Origin IGS: aatgaagaaaacttgacaaaatcttcaagcagcccaaggagcaatagaggaaataaatatgattaacacgataaattttgctgcaactcatgagtccaagcagagtacagcacgggcaaaacttgtattttacccttatagtcattggcaggtcttacggctcggaggtcatcattgattttcgccttcccggaataaaccagtggcattttgaaaaacaactctctcacttacgtcagccggactgctcaggactttcacctgattcccttttcactccttagctaaaaggagcaccaagaccgaaaccgttatttaatcataattctatacttttataaaaaataagtcaagataccaaaatcggtattccaatctagattcaacacactgataattgaaaaatactctattctatgatataatcaggctatagtggtattaaggaggcgtgt .........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 acacgcctccttaataccactatagcctgattatatcatagaatagagtatttttcaattatcagtgtgttgaatctagattggaataccgattttggtatcttgacttattttttataaaagtatagaattatgattaaataacggtttcggtcttggtgctccttttagctaaggagtgaaaagggaatcaggtgaaagtcctgagcagtccggctgacgtaagtgagagagttgtttttcaaaatgccactggtttattccgggaaggcgaaaatcaatgatgacctccgagccgtaagacctgccaatgactataagggtaaaatacaagttttgcccgtgctgtactctgcttggactcatgagttgcagcaaaatttatcgtgttaatcatatttatttcctctattgctccttgggctgcttgaagattttgtcaagttttcttcatt Mask Tandem Repeat Region ================================================ aatgaagaaaacttgacaaaatcttcaagcagcccaaggagcaatagaggaaataaatatgattaacacgataaattttgctgcaactcatgagtccaagcagagtacagcacgggcaaaacttgtattttacccttatagtcattggcaggtcttacggctcggaggtcatcattgattttcgccttcccggaataaaccagtggcattttgaaaaacaactctctcacttacgtcagccggactgctcaggactttcacctgattcccttttcactccttagctaaaaggagcaccaagaccgaaaccgttatttaatcataattctatacttttataaaaaataagtcaagataccaaaatcggtattccaatctagattcaacacactgataattgaaaaatactctattctatgatataatcaggctatagtggtattaaggaggcgtgt Find is-nt database================================================ Query_seq: TDE0998:TDE0999|TDE0998:TDE0999:hypothetical protein:formate/nitrite transporter:->->:1025555..1026009 455 aatgaagaaaacttgacaaaatcttcaagcagcccaaggagcaatagaggaaataaatatgattaacacgataaattttgctgcaactcatgagtccaagcagagtacagcacgggcaaaacttgtattttacccttatagtcattggcaggtcttacggctcggaggtcatcattgattttcgccttcccggaataaaccagtggcattttgaaaaacaactctctcacttacgtcagccggactgctcaggactttcacctgattcccttttcactccttagctaaaaggagcaccaagaccgaaaccgttatttaatcataattctatacttttataaaaaataagtcaagataccaaaatcggtattccaatctagattcaacacactgataattgaaaaatactctattctatgatataatcaggctatagtggtattaaggaggcgtgt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE0998:TDE0999|TDE0998:TDE0999:hypothetical protein:formate/nitrite transporter:->->:1025555..1026009 455 aatgaagaaaacttgacaaaatcttcaagcagcccaaggagcaatagaggaaataaatatgattaacacgataaattttgctgcaactcatgagtccaagcagagtacagcacgggcaaaacttgtattttacccttatagtcattggcaggtcttacggctcggaggtcatcattgattttcgccttcccggaataaaccagtggcattttgaaaaacaactctctcacttacgtcagccggactgctcaggactttcacctgattcccttttcactccttagctaaaaggagcaccaagaccgaaaccgttatttaatcataattctatacttttataaaaaataagtcaagataccaaaatcggtattccaatctagattcaacacactgataattgaaaaatactctattctatgatataatcaggctatagtggtattaaggaggcgtgt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE0998:TDE0999|TDE0998:TDE0999:hypothetical protein:formate/nitrite transporter:->->:1025555..1026009 455 