Origin IGS: atctccctcaaaaaaactctccttaagctttcctaattcttttatttaagatacggtacttacataaggagagcactctttatttgtacttactgtacacgatatggatggttcacacaatttgtgtgagctcaagggccgacaagccaagcggaagccaagattgttgttcctgttgtcaggactgttgttattccgtttgcctacagtgcagttgttcgcgttgttgttccagctgccgccgcgtttaacacggttagagcctgacgcggcaccttatacggtccataccgttttttagccaaaaaattttcgagccgctaaagcggctgacatagtgcaggttaatcattattt .........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 aaataatgattaacctgcactatgtcagccgctttagcggctcgaaaattttttggctaaaaaacggtatggaccgtataaggtgccgcgtcaggctctaaccgtgttaaacgcggcggcagctggaacaacaacgcgaacaactgcactgtaggcaaacggaataacaacagtcctgacaacaggaacaacaatcttggcttccgcttggcttgtcggcccttgagctcacacaaattgtgtgaaccatccatatcgtgtacagtaagtacaaataaagagtgctctccttatgtaagtaccgtatcttaaataaaagaattaggaaagcttaaggagagtttttttgagggagat Mask Tandem Repeat Region ================================================ atctccctcaaaaaaactctccttaagctttcctaattcttttatttaagatacggtacttacataaggagagcactctttatttgtacttactgtacacgatatggatggttcacacaatttgtgtgagctcaagggccgacaagccaagcggaagccaagattgttgttcctgttgtcaggactgttgttattccgtttgcctacagtgcagttgttcgcgttgttgttccagctgccgccgcgtttaacacggttagagcctgacgcggcaccttatacggtccataccgttttttagccaaaaaattttcgagccgctaaagcggctgacatagtgcaggttaatcattattt Find is-nt database================================================ Query_seq: TDE2267:TDE2268|TDE2267:TDE2268:HRDC domain protein:hypothetical protein:<-<-:2304555..2304911 357 atctccctcaaaaaaactctccttaagctttcctaattcttttatttaagatacggtacttacataaggagagcactctttatttgtacttactgtacacgatatggatggttcacacaatttgtgtgagctcaagggccgacaagccaagcggaagccaagattgttgttcctgttgtcaggactgttgttattccgtttgcctacagtgcagttgttcgcgttgttgttccagctgccgccgcgtttaacacggttagagcctgacgcggcaccttatacggtccataccgttttttagccaaaaaattttcgagccgctaaagcggctgacatagtgcaggttaatcattattt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE2267:TDE2268|TDE2267:TDE2268:HRDC domain protein:hypothetical protein:<-<-:2304555..2304911 357 atctccctcaaaaaaactctccttaagctttcctaattcttttatttaagatacggtacttacataaggagagcactctttatttgtacttactgtacacgatatggatggttcacacaatttgtgtgagctcaagggccgacaagccaagcggaagccaagattgttgttcctgttgtcaggactgttgttattccgtttgcctacagtgcagttgttcgcgttgttgttccagctgccgccgcgtttaacacggttagagcctgacgcggcaccttatacggtccataccgttttttagccaaaaaattttcgagccgctaaagcggctgacatagtgcaggttaatcattattt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE2267:TDE2268|TDE2267:TDE2268:HRDC domain protein:hypothetical protein:<-<-:2304555..2304911 357 atctccctcaaaaaaactctccttaagctttcctaattcttttatttaagatacggtacttacataaggagagcactctttatttgtacttactgtacacgatatggatggttcacacaatttgtgtgagctcaagggccgacaagccaagcggaagccaagattgttgttcctgttgtcaggactgttgttattccgtttgcctacagtgcagttgttcgcgttgttgttccagctgccgccgcgtttaacacggttagagcctgacgcggcaccttatacggtccataccgttttttagccaaaaaattttcgagccgctaaagcggctgacatagtgcaggttaatcattattt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 6 Min: 136 Max: 276 Len: 141 Subject: UniRef90_Q73JX2 Cluster: Hypothetical protein; n=1; Treponema denticola|Rep: Hypothetical protein - Treponema denticola HSP 1 e-value: 6.0E-9 bit: 62.0 Len: 141 Query Start:136 Query End:276 Subject Strand: null Subject Start: 315 Subject End: 361 ....................................................................................................................................... G A A S G S N R V K R G G S W N N N A N N C T V G K R X X X X X X X X X X N L G F R L A C R P ................................................................................. ....................................................................................................................................... G A A S G S N R V L R G G S W D N Y A E G C T V G T R G N G N P G N R G N L L G F R L A C R P ................................................................................. Subject: UniRef90_Q73KW6 Cluster: Hypothetical protein; n=1; Treponema denticola|Rep: Hypothetical protein - Treponema denticola HSP 1 e-value: 2.0E-7 