Origin IGS: atgaacctccataaaaactttttgcaggaaatatcaatttccaaaaaaagttttttcacgcagtttgtttacaaactgcatacaataatgcgacgttttgtacctttggtacaaaactcggcagataaacagagcggaaccatttgtgccgaactgtttatcatacctcctatatgttacttcaataaattttcggcttatttttaagatgggtttaggaaaaaagtctatacaagctttaaattaagaattttaaagtttcttaaaaaaaattaccatatattacaaaaaatttgaataataatagtgagagcagcaaaaataatttgctgttttaaggagaagtataat .........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 attatacttctccttaaaacagcaaattatttttgctgctctcactattattattcaaattttttgtaatatatggtaattttttttaagaaactttaaaattcttaatttaaagcttgtatagacttttttcctaaacccatcttaaaaataagccgaaaatttattgaagtaacatataggaggtatgataaacagttcggcacaaatggttccgctctgtttatctgccgagttttgtaccaaaggtacaaaacgtcgcattattgtatgcagtttgtaaacaaactgcgtgaaaaaactttttttggaaattgatatttcctgcaaaaagtttttatggaggttcat Mask Tandem Repeat Region ================================================ atgaacctccataaaaactttttgcaggaaatatcaatttccaaaaaaagttttttcacgcagtttgtttacaaactgcatacaataatgcgacgttttgtacctttggtacaaaactcggcagataaacagagcggaaccatttgtgccgaactgtttatcatacctcctatatgttacttcaataaattttcggcttatttttaagatgggtttaggaaaaaagtctatacaagctttaaattaagaattttaaagtttcttaaaaaaaattaccatatattacaaaaaatttgaataataatagtgagagcagcaaaaataatttgctgttttaaggagaagtataat Find is-nt database================================================ Query_seq: TDE2770:TDE2771|TDE2770:TDE2771:flagellar hook-length control protein FliK:hypothetical protein:<-->:2824508..2824858 351 atgaacctccataaaaactttttgcaggaaatatcaatttccaaaaaaagttttttcacgcagtttgtttacaaactgcatacaataatgcgacgttttgtacctttggtacaaaactcggcagataaacagagcggaaccatttgtgccgaactgtttatcatacctcctatatgttacttcaataaattttcggcttatttttaagatgggtttaggaaaaaagtctatacaagctttaaattaagaattttaaagtttcttaaaaaaaattaccatatattacaaaaaatttgaataataatagtgagagcagcaaaaataatttgctgttttaaggagaagtataat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE2770:TDE2771|TDE2770:TDE2771:flagellar hook-length control protein FliK:hypothetical protein:<-->:2824508..2824858 351 atgaacctccataaaaactttttgcaggaaatatcaatttccaaaaaaagttttttcacgcagtttgtttacaaactgcatacaataatgcgacgttttgtacctttggtacaaaactcggcagataaacagagcggaaccatttgtgccgaactgtttatcatacctcctatatgttacttcaataaattttcggcttatttttaagatgggtttaggaaaaaagtctatacaagctttaaattaagaattttaaagtttcttaaaaaaaattaccatatattacaaaaaatttgaataataatagtgagagcagcaaaaataatttgctgttttaaggagaagtataat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE2770:TDE2771|TDE2770:TDE2771:flagellar hook-length control protein FliK:hypothetical protein:<-->:2824508..2824858 351 atgaacctccataaaaactttttgcaggaaatatcaatttccaaaaaaagttttttcacgcagtttgtttacaaactgcatacaataatgcgacgttttgtacctttggtacaaaactcggcagataaacagagcggaaccatttgtgccgaactgtttatcatacctcctatatgttacttcaataaattttcggcttatttttaagatgggtttaggaaaaaagtctatacaagctttaaattaagaattttaaagtttcttaaaaaaaattaccatatattacaaaaaatttgaataataatagtgagagcagcaaaaataatttgctgttttaaggagaagtataat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 1 Min: 10 Max: 143 Len: 134 Subject: UniRef90_Q73M17 Cluster: Hypothetical protein; n=1; Treponema denticola|Rep: Hypothetical protein - Treponema denticola HSP 1 e-value: 5.0E-9 bit: 56.6 Len: 90 Query Start:10 Query End:99 Subject Strand: null Subject Start: 14 Subject End: 43 ......... K T S H Y C M Q F V N K L R E K T F F G N * Y F L Q K V F M ............................................................................................................................................................................................................................................................ ......... Q T S H Y C M Q F V N K L R E K T F F A N C Y L L Q K V F I ............................................................................................................................................................................................................................................................ HSP 2 e-value: 5.0E-9 bit: 25.8 Len: 45 Query Start:99 Query End:143 Subject Strand: null Subject Start: 1 Subject End: 15 .................................................................................................. M V P L C L S A E F C T K G T ................................................................................................................................................................................................................ .................................................................................................. M