Origin IGS: tcttttataaaaggggtgctgaggttctatacttcgcttttgctaaactccttgtccgactttgagcttcgagttttaggcggtgcacgcactgcctaaaacatctcaagaatggaaccaccgctgtttaccaatttaactttccgcctcaccctattgacaaatttaaaatatagctcaaaatacaataatgagtaaa .........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 tttactcattattgtattttgagctatattttaaatttgtcaatagggtgaggcggaaagttaaattggtaaacagcggtggttccattcttgagatgttttaggcagtgcgtgcaccgcctaaaactcgaagctcