Origin IGS: taacggctaatggttaattccaatggataatggataattggtaattggtaattatgtggaaaagtcaattacacattagcaattaccaattgagttacaaattacaaattaaatcgaccgctctcaagccggggaaagctccggctcggggcggttttttttgcaccgtattttacattgcctgcaaaaggtcttcggtaatttaccggtttttagggatatgttgattagaacaatcggaatgttcgggcagtatggacaaaaatgggtgctgcttcaggttctaaccgtttcggtatctccgaggatgacgattgttctatgcggaagtacggtagatgccattcaaaactttgcaaaacagtattcatacaccgtaaatataataaagcaaacttatgagaaaaacggctgtaagt .........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 acttacagccgtttttctcataagtttgctttattatatttacggtgtatgaatactgttttgcaaagttttgaatggcatctaccgtacttccgcatagaacaatcgtcatcctcggagataccgaaacggttagaacctgaagcagcacccatttttgtccatactgcccgaacattccgattgttctaatcaacatatccctaaaaaccggtaaattaccgaagaccttttgcaggcaatgtaaaatacggtgcaaaaaaaaccgccccgagccggagctttccccggcttgagagcggtcgatttaatttgtaatttgtaactcaattggtaattgctaatgtgtaattgacttttccacataattaccaattaccaattatccattatccattggaattaaccattagccgtta Mask Tandem Repeat Region ================================================ taacggctaatggttaattccaatggataatggataattggtaattggtaattatgtggaaaagtcaattacacattagcaattaccaattgagttacaaattacaaattaaatcgaccgctctcaagccggggaaagctccggctcggggcggttttttttgcaccgtattttacattgcctgcaaaaggtcttcggtaatttaccggtttttagggatatgttgattagaacaatcggaatgttcgggcagtatggacaaaaatgggtgctgcttcaggttctaaccgtttcggtatctccgaggatgacgattgttctatgcggaagtacggtagatgccattcaaaactttgcaaaacagtattcatacaccgtaaatataataaagcaaacttatgagaaaaacggctgtaagt Find is-nt database================================================ Query_seq: TDE0574:TDE0575|TDE0574:TDE0575:surface protein, putative:aspartyl/glutamyl-tRNA amidotransferase subunit B:-><-:605923..606341 419 taacggctaatggttaattccaatggataatggataattggtaattggtaattatgtggaaaagtcaattacacattagcaattaccaattgagttacaaattacaaattaaatcgaccgctctcaagccggggaaagctccggctcggggcggttttttttgcaccgtattttacattgcctgcaaaaggtcttcggtaatttaccggtttttagggatatgttgattagaacaatcggaatgttcgggcagtatggacaaaaatgggtgctgcttcaggttctaaccgtttcggtatctccgaggatgacgattgttctatgcggaagtacggtagatgccattcaaaactttgcaaaacagtattcatacaccgtaaatataataaagcaaacttatgagaaaaacggctgtaagt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE0574:TDE0575|TDE0574:TDE0575:surface protein, putative:aspartyl/glutamyl-tRNA amidotransferase subunit B:-><-:605923..606341 419 taacggctaatggttaattccaatggataatggataattggtaattggtaattatgtggaaaagtcaattacacattagcaattaccaattgagttacaaattacaaattaaatcgaccgctctcaagccggggaaagctccggctcggggcggttttttttgcaccgtattttacattgcctgcaaaaggtcttcggtaatttaccggtttttagggatatgttgattagaacaatcggaatgttcgggcagtatggacaaaaatgggtgctgcttcaggttctaaccgtttcggtatctccgaggatgacgattgttctatgcggaagtacggtagatgccattcaaaactttgcaaaacagtattcatacaccgtaaatataataaagcaaacttatgagaaaaacggctgtaagt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE0574:TDE0575|TDE0574:TDE0575:surface protein, putative:aspartyl/glutamyl-tRNA amidotransferase subunit B:-><-:605923..606341 419 