Origin IGS: tccgacatacacggccggatctaaagttgtccctcctcacgaagcacacatattaagcatacagtgaaccgtatccgcgtttttcgctctaattttgtctctagcagaatcttcaactatgatattcatttttggcctccaaaaaataattgtaatctacctttatgaattgtttcaaggctcttacaaacctaagataaaaactttttgaatgaaagtcaagacgtttaagaaagttttttgatatga .........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 tcatatcaaaaaactttcttaaacgtcttgactttcattcaaaaagtttttatcttaggtttgtaagagccttgaaacaattcataaaggtagattacaattattttttggaggccaaaaatgaatatcatagttgaagattctgctagagacaaaattagagcgaaaaacgcggatacggttcactgtatgcttaatatgtgtgcttcgtgaggagggacaactttagatccggccgtgtatgtcgga Mask Tandem Repeat Region ================================================ tccgacatacacggccggatctaaagttgtccctcctcacgaagcacacatattaagcatacagtgaaccgtatccgcgtttttcgctctaattttgtctctagcagaatcttcaactatgatattcatttttggcctccaaaaaataattgtaatctacctttatgaattgtttcaaggctcttacaaacctaagataaaaactttttgaatgaaagtcaagacgtttaagaaagttttttgatatga Find is-nt database================================================ Query_seq: TDE0697:TDE0698|TDE0697:TDE0698:hypothetical protein:PIN domain protein:<-<-:734463..734711 249 tccgacatacacggccggatctaaagttgtccctcctcacgaagcacacatattaagcatacagtgaaccgtatccgcgtttttcgctctaattttgtctctagcagaatcttcaactatgatattcatttttggcctccaaaaaataattgtaatctacctttatgaattgtttcaaggctcttacaaacctaagataaaaactttttgaatgaaagtcaagacgtttaagaaagttttttgatatga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE0697:TDE0698|TDE0697:TDE0698:hypothetical protein:PIN domain protein:<-<-:734463..734711 249 tccgacatacacggccggatctaaagttgtccctcctcacgaagcacacatattaagcatacagtgaaccgtatccgcgtttttcgctctaattttgtctctagcagaatcttcaactatgatattcatttttggcctccaaaaaataattgtaatctacctttatgaattgtttcaaggctcttacaaacctaagataaaaactttttgaatgaaagtcaagacgtttaagaaagttttttgatatga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE0697:TDE0698|TDE0697:TDE0698:hypothetical protein:PIN domain protein:<-<-:734463..734711 249 tccgacatacacggccggatctaaagttgtccctcctcacgaagcacacatattaagcatacagtgaaccgtatccgcgtttttcgctctaattttgtctctagcagaatcttcaactatgatattcatttttggcctccaaaaaataattgtaatctacctttatgaattgtttcaaggctcttacaaacctaagataaaaactttttgaatgaaagtcaagacgtttaagaaagttttttgatatga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tccgacatacacggccggatctaaagttgtccctcctcacgaagcacacatattaagcatacagtgaaccgtatccgcgtttttcgctctaattttgtctctagcagaatcttcaactatgatattcatttttggcctccaaaaaataattgtaatctacctttatgaattgtttcaaggctcttacaaacctaagataaaaactttttgaatgaaagtcaagacgtttaagaaagttttttgatatga Predict ORF larger than 30AA ================================================ Protein_Len: 38 Strand: + Start: 52 End: 165 ................................................... M K H T V N R I R V F R S N F V S S R I F N Y D I H F W P P K N N C N L P L .................................................................................... Protein_Len: 39 Strand: + Start: 92 End: 208 ........................................................................................... M L S L A E S S T M I F I F G L Q K I I V I Y L Y E L F Q G S Y K P K I K T F ......................................... Protein_Len: 44 Strand: - Start: 116 End: 247 ................................................................................................................... S H Y E N K A E L F Y N Y D V K I F Q K L A R V F R L Y F S K S H F D L R K L F N K S M .. Protein_Len: 39 Strand: - Start: 40 End: 156 ....................................... S A C M N L M C H V T D A N K A R I K D R A S D E V I I N M K P R W F I I T M ............................................................................................. Protein_Len: 31 Strand: - Start: 24 End: 116 ....................... L Q G E E R L V C I L C V T F R I R T K R E L K T E L L I K M ..................................................................................................................................... tccgacatacacggccggatctaaagttgtccctcctcacgaagcacacatattaagcatacagtgaaccgtatccgcgtttttcgctctaattttgtctctagcagaatcttcaactatgatattcatttttggcctccaaaaaataattgtaatctacctttatgaattgtttcaaggctcttacaaacctaagataaaaactttttgaatgaaagtcaagacgtttaagaaagttttttgatatga 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: 82 Start: 94 End: 123 .............................................................................................TTTGTCTCTAGCAGAATCTTCAACTATGAT.............................................................................................................................. PromScan Matrix: RpoD-17 Strand: - Score: 82 Start: 194 End: 223 .................................................................................................................................................................................................CTTGACTTTCATTCAAAAAGTTTTTATCTT.......................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tccgacatacacggccggatctaaagttgtccctcctcacgaagcacacatattaagcatacagtgaaccgtatccgcgtttttcgctctaattttgtctctagcagaatcttcaactatgatattcatttttggcctccaaaaaataattgtaatctacctttatgaattgtttcaaggctcttacaaacctaagataaaaactttttgaatgaaagtcaagacgtttaagaaagttttttgatatga Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE0697:TDE0698|TDE0697:TDE0698:hypothetical protein:PIN domain protein:<-<-:734463..734711 249 tccgacatacacggccggatctaaagttgtccctcctcacgaagcacacatattaagcatacagtgaaccgtatccgcgtttttcgctctaattttgtctctagcagaatcttcaactatgatattcatttttggcctccaaaaaataattgtaatctacctttatgaattgtttcaaggctcttacaaacctaagataaaaactttttgaatgaaagtcaagacgtttaagaaagttttttgatatga Intra-Species Hit: Count: 1 Min: 1 Max: 249 Len: 249 Subject: NC_002967_TDE0697_TDE0698|hypothetical protein:PIN domain protein|NEGATIVE:NEGATIVE|[734463,734711]|249 HSP 1 e-value: 1.0E-139 bit: 494.0 Len: 249 Query Start:1 Query End:249 Subject Strand: POSITIVE Subject Start: 1 Subject End: 249 tccgacatacacggccggatctaaagttgtccctcctcacgaagcacacatattaagcatacagtgaaccgtatccgcgtttttcgctctaattttgtctctagcagaatcttcaactatgatattcatttttggcctccaaaaaataattgtaatctacctttatgaattgtttcaaggctcttacaaacctaagataaaaactttttgaatgaaagtcaagacgtttaagaaagttttttgatatga tccgacatacacggccggatctaaagttgtccctcctcacgaagcacacatattaagcatacagtgaaccgtatccgcgtttttcgctctaattttgtctctagcagaatcttcaactatgatattcatttttggcctccaaaaaataattgtaatctacctttatgaattgtttcaaggctcttacaaacctaagataaaaactttttgaatgaaagtcaagacgtttaagaaagttttttgatatga Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCCGACAUACACGGCCGGAUCUAAAGUUGUCCCUCCUCACGAAGCACACAUAUUAAGCAUACAGUGAACCGUAUCCGCGUUUUUCGCUCUAAUUUUGUCUCUAGCAGAAUCUUCAACUAUGAUAUUCAUUUUUGGCCUCCAAAAAAUAAUUGUAAUCUACCUUUAUGAAUUGUUUCAAGGCUCUUACAAACCUAAGAUAAAAACUUUUUGAAUGAAAGUCAAGACGUUUAAGAAAGUUUUUUGAUAUGA .....((((...(((((((..((((((((.......((((...((...........)).....)))).........(((.....)))..)))))))).........((((..(((....))).))))...)))))))..((((((((..((((((....(((...((((....)))))))...))))))...........((((.((((((.(....))))))).))))......)))))))).)))). (-41.00) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCAUAUCAAAAAACUUUCUUAAACGUCUUGACUUUCAUUCAAAAAGUUUUUAUCUUAGGUUUGUAAGAGCCUUGAAACAAUUCAUAAAGGUAGAUUACAAUUAUUUUUUGGAGGCCAAAAAUGAAUAUCAUAGUUGAAGAUUCUGCUAGAGACAAAAUUAGAGCGAAAAACGCGGAUACGGUUCACUGUAUGCUUAAUAUGUGUGCUUCGUGAGGAGGGACAACUUUAGAUCCGGCCGUGUAUGUCGGA .............(((((((....(((((................(((((......((((((....)))))).)))))..........((((((...((((((((((((((...)))))))........))))))).....)))))).))))).........(((((..(((((.((((((....)))))).).......))))..))))))))))))............