Origin IGS: aatttgcatctccatgataccgttatattttatcagaatactcaatattagtctactgcctcacagaaatcaattttgtaatattttttttaataaaagaggtattcataagagctatcttatttgagcattttatgttgacgcctatcgggttttatgatatagtgaagaagggtcgaagtaatctgactaaaggcaggtaggtgcggaaccgacctataacatttatttcgatctaaaaataaatttataggaggtcaagt .........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 acttgacctcctataaatttatttttagatcgaaataaatgttataggtcggttccgcacctacctgcctttagtcagattacttcgacccttcttcactatatcataaaacccgataggcgtcaacataaaatgctcaaataagatagctcttatgaatacctcttttattaaaaaaaatattacaaaattgatttctgtgaggcagtagactaatattgagtattctgataaaatataacggtatcatggagatgcaaatt Mask Tandem Repeat Region ================================================ aatttgcatctccatgataccgttatattttatcagaatactcaatattagtctactgcctcacagaaatcaattttgtaatattttttttaataaaagaggtattcataagagctatcttatttgagcattttatgttgacgcctatcgggttttatgatatagtgaagaagggtcgaagtaatctgactaaaggcaggtaggtgcggaaccgacctataacatttatttcgatctaaaaataaatttataggaggtcaagt Find is-nt database================================================ Query_seq: TDE1955:TDE1956|TDE1955:TDE1956:hypothetical protein:hypothetical protein:<-->:1970991..1971253 263 aatttgcatctccatgataccgttatattttatcagaatactcaatattagtctactgcctcacagaaatcaattttgtaatattttttttaataaaagaggtattcataagagctatcttatttgagcattttatgttgacgcctatcgggttttatgatatagtgaagaagggtcgaagtaatctgactaaaggcaggtaggtgcggaaccgacctataacatttatttcgatctaaaaataaatttataggaggtcaagt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE1955:TDE1956|TDE1955:TDE1956:hypothetical protein:hypothetical protein:<-->:1970991..1971253 263 aatttgcatctccatgataccgttatattttatcagaatactcaatattagtctactgcctcacagaaatcaattttgtaatattttttttaataaaagaggtattcataagagctatcttatttgagcattttatgttgacgcctatcgggttttatgatatagtgaagaagggtcgaagtaatctgactaaaggcaggtaggtgcggaaccgacctataacatttatttcgatctaaaaataaatttataggaggtcaagt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE1955:TDE1956|TDE1955:TDE1956:hypothetical protein:hypothetical protein:<-->:1970991..1971253 263 aatttgcatctccatgataccgttatattttatcagaatactcaatattagtctactgcctcacagaaatcaattttgtaatattttttttaataaaagaggtattcataagagctatcttatttgagcattttatgttgacgcctatcgggttttatgatatagtgaagaagggtcgaagtaatctgactaaaggcaggtaggtgcggaaccgacctataacatttatttcgatctaaaaataaatttataggaggtcaagt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aatttgcatctccatgataccgttatattttatcagaatactcaatattagtctactgcctcacagaaatcaattttgtaatattttttttaataaaagaggtattcataagagctatcttatttgagcattttatgttgacgcctatcgggttttatgatatagtgaagaagggtcgaagtaatctgactaaaggcaggtaggtgcggaaccgacctataacatttatttcgatctaaaaataaatttataggaggtcaagt Predict ORF larger than 30AA ================================================ Protein_Len: 41 Strand: + Start: 2 End: 124 . M C I S M I P L Y F I R I L N I S L L P H R N Q F C N I F F N K R G I H K S Y L I ........................................................................................................................................... Protein_Len: 58 Strand: + Start: 27 End: 200 .......................... M L S E Y S I L V Y C L T E I N F V I F F L I K E V F I R A I L F E H F M L T P I G F Y D I V K K G R S N L T K G R ............................................................... Protein_Len: 43 Strand: - Start: 123 End: 251 .......................................................................................................................... K L M K H Q R R D P K I I Y H L L T S T I Q S F A P L H P V S R Y C K N R D L F L N M ............ Protein_Len: 31 Strand: - Start: 56 End: 148 ....................................................... Q R V S I L K T I N K K I F S T N M L A I K N S C K I N V G M ................................................................................................................... aatttgcatctccatgataccgttatattttatcagaatactcaatattagtctactgcctcacagaaatcaattttgtaatattttttttaataaaagaggtattcataagagctatcttatttgagcattttatgttgacgcctatcgggttttatgatatagtgaagaagggtcgaagtaatctgactaaaggcaggtaggtgcggaaccgacctataacatttatttcgatctaaaaataaatttataggaggtcaagt 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: 86 Start: 137 End: 166 ........................................................................................................................................GTTGACGCCTATCGGGTTTTATGATATAGT................................................................................................. PromScan Matrix: RpoD-17 Strand: - Score: 82 Start: 27 End: 56 ..........................GTAGACTAATATTGAGTATTCTGATAAAAT............................................................................................................................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aatttgcatctccatgataccgttatattttatcagaatactcaatattagtctactgcctcacagaaatcaattttgtaatattttttttaataaaagaggtattcataagagctatcttatttgagcattttatgttgacgcctatcgggttttatgatatagtgaagaagggtcgaagtaatctgactaaaggcaggtaggtgcggaaccgacctataacatttatttcgatctaaaaataaatttataggaggtcaagt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE1955:TDE1956|TDE1955:TDE1956:hypothetical protein:hypothetical protein:<-->:1970991..1971253 263 aatttgcatctccatgataccgttatattttatcagaatactcaatattagtctactgcctcacagaaatcaattttgtaatattttttttaataaaagaggtattcataagagctatcttatttgagcattttatgttgacgcctatcgggttttatgatatagtgaagaagggtcgaagtaatctgactaaaggcaggtaggtgcggaaccgacctataacatttatttcgatctaaaaataaatttataggaggtcaagt Intra-Species Hit: Count: 1 Min: 1 Max: 263 Len: 263 Subject: NC_002967_TDE1955_TDE1956|hypothetical protein:hypothetical protein|NEGATIVE:POSITIVE|[1970991,1971253]|263 HSP 1 e-value: 1.0E-133 bit: 474.0 Len: 263 Query Start:1 Query End:263 Subject Strand: POSITIVE Subject Start: 1 Subject End: 263 aatttgcatctccatgataccgttatattttatcagaatactcaatattagtctactgcctcacagaaatcaattttgtaatannnnnnnnaataaaagaggtattcataagagctatcttatttgagcattttatgttgacgcctatcgggttttatgatatagtgaagaagggtcgaagtaatctgactaaaggcaggtaggtgcggaaccgacctataacatttatttcgatctaaaaataaatttataggaggtcaagt aatttgcatctccatgataccgttatattttatcagaatactcaatattagtctactgcctcacagaaatcaattttgtaatattttttttaataaaagaggtattcataagagctatcttatttgagcattttatgttgacgcctatcgggttttatgatatagtgaagaagggtcgaagtaatctgactaaaggcaggtaggtgcggaaccgacctataacatttatttcgatctaaaaataaatttataggaggtcaagt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUUUGCAUCUCCAUGAUACCGUUAUAUUUUAUCAGAAUACUCAAUAUUAGUCUACUGCCUCACAGAAAUCAAUUUUGUAAUAUUUUUUUUAAUAAAAGAGGUAUUCAUAAGAGCUAUCUUAUUUGAGCAUUUUAUGUUGACGCCUAUCGGGUUUUAUGAUAUAGUGAAGAAGGGUCGAAGUAAUCUGACUAAAGGCAGGUAGGUGCGGAACCGACCUAUAACAUUUAUUUCGAUCUAAAAAUAAAUUUAUAGGAGGUCAAGU .(((((.((((((((((........((((.(((((....((((.(((...(((...((((((((((((.....))))))..((((......))))...))))))..((((((((((..........))).)))))))..)))...))).))))....))))).)))).....((((((((((((.(((.(.....))))((((((.((....)))))))).....))))))))))))..........)))).))))))))))) (-61.90) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACUUGACCUCCUAUAAAUUUAUUUUUAGAUCGAAAUAAAUGUUAUAGGUCGGUUCCGCACCUACCUGCCUUUAGUCAGAUUACUUCGACCCUUCUUCACUAUAUCAUAAAACCCGAUAGGCGUCAACAUAAAAUGCUCAAAUAAGAUAGCUCUUAUGAAUACCUCUUUUAUUAAAAAAAAUAUUACAAAAUUGAUUUCUGUGAGGCAGUAGACUAAUAUUGAGUAUUCUGAUAAAAUAUAACGGUAUCAUGGAGAUGCAAAUU ....((((.((((((((((((((((......))))))))).)))))))..))))..(((.((.((((((.(((((((((.(((..........((((((...((((....((((....)).))...(((((...(((..........)))..)))))..................................))))....))))))(((((......))))).))).))))))......))).))))....)))).)))