aatgaagaaaacttgacaaaatcttcaagcagcccaaggagcaatagaggaaataaatatgattaacacgataaattttgctgcaactcatgagtccaagcagagtacagcacgggcaaaacttgtattttacccttatagtcattggcaggtcttacggctcggaggtcatcattgattttcgccttcccggaataaaccagtggcattttgaaaaacaactctctcacttacgtcagccggactgctcaggactttcacctgattcccttttcactccttagctaaaaggagcaccaagaccgaaaccgttatttaatcataattctatacttttataaaaaataagtcaagataccaaaatcggtattccaatctagattcaacacactgataattgaaaaatactctattctatgatataatcaggctatagtggtattaaggaggcgtgt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aatgaagaaaacttgacaaaatcttcaagcagcccaaggagcaatagaggaaataaatatgattaacacgataaattttgctgcaactcatgagtccaagcagagtacagcacgggcaaaacttgtattttacccttatagtcattggcaggtcttacggctcggaggtcatcattgattttcgccttcccggaataaaccagtggcattttgaaaaacaactctctcacttacgtcagccggactgctcaggactttcacctgattcccttttcactccttagctaaaaggagcaccaagaccgaaaccgttatttaatcataattctatacttttataaaaaataagtcaagataccaaaatcggtattccaatctagattcaacacactgataattgaaaaatactctattctatgatataatcaggctatagtggtattaaggaggcgtgt Predict ORF larger than 30AA ================================================ Protein_Len: 44 Strand: + Start: 44 End: 175 ........................................... M E E I N M I N T I N F A A T H E S K Q S T A R A K L V F Y P Y S H W Q V L R L G G H H ........................................................................................................................................................................................................................................................................................ Protein_Len: 60 Strand: + Start: 75 End: 281 .......................................................................... M L L Q L M S P S R V Q H G Q N L Y F T L I V I G R S Y G S E V I I D F R L P G I N Q W H F E K Q L S H L R Q P D C S G .............................................................................................................................................................................. Protein_Len: 55 Strand: - Start: 66 End: 230 ................................................................. C S L N Q Q L E H T W A S Y L V P L V Q I K G K Y D N A P R V A R L D D N I K A K G S Y V L P M K F F L E R M ................................................................................................................................................................................................................................. Protein_Len: 50 Strand: - Start: 2 End: 151 . H L F S S L I K L C G L S C Y L F Y I H N V R Y I K S C S M L G L L T C C P C F K Y K V R I T M P M ................................................................................................................................................................................................................................................................................................................ aatgaagaaaacttgacaaaatcttcaagcagcccaaggagcaatagaggaaataaatatgattaacacgataaattttgctgcaactcatgagtccaagcagagtacagcacgggcaaaacttgtattttacccttatagtcattggcaggtcttacggctcggaggtcatcattgattttcgccttcccggaataaaccagtggcattttgaaaaacaactctctcacttacgtcagccggactgctcaggactttcacctgattcccttttcactccttagctaaaaggagcaccaagaccgaaaccgttatttaatcataattctatacttttataaaaaataagtcaagataccaaaatcggtattccaatctagattcaacacactgataattgaaaaatactctattctatgatataatcaggctatagtggtattaaggaggcgtgt 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: 93 Start: 397 End: 426 ............................................................................................................................................................................................................................................................................................................................................................................................................ATTGAAAAATACTCTATTCTATGATATAAT............................. PromScan Matrix: RpoD-17 Strand: - Score: 87 Start: 325 End: 354 ....................................................................................................................................................................................................................................................................................................................................CTTGACTTATTTTTTATAAAAGTATAGAAT..................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aatgaagaaaacttgacaaaatcttcaagcagcccaaggagcaatagaggaaataaatatgattaacacgataaattttgctgcaactcatgagtccaagcagagtacagcacgggcaaaacttgtattttacccttatagtcattggcaggtcttacggctcggaggtcatcattgattttcgccttcccggaataaaccagtggcattttgaaaaacaactctctcacttacgtcagccggactgctcaggactttcacctgattcccttttcactccttagctaaaaggagcaccaagaccgaaaccgttatttaatcataattctatacttttataaaaaataagtcaagataccaaaatcggtattccaatctagattcaacacactgataattgaaaaatactctattctatgatataatcaggctatagtggtattaaggaggcgtgt Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 47 HP_score: -3.0 Tail_Score: -3.47227 Start: 114 End: 135 Full_Region: AGCAGAGTACAGCAC GGGCAAAA CTTGTA TTTTACCC TTATAGTCATTGGCA .................................................................................................................GGGCAAAACTTGTATTTTACCC................................................................................................................................................................................................................................................................................................................................ Find igs database================================================ Query_seq: TDE0998:TDE0999|TDE0998:TDE0999:hypothetical protein:formate/nitrite transporter:->->:1025555..1026009 455 aatgaagaaaacttgacaaaatcttcaagcagcccaaggagcaatagaggaaataaatatgattaacacgataaattttgctgcaactcatgagtccaagcagagtacagcacgggcaaaacttgtattttacccttatagtcattggcaggtcttacggctcggaggtcatcattgattttcgccttcccggaataaaccagtggcattttgaaaaacaactctctcacttacgtcagccggactgctcaggactttcacctgattcccttttcactccttagctaaaaggagcaccaagaccgaaaccgttatttaatcataattctatacttttataaaaaataagtcaagataccaaaatcggtattccaatctagattcaacacactgataattgaaaaatactctattctatgatataatcaggctatagtggtattaaggaggcgtgt Intra-Species Hit: Count: 1 Min: 1 Max: 455 Len: 455 Subject: NC_002967_TDE0998_TDE0999|hypothetical protein:formate/nitrite transporter|POSITIVE:POSITIVE|[1025555,1026009]|455 HSP 1 e-value: 0.0 bit: 902.0 Len: 455 Query Start:1 Query End:455 Subject Strand: POSITIVE Subject Start: 1 Subject End: 455 aatgaagaaaacttgacaaaatcttcaagcagcccaaggagcaatagaggaaataaatatgattaacacgataaattttgctgcaactcatgagtccaagcagagtacagcacgggcaaaacttgtattttacccttatagtcattggcaggtcttacggctcggaggtcatcattgattttcgccttcccggaataaaccagtggcattttgaaaaacaactctctcacttacgtcagccggactgctcaggactttcacctgattcccttttcactccttagctaaaaggagcaccaagaccgaaaccgttatttaatcataattctatacttttataaaaaataagtcaagataccaaaatcggtattccaatctagattcaacacactgataattgaaaaatactctattctatgatataatcaggctatagtggtattaaggaggcgtgt