Origin IGS: agcttcctcctaaaaataaacgatgtttcatcaggcgacagcctgatgaaactcgaagttgaagcgagaggcactatttgagccgtgagcttcaaccgtccccctgtttttcattatatcacagattaaatgactttaaaagggagtgatgtaaaccgtgcagaacgcacgcatttt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aaaatgcgtgcgttctgcacggtttacatcactcccttttaaagtcatttaatctgtgatataatgaaaaacagggggacggttgaagctcacggctcaaatagtgcctctcgcttcaacttcgagtttcatcaggctgtcgcctgatgaaacatcgtttatttttaggaggaagct Mask Tandem Repeat Region ================================================ agcttcctcctaaaaataaacgatgtttcatcaggcgacagcctgatgaaactcgaagttgaagcgagaggcactatttgagccgtgagcttcaaccgtccccctgtttttcattatatcacagattaaatgactttaaaagggagtgatgtaaaccgtgcagaacgcacgcatttt Find is-nt database================================================ Query_seq: TDE0736:TDE0737|TDE0736:TDE0737:hypothetical protein:hypothetical protein:<-<-:775321..775497 177 agcttcctcctaaaaataaacgatgtttcatcaggcgacagcctgatgaaactcgaagttgaagcgagaggcactatttgagccgtgagcttcaaccgtccccctgtttttcattatatcacagattaaatgactttaaaagggagtgatgtaaaccgtgcagaacgcacgcatttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE0736:TDE0737|TDE0736:TDE0737:hypothetical protein:hypothetical protein:<-<-:775321..775497 177 agcttcctcctaaaaataaacgatgtttcatcaggcgacagcctgatgaaactcgaagttgaagcgagaggcactatttgagccgtgagcttcaaccgtccccctgtttttcattatatcacagattaaatgactttaaaagggagtgatgtaaaccgtgcagaacgcacgcatttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE0736:TDE0737|TDE0736:TDE0737:hypothetical protein:hypothetical protein:<-<-:775321..775497 177 agcttcctcctaaaaataaacgatgtttcatcaggcgacagcctgatgaaactcgaagttgaagcgagaggcactatttgagccgtgagcttcaaccgtccccctgtttttcattatatcacagattaaatgactttaaaagggagtgatgtaaaccgtgcagaacgcacgcatttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 agcttcctcctaaaaataaacgatgtttcatcaggcgacagcctgatgaaactcgaagttgaagcgagaggcactatttgagccgtgagcttcaaccgtccccctgtttttcattatatcacagattaaatgactttaaaagggagtgatgtaaaccgtgcagaacgcacgcatttt Predict ORF larger than 30AA ================================================ Protein_Len: 31 Strand: - Start: 34 End: 126 ................................. A V A Q H F E F N F R S A S N S G H A E V T G R N K M I D C M ................................................... Protein_Len: 31 Strand: - Start: 3 End: 95 .. K R R F I F S T E D P S L R I F S S T S A L P V I Q A T L K M .................................................................................. agcttcctcctaaaaataaacgatgtttcatcaggcgacagcctgatgaaactcgaagttgaagcgagaggcactatttgagccgtgagcttcaaccgtccccctgtttttcattatatcacagattaaatgactttaaaagggagtgatgtaaaccgtgcagaacgcacgcatttt 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: 85 Start: 113 End: 142 ................................................................................................................CTTTTAAAGTCATTTAATCTGTGATATAAT................