Origin IGS: atcaagacaaacctcaaaaactggagttttttgaggtttgtctttgtgcggagatattatgaaaaacagttattatatacgcacaaaaattttcttctcatttaaaaagtaaagattttgccgttttagaatcgatcatttgaatgtaaggactttgatacctacggcctatttaaattcttcggcgacctagccaaagggcatcccaatgctaaagacattgaaaatgccgtaacatttataaaagatattgaataggttaaaatacggtaaagctcaaaagtattgcggccgtttctagtacatatccgattttgaaatacccaaaattgtattgatgacctggagattttataa .........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 ttataaaatctccaggtcatcaatacaattttgggtatttcaaaatcggatatgtactagaaacggccgcaatacttttgagctttaccgtattttaacctattcaatatcttttataaatgttacggcattttcaatgtctttagcattgggatgccctttggctaggtcgccgaagaatttaaataggccgtaggtatcaaagtccttacattcaaatgatcgattctaaaacggcaaaatctttactttttaaatgagaagaaaatttttgtgcgtatataataactgtttttcataatatctccgcacaaagacaaacctcaaaaaactccagtttttgaggtttgtcttgat Mask Tandem Repeat Region ================================================ atcaagacaaacctcaaaaactggagttttttgaggtttgtctttgtgcggagatattatgaaaaacagttattatatacgcacaaaaattttcttctcatttaaaaagtaaagattttgccgttttagaatcgatcatttgaatgtaaggactttgatacctacggcctatttaaattcttcggcgacctagccaaagggcatcccaatgctaaagacattgaaaatgccgtaacatttataaaagatattgaataggttaaaatacggtaaagctcaaaagtattgcggccgtttctagtacatatccgattttgaaatacccaaaattgtattgatgacctggagattttataa Find is-nt database================================================ Query_seq: TDE0525:TDE0526|TDE0525:TDE0526:hypothetical protein:hypothetical protein:->->:571224..571580 357 atcaagacaaacctcaaaaactggagttttttgaggtttgtctttgtgcggagatattatgaaaaacagttattatatacgcacaaaaattttcttctcatttaaaaagtaaagattttgccgttttagaatcgatcatttgaatgtaaggactttgatacctacggcctatttaaattcttcggcgacctagccaaagggcatcccaatgctaaagacattgaaaatgccgtaacatttataaaagatattgaataggttaaaatacggtaaagctcaaaagtattgcggccgtttctagtacatatccgattttgaaatacccaaaattgtattgatgacctggagattttataa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE0525:TDE0526|TDE0525:TDE0526:hypothetical protein:hypothetical protein:->->:571224..571580 357 atcaagacaaacctcaaaaactggagttttttgaggtttgtctttgtgcggagatattatgaaaaacagttattatatacgcacaaaaattttcttctcatttaaaaagtaaagattttgccgttttagaatcgatcatttgaatgtaaggactttgatacctacggcctatttaaattcttcggcgacctagccaaagggcatcccaatgctaaagacattgaaaatgccgtaacatttataaaagatattgaataggttaaaatacggtaaagctcaaaagtattgcggccgtttctagtacatatccgattttgaaatacccaaaattgtattgatgacctggagattttataa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE0525:TDE0526|TDE0525:TDE0526:hypothetical protein:hypothetical protein:->->:571224..571580 357 atcaagacaaacctcaaaaactggagttttttgaggtttgtctttgtgcggagatattatgaaaaacagttattatatacgcacaaaaattttcttctcatttaaaaagtaaagattttgccgttttagaatcgatcatttgaatgtaaggactttgatacctacggcctatttaaattcttcggcgacctagccaaagggcatcccaatgctaaagacattgaaaatgccgtaacatttataaaagatattgaataggttaaaatacggtaaagctcaaaagtattgcggccgtttctagtacatatccgattttgaaatacccaaaattgtattgatgacctggagattttataa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 atcaagacaaacctcaaaaactggagttttttgaggtttgtctttgtgcggagatattatgaaaaacagttattatatacgcacaaaaattttcttctcatttaaaaagtaaagattttgccgttttagaatcgatcatttgaatgtaaggactttgatacctacggcctatttaaattcttcggcgacctagccaaagggcatcccaatgctaaagacattgaaaatgccgtaacatttataaaagatattgaataggttaaaatacggtaaagctcaaaagtattgcggccgtttctagtacatatccgattttgaaatacccaaaattgtattgatgacctggagattttataa Predict ORF larger than 30AA ================================================ Protein_Len: 34 Strand: + Start: 1 End: 102 M K T N L K N W S F L R F V F V R R Y Y E K Q L L Y T H K N F L L I ............................................................................................................................................................................................................................................................... Protein_Len: 31 Strand: - Start: 263 End: 355 ...................................................................................................................................................................................................................................................................... F V T F S L L I A A T E L V Y G I K F Y G F N Y Q H G P S K M .. Protein_Len: 60 Strand: - Start: 165 End: 350 .................................................................................................................................................................... N L N K P S R A L P C G L A L S M S F A T V N I F S I S Y T L I R Y L E F T N R G N R T C I R N Q F V W F Q I S S R S M ....... atcaagacaaacctcaaaaactggagttttttgaggtttgtctttgtgcggagatattatgaaaaacagttattatatacgcacaaaaattttcttctcatttaaaaagtaaagattttgccgttttagaatcgatcatttgaatgtaaggactttgatacctacggcctatttaaattcttcggcgacctagccaaagggcatcccaatgctaaagacattgaaaatgccgtaacatttataaaagatattgaataggttaaaatacggtaaagctcaaaagtattgcggccgtttctagtacatatccgattttgaaatacccaaaattgtattgatgacctggagattttataa 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: 85 Start: 237 End: 266 ............................................................................................................................................................................................................................................ATTTATAAAAGATATTGAATAGGTTAAAAT........................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ atcaagacaaacctcaaaaactggagttttttgaggtttgtctttgtgcggagatattatgaaaaacagttattatatacgcacaaaaattttcttctcatttaaaaagtaaagattttgccgttttagaatcgatcatttgaatgtaaggactttgatacctacggcctatttaaattcttcggcgacctagccaaagggcatcccaatgctaaagacattgaaaatgccgtaacatttataaaagatattgaataggttaaaatacggtaaagctcaaaagtattgcggccgtttctagtacatatccgattttgaaatacccaaaattgtattgatgacctggagattttataa Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 43 HP_score: -2.8 Tail_Score: -3.14602 Start: 310 End: 332 Full_Region: TTTCTAGTACATATC CGATTTTG AAATACC CAAAATTG TATTGATGACCTGGA .....................................................................................................................................................................................................................................................................................................................CGATTTTGAAATACCCAAAATTG......................... Find igs database================================================ Query_seq: TDE0525:TDE0526|TDE0525:TDE0526:hypothetical protein:hypothetical protein:->->:571224..571580 357 atcaagacaaacctcaaaaactggagttttttgaggtttgtctttgtgcggagatattatgaaaaacagttattatatacgcacaaaaattttcttctcatttaaaaagtaaagattttgccgttttagaatcgatcatttgaatgtaaggactttgatacctacggcctatttaaattcttcggcgacctagccaaagggcatcccaatgctaaagacattgaaaatgccgtaacatttataaaagatattgaataggttaaaatacggtaaagctcaaaagtattgcggccgtttctagtacatatccgattttgaaatacccaaaattgtattgatgacctggagattttataa