((((((.......)))))) (-51.81) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 1037 50 1 141 92 NC_002967:TDE0697|5end_hypothetical_protein_734372..734602_NEGATIVE 434 48 2 127 82 NC_002967:TDE0132|5end_hypothetical_protein_152046..152276_POSITIVE 358 99 57 225 187 NC_002967:TDE0573|5end_hypothetical_protein_604681..604911_POSITIVE 346 46 2 50 3 NC_002967:TDE0239|5end_glycine_reductase_complex_protein_GrdD_272982..273212_NEGATIVE 331 59 12 175 116 NC_002967:TDE1876|5end_glycosyl_transferase,_WecB/TagA/CpsF_family_1897679..1897909_NEGATIVE 302 75 33 77 17 NC_002967:TDE2629|5end_peptide_ABC_transporter,_periplasmic_peptide-binding_protein,_putative_2669329..2669559_POSITIVE 289 58 12 208 154 NC_002967:TDE1935|5end_hypothetical_protein_1952994..1953224_POSITIVE 287 137 98 53 13 NC_002967:TDE2187|5end_ParB-like_nuclease_domain_protein_2221548..2221778_NEGATIVE 287 100 63 118 73 NC_002967:TDE1188|5end_NAD(P)_transhydrogenase,_beta_subunit_1216622..1216852_NEGATIVE 286 41 2 80 37 NC_002967:TDE2131|5end_cobalamin_biosynthesis_protein_CbiM,_putative_2162683..2162913_NEGATIVE 285 68 27 71 22 NC_002967:TDE2709|5end_BNR_domain_protein_2766358..2766588_NEGATIVE 285 49 10 212 164 NC_002967:TDE2583|5end_hypothetical_protein_2616322..2616552_POSITIVE 284 47 3 210 158 NC_002967:TDE0283|5end_transporter,_putative_312825..313055_NEGATIVE 282 45 3 73 31 NC_002967:TDE2485|5end_hypothetical_protein_2509123..2509353_NEGATIVE 280 114 74 37 3 NC_002967:TDE2770|5end_flagellar_hook-length_control_protein_FliK_2824417..2824647_NEGATIVE 279 119 80 74 36 NC_002967:TDE1443|5end_RNA_methyltransferase,_TrmH_family,_group_3_1489585..1489815_NEGATIVE 277 79 34 114 78 NC_002967:TDE1847|5end_hypothetical_protein_1875664..1875894_POSITIVE 277 89 60 189 164 NC_002967:TDE0945|5end_hypothetical_protein_967128..967358_POSITIVE 275 58 13 71 22 NC_002967:TDE1505|5end_hypothetical_protein_1553614..1553844_POSITIVE 273 100 57 65 21 NC_002967:TDE1595|5end_cobalamin_biosynthesis_protein_CbiD_1646039..1646269_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 434 48 2 102 57 NC_002967:TDE0131|3end_hypothetical_protein_152101..152251_POSITIVE 334 41 14 139 112 NC_002967:TDE2527|3end_hypothetical_protein_2555449..2555599_NEGATIVE 296 46 12 37 2 NC_002967:TDE0240|3end_glycine_reductase_complex_protein_GrdC_272995..273145_NEGATIVE 289 45 2 118 76 NC_002967:TDE1848|3end_hypothetical_protein_1875897..1876047_NEGATIVE 279 119 80 67 29 NC_002967:TDE1444|3end_metallo-beta-lactamase_family_protein_1489592..1489742_NEGATIVE 273 88 61 57 34 NC_002967:TDE2621|3end_hypothetical_protein_2662197..2662347_POSITIVE 272 43 1 142 100 NC_002967:TDE0956|3end_hypothetical_protein_980330..980480_POSITIVE 268 47 2 79 37 NC_002967:TDE0689|3end_5-methylthioribose_kinase_726972..727122_POSITIVE 267 102 62 104 62 NC_002967:TDE0788|3end_ribosomal_protein_L36_816625..816775_POSITIVE 265 109 65 150 109 NC_002967:TDE1274|3end_oligopeptide/dipeptide_ABC_transporter,_permease_protein_1308643..1308793_NEGATIVE 255 37 2 132 97 NC_002967:TDE2101|3end_hypothetical_protein_2125549..2125699_NEGATIVE 254 109 69 144 111 NC_002967:TDE2005|3end_hypothetical_protein_2024410..2024560_POSITIVE 253 115 75 144 107 NC_002967:TDE1001|3end_orotate_phosphoribosyltransferase_1028437..1028587_POSITIVE 252 109 70 44 5 NC_002967:TDE0740|3end_hypothetical_protein_776204..776354_POSITIVE 252 45 3 59 9 NC_002967:TDE0693|3end_phosphomethylpyrimidine_kinase_730831..730981_POSITIVE 251 39 2 72 40 NC_002967:TDE2084|3end_RNA_methyltransferase,_TrmH_family_2114229..2114379_POSITIVE 250 42 1 96 51 NC_002967:TDE1934|3end_hypothetical_protein_1952804..1952954_POSITIVE 248 115 72 145 92 NC_002967:TDE1309|3end_modulator_of_DNA_gyrase_family_protein_1346042..1346192_POSITIVE 246 89 48 151 105 NC_002967:TDE1128|3end_hypothetical_protein_1161785..1161935_POSITIVE 245 45 1 149 98 NC_002967:TDE2762|3end_flagellar_motor_switch_protein_FliY_2816563..2816713_NEGATIVE