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ agcttcctcctaaaaataaacgatgtttcatcaggcgacagcctgatgaaactcgaagttgaagcgagaggcactatttgagccgtgagcttcaaccgtccccctgtttttcattatatcacagattaaatgactttaaaagggagtgatgtaaaccgtgcagaacgcacgcatttt Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 100 HP_score: -16.7 Tail_Score: -4.85782 Start: 21 End: 55 Full_Region: ctctcgcttcaactt cgagtttcatcaggc tgtc gcctgatgaaacatcg tttatttttaggagg ....................cgagtttcatcaggctgtcgcctgatgaaacatcg.......................................................................................................................... TransTerm Strand: - Conf: 100 HP_score: -17.2 Tail_Score: -2.57916 Start: 25 End: 52 Full_Region: tcgcttcaacttcga gtttcatcaggc tgtc gcctgatgaaac atcgtttatttttag ........................gtttcatcaggctgtcgcctgatgaaac............................................................................................................................. Find igs database================================================ Query_seq: TDE0736:TDE0737|TDE0736:TDE0737:hypothetical protein:hypothetical protein:<-<-:775321..775497 177 agcttcctcctaaaaataaacgatgtttcatcaggcgacagcctgatgaaactcgaagttgaagcgagaggcactatttgagccgtgagcttcaaccgtccccctgtttttcattatatcacagattaaatgactttaaaagggagtgatgtaaaccgtgcagaacgcacgcatttt Intra-Species Hit: Count: 1 Min: 1 Max: 177 Len: 177 Subject: NC_002967_TDE0736_TDE0737|hypothetical protein:hypothetical protein|NEGATIVE:NEGATIVE|[775321,775497]|177 HSP 1 e-value: 5.0E-96 bit: 351.0 Len: 177 Query Start:1 Query End:177 Subject Strand: POSITIVE Subject Start: 1 Subject End: 177 agcttcctcctaaaaataaacgatgtttcatcaggcgacagcctgatgaaactcgaagttgaagcgagaggcactatttgagccgtgagcttcaaccgtccccctgtttttcattatatcacagattaaatgactttaaaagggagtgatgtaaaccgtgcagaacgcacgcatttt agcttcctcctaaaaataaacgatgtttcatcaggcgacagcctgatgaaactcgaagttgaagcgagaggcactatttgagccgtgagcttcaaccgtccccctgtttttcattatatcacagattaaatgactttaaaagggagtgatgtaaaccgtgcagaacgcacgcatttt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGCUUCCUCCUAAAAAUAAACGAUGUUUCAUCAGGCGACAGCCUGAUGAAACUCGAAGUUGAAGCGAGAGGCACUAUUUGAGCCGUGAGCUUCAACCGUCCCCCUGUUUUUCAUUAUAUCACAGAUUAAAUGACUUUAAAAGGGAGUGAUGUAAACCGUGCAGAACGCACGCAUUUU .((.(((((((.((((((..(((.((((((((((((....)))))))))))))))..((((((((....(((.(.....).)))....))))))))........))))))(((((..(((...)))..)))))........))))).)).))....(((((.....)))))...... (-59.90) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAAUGCGUGCGUUCUGCACGGUUUACAUCACUCCCUUUUAAAGUCAUUUAAUCUGUGAUAUAAUGAAAAACAGGGGGACGGUUGAAGCUCACGGCUCAAAUAGUGCCUCUCGCUUCAACUUCGAGUUUCAUCAGGCUGUCGCCUGAUGAAACAUCGUUUAUUUUUAGGAGGAAGCU ......(((((.....)))))..........((.((((((((((((......(((((.............)))))..))).((((((((....(((.(.....).)))....))))))))..(((((((((((((((....)))))))))))).)))......))))))))).)).. (-58.92) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 1032 110 61 201 152 NC_002967:TDE0736|5end_hypothetical_protein_775230..775460_NEGATIVE 407 97 51 115 64 NC_002967:TDE1694|5end_hypothetical_protein_1749366..1749596_NEGATIVE 402 97 51 94 43 NC_002967:TDE2019|5end_hypothetical_protein_2040719..2040949_NEGATIVE 381 96 57 67 26 NC_002967:TDE2543|5end_hypothetical_protein_2570950..2571180_NEGATIVE 381 96 57 191 150 NC_002967:TDE2542|5end_antigen,_putative_2570826..2571056_NEGATIVE 377 95 54 185 137 NC_002967:TDE1613|5end_hypothetical_protein_1661625..1661855_POSITIVE 376 90 53 230 189 NC_002967:TDE1769|5end_hypothetical_protein_1814377..1814607_NEGATIVE 