Origin IGS: atttttaggattattttacttgacaattgcaataattatgttagaattatattaagagggagatgtgagtatccgtcttaggcggttcaaagcacaactcccataaggggcatgacttcatgcccctttttagtttttaataagcctgcctcggattagacctcagtttttacaccttattt .........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 aaataaggtgtaaaaactgaggtctaatccgaggcaggcttattaaaaactaaaaaggggcatgaagtcatgccccttatgggagttgtgctttgaaccgcctaagacggatactcacatctccctcttaatataattctaacataattattgcaattgtcaagtaaaataatcctaaaaat Mask Tandem Repeat Region ================================================ atttttaggattattttacttgacaattgcaataattatgttagaattatattaagagggagatgtgagtatccgtcttaggcggttcaaagcacaactcccataaggggcatgacttcatgcccctttttagtttttaataagcctgcctcggattagacctcagtttttacaccttattt Find is-nt database================================================ Query_seq: TDE2227:TDE2228|TDE2227:TDE2228:hypothetical protein:aminoacyl-histidine dipeptidase, putative:-><-:2267195..2267376 182 atttttaggattattttacttgacaattgcaataattatgttagaattatattaagagggagatgtgagtatccgtcttaggcggttcaaagcacaactcccataaggggcatgacttcatgcccctttttagtttttaataagcctgcctcggattagacctcagtttttacaccttattt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE2227:TDE2228|TDE2227:TDE2228:hypothetical protein:aminoacyl-histidine dipeptidase, putative:-><-:2267195..2267376 182 atttttaggattattttacttgacaattgcaataattatgttagaattatattaagagggagatgtgagtatccgtcttaggcggttcaaagcacaactcccataaggggcatgacttcatgcccctttttagtttttaataagcctgcctcggattagacctcagtttttacaccttattt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE2227:TDE2228|TDE2227:TDE2228:hypothetical protein:aminoacyl-histidine dipeptidase, putative:-><-:2267195..2267376 182 atttttaggattattttacttgacaattgcaataattatgttagaattatattaagagggagatgtgagtatccgtcttaggcggttcaaagcacaactcccataaggggcatgacttcatgcccctttttagtttttaataagcctgcctcggattagacctcagtttttacaccttattt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 atttttaggattattttacttgacaattgcaataattatgttagaattatattaagagggagatgtgagtatccgtcttaggcggttcaaagcacaactcccataaggggcatgacttcatgcccctttttagtttttaataagcctgcctcggattagacctcagtttttacaccttattt Predict ORF larger than 30AA ================================================ atttttaggattattttacttgacaattgcaataattatgttagaattatattaagagggagatgtgagtatccgtcttaggcggttcaaagcacaactcccataaggggcatgacttcatgcccctttttagtttttaataagcctgcctcggattagacctcagtttttacaccttattt 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================================================ atttttaggattattttacttgacaattgcaataattatgttagaattatattaagagggagatgtgagtatccgtcttaggcggttcaaagcacaactcccataaggggcatgacttcatgcccctttttagtttttaataagcctgcctcggattagacctcagtttttacaccttattt Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 100 HP_score: -13.6 Tail_Score: -5.1971 Start: 107 End: 126 Full_Region: GCACAACTCCCATAA GGGGCATG ACTT CATGCCCC TTTTTAGTTTTTAAT ..........................................................................................................GGGGCATGACTTCATGCCCC........................................................ TransTerm Strand: - Conf: 100 HP_score: -13.6 Tail_Score: -3.34233 Start: 107 End: 126 Full_Region: attaaaaactaaaaa ggggcatg aagt catgcccc ttatgggagttgtgc ..........................................................................................................ggggcatgaagtcatgcccc........................................................ Find igs database================================================ Query_seq: TDE2227:TDE2228|TDE2227:TDE2228:hypothetical protein:aminoacyl-histidine dipeptidase, putative:-><-:2267195..2267376 182 atttttaggattattttacttgacaattgcaataattatgttagaattatattaagagggagatgtgagtatccgtcttaggcggttcaaagcacaactcccataaggggcatgacttcatgcccctttttagtttttaataagcctgcctcggattagacctcagtttttacaccttattt Intra-Species Hit: Count: 1 Min: 1 Max: 182 Len: 182 Subject: NC_002967_TDE2227_TDE2228|hypothetical protein:aminoacyl-histidine dipeptidase, putative|POSITIVE:NEGATIVE|[2267195,2267376]|182 HSP 1 e-value: 5.0E-99 bit: 361.0 Len: 182 Query Start:1 Query End:182 Subject Strand: POSITIVE Subject Start: 1 Subject End: 182 atttttaggattattttacttgacaattgcaataattatgttagaattatattaagagggagatgtgagtatccgtcttaggcggttcaaagcacaactcccataaggggcatgacttcatgcccctttttagtttttaataagcctgcctcggattagacctcagtttttacaccttattt atttttaggattattttacttgacaattgcaataattatgttagaattatattaagagggagatgtgagtatccgtcttaggcggttcaaagcacaactcccataaggggcatgacttcatgcccctttttagtttttaataagcctgcctcggattagacctcagtttttacaccttattt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUUUUUAGGAUUAUUUUACUUGACAAUUGCAAUAAUUAUGUUAGAAUUAUAUUAAGAGGGAGAUGUGAGUAUCCGUCUUAGGCGGUUCAAAGCACAACUCCCAUAAGGGGCAUGACUUCAUGCCCCUUUUUAGUUUUUAAUAAGCCUGCCUCGGAUUAGACCUCAGUUUUUACACCUUAUUU ......(((...................(((....((((...(((((((........(((((.((((.....((((.....)))).......)))).)))))..((((((((((....))))))))))..)))))))..))))...)))...((......))............)))..... (-47.80) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAUAAGGUGUAAAAACUGAGGUCUAAUCCGAGGCAGGCUUAUUAAAAACUAAAAAGGGGCAUGAAGUCAUGCCCCUUAUGGGAGUUGUGCUUUGAACCGCCUAAGACGGAUACUCACAUCUCCCUCUUAAUAUAAUUCUAACAUAAUUAUUGCAAUUGUCAAGUAAAAUAAUCCUAAAAAU .....(((.......(((..((......))..((((.((..((((.........((((((((((....))))))))))..(((((.((((.......(((.......))).....)))).)))))...................))))....))...)))).)))........)))...... (-43.26) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 315 100 55 154 109 NC_002967:TDE2735|5end_surface_antigen,_putative_2790154..2790384_POSITIVE 296 120 72 77 36 NC_002967:TDE0317|5end_hypothetical_protein_350656..350886_POSITIVE 295 124 81 102 50 NC_002967:TDE2715|5end_hypothetical_protein_2772668..2772898_POSITIVE 291 128 89 168 126 NC_002967:TDE2736|5end_hypothetical_protein_2791812..2792042_NEGATIVE 290 165 122 105 61 NC_002967:TDE0606|5end_ParB_family_protein_644132..644362_NEGATIVE 288 149 115 36 1 NC_002967:TDE1763|5end_hypothetical_protein_1811205..1811435_NEGATIVE 286 124 83 116 77 NC_002967:TDE2326|5end_cobyric_acid_synthase_CobQ,_putative_2361087..2361317_POSITIVE 286 138 99 39 6 NC_002967:TDE2286|5end_MazG_family_protein_2323354..2323584_POSITIVE 285 113 71 91 47 