Origin IGS: gattttaagattgtaatttaaatcgagatgccttgaagctgggcatttctaaaagtctaaccggttttttagagatgcccaaaaggctttgaggcattttgagttttttagcagtaatgtgccttgagctcaaagcctaaattttgtaggagactttt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aaaagtctcctacaaaatttaggctttgagctcaaggcacattactgctaaaaaactcaaaatgcctcaaagccttttgggcatctctaaaaaaccggttagacttttagaaatgcccagcttcaaggcatctcgatttaaattacaatcttaaaatc Mask Tandem Repeat Region ================================================ gattttaagattgtaatttaaatcgagatgccttgaagctgggcatttctaaaagtctaaccggttttttagagatgcccaaaaggctttgaggcattttgagttttttagcagtaatgtgccttgagctcaaagcctaaattttgtaggagactttt Find is-nt database================================================ Query_seq: TDE1072:TDE1073|TDE1072:TDE1073:lipoprotein, putative:oligopeptide/dipeptide ABC transporter, permease protein:->->:1103497..1103654 158 gattttaagattgtaatttaaatcgagatgccttgaagctgggcatttctaaaagtctaaccggttttttagagatgcccaaaaggctttgaggcattttgagttttttagcagtaatgtgccttgagctcaaagcctaaattttgtaggagactttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE1072:TDE1073|TDE1072:TDE1073:lipoprotein, putative:oligopeptide/dipeptide ABC transporter, permease protein:->->:1103497..1103654 158 gattttaagattgtaatttaaatcgagatgccttgaagctgggcatttctaaaagtctaaccggttttttagagatgcccaaaaggctttgaggcattttgagttttttagcagtaatgtgccttgagctcaaagcctaaattttgtaggagactttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE1072:TDE1073|TDE1072:TDE1073:lipoprotein, putative:oligopeptide/dipeptide ABC transporter, permease protein:->->:1103497..1103654 158 gattttaagattgtaatttaaatcgagatgccttgaagctgggcatttctaaaagtctaaccggttttttagagatgcccaaaaggctttgaggcattttgagttttttagcagtaatgtgccttgagctcaaagcctaaattttgtaggagactttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gattttaagattgtaatttaaatcgagatgccttgaagctgggcatttctaaaagtctaaccggttttttagagatgcccaaaaggctttgaggcattttgagttttttagcagtaatgtgccttgagctcaaagcctaaattttgtaggagactttt Predict ORF larger than 30AA ================================================ Protein_Len: 42 Strand: - Start: 8 End: 133 ....... S Q L K F R S A K F S P M E L L R V P K K S I G L L S Q P M K L K K A T I H R S S M ......................... gattttaagattgtaatttaaatcgagatgccttgaagctgggcatttctaaaagtctaaccggttttttagagatgcccaaaaggctttgaggcattttgagttttttagcagtaatgtgccttgagctcaaagcctaaattttgtaggagactttt 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================================================ gattttaagattgtaatttaaatcgagatgccttgaagctgggcatttctaaaagtctaaccggttttttagagatgcccaaaaggctttgaggcattttgagttttttagcagtaatgtgccttgagctcaaagcctaaattttgtaggagactttt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE1072:TDE1073|TDE1072:TDE1073:lipoprotein, putative:oligopeptide/dipeptide ABC transporter, permease protein:->->:1103497..1103654 158 gattttaagattgtaatttaaatcgagatgccttgaagctgggcatttctaaaagtctaaccggttttttagagatgcccaaaaggctttgaggcattttgagttttttagcagtaatgtgccttgagctcaaagcctaaattttgtaggagactttt Intra-Species Hit: Count: 1 Min: 1 Max: 158 Len: 158 Subject: NC_002967_TDE1072_TDE1073|lipoprotein, putative:oligopeptide/dipeptide ABC transporter, permease protein|POSITIVE:POSITIVE|[1103497,1103654]|158 HSP 1 e-value: 9.0E-85 bit: 313.0 Len: 158 Query Start:1 Query End:158 Subject Strand: POSITIVE Subject Start: 1 Subject End: 158 gattttaagattgtaatttaaatcgagatgccttgaagctgggcatttctaaaagtctaaccggttttttagagatgcccaaaaggctttgaggcattttgagttttttagcagtaatgtgccttgagctcaaagcctaaattttgtaggagactttt gattttaagattgtaatttaaatcgagatgccttgaagctgggcatttctaaaagtctaaccggttttttagagatgcccaaaaggctttgaggcattttgagttttttagcagtaatgtgccttgagctcaaagcctaaattttgtaggagactttt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAUUUUAAGAUUGUAAUUUAAAUCGAGAUGCCUUGAAGCUGGGCAUUUCUAAAAGUCUAACCGGUUUUUUAGAGAUGCCCAAAAGGCUUUGAGGCAUUUUGAGUUUUUUAGCAGUAAUGUGCCUUGAGCUCAAAGCCUAAAUUUUGUAGGAGACUUUU ((.((((((.............(((((((((((..((((((((((((((((((((.((....)).)))))))))))))))....)))))..)))))))))))........(((....)))..)))))).))....((((.......))))........ (-56.40) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAAGUCUCCUACAAAAUUUAGGCUUUGAGCUCAAGGCACAUUACUGCUAAAAAACUCAAAAUGCCUCAAAGCCUUUUGGGCAUCUCUAAAAAACCGGUUAGACUUUUAGAAAUGCCCAGCUUCAAGGCAUCUCGAUUUAAAUUACAAUCUUAAAAUC ..(((((.............((((((((((.....((((......))))......))))))..))))....(((((((((((((.(((((((............))))))).))))))))....))))).....)))))................... (-38.50) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 385 87 44 168 124 NC_002967:TDE1098|5end_hypothetical_protein_1133678..1133908_NEGATIVE 352 126 81 228 184 NC_002967:TDE1944|5end_hypothetical_protein_1960434..1960664_POSITIVE 336 95 55 46 2 NC_002967:TDE1278|5end_conserved_hypothetical_protein_TIGR01440_1312788..1313018_NEGATIVE 315 100 54 198 152 NC_002967:TDE1045|5end_hypothetical_protein_1073240..1073470_POSITIVE 310 99 54 77 31 NC_002967:TDE1689|5end_ABC_transporter,_ATP-binding_protein_1746565..1746795_NEGATIVE 306 150 111 102 59 NC_002967:TDE0970|5end_hypothetical_protein_994769..994999_POSITIVE 304 102 61 132 97 NC_002967:TDE1146|5end_hypothetical_protein_1185414..1185644_NEGATIVE 303 80 45 186 151 NC_002967:TDE0106|5end_hypothetical_protein_126546..126776_NEGATIVE 296 96 53 77 27 NC_002967:TDE0473|5end_heavy_metal_translocating_P-type_ATPase_528621..528851_POSITIVE 292 115 71 74 26 NC_002967:TDE2143|5end_penicillin-binding_protein_2178107..2178337_POSITIVE 292 80 34 213 165 NC_002967:TDE1919|5end_hypothetical_protein_1939890..1940120_NEGATIVE 286 95 56 168 119 NC_002967:TDE0596|5end_hypothetical_protein_636010..636240_NEGATIVE 281 48 5 159 118 NC_002967:TDE0808|5end_acetyltransferase,_GNAT_family_829650..829880_NEGATIVE 281 73 32 64 28 NC_002967:TDE0791|5end_DNA-directed_RNA_polymerase_alpha_subunit_817342..817572_POSITIVE 281 80 38 62 20 NC_002967:TDE0311|5end_thymidylate_synthase_342816..343046_POSITIVE 280 78 32 62 4 NC_002967:TDE0026|5end_TraB_family_protein_33016..33246_NEGATIVE 276 138 91 206 161 NC_002967:TDE0199|5end_hypothetical_protein_234708..234938_NEGATIVE 269 67 21 218 166 NC_002967:TDE2150|5end_hypothetical_protein_2188276..2188506_NEGATIVE 269 68 25 66 31 NC_002967:TDE1294|5end_phosphocarrier_protein_HPr_1332321..1332551_NEGATIVE 268 70 28 53 21 NC_002967:TDE2634|5end_hypothetical_protein_2674625..2674855_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 517 87 41 61 11 NC_002967:TDE1072|3end_lipoprotein,_putative_1103436..1103586_POSITIVE 479 89 41 98 50 NC_002967:TDE2206|3end_hypothetical_protein_2244921..2245071_NEGATIVE 385 87 44 110 66 NC_002967:TDE1099|3end_acetyltransferase,_GNAT_family_1133736..1133886_NEGATIVE 360 80 34 88 43 NC_002967:TDE1264|3end_hypothetical_protein_1298152..1298302_NEGATIVE 352 80 39 64 5 NC_002967:TDE1091|3end_hypothetical_protein_1123017..1123167_NEGATIVE 342 79 32 88 44 NC_002967:TDE2465|3end_hypothetical_protein_2489391..2489541_NEGATIVE 327 79 33 80 29 NC_002967:TDE2464|3end_hypothetical_protein_2489369..2489519_POSITIVE 326 80 33 70 9 NC_002967:TDE1090|3end_threonyl-tRNA_synthetase_1122943..1123093_POSITIVE 324 95 51 61 10 NC_002967:TDE0043|3end_TPR_domain_protein_51651..51801_POSITIVE 315 100 54 106 60 NC_002967:TDE1044|3end_hypothetical_protein_1073228..1073378_POSITIVE 310 99 54 59 13 NC_002967:TDE1690|3end_hypothetical_protein_1746583..1746733_NEGATIVE 303 80 45 91 56 NC_002967:TDE0107|3end_alpha-amylase_family_protein_126641..126791_NEGATIVE 287 96 54 50 1 NC_002967:TDE0472|3end_hypothetical_protein_528674..528824_POSITIVE 284 110 67 139 94 NC_002967:TDE1255|3end_hypothetical_protein_1288977..1289127_NEGATIVE 281 73 32 53 17 NC_002967:TDE0790|3end_30S_ribosomal_protein_S11_817411..817561_POSITIVE 280 78 32 75 17 NC_002967:TDE0027|3end_DHH_superfamily_protein,_subfamily_1_33003..33153_NEGATIVE 268 70 28 50 18 NC_002967:TDE2633|3end_hypothetical_protein_2674702..2674852_POSITIVE 268 79 31 54 18 NC_002967:TDE1880|3end_hypothetical_protein_1903058..1903208_POSITIVE 265 128 85 113 68 NC_002967:TDE1950|3end_membrane_lipoprotein_TmpC,_putative_1966191..1966341_NEGATIVE 264 95 51 91 28 NC_002967:TDE2692|3end_CTP_synthetase_2731111..2731261_POSITIVE