bit: 57.4 Len: 141 Query Start:136 Query End:276 Subject Strand: null Subject Start: 310 Subject End: 356 ....................................................................................................................................... G A A S G S N R V K R G G S W N N N A N N C T V G K R X X X X X X X X X X N L G F R L A C R P ................................................................................. ....................................................................................................................................... G A A S G S A R V E R G G S W L N Y A Y G C T V G V R Y C V T P G S R S D N L G F R L A C R P ................................................................................. Subject: UniRef90_Q73KE9 Cluster: Hypothetical protein; n=1; Treponema denticola|Rep: Hypothetical protein - Treponema denticola HSP 1 e-value: 2.0E-6 bit: 53.9 Len: 141 Query Start:136 Query End:276 Subject Strand: null Subject Start: 283 Subject End: 329 ....................................................................................................................................... G A A S G S N R V K R G G S W N N N A N N C T V G K R X X X X X X X X X X N L G F R L A C R P ................................................................................. ....................................................................................................................................... G P A S G S G R V L R G G S W A G S A D Y C A V G E R V N I S P G V R C S D L G F R L A C R P ................................................................................. Subject: UniRef90_Q73Q71 Cluster: Conserved domain protein; n=1; Treponema denticola|Rep: Conserved domain protein - Treponema denticola HSP 1 e-value: 2.0E-6 bit: 53.9 Len: 141 Query Start:136 Query End:276 Subject Strand: null Subject Start: 340 Subject End: 386 ....................................................................................................................................... G A A S G S N R V K R G G S W N N N A N N C T V G K R X X X X X X X X X X N L G F R L A C R P ................................................................................. ....................................................................................................................................... G A A S G P Y R V R R G G S W G G S A G G C T V G R R E D Y S P D S R Y N Y L G F R L A W R P ................................................................................. Subject: UniRef90_Q73NU6 Cluster: Conserved domain protein; n=1; Treponema denticola|Rep: Conserved domain protein - Treponema denticola HSP 1 e-value: 2.0E-6 bit: 53.5 Len: 141 Query Start:136 Query End:276 Subject Strand: null Subject Start: 155 Subject End: 201 ....................................................................................................................................... G A A S G S N R V K R G G S W N N N A N N C T V G K R X X X X X X X X X X N L G F R L A C R P ................................................................................. ....................................................................................................................................... G A A S G S Y R V L R G G S W Y D S A K N C T V G F R F N R D P G Y G N L D I G F R L A W R P ................................................................................. Subject: UniRef90_Q73P54 Cluster: Hypothetical protein; n=1; Treponema denticola|Rep: Hypothetical protein - Treponema denticola HSP 1 e-value: 6.0E-6 bit: 52.0 Len: 141 Query Start:136 Query End:276 Subject Strand: null Subject Start: 324 Subject End: 370 ....................................................................................................................................... G A A S G S N R V K R G G S W N N N A N N C T V G K R X X X X X X X X X X N L G F R L A C R P ................................................................................. ....................................................................................................................................... G G A S G S Y R V L R G G S W Y F Y A H Y C T V G V R G Y Y S P D Y W S F Y L G F R L A C R P ................................................................................. atctccctcaaaaaaactctccttaagctttcctaattcttttatttaagatacggtacttacataaggagagcactctttatttgtacttactgtacacgatatggatggttcacacaatttgtgtgagctcaannnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnttatacggtccataccgttttttagccaaaaaattttcgagccgctaaagcggctgacatagtgcaggttaatcattattt Predict ORF larger than 30AA ================================================ Protein_Len: 60 Strand: + Start: 36 End: 248 ................................... M L L F K I R Y L H K E S T L Y L Y L L Y T I W M V H T I C V S S R A D K P S G S Q D C C S C C Q D C C Y S V C L Q C S ............................................................................................................. Protein_Len: 34 Strand: + Start: 163 End: 264 .................................................................................................................................................................. M V V P V V R T V V I P F A Y S A V V R V V V P A A A A F N T V R A ............................................................................................. Protein_Len: 60 Strand: + Start: 104 End: 298 ....................................................................................................... M D G S H N L C E L K G R Q A K R K P R L L F L L S G L L L F R L P T V Q L F A L L F Q L P P R L T R L E P D A A P Y T ........................................................... Protein_Len: 32 Strand: - Start: 260 End: 355 ................................................................................................................................................................................................................................................................... L R V R C R I R D M G N K L W F I K S G S F R S V Y H L N I M M .. Protein_Len: 33 Strand: - Start: 207 End: 305 .............................................................................................................................................................................................................. L A T T R T T T G A A A A N L V T L A Q R P V K Y P G Y R K K A M .................................................... Protein_Len: 34 Strand: - Start: 49 End: 150 ................................................ S V T S V Y P S C E K N T S V T C S I S P E C L K H S S L P R C A M ............................................................................................................................................................................................................... atctccctcaaaaaaactctccttaagctttcctaattcttttatttaagatacggtacttacataaggagagcactctttatttgtacttactgtacacgatatggatggttcacacaatttgtgtgagctcaannnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnttatacggtccataccgttttttagccaaaaaattttcgagccgctaaagcggctgacatagtgcaggttaatcattattt 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================================================ atctccctcaaaaaaactctccttaagctttcctaattcttttatttaagatacggtacttacataaggagagcactctttatttgtacttactgtacacgatatggatggttcacacaatttgtgtgagctcaannnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnttatacggtccataccgttttttagccaaaaaattttcgagccgctaaagcggctgacatagtgcaggttaatcattattt Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 78 HP_score: -5.8 Tail_Score: -5.00616 Start: 282 End: 293 Full_Region: ACGCGGCACCTTATA CGGT CCAT ACCG TTTTTTAGCCAAAAA .........................................................................................................................................................................................................................................................................................CGGTCCATACCG................................................................ Find igs database================================================ Query_seq: TDE2267:TDE2268|TDE2267:TDE2268:HRDC domain protein:hypothetical protein:<-<-:2304555..2304911 357 atctccctcaaaaaaactctccttaagctttcctaattcttttatttaagatacggtacttacataaggagagcactctttatttgtacttactgtacacgatatggatggttcacacaatttgtgtgagctcaannnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnttatacggtccataccgttttttagccaaaaaattttcgagccgctaaagcggctgacatagtgcaggttaatcattattt Intra-Species Hit: Count: 1 Min: 17 Max: 357 Len: 341 Subject: NC_002967_TDE2267_TDE2268|HRDC domain protein:hypothetical protein|NEGATIVE:NEGATIVE|[2304555,2304911]|357 HSP 1 e-value: 4.0E-61 bit: 236.0 Len: 119 Query Start:17 Query End:135 Subject Strand: POSITIVE Subject Start: 17 Subject End: 135 ................ctctccttaagctttcctaattcttttatttaagatacggtacttacataaggagagcactctttatttgtacttactgtacacgatatggatggttcacacaatttgtgtgagctcaa.............................................................................................................................................................................................................................. ................ctctccttaagctttcctaattcttttatttaagatacggtacttacataaggagagcactctttatttgtacttactgtacacgatatggatggttcacacaatttgtgtgagctcaa.............................................................................................................................................................................................................................. HSP 2 e-value: 2.0E-38 bit: 161.0 Len: 81 Query Start:277 Query End:357 Subject Strand: POSITIVE Subject Start: 277 Subject End: 357 ....................................................................................................................................................................................................................................................................................ttatacggtccataccgttttttagccaaaaaattttcgagccgctaaagcggctgacatagtgcaggttaatcattattt ....................................................................................................................................................................................................................................................................................ttatacggtccataccgttttttagccaaaaaattttcgagccgctaaagcggctgacatagtgcaggttaatcattattt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUCUCCUUAAGCUUUCCUAAUUCUUUUAUUUAAGAUACGGUACUUACAUAAGGAGAGCACUCUUUAUUUGUACUUACUGUACACGAUAUGGAUGGUUCACACAAUUUGUGUGAGCUCAAGGGCCGACAAGCCAAGCGGAAGCCAAGAUUGUUGUUCCUGUUGUCAGGACUGUUGUUAUUCCGUUUGCCUACAGUGCAGUUGUUCGCGUUGUUGUUCCAGCUGCCGCCGCGUUUAACACGGUUAGAGCCUGACGCGGCACCUUAUACGGUCCAUACCGUUUUUUAGCCAAAAAAUUUUCGAGCCGCUAAAGCGGCUGACAUAGUGCAGGUUAAUCAUUAUUU (((((((((......((....((((......))))...))........)))))))))...(((.(((((((((.....))))).)))).))).(((((((((.....)))))))))...((((((...((.(((((((((.....(((....((.((((....)))))).)))....))))))))).)).....(((((((...(((....)))..))))))).((((((((......(((....))).))))))))........))))))..........((((((.........((.((((((....)))))))).........))))))......... (-107.91) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAUAAUGAUUAACCUGCACUAUGUCAGCCGCUUUAGCGGCUCGAAAAUUUUUUGGCUAAAAAACGGUAUGGACCGUAUAAGGUGCCGCGUCAGGCUCUAACCGUGUUAAACGCGGCGGCAGCUGGAACAACAACGCGAACAACUGCACUGUAGGCAAACGGAAUAACAACAGUCCUGACAACAGGAACAACAAUCUUGGCUUCCGCUUGGCUUGUCGGCCCUUGAGCUCACACAAAUUGUGUGAACCAUCCAUAUCGUGUACAGUAAGUACAAAUAAAGAGUGCUCUCCUUAUGUAAGUACCGUAUCUUAAAUAAAAGAAUUAGGAAAGCUUAAGGAGAG ................(((((...((((((((....)))))).))..................((((((((((..((.(((((.((((...((((((.....((((.....))))((((.(((..(.........(((......))).((((......))))...........(((((....))))).........)..))).))))..)))))).))))))))).))((((((.....))))))....))))))))))((((.....))))........)))))