Intra-Species Hit: Count: 1 Min: 1 Max: 357 Len: 357 Subject: NC_002967_TDE0525_TDE0526|hypothetical protein:hypothetical protein|POSITIVE:POSITIVE|[571224,571580]|357 HSP 1 e-value: 0.0 bit: 708.0 Len: 357 Query Start:1 Query End:357 Subject Strand: POSITIVE Subject Start: 1 Subject End: 357 atcaagacaaacctcaaaaactggagttttttgaggtttgtctttgtgcggagatattatgaaaaacagttattatatacgcacaaaaattttcttctcatttaaaaagtaaagattttgccgttttagaatcgatcatttgaatgtaaggactttgatacctacggcctatttaaattcttcggcgacctagccaaagggcatcccaatgctaaagacattgaaaatgccgtaacatttataaaagatattgaataggttaaaatacggtaaagctcaaaagtattgcggccgtttctagtacatatccgattttgaaatacccaaaattgtattgatgacctggagattttataa atcaagacaaacctcaaaaactggagttttttgaggtttgtctttgtgcggagatattatgaaaaacagttattatatacgcacaaaaattttcttctcatttaaaaagtaaagattttgccgttttagaatcgatcatttgaatgtaaggactttgatacctacggcctatttaaattcttcggcgacctagccaaagggcatcccaatgctaaagacattgaaaatgccgtaacatttataaaagatattgaataggttaaaatacggtaaagctcaaaagtattgcggccgtttctagtacatatccgattttgaaatacccaaaattgtattgatgacctggagattttataa Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUCAAGACAAACCUCAAAAACUGGAGUUUUUUGAGGUUUGUCUUUGUGCGGAGAUAUUAUGAAAAACAGUUAUUAUAUACGCACAAAAAUUUUCUUCUCAUUUAAAAAGUAAAGAUUUUGCCGUUUUAGAAUCGAUCAUUUGAAUGUAAGGACUUUGAUACCUACGGCCUAUUUAAAUUCUUCGGCGACCUAGCCAAAGGGCAUCCCAAUGCUAAAGACAUUGAAAAUGCCGUAACAUUUAUAAAAGAUAUUGAAUAGGUUAAAAUACGGUAAAGCUCAAAAGUAUUGCGGCCGUUUCUAGUACAUAUCCGAUUUUGAAAUACCCAAAAUUGUAUUGAUGACCUGGAGAUUUUAUAA (((((((((((((((((((((....).))))))))))))))).(((((((...((((.((((.......)))).)))).)))))))......((((..((((((((..((...(((((((......))))))).))..))))))))..))))..)))))......(((((((((((..((((.(((......)))....(((((..((((((....).)))))...))))).............))))..))))))))))).....(((((...((...........)).)))))((((((..(((...((((((((.......)))))))).....)))..))))))......... (-95.00) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUAUAAAAUCUCCAGGUCAUCAAUACAAUUUUGGGUAUUUCAAAAUCGGAUAUGUACUAGAAACGGCCGCAAUACUUUUGAGCUUUACCGUAUUUUAACCUAUUCAAUAUCUUUUAUAAAUGUUACGGCAUUUUCAAUGUCUUUAGCAUUGGGAUGCCCUUUGGCUAGGUCGCCGAAGAAUUUAAAUAGGCCGUAGGUAUCAAAGUCCUUACAUUCAAAUGAUCGAUUCUAAAACGGCAAAAUCUUUACUUUUUAAAUGAGAAGAAAAUUUUUGUGCGUAUAUAAUAACUGUUUUUCAUAAUAUCUCCGCACAAAGACAAACCUCAAAAAACUCCAGUUUUUGAGGUUUGUCUUGAU (((((.........((((((.......(((((((.....))))))).((((..(((((....((((((..(((((..............)))))......................(((((.....((((.(..((((((.....))))))..)))))(((((((......))))))).)))))....)))))).)))))....))))..........)))))).........(((((((((..(((.((((((....)))))))))..)))))).))).)))))............................(((((((((((((((((.(....))))))))))))))))))... (-81.44) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 365 49 1 223 169 NC_002967:TDE0332|5end_transcriptional_regulator,_TetR_family_370940..371170_POSITIVE 337 207 161 124 79 NC_002967:TDE2265|5end_hypothetical_protein_2302165..2302395_POSITIVE 336 320 275 225 180 NC_002967:TDE1850|5end_ABC_transporter,_permease_protein,_putative_1879561..1879791_NEGATIVE 325 205 162 166 121 NC_002967:TDE2488|5end_modification_methylase,_HemK_family_2511384..2511614_NEGATIVE 323 54 11 62 7 NC_002967:TDE2027|5end_hypothetical_protein_2052649..2052879_POSITIVE 322 207 161 103 58 NC_002967:TDE0402|5end_hypothetical_protein_454352..454582_NEGATIVE 