(((....))).....)))))).)))))). (-89.40) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 779 50 1 141 92 NC_002967:TDE1617|5end_hypothetical_protein_1664859..1665089_NEGATIVE 292 346 302 88 35 NC_002967:TDE2731|5end_TIM-barrel_protein,_putative,_NifR3_family_2787372..2787602_POSITIVE 276 369 321 64 10 NC_002967:TDE0632|5end_anti-anti-sigma_factor_667431..667661_POSITIVE 275 348 309 226 183 NC_002967:TDE0474|5end_hypothetical_protein_530740..530970_POSITIVE 258 107 61 53 3 NC_002967:TDE0906|5end_ABC_transporter,_ATP-binding_protein_923164..923394_POSITIVE 257 210 164 88 27 NC_002967:TDE1401|5end_DedA_family_protein_1442365..1442595_POSITIVE 255 182 149 179 145 NC_002967:TDE1688|5end_hypothetical_protein_1745791..1746021_NEGATIVE 255 340 293 54 3 NC_002967:TDE1299|5end_hypothetical_protein_1336613..1336843_NEGATIVE 254 47 3 112 56 NC_002967:TDE2281|5end_LysM_domain_protein_2318493..2318723_NEGATIVE 250 220 177 192 141 NC_002967:TDE1624|5end_glycine_dehydrogenase_subunit_2_1673519..1673749_NEGATIVE 248 370 325 179 137 NC_002967:TDE2619|5end_RNA_methyltransferase,_TrmA_family,_putative_2660280..2660510_POSITIVE 247 370 329 35 1 NC_002967:TDE0847|5end_hypothetical_protein_870894..871124_POSITIVE 245 206 161 128 82 NC_002967:TDE1584|5end_lipoprotein,_putative_1632025..1632255_POSITIVE 244 207 165 78 38 NC_002967:TDE0010|5end_MutT/nudix_family_protein_14580..14810_POSITIVE 242 219 171 64 20 NC_002967:TDE2712|5end_hypothetical_protein_2769008..2769238_POSITIVE 241 102 72 211 184 NC_002967:TDE1340|5end_ribosomal_5S_rRNA_E-loop_binding_protein_Ctc/L25/TL5_1376317..1376547_POSITIVE 239 369 322 158 114 NC_002967:TDE2138|5end_ankyrin_repeat_protein_2171631..2171861_POSITIVE 237 286 249 108 68 NC_002967:TDE2142|5end_methyl-accepting_chemotaxis_protein_2175769..2175999_POSITIVE 237 220 171 59 11 NC_002967:TDE0129|5end_PyrBI_protein_150299..150529_NEGATIVE 236 350 308 169 123 NC_002967:TDE0411|5end_adenylate/guanylate_cyclase_catalytic_domain_protein_462931..463161_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 292 346 302 75 22 NC_002967:TDE2730|3end_hydrolase,_TatD_family_2787439..2787589_POSITIVE 264 135 97 143 102 NC_002967:TDE2066|3end_exodeoxyribonuclease_VII,_small_subunit_2092222..2092372_POSITIVE 263 369 322 54 1 NC_002967:TDE0631|3end_sigma_factor_regulatory_protein,_putative_667501..667651_POSITIVE 260 345 307 67 32 NC_002967:TDE0352|3end_ribose_5-phosphate_isomerase_B_396739..396889_POSITIVE 258 104 65 90 49 NC_002967:TDE2319|3end_hypothetical_protein_2355835..2355985_NEGATIVE 257 210 164 77 16 NC_002967:TDE1400|3end_NAD(+)_synthetase_1442434..1442584_POSITIVE 255 340 293 57 6 NC_002967:TDE1300|3end_hypothetical_protein_1336610..1336760_NEGATIVE 255 119 73 59 7 NC_002967:TDE0826|3end_hypothetical_protein_847860..848010_POSITIVE 249 339 293 44 2 NC_002967:TDE1593|3end_Fe-hydrogenase_1641209..1641359_NEGATIVE 239 368 323 46 1 NC_002967:TDE1336|3end_hypothetical_protein_1373780..1373930_POSITIVE 230 369 325 76 34 NC_002967:TDE1931|3end_cytidine_deaminase_1949020..1949170_POSITIVE 230 53 11 87 36 NC_002967:TDE0769|3end_ribosomal_protein_L23_807998..808148_POSITIVE 227 342 310 88 54 NC_002967:TDE0339|3end_transcriptional_regulator,_TetR_family_378568..378718_POSITIVE 226 135 95 111 69 NC_002967:TDE1364|3end_valyl-tRNA_synthetase_1407572..1407722_POSITIVE 224 151 119 57 25 NC_002967:TDE2684|3end_hypothetical_protein_2724180..2724330_NEGATIVE 223 109 75 120 95 NC_002967:TDE1434|3end_hypothetical_protein_1478238..1478388_NEGATIVE 222 193 151 87 50 NC_002967:TDE0735|3end_hypothetical_protein_774746..774896_NEGATIVE 222 252 213 36 1 NC_002967:TDE0021|3end_CDP-alcohol_phosphatidyltransferase_family_protein_27895..28045_POSITIVE 221 370 322 71 3 NC_002967:TDE1540|3end_hypothetical_protein_1584948..1585098_POSITIVE 221 107 73 37 3 NC_002967:TDE0905|3end_hypothetical_protein_923228..923378_POSITIVE