V P L C L S A E F A F R Q T ................................................................................................................................................................................................................ atgaacctcnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnatgttacttcaataaattttcggcttatttttaagatgggtttaggaaaaaagtctatacaagctttaaattaagaattttaaagtttcttaaaaaaaattaccatatattacaaaaaatttgaataataatagtgagagcagcaaaaataatttgctgttttaaggagaagtataat Predict ORF larger than 30AA ================================================ Protein_Len: 31 Strand: + Start: 33 End: 125 ................................ M N F Q K K F F H A V C L Q T A Y N N A T F C T F G T K L G R .................................................................................................................................................................................................................................. Protein_Len: 60 Strand: + Start: 1 End: 204 M N L H K N F L Q E I S I S K K S F F T Q F V Y K L H T I M R R F V P L V Q N S A D K Q S G T I C A E L F I I P P I C Y ................................................................................................................................................... Protein_Len: 49 Strand: + Start: 98 End: 244 ................................................................................................. M Y L W Y K T R Q I N R A E P F V P N C L S Y L L Y V T S I N F R L I F K M G L G K K S I Q A L N ........................................................................................................... Protein_Len: 34 Strand: - Start: 72 End: 173 ....................................................................... L S C V I I R R K T G K T C F E A S L C L P V M Q A S S N I M G G M .................................................................................................................................................................................. Protein_Len: 60 Strand: - Start: 37 End: 231 .................................... K E R L K N V F Q M C Y H S T K Y R Q Y L V R C I F L A S G N T G F Q K D Y R R Y T V E I F K R S I K L I P K P F F D M ........................................................................................................................ atgaacctcnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnatgttacttcaataaattttcggcttatttttaagatgggtttaggaaaaaagtctatacaagctttaaattaagaattttaaagtttcttaaaaaaaattaccatatattacaaaaaatttgaataataatagtgagagcagcaaaaataatttgctgttttaaggagaagtataat 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================================================ atgaacctcnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnatgttacttcaataaattttcggcttatttttaagatgggtttaggaaaaaagtctatacaagctttaaattaagaattttaaagtttcttaaaaaaaattaccatatattacaaaaaatttgaataataatagtgagagcagcaaaaataatttgctgttttaaggagaagtataat Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 70 HP_score: -2.2 Tail_Score: -5.43866 Start: 50 End: 89 Full_Region: ggtacaaaacgtcgc attattgtatgcagtttg taaa caaactgcgtgaaaaaac tttttttggaaattg .................................................attattgtatgcagtttgtaaacaaactgcgtgaaaaaac...................................................................................................................................................................................................................................................................... TransTerm Strand: - Conf: 95 HP_score: -10.8 Tail_Score: -3.89348 Start: 89 End: 123 Full_Region: tccgctctgtttatc tgccgagttttgtacc aaa ggtacaaaacgtcgca ttattgtatgcagtt ........................................................................................tgccgagttttgtaccaaaggtacaaaacgtcgca.................................................................................................................................................................................................................................... TransTerm Strand: - Conf: 43 HP_score: -3.6 Tail_Score: -2.52946 Start: 119 End: 168 Full_Region: gaagtaacatatagg aggtatgataaacagttcggcac aaatg gttccgctctgtttatctgccg agttttgtaccaaag ......................................................................................................................aggtatgataaacagttcggcacaaatggttccgctctgtttatctgccg....................................................................................................................................................................................... TransTerm Strand: + Conf: 50 HP_score: -4.9 Tail_Score: -2.7709 Start: 120 End: 167 Full_Region: TTTGGTACAAAACTC GGCAGATAAACAGAGCGGAAC CATTT GTGCCGAACTGTTTATCATACC TCCTATATGTTACTT .......................................................................................................................GGCAGATAAACAGAGCGGAACCATTTGTGCCGAACTGTTTATCATACC........................................................................................................................................................................................ TransTerm Strand: + Conf: 50 HP_score: -2.1 Tail_Score: -3.98214 Start: 130 End: 156 Full_Region: AACTCGGCAGATAAA CAGAGCGGAAC CATTT GTGCCGAACTG TTTATCATACCTCCT .................................................................................................................................CAGAGCGGAACCATTTGTGCCGAACTG................................................................................................................................................................................................... TransTerm Strand: - Conf: 50 HP_score: -2.1 Tail_Score: -4.03978 Start: 130 End: 156 Full_Region: aggaggtatgataaa cagttcggcac aaatg gttccgctctg tttatctgccgagtt .................................................................................................................................cagttcggcacaaatggttccgctctg................................................................................................................................................................................................... TransTerm Strand: + Conf: 77 HP_score: -7.5 Tail_Score: -4.07885 Start: 314 End: 332 Full_Region: TAATAATAGTGAGAG CAGCAAA AATAA TTTGCTG TTTTAAGGAGAAGTA .........................................................................................................................................................................................................................................................................................................................CAGCAAAAATAATTTGCTG................... Find igs database================================================ Query_seq: TDE2770:TDE2771|TDE2770:TDE2771:flagellar hook-length control protein FliK:hypothetical protein:<-->:2824508..2824858 351 atgaacctcnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnatgttacttcaataaattttcggcttatttttaagatgggtttaggaaaaaagtctatacaagctttaaattaagaattttaaagtttcttaaaaaaaattaccatatattacaaaaaatttgaataataatagtgagagcagcaaaaataatttgctgttttaaggagaagtataat Intra-Species Hit: Count: 1 Min: 174 Max: 351 Len: 178 Subject: NC_002967_TDE2770_TDE2771|flagellar hook-length control protein FliK:hypothetical protein|NEGATIVE:POSITIVE|[2824508,2824858]|351 HSP 1 e-value: 5.0E-82 bit: 305.0 Len: 178 Query Start:174 Query End:351 Subject Strand: POSITIVE Subject Start: 174 Subject End: 351 .............................................................................................................................................................................atgttacttcaataaattttcggcttatttttaagatgggtttaggaaaaaagtctatacaagctttaaattaagaattttaaagtttcttnnnnnnnnttaccatatattacaaaaaatttgaataataatagtgagagcagcaaaaataatttgctgttttaaggagaagtataat .............................................................................................................................................................................atgttacttcaataaattttcggcttatttttaagatgggtttaggaaaaaagtctatacaagctttaaattaagaattttaaagtttcttaaaaaaaattaccatatattacaaaaaatttgaataataatagtgagagcagcaaaaataatttgctgttttaaggagaagtataat Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUGUUACUUCAAUAAAUUUUCGGCUUAUUUUUAAGAUGGGUUUAGGAAAAAAGUCUAUACAAGCUUUAAAUUAAGAAUUUUAAAGUUUCUUAAAAAAAAUUACCAUAUAUUACAAAAAAUUUGAAUAAUAAUAGUGAGAGCAGCAAAAAUAAUUUGCUGUUUUAAGGAGAAGUAUAAU ....((((((.................(((((((((...((.((((.......)))).)).(((((((((........))))))))))))))))))......((...((((.(((.....))))))).........(((((((((((.....)))))))))))