((((((((.((...(.((...((((......))))....)))..)).)))))))). (-101.70) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 1023 230 181 231 182 NC_002967:TDE0573|5end_hypothetical_protein_604681..604911_POSITIVE 878 100 51 207 158 NC_002967:TDE2267|5end_HRDC_domain_protein_2304464..2304694_NEGATIVE 741 170 121 116 67 NC_002967:TDE0946|5end_hypothetical_protein_968212..968442_POSITIVE 393 289 246 231 189 NC_002967:TDE0589|5end_acetyl-CoA_carboxylase,_carboxyl_transferase,_alpha_subunit_629044..629274_NEGATIVE 377 227 181 206 162 NC_002967:TDE2491|5end_DNA_polymerase_domain_protein_2515499..2515729_NEGATIVE 374 228 181 108 67 NC_002967:TDE1139|5end_hypothetical_protein_1168615..1168845_NEGATIVE 371 258 216 46 4 NC_002967:TDE1595|5end_cobalamin_biosynthesis_protein_CbiD_1646039..1646269_NEGATIVE 367 320 276 184 130 NC_002967:TDE1492|5end_chemotaxis_protein_CheW_1537231..1537461_POSITIVE 363 260 219 213 167 NC_002967:TDE1769|5end_hypothetical_protein_1814377..1814607_NEGATIVE 362 260 218 169 121 NC_002967:TDE2542|5end_antigen,_putative_2570826..2571056_NEGATIVE 360 160 115 58 1 NC_002967:TDE0163|5end_flavodoxin_193383..193613_NEGATIVE 357 160 117 108 58 NC_002967:TDE0436|5end_Recombination_protein_O_492133..492363_NEGATIVE 354 158 117 228 183 NC_002967:TDE1864|5end_crossover_junction_endodeoxyribonuclease_RuvC_1889108..1889338_NEGATIVE 352 196 153 226 179 NC_002967:TDE2499|5end_hypothetical_protein_2523952..2524182_NEGATIVE 352 260 219 200 137 NC_002967:TDE1340|5end_ribosomal_5S_rRNA_E-loop_binding_protein_Ctc/L25/TL5_1376317..1376547_POSITIVE 352 158 114 51 12 NC_002967:TDE0210|5end_cob(I)yrinic_acid_a,c-diamide_adenosyltransferase_245551..245781_POSITIVE 351 228 182 198 148 NC_002967:TDE2640|5end_hypothetical_protein_2680034..2680264_POSITIVE 351 229 182 179 117 NC_002967:TDE0921|5end_ABC_transporter,_ATP-binding/permease_protein_941857..942087_NEGATIVE 351 240 195 202 150 NC_002967:TDE0545|5end_hypothetical_protein_584774..585004_POSITIVE 348 259 221 57 4 NC_002967:TDE1736|5end_ferredoxin,_2(4Fe-4S)_1789908..1790138_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 917 168 121 142 95 NC_002967:TDE2101|3end_hypothetical_protein_2125549..2125699_NEGATIVE 825 167 121 141 95 NC_002967:TDE2515|3end_hypothetical_protein_2540972..2541122_NEGATIVE 771 170 121 144 95 NC_002967:TDE2269|3end_hypothetical_protein_2304931..2305081_NEGATIVE 741 170 121 144 95 NC_002967:TDE0945|3end_hypothetical_protein_968320..968470_POSITIVE 734 170 121 144 96 NC_002967:TDE0572|3end_hypothetical_protein_604734..604884_POSITIVE 729 170 121 144 95 NC_002967:TDE2239|3end_hypothetical_protein_2276554..2276704_NEGATIVE 661 170 121 144 96 NC_002967:TDE0977|3end_hypothetical_protein_1001640..1001790_POSITIVE 655 167 121 141 95 NC_002967:TDE1056|3end_hypothetical_protein_1085895..1086045_POSITIVE 505 156 112 130 86 NC_002967:TDE0833|3end_lipoprotein,_putative_854097..854247_POSITIVE 373 228 181 69 14 NC_002967:TDE0320|3end_CBS_domain_protein_352480..352630_NEGATIVE 366 230 181 68 12 NC_002967:TDE1770|3end_hypothetical_protein_1814468..1814618_POSITIVE 362 260 218 60 12 NC_002967:TDE2544|3end_hypothetical_protein_2570935..2571085_NEGATIVE 358 226 181 108 52 NC_002967:TDE0493|3end_hypothetical_protein_548581..548731_NEGATIVE 357 219 180 151 98 NC_002967:TDE1238|3end_translocase_1271245..1271395_POSITIVE 357 160 117 105 55 NC_002967:TDE0437|3end_PBS_lyase_HEAT-like_repeat_domain_protein_492136..492286_NEGATIVE 351 259 212 67 10 NC_002967:TDE1735|3end_hypothetical_protein_1789998..1790148_POSITIVE 348 267 221 41 5 NC_002967:TDE1540|3end_hypothetical_protein_1584948..1585098_POSITIVE 348 189 141 125 73 NC_002967:TDE0786|3end_ribosomal_protein_L15_815134..815284_POSITIVE 343 237 196 139 92 NC_002967:TDE0514|3end_hypothetical_protein_562420..562570_NEGATIVE 338 157 111 97 36 NC_002967:TDE1487|3end_conserved_hypothetical_protein_TIGR01033_1531528..1531678_POSITIVE