taacggctaatggttaattccaatggataatggataattggtaattggtaattatgtggaaaagtcaattacacattagcaattaccaattgagttacaaattacaaattaaatcgaccgctctcaagccggggaaagctccggctcggggcggttttttttgcaccgtattttacattgcctgcaaaaggtcttcggtaatttaccggtttttagggatatgttgattagaacaatcggaatgttcgggcagtatggacaaaaatgggtgctgcttcaggttctaaccgtttcggtatctccgaggatgacgattgttctatgcggaagtacggtagatgccattcaaaactttgcaaaacagtattcatacaccgtaaatataataaagcaaacttatgagaaaaacggctgtaagt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taacggctaatggttaattccaatggataatggataattggtaattggtaattatgtggaaaagtcaattacacattagcaattaccaattgagttacaaattacaaattaaatcgaccgctctcaagccggggaaagctccggctcggggcggttttttttgcaccgtattttacattgcctgcaaaaggtcttcggtaatttaccggtttttagggatatgttgattagaacaatcggaatgttcgggcagtatggacaaaaatgggtgctgcttcaggttctaaccgtttcggtatctccgaggatgacgattgttctatgcggaagtacggtagatgccattcaaaactttgcaaaacagtattcatacaccgtaaatataataaagcaaacttatgagaaaaacggctgtaagt Predict ORF larger than 30AA ================================================ Protein_Len: 60 Strand: + Start: 45 End: 224 ............................................ M V I M W K S Q L H I S N Y Q L S Y K L Q I K S T A L K P G K A P A R G G F F C T V F Y I A C K R S S V I Y R F L G I C ................................................................................................................................................................................................... Protein_Len: 45 Strand: + Start: 265 End: 399 ........................................................................................................................................................................................................................................................................ M G A A S G S N R F G I S E D D D C S M R K Y G R C H S K L C K T V F I H R K Y N K A N L .................... Protein_Len: 60 Strand: + Start: 113 End: 418 ................................................................................................................ M D R S Q A G E S S G S G R F F L H R I L H C L Q K V F G N L P V F R D M L I R T I G M F G Q Y G Q K W V L L Q V L T V . Protein_Len: 47 Strand: - Start: 231 End: 371 ...................................................................................................................................................................................................................................... F L R F T R A T H V F I P A A E P E L R K P I E S S S S Q E I R F Y P L H W E F S Q L V T N M ................................................ Protein_Len: 39 Strand: - Start: 127 End: 243 .............................................................................................................................. A P S L E P E P R N K K C R I K C Q R C F T K P L K G T K L S I N I L V I P M ................................................................................................................................................................................ taacggctaatggttaattccaatggataatggataattggtaattggtaattatgtggaaaagtcaattacacattagcaattaccaattgagttacaaattacaaattaaatcgaccgctctcaagccggggaaagctccggctcggggcggttttttttgcaccgtattttacattgcctgcaaaaggtcttcggtaatttaccggtttttagggatatgttgattagaacaatcggaatgttcgggcagtatggacaaaaatgggtgctgcttcaggttctaaccgtttcggtatctccgaggatgacgattgttctatgcggaagtacggtagatgccattcaaaactttgcaaaacagtattcatacaccgtaaatataataaagcaaacttatgagaaaaacggctgtaagt Predict Promoter with matrix: RpoD-15 score > 80================================================ Predict Promoter with matrix: RpoD-16 score > 80================================================ Predict Promoter with matrix: RpoD-17 score > 80================================================ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ taacggctaatggttaattccaatggataatggataattggtaattggtaattatgtggaaaagtcaattacacattagcaattaccaattgagttacaaattacaaattaaatcgaccgctctcaagccggggaaagctccggctcggggcggttttttttgcaccgtattttacattgcctgcaaaaggtcttcggtaatttaccggtttttagggatatgttgattagaacaatcggaatgttcgggcagtatggacaaaaatgggtgctgcttcaggttctaaccgtttcggtatctccgaggatgacgattgttctatgcggaagtacggtagatgccattcaaaactttgcaaaacagtattcatacaccgtaaatataataaagcaaacttatgagaaaaacggctgtaagt Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 100 HP_score: -14.4 Tail_Score: -5.75945 Start: 118 End: 154 Full_Region: TACAAATTAAATCGA CCGCTCTCAAGCCGGGG AAAG CTCCGGCTCGGGGCGG TTTTTTTTGCACCGT .....................................................................................................................CCGCTCTCAAGCCGGGGAAAGCTCCGGCTCGGGGCGG......................................................................................................................................................................................................................................................................... TransTerm Strand: - Conf: 81 HP_score: -12.2 Tail_Score: -2.74747 Start: 118 End: 154 Full_Region: acggtgcaaaaaaaa ccgccccgagccggag cttt ccccggcttgagagcgg tcgatttaatttgta .....................................................................................................................ccgccccgagccggagctttccccggcttgagagcgg......................................................................................................................................................................................................................................................................... TransTerm Strand: + Conf: 77 HP_score: -6.4 Tail_Score: -4.61633 Start: 195 End: 209 Full_Region: GCCTGCAAAAGGTCT TCGGTA ATT TACCGG TTTTTAGGGATATGT ..................................................................................................................................................................................................TCGGTAATTTACCGG.................................................................................................................................................................................................................. Find igs database================================================ Query_seq: TDE0574:TDE0575|TDE0574:TDE0575:surface protein, putative:aspartyl/glutamyl-tRNA amidotransferase subunit B:-><-:605923..606341 419 taacggctaatggttaattccaatggataatggataattggtaattggtaattatgtggaaaagtcaattacacattagcaattaccaattgagttacaaattacaaattaaatcgaccgctctcaagccggggaaagctccggctcggggcggttttttttgcaccgtattttacattgcctgcaaaaggtcttcggtaatttaccggtttttagggatatgttgattagaacaatcggaatgttcgggcagtatggacaaaaatgggtgctgcttcaggttctaaccgtttcggtatctccgaggatgacgattgttctatgcggaagtacggtagatgccattcaaaactttgcaaaacagtattcatacaccgtaaatataataaagcaaacttatgagaaaaacggctgtaagt Intra-Species Hit: Count: 1 Min: 1 Max: 419 Len: 419 Subject: NC_002967_TDE0574_TDE0575|surface protein, putative:aspartyl/glutamyl-tRNA amidotransferase subunit B|POSITIVE:NEGATIVE|[605923,606341]|419 HSP 1 e-value: 0.0 bit: 783.0 Len: 419 Query Start:1 Query End:419 Subject Strand: POSITIVE Subject Start: 1 Subject End: 419 