NC_002967:TDE1451|5end_hypothetical_protein_1498968..1499198_NEGATIVE 283 92 56 71 33 NC_002967:TDE2451|5end_S-adenosylmethionine:tRNA_ribosyltransferase-isomerase_2479832..2480062_POSITIVE 283 103 72 47 8 NC_002967:TDE1693|5end_hypothetical_protein_1749226..1749456_NEGATIVE 282 115 74 53 10 NC_002967:TDE1657|5end_transcription_antitermination_protein_NusB_1707640..1707870_NEGATIVE 280 97 55 83 48 NC_002967:TDE2722|5end_carhohydrate_kinase,_FGGY_family_2780874..2781104_NEGATIVE 277 166 121 96 38 NC_002967:TDE2153|5end_hypothetical_protein_2189573..2189803_NEGATIVE 275 94 54 90 51 NC_002967:TDE2357|5end_iron_compound_ABC_transporter,_permease_protein_2392038..2392268_POSITIVE 273 110 61 208 144 NC_002967:TDE0722|5end_lipoprotein,_putative_758519..758749_POSITIVE 272 114 73 211 174 NC_002967:TDE2438|5end_hypothetical_protein_2469257..2469487_NEGATIVE 271 118 71 198 149 NC_002967:TDE1129|5end_lipoprotein,_putative_1161730..1161960_POSITIVE 270 155 112 58 9 NC_002967:TDE0294|5end_TrkA_domain_protein_324210..324440_NEGATIVE 269 93 67 29 1 NC_002967:TDE2550|5end_hypothetical_protein_2576215..2576445_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 313 119 71 59 8 NC_002967:TDE0740|3end_hypothetical_protein_776204..776354_POSITIVE 298 88 44 146 104 NC_002967:TDE2081|3end_hypothetical_protein_2112529..2112679_POSITIVE 290 165 122 112 68 NC_002967:TDE0607|3end_ParA_family_ATPase_644125..644275_NEGATIVE 290 119 72 132 69 NC_002967:TDE0049|3end_hypothetical_protein_58199..58349_NEGATIVE 288 150 101 60 17 NC_002967:TDE2682|3end_hypothetical_protein_2721388..2721538_NEGATIVE 287 93 57 32 1 NC_002967:TDE2551|3end_hypothetical_protein_2576212..2576362_NEGATIVE 286 124 83 126 87 NC_002967:TDE2325|3end_hypothetical_protein_2361177..2361327_POSITIVE 286 87 54 54 17 NC_002967:TDE1803|3end_hypothetical_protein_1838395..1838545_NEGATIVE 283 92 56 46 8 NC_002967:TDE2450|3end_ankyrin_repeat_protein_2479887..2480037_POSITIVE 283 103 72 50 11 NC_002967:TDE1694|3end_hypothetical_protein_1749223..1749373_NEGATIVE 282 124 82 67 10 NC_002967:TDE0065|3end_hypothetical_protein_72822..72972_NEGATIVE 280 97 55 86 51 NC_002967:TDE2723|3end_phosphoribosylpyrophosphate_synthetase_2780871..2781021_NEGATIVE 280 124 82 70 12 NC_002967:TDE0591|3end_acetyl-CoA_carboxylase,_biotin_carboxylase_630033..630183_NEGATIVE 278 93 56 66 21 NC_002967:TDE1613|3end_hypothetical_protein_1662319..1662469_POSITIVE 277 166 121 94 36 NC_002967:TDE2154|3end_50S_ribosomal_protein_L20_2189575..2189725_NEGATIVE 277 130 81 110 51 NC_002967:TDE1914|3end_Holliday_junction_DNA_helicase_RuvB_1930889..1931039_NEGATIVE 275 94 54 70 31 NC_002967:TDE2356|3end_iron_compound_ABC_transporter,_periplasmic_iron_compound-binding_protein,_putative_2392098..2392248_POSITIVE 265 123 81 113 66 NC_002967:TDE2622|3end_ABC_transporter,_ATP-binding_protein_2662178..2662328_NEGATIVE 264 124 81 71 29 NC_002967:TDE1546|3end_hypothetical_protein_1591204..1591354_POSITIVE 261 149 102 74 37 NC_002967:TDE0792|3end_ribosomal_protein_L17_819006..819156_POSITIVE