322 207 161 225 180 NC_002967:TDE0401|5end_adenylate/guanylate_cyclase_catalytic_domain_protein_454230..454460_NEGATIVE 312 210 164 64 17 NC_002967:TDE0743|5end_thioredoxin_reductase_778718..778948_POSITIVE 300 204 162 227 183 NC_002967:TDE0735|5end_hypothetical_protein_775003..775233_NEGATIVE 296 45 10 203 169 NC_002967:TDE0943|5end_hypothetical_protein_965983..966213_POSITIVE 294 207 161 75 32 NC_002967:TDE2435|5end_hypothetical_protein_2466462..2466692_NEGATIVE 293 306 268 185 148 NC_002967:TDE2555|5end_precorrin-8X_methylmutase_2581613..2581843_POSITIVE 292 220 178 71 23 NC_002967:TDE1712|5end_flagellar_filament_outer_layer_protein_1767915..1768145_NEGATIVE 288 190 142 174 135 NC_002967:TDE0650|5end_hypothetical_protein_684697..684927_POSITIVE 287 209 165 62 12 NC_002967:TDE0006|5end_Snf2_family_protein_9694..9924_NEGATIVE 285 207 161 193 146 NC_002967:TDE0741|5end_hypothetical_protein_778158..778388_NEGATIVE 284 48 12 164 135 NC_002967:TDE1718|5end_GMP_synthase_1772160..1772390_POSITIVE 284 47 9 152 113 NC_002967:TDE0346|5end_protease_PrtB_387897..388127_NEGATIVE 283 295 267 37 7 NC_002967:TDE0571|5end_hypothetical_protein_601135..601365_POSITIVE 280 233 197 91 53 NC_002967:TDE0031|5end_hypothetical_protein_39095..39325_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 432 44 4 87 47 NC_002967:TDE0525|3end_hypothetical_protein_571163..571313_POSITIVE 337 49 1 91 43 NC_002967:TDE0356|3end_hypothetical_protein_399732..399882_NEGATIVE 328 45 1 67 24 NC_002967:TDE0186|3end_hypothetical_protein_222373..222523_NEGATIVE 315 203 164 86 56 NC_002967:TDE1533|3end_hypothetical_protein_1578657..1578807_POSITIVE 296 45 10 79 45 NC_002967:TDE0942|3end_long-chain-fatty-acid--CoA_ligase,_putative_965939..966089_POSITIVE 296 158 111 58 5 NC_002967:TDE0151|3end_integral_membrane_protein,_YeeE/YedE_family_171845..171995_NEGATIVE 291 50 10 103 51 NC_002967:TDE0185|3end_ABC_transporter,_ATP-binding_protein,_HlyB_family_222335..222485_POSITIVE 284 48 12 85 56 NC_002967:TDE1717|3end_hypothetical_protein_1772161..1772311_POSITIVE 279 230 183 43 4 NC_002967:TDE1658|3end_basic_membrane_protein,_putative_1707655..1707805_NEGATIVE 279 208 161 127 78 NC_002967:TDE1142|3end_phage_minor_structural_protein,_putative_1171468..1171618_NEGATIVE 278 42 4 88 45 NC_002967:TDE1993|3end_aspartate_ammonia-lyase,_putative_2010917..2011067_NEGATIVE 275 240 198 66 27 NC_002967:TDE0953|3end_branched-chain_amino_acid_ABC_transporter,_permease_protein_978007..978157_POSITIVE 274 230 184 51 3 NC_002967:TDE2308|3end_hypothetical_protein_2346313..2346463_POSITIVE 273 227 184 82 24 NC_002967:TDE1028|3end_hypothetical_protein_1058661..1058811_POSITIVE 273 209 161 119 67 NC_002967:TDE0572|3end_hypothetical_protein_604734..604884_POSITIVE 273 206 163 142 102 NC_002967:TDE0387|3end_(R)-hydroxyglutaryl-CoA_dehydratase_activator_439256..439406_POSITIVE 271 49 9 95 55 NC_002967:TDE1992|3end_OmpA_family_protein_2010902..2011052_POSITIVE 265 207 168 75 33 NC_002967:TDE1059|3end_hypothetical_protein_1086498..1086648_NEGATIVE 265 207 165 51 14 NC_002967:TDE1052|3end_rubredoxin_1078712..1078862_NEGATIVE 263 209 161 48 4 NC_002967:TDE2403|3end_metallo-beta-lactamase_family_protein_2428641..2428791_NEGATIVE