..)).)))))).... (-33.70) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUUAUACUUCUCCUUAAAACAGCAAAUUAUUUUUGCUGCUCUCACUAUUAUUAUUCAAAUUUUUUGUAAUAUAUGGUAAUUUUUUUUAAGAAACUUUAAAAUUCUUAAUUUAAAGCUUGUAUAGACUUUUUUCCUAAACCCAUCUUAAAAAUAAGCCGAAAAUUUAUUGAAGUAACAU ....((((((.........(((((((.....))))))).....(((((((((((...........)))))).))))).....(((((((((..(((((((........)))))))...((.(((.........))).))...))))))))).................)))))).... (-26.80) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 252 47 17 227 192 NC_002967:TDE1968|5end_cell_division_protein_FtsJ_1983092..1983322_NEGATIVE 250 159 116 169 132 NC_002967:TDE0466|5end_hypothetical_protein_518854..519084_NEGATIVE 232 65 22 157 115 NC_002967:TDE2786|5end_DNA_polymerase_III_subunit_alpha_2842672..2842902_NEGATIVE 219 56 13 165 124 NC_002967:TDE0119|5end_flagellar_protein_FliS_137498..137728_NEGATIVE 212 155 119 84 47 NC_002967:TDE0386|5end_ABC_transporter,_periplasmic_substrate-binding_protein_438321..438551_NEGATIVE 208 43 4 110 66 NC_002967:TDE2239|5end_hypothetical_protein_2277546..2277776_NEGATIVE 206 47 8 181 134 NC_002967:TDE1253|5end_hypothetical_protein_1286963..1287193_POSITIVE 203 47 5 143 97 NC_002967:TDE2117|5end_hypothetical_protein_2147806..2148036_POSITIVE 201 160 122 70 31 NC_002967:TDE0108|5end_hypothetical_protein_128399..128629_POSITIVE 199 162 132 184 150 NC_002967:TDE2608|5end_hypothetical_protein_2649275..2649505_POSITIVE 197 66 21 230 174 NC_002967:TDE1941|5end_hypothetical_protein_1959285..1959515_NEGATIVE 194 60 34 218 194 NC_002967:TDE0743|5end_thioredoxin_reductase_778718..778948_POSITIVE 194 91 52 84 48 NC_002967:TDE0311|5end_thymidylate_synthase_342816..343046_POSITIVE 192 41 17 227 206 NC_002967:TDE0884|5end_tRNA_(guanine-N(1)-)-methyltransferase_902221..902451_POSITIVE 192 44 6 170 129 NC_002967:TDE0777|5end_50S_ribosomal_protein_L14_811109..811339_POSITIVE 192 168 121 152 106 NC_002967:TDE0752|5end_hypothetical_protein_791353..791583_POSITIVE 191 55 14 191 149 NC_002967:TDE2620|5end_hypothetical_protein_2661538..2661768_POSITIVE 191 67 24 146 101 NC_002967:TDE1519|5end_hypothetical_protein_1565601..1565831_POSITIVE 191 166 127 88 50 NC_002967:TDE0304|5end_hypothetical_protein_333883..334113_POSITIVE 190 55 20 220 166 NC_002967:TDE2349|5end_hypothetical_protein_2385940..2386170_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 252 70 22 87 42 NC_002967:TDE2539|3end_hypothetical_protein_2564274..2564424_NEGATIVE 250 169 130 85 42 NC_002967:TDE2358|3end_hypothetical_protein_2393129..2393279_NEGATIVE 218 47 1 133 88 NC_002967:TDE2756|3end_bacterial_extracellular_solute-binding_protein,_family_5_2811898..2812048_NEGATIVE 212 159 117 50 14 NC_002967:TDE2396|3end_putative_inner_membrane_protein_translocase_component_YidC_2423650..2423800_NEGATIVE 210 46 5 58 18 NC_002967:TDE1290|3end_hypothetical_protein_1328648..1328798_POSITIVE 204 65 22 79 29 NC_002967:TDE1499|3end_adenylosuccinate_lyase,_putative_1546788..1546938_POSITIVE 197 66 21 79 23 NC_002967:TDE1943|3end_30S_ribosomal_protein_S4_1959436..1959586_NEGATIVE 196 56 22 98 65 NC_002967:TDE2660|3end_hypothetical_protein_2697158..2697308_NEGATIVE 195 55 18 37 1 NC_002967:TDE1939|3end_hypothetical_protein_1955435..1955585_POSITIVE 195 159 116 68 31 NC_002967:TDE0065|3end_hypothetical_protein_72822..72972_NEGATIVE 194 49 7 108 71 NC_002967:TDE1323|3end_hypothetical_protein_1360968..1361118_POSITIVE 192 44 6 151 110 NC_002967:TDE0776|3end_ribosomal_protein_S17_811170..811320_POSITIVE 191 55 14 147 105 NC_002967:TDE2619|3end_RNA_methyltransferase,_TrmA_family,_putative_2661574..2661724_POSITIVE 191 68 25 60 9 NC_002967:TDE2327|3end_ATP-dependent_Clp_protease,_ATP-binding_subunit_ClpB_2362048..2362198_NEGATIVE 190 55 20 107 53 NC_002967:TDE2350|3end_lipoprotein,_putative_2386053..2386203_NEGATIVE 189 146 102 76 28 NC_002967:TDE1198|3end_S-adenosyl-methyltransferase_MraW_1231419..1231569_POSITIVE 189 46 21 147 119 NC_002967:TDE0040|3end_AMP-binding_protein_45776..45926_NEGATIVE 187 80 35 64 11 NC_002967:TDE2433|3end_treponemal_membrane_protein,_putative_2463265..2463415_POSITIVE 187 61 22 95 59 NC_002967:TDE1844|3end_DNA_integrase_1873197..1873347_NEGATIVE 187 57 16 62 9 NC_002967:TDE1360|3end_xanthine/uracil_permease_family_protein_1400681..1400831_POSITIVE