taacggctaatggttaattccaatggataatggataattggtaattggtaattatgtggaaaagtcaattacacattagcaattaccaattgagttacaaattacaaattaaatcgaccgctctcaagccggggaaagctccggctcggggcggnnnnnnnngcaccgtattttacattgcctgcaaaaggtcttcggtaatttaccggtttttagggatatgttgattagaacaatcggaatgttcgggcagtatggacaaaaatgggtgctgcttcaggttctaaccgtttcggtatctccgaggatgacgattgttctatgcggaagtacggtagatgccattcaaaactttgcaaaacagtattcatacaccgtaaatataataaagcaaacttatgagaaaaacggctgtaagt taacggctaatggttaattccaatggataatggataattggtaattggtaattatgtggaaaagtcaattacacattagcaattaccaattgagttacaaattacaaattaaatcgaccgctctcaagccggggaaagctccggctcggggcggttttttttgcaccgtattttacattgcctgcaaaaggtcttcggtaatttaccggtttttagggatatgttgattagaacaatcggaatgttcgggcagtatggacaaaaatgggtgctgcttcaggttctaaccgtttcggtatctccgaggatgacgattgttctatgcggaagtacggtagatgccattcaaaactttgcaaaacagtattcatacaccgtaaatataataaagcaaacttatgagaaaaacggctgtaagt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAACGGCUAAUGGUUAAUUCCAAUGGAUAAUGGAUAAUUGGUAAUUGGUAAUUAUGUGGAAAAGUCAAUUACACAUUAGCAAUUACCAAUUGAGUUACAAAUUACAAAUUAAAUCGACCGCUCUCAAGCCGGGGAAAGCUCCGGCUCGGGGCGGUUUUUUUUGCACCGUAUUUUACAUUGCCUGCAAAAGGUCUUCGGUAAUUUACCGGUUUUUAGGGAUAUGUUGAUUAGAACAAUCGGAAUGUUCGGGCAGUAUGGACAAAAAUGGGUGCUGCUUCAGGUUCUAACCGUUUCGGUAUCUCCGAGGAUGACGAUUGUUCUAUGCGGAAGUACGGUAGAUGCCAUUCAAAACUUUGCAAAACAGUAUUCAUACACCGUAAAUAUAAUAAAGCAAACUUAUGAGAAAAACGGCUGUAAGU ..((((((..(((......))).......((((..((((((((((((.((...(((((.............))))))).))))))))))))((((.((.................(((((((((..((((((((....)))))))).)))))))))..(((((((..((..........((((.....))))....((((.(((((((....................(((((((((((..((.((((((((((((...((....)).)))))))...........((((...))))....))))).))..))))))))))).((....)).))))))))))).......))..)))))))..)))))).....))))...............................)))))).... (-124.52) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACUUACAGCCGUUUUUCUCAUAAGUUUGCUUUAUUAUAUUUACGGUGUAUGAAUACUGUUUUGCAAAGUUUUGAAUGGCAUCUACCGUACUUCCGCAUAGAACAAUCGUCAUCCUCGGAGAUACCGAAACGGUUAGAACCUGAAGCAGCACCCAUUUUUGUCCAUACUGCCCGAACAUUCCGAUUGUUCUAAUCAACAUAUCCCUAAAAACCGGUAAAUUACCGAAGACCUUUUGCAGGCAAUGUAAAAUACGGUGCAAAAAAAACCGCCCCGAGCCGGAGCUUUCCCCGGCUUGAGAGCGGUCGAUUUAAUUUGUAAUUUGUAACUCAAUUGGUAAUUGCUAAUGUGUAAUUGACUUUUCCACAUAAUUACCAAUUACCAAUUAUCCAUUAUCCAUUGGAAUUAACCAUUAGCCGUUA ..((((((((((.....(((.((.(((((............(((((((....)))))))...))))).)).))))))))...(((((((........(((((((((((..((..((((....((((...))))...........((((....((....))......))))))))..))..)))))))))))....((((............(((((...)))))..(.(((.....)))).))))....)))))))........((((((.((((((((........)))))))).).)))))..........)))))....((((..((((((((((((.((((((((.............)))).)))).)))))))))))).((((........))))..............)))) (-103.18) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 524 160 111 59 13 NC_002967:TDE0573|5end_hypothetical_protein_604681..604911_POSITIVE 456 168 121 162 98 NC_002967:TDE1048|5end_30S_ribosomal_protein_S7_1074482..1074712_POSITIVE 434 165 126 72 33 NC_002967:TDE0682|5end_preprotein_translocase,_YajC_subunit_721078..721308_NEGATIVE 425 159 111 165 104 NC_002967:TDE2103|5end_glycosyl_transferase,_group_2_family_protein_2128393..2128623_NEGATIVE 425 160 111 131 81 NC_002967:TDE1924|5end_hypothetical_protein_1941886..1942116_NEGATIVE 421 158 117 58 14 NC_002967:TDE2715|5end_hypothetical_protein_2772668..2772898_POSITIVE 410 155 121 216 165 