aatgaagaaaacttgacaaaatcttcaagcagcccaaggagcaatagaggaaataaatatgattaacacgataaattttgctgcaactcatgagtccaagcagagtacagcacgggcaaaacttgtattttacccttatagtcattggcaggtcttacggctcggaggtcatcattgattttcgccttcccggaataaaccagtggcattttgaaaaacaactctctcacttacgtcagccggactgctcaggactttcacctgattcccttttcactccttagctaaaaggagcaccaagaccgaaaccgttatttaatcataattctatacttttataaaaaataagtcaagataccaaaatcggtattccaatctagattcaacacactgataattgaaaaatactctattctatgatataatcaggctatagtggtattaaggaggcgtgt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUGAAGAAAACUUGACAAAAUCUUCAAGCAGCCCAAGGAGCAAUAGAGGAAAUAAAUAUGAUUAACACGAUAAAUUUUGCUGCAACUCAUGAGUCCAAGCAGAGUACAGCACGGGCAAAACUUGUAUUUUACCCUUAUAGUCAUUGGCAGGUCUUACGGCUCGGAGGUCAUCAUUGAUUUUCGCCUUCCCGGAAUAAACCAGUGGCAUUUUGAAAAACAACUCUCUCACUUACGUCAGCCGGACUGCUCAGGACUUUCACCUGAUUCCCUUUUCACUCCUUAGCUAAAAGGAGCACCAAGACCGAAACCGUUAUUUAAUCAUAAUUCUAUACUUUUAUAAAAAAUAAGUCAAGAUACCAAAAUCGGUAUUCCAAUCUAGAUUCAACACACUGAUAAUUGAAAAAUACUCUAUUCUAUGAUAUAAUCAGGCUAUAGUGGUAUUAAGGAGGCGUGU ...........((((((....(((((.....(((....).))....)))))......(((((((((...(((..((((((((...(((....)))...)))))))).......(((.((((......)))).))).....)))...((..((((((..(((..((((((((....)))))))))))...((((........(((((....(((.....))).....)))))........)))).....(((((.......)))))...........((((((......))))))....))))))....)).....)))))))))........................)))))).((((......)))).(((..((.....(((......))).....))..((((((((((....((((...))))....)))).))))))..)))....... (-93.69) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACACGCCUCCUUAAUACCACUAUAGCCUGAUUAUAUCAUAGAAUAGAGUAUUUUUCAAUUAUCAGUGUGUUGAAUCUAGAUUGGAAUACCGAUUUUGGUAUCUUGACUUAUUUUUUAUAAAAGUAUAGAAUUAUGAUUAAAUAACGGUUUCGGUCUUGGUGCUCCUUUUAGCUAAGGAGUGAAAAGGGAAUCAGGUGAAAGUCCUGAGCAGUCCGGCUGACGUAAGUGAGAGAGUUGUUUUUCAAAAUGCCACUGGUUUAUUCCGGGAAGGCGAAAAUCAAUGAUGACCUCCGAGCCGUAAGACCUGCCAAUGACUAUAAGGGUAAAAUACAAGUUUUGCCCGUGCUGUACUCUGCUUGGACUCAUGAGUUGCAGCAAAAUUUAUCGUGUUAAUCAUAUUUAUUUCCUCUAUUGCUCCUUGGGCUGCUUGAAGAUUUUGUCAAGUUUUCUUCAUU ....(((...(((((((.(((((((..(((..(((((........)).)))...))).)))).))))))))))....(((((((....))))))).)))..((((((..((((((.....((((.......(((((((((...(((((...((((((((((((((((......)))))))....(((...((((((....).)))))......(((((.((....))..(((.((..((........((((.((((......))))...)))).........))..)))))..))))).....)))))))).))))....(((((((((....))))))))).((((((((((((........)).))).)))))))......))))).)))))))))...............(((.....))).))))))))))...))))))........... (-115.03) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 342 170 141 178 147 NC_002967:TDE1085|5end_UDP-N-acetylmuramate--L-alanine_ligase_1116328..1116558_POSITIVE 339 169 122 59 9 NC_002967:TDE2320|5end_RNA_polymerase_sigma-24_factor,_putative_2356951..2357181_NEGATIVE 331 169 123 64 13 NC_002967:TDE0980|5end_asparaginyl-tRNA_synthetase_1005400..1005630_NEGATIVE 325 195 153 188 146 NC_002967:TDE1168|5end_hypothetical_protein_1199482..1199712_NEGATIVE 324 132 92 110 71 NC_002967:TDE2070|5end_hypothetical_protein_2097035..2097265_POSITIVE 320 168 127 204 156 NC_002967:TDE1708|5end_apolipoprotein_N-acyltransferase_1764822..1765052_NEGATIVE 315 195 151 204 157 NC_002967:TDE2583|5end_hypothetical_protein_2616322..2616552_POSITIVE 