..... (-49.40) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 796 60 11 151 102 NC_002967:TDE1955|5end_hypothetical_protein_1970900..1971130_NEGATIVE 506 110 61 221 173 NC_002967:TDE0155|5end_adenylate/guanylate_cyclase_catalytic_domain_protein_180154..180384_NEGATIVE 365 227 184 212 173 NC_002967:TDE0440|5end_DNA-binding_protein_495951..496181_POSITIVE 364 180 151 68 38 NC_002967:TDE0271|5end_hypothetical_protein_301976..302206_POSITIVE 361 89 50 231 185 NC_002967:TDE0462|5end_metallo-beta-lactamase_family_protein_516987..517217_NEGATIVE 330 215 172 160 126 NC_002967:TDE1233|5end_hypothetical_protein_1267203..1267433_POSITIVE 320 215 172 56 2 NC_002967:TDE2673|5end_hypothetical_protein_2712377..2712607_NEGATIVE 309 237 193 81 43 NC_002967:TDE0683|5end_hypothetical_protein_721303..721533_NEGATIVE 308 218 172 183 129 NC_002967:TDE0450|5end_hypothetical_protein_508529..508759_NEGATIVE 300 205 164 178 141 NC_002967:TDE1023|5end_methylaspartate_mutase_subunit_S_1055123..1055353_POSITIVE 300 150 105 126 87 NC_002967:TDE0118|5end_hypothetical_protein_137047..137277_NEGATIVE 298 210 164 172 126 NC_002967:TDE1005|5end_hypothetical_protein_1030206..1030436_POSITIVE 295 178 134 53 4 NC_002967:TDE0848|5end_hypothetical_protein_871269..871499_POSITIVE 285 215 172 211 162 NC_002967:TDE2070|5end_hypothetical_protein_2097035..2097265_POSITIVE 275 240 191 74 26 NC_002967:TDE0575|5end_aspartyl/glutamyl-tRNA_amidotransferase_subunit_B_607733..607963_NEGATIVE 271 215 174 91 47 NC_002967:TDE2268|5end_hypothetical_protein_2304959..2305189_NEGATIVE 271 215 174 91 47 NC_002967:TDE0946|5end_hypothetical_protein_968212..968442_POSITIVE 269 203 164 170 129 NC_002967:TDE2607|5end_hypothetical_protein_2648586..2648816_POSITIVE 267 217 172 208 160 NC_002967:TDE1884|5end_hypothetical_protein_1906857..1907087_NEGATIVE 266 209 171 57 16 NC_002967:TDE1644|5end_methionyl-tRNA_formyltransferase_1695546..1695776_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 351 114 79 35 1 NC_002967:TDE0156|3end_adenylate/guanylate_cyclase_catalytic_domain_protein_180344..180494_NEGATIVE 318 217 172 76 34 NC_002967:TDE0923|3end_ABC_transporter,_ATP-binding/permease_protein_943920..944070_NEGATIVE 310 230 185 144 105 NC_002967:TDE0693|3end_phosphomethylpyrimidine_kinase_730831..730981_POSITIVE 300 150 105 115 76 NC_002967:TDE0119|3end_flagellar_protein_FliS_137058..137208_NEGATIVE 287 215 174 119 75 NC_002967:TDE2515|3end_hypothetical_protein_2540972..2541122_NEGATIVE 278 207 164 149 112 NC_002967:TDE2357|3end_iron_compound_ABC_transporter,_permease_protein_2393101..2393251_POSITIVE 277 178 140 46 2 NC_002967:TDE0847|3end_hypothetical_protein_871342..871492_POSITIVE 276 209 162 51 8 NC_002967:TDE2266|3end_reverse_transcriptase_family_protein_2303042..2303192_NEGATIVE 275 218 180 146 100 NC_002967:TDE2292|3end_2C-methyl-D-erythritol_2,4-cyclodiphosphate_synthase_2329383..2329533_POSITIVE 275 240 191 81 33 NC_002967:TDE0576|3end_glutamyl-tRNA(Gln)_amidotransferase,_A_subunit_607726..607876_NEGATIVE 271 215 174 119 75 NC_002967:TDE2269|3end_hypothetical_protein_2304931..2305081_NEGATIVE 271 215 174 119 75 NC_002967:TDE0945|3end_hypothetical_protein_968320..968470_POSITIVE 269 203 164 55 14 NC_002967:TDE2606|3end_urocanate_hydratase_2648551..2648701_POSITIVE 268 213 171 116 80 NC_002967:TDE1019|3end_dicarboxylate_transporter,_DctM_subunit,_putative_1049702..1049852_NEGATIVE 268 210 168 127 93 NC_002967:TDE0583|3end_hypothetical_protein_621426..621576_NEGATIVE 266 209 171 60 19 NC_002967:TDE1645|3end_polypeptide_deformylase_1695543..1695693_NEGATIVE 262 219 172 83 32 NC_002967:TDE2491|3end_DNA_polymerase_domain_protein_2514705..2514855_NEGATIVE 259 217 173 68 14 NC_002967:TDE0353|3end_lipase/acylhydrolase,_GDSL_family_396743..396893_NEGATIVE 254 218 173 45 5 NC_002967:TDE2259|3end_hypothetical_protein_2296527..2296677_NEGATIVE 254 219 173 118 69 NC_002967:TDE0203|3end_hypothetical_protein_237058..237208_POSITIVE