353 90 41 132 83 NC_002967:TDE1325|5end_hypothetical_protein_1361721..1361951_NEGATIVE 339 99 51 91 34 NC_002967:TDE1513|5end_hypothetical_protein_1560484..1560714_POSITIVE 338 77 35 231 183 NC_002967:TDE1693|5end_hypothetical_protein_1749226..1749456_NEGATIVE 337 108 63 227 170 NC_002967:TDE2701|5end_hypothetical_protein_2745689..2745919_POSITIVE 328 85 41 79 29 NC_002967:TDE1750|5end_hypothetical_protein_1803825..1804055_NEGATIVE 327 100 54 67 19 NC_002967:TDE1782|5end_hypothetical_protein_1823417..1823647_NEGATIVE 327 100 54 224 176 NC_002967:TDE1781|5end_hypothetical_protein_1823260..1823490_NEGATIVE 325 99 57 194 149 NC_002967:TDE2309|5end_sigma-54_dependent_transcriptional_regulator,_putative_2348099..2348329_NEGATIVE 325 102 63 64 22 NC_002967:TDE0172|5end_undecaprenyl_pyrophosphate_phosphatase_203136..203366_POSITIVE 321 85 41 147 105 NC_002967:TDE0319|5end_hypothetical_protein_351460..351690_POSITIVE 314 49 2 176 132 NC_002967:TDE0957|5end_glycerophosphoryl_diester_phosphodiesterase_family_protein_980252..980482_POSITIVE 311 108 73 65 27 NC_002967:TDE2485|5end_hypothetical_protein_2509123..2509353_NEGATIVE 308 114 71 108 62 NC_002967:TDE0058|5end_hypothetical_protein_66986..67216_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 546 145 101 76 31 NC_002967:TDE0735|3end_hypothetical_protein_774746..774896_NEGATIVE 402 97 51 79 28 NC_002967:TDE2020|3end_YD_repeat_protein_2040734..2040884_NEGATIVE 381 96 57 82 41 NC_002967:TDE2544|3end_hypothetical_protein_2570935..2571085_NEGATIVE 370 90 41 53 3 NC_002967:TDE2396|3end_putative_inner_membrane_protein_translocase_component_YidC_2423650..2423800_NEGATIVE 353 90 41 64 15 NC_002967:TDE1327|3end_hypothetical_protein_1361789..1361939_NEGATIVE 339 99 51 78 21 NC_002967:TDE1512|3end_hypothetical_protein_1560551..1560701_POSITIVE 328 85 41 73 23 NC_002967:TDE1751|3end_ribosomal_protein_L21_1803831..1803981_NEGATIVE 328 63 32 31 1 NC_002967:TDE0741|3end_hypothetical_protein_776185..776335_NEGATIVE 323 69 21 71 19 NC_002967:TDE2735|3end_surface_antigen,_putative_2791616..2791766_POSITIVE 322 75 35 73 30 NC_002967:TDE0340|3end_fructose-bisphosphate_aldolase_379606..379756_POSITIVE 321 85 41 83 41 NC_002967:TDE0318|3end_hypothetical_protein_351476..351626_POSITIVE 307 108 63 123 80 NC_002967:TDE0133|3end_transcriptional_regulator,_GntR_family_153202..153352_POSITIVE 305 72 31 135 91 NC_002967:TDE0616|3end_hypothetical_protein_650079..650229_POSITIVE 301 90 41 67 16 NC_002967:TDE1916|3end_glycerol_kinase_1933277..1933427_NEGATIVE 301 70 34 145 112 NC_002967:TDE0038|3end_3-oxoacyl-(acyl-carrier-protein)_synthase_II_43036..43186_NEGATIVE 300 75 33 91 25 NC_002967:TDE1771|3end_hypothetical_protein_1814579..1814729_NEGATIVE 300 106 68 140 104 NC_002967:TDE0956|3end_hypothetical_protein_980330..980480_POSITIVE 296 109 61 111 49 NC_002967:TDE2561|3end_ABC_transporter,_ATP-binding_protein_2588977..2589127_POSITIVE 294 70 21 121 71 NC_002967:TDE2714|3end_hypothetical_protein_2770627..2770777_NEGATIVE 292 88 42 73 26 NC_002967:TDE2347|3end_30S_ribosomal_protein_S2_2383503..2383653_NEGATIVE