315 280 238 86 35 NC_002967:TDE1892|5end_hypothetical_protein_1912065..1912295_POSITIVE 314 194 151 83 37 NC_002967:TDE1242|5end_hypothetical_protein_1274565..1274795_POSITIVE 313 300 251 211 150 NC_002967:TDE2150|5end_hypothetical_protein_2188276..2188506_NEGATIVE 310 127 81 221 174 NC_002967:TDE2669|5end_CDP-alcohol_phosphatidyltransferase_family_protein_2706943..2707173_NEGATIVE 310 280 234 156 113 NC_002967:TDE0957|5end_glycerophosphoryl_diester_phosphodiesterase_family_protein_980252..980482_POSITIVE 306 50 2 174 124 NC_002967:TDE2660|5end_hypothetical_protein_2697517..2697747_NEGATIVE 303 286 245 43 6 NC_002967:TDE2515|5end_hypothetical_protein_2542057..2542287_NEGATIVE 302 190 145 63 16 NC_002967:TDE0740|5end_hypothetical_protein_775987..776217_POSITIVE 301 207 164 150 95 NC_002967:TDE2059|5end_hypothetical_protein_2086509..2086739_NEGATIVE 299 186 141 110 68 NC_002967:TDE2268|5end_hypothetical_protein_2304959..2305189_NEGATIVE 299 129 82 60 8 NC_002967:TDE0360|5end_ABC_transporter,_ATP-binding/permease_protein_405844..406074_NEGATIVE 295 263 223 75 30 NC_002967:TDE1914|5end_Holliday_junction_DNA_helicase_RuvB_1931920..1932150_NEGATIVE 295 264 223 225 172 NC_002967:TDE0572|5end_hypothetical_protein_603494..603724_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 339 169 122 62 12 NC_002967:TDE2321|3end_hypothetical_protein_2356948..2357098_NEGATIVE 328 190 144 139 64 NC_002967:TDE0362|3end_bacterial_Ig-like_domain_protein_407501..407651_NEGATIVE 324 132 92 84 45 NC_002967:TDE2069|3end_endoribonuclease_L-PSP,_putative_2097089..2097239_POSITIVE 324 170 121 145 89 NC_002967:TDE1850|3end_ABC_transporter,_permease_protein,_putative_1878227..1878377_NEGATIVE 319 280 233 148 88 NC_002967:TDE2527|3end_hypothetical_protein_2555449..2555599_NEGATIVE 314 194 151 90 44 NC_002967:TDE1241|3end_HD_domain_protein_1274652..1274802_POSITIVE 313 300 251 147 86 NC_002967:TDE2151|3end_hypothetical_protein_2188340..2188490_NEGATIVE 313 190 147 109 65 NC_002967:TDE0759|3end_hypothetical_protein_799128..799278_NEGATIVE 310 280 231 54 12 NC_002967:TDE2719|3end_hypothetical_protein_2777015..2777165_POSITIVE 305 270 222 150 99 NC_002967:TDE0956|3end_hypothetical_protein_980330..980480_POSITIVE 304 190 149 134 84 NC_002967:TDE0833|3end_lipoprotein,_putative_854097..854247_POSITIVE 302 166 133 78 39 NC_002967:TDE1857|3end_hypothetical_protein_1883929..1884079_NEGATIVE 301 190 145 57 16 NC_002967:TDE0977|3end_hypothetical_protein_1001640..1001790_POSITIVE 299 186 141 138 96 NC_002967:TDE2269|3end_hypothetical_protein_2304931..2305081_NEGATIVE 297 280 234 133 72 NC_002967:TDE1450|3end_MutS2_family_protein_1497856..1498006_POSITIVE 295 190 144 137 80 NC_002967:TDE2609|3end_MiaB-like_tRNA_modifying_enzyme_YliG,_TIGR01125_2651904..2652054_POSITIVE 295 263 223 67 22 NC_002967:TDE1915|3end_alcohol_dehydrogenase,_iron-containing_1931928..1932078_NEGATIVE 295 264 223 148 95 NC_002967:TDE0571|3end_hypothetical_protein_603497..603647_POSITIVE 294 249 202 64 11 NC_002967:TDE2363|3end_high-affinity_branched_chain_amino_acid_ABC_transporter,_ATP-binding_protein_2397472..2397622_NEGATIVE 289 190 141 104 52 NC_002967:TDE2542|3end_antigen,_putative_2569441..2569591_NEGATIVE