NC_002967:TDE2438|5end_hypothetical_protein_2469257..2469487_NEGATIVE 397 173 135 44 1 NC_002967:TDE0832|5end_hypothetical_protein_852549..852779_POSITIVE 385 168 128 69 22 NC_002967:TDE1513|5end_hypothetical_protein_1560484..1560714_POSITIVE 384 317 272 60 19 NC_002967:TDE1034|5end_magnesium_and_cobalt_transporter,_putative_1062454..1062684_POSITIVE 380 169 127 165 129 NC_002967:TDE1313|5end_signal_peptidase_I_1350650..1350880_POSITIVE 375 159 114 56 7 NC_002967:TDE1847|5end_hypothetical_protein_1875664..1875894_POSITIVE 370 169 124 185 135 NC_002967:TDE2210|5end_hypothetical_protein_2250701..2250931_NEGATIVE 369 154 118 150 119 NC_002967:TDE1113|5end_hypothetical_protein_1148250..1148480_NEGATIVE 365 157 112 65 2 NC_002967:TDE1895|5end_GTP-binding_protein_Era_1914963..1915193_POSITIVE 363 168 126 225 190 NC_002967:TDE0043|5end_TPR_domain_protein_49688..49918_POSITIVE 362 159 118 70 27 NC_002967:TDE0144|5end_thiamine_ABC_transporter,_permease_protein_165007..165237_POSITIVE 360 159 126 144 112 NC_002967:TDE2565|5end_hypothetical_protein_2591273..2591503_NEGATIVE 360 308 266 164 106 NC_002967:TDE2516|5end_hypothetical_protein_2542021..2542251_POSITIVE 359 155 113 58 8 NC_002967:TDE0886|5end_hypothetical_protein_903341..903571_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 456 168 121 151 87 NC_002967:TDE1047|3end_30S_ribosomal_protein_S12_1074551..1074701_POSITIVE 385 168 128 56 9 NC_002967:TDE1512|3end_hypothetical_protein_1560551..1560701_POSITIVE 382 159 115 76 31 NC_002967:TDE0340|3end_fructose-bisphosphate_aldolase_379606..379756_POSITIVE 380 169 127 150 114 NC_002967:TDE1312|3end_hypothetical_protein_1350715..1350865_POSITIVE 362 159 118 86 43 NC_002967:TDE0143|3end_thiamine_ABC_transporter,_thiamine-binding_protein_165103..165253_POSITIVE 360 159 126 85 53 NC_002967:TDE2566|3end_hypothetical_protein_2591332..2591482_NEGATIVE 356 157 113 63 1 NC_002967:TDE1894|3end_ferredoxin_1915041..1915191_POSITIVE 352 156 120 133 95 NC_002967:TDE0598|3end_3-oxoacyl-(acyl-carrier-protein)_reductase_637358..637508_NEGATIVE 345 156 114 150 91 NC_002967:TDE1056|3end_hypothetical_protein_1085895..1086045_POSITIVE 343 147 112 98 54 NC_002967:TDE2729|3end_hypothetical_protein_2785756..2785906_NEGATIVE 343 167 130 141 97 NC_002967:TDE1590|3end_aminotransferase,_DegT/DnrJ/EryC1/StrS_family_1638621..1638771_POSITIVE 342 170 131 44 4 NC_002967:TDE2104|3end_hypothetical_protein_2128525..2128675_NEGATIVE 339 157 112 64 6 NC_002967:TDE0693|3end_phosphomethylpyrimidine_kinase_730831..730981_POSITIVE 339 339 292 149 94 NC_002967:TDE0172|3end_undecaprenyl_pyrophosphate_phosphatase_204025..204175_POSITIVE 336 156 114 148 108 NC_002967:TDE1847|3end_hypothetical_protein_1875845..1875995_POSITIVE 335 160 130 32 1 NC_002967:TDE0572|3end_hypothetical_protein_604734..604884_POSITIVE 334 159 111 65 18 NC_002967:TDE2477|3end_selenocysteine_synthase_2500949..2501099_POSITIVE 330 156 113 130 77 NC_002967:TDE1079|3end_DNA-binding_protein/PTS_system,_IIA_component_1111805..1111955_POSITIVE 329 154 114 101 46 NC_002967:TDE2735|3end_surface_antigen,_putative_2791616..2791766_POSITIVE 329 165 122 151 98 NC_002967:TDE0823|3end_(3R)-hydroxymyristoyl-(acyl-carrier-protein)_dehydratase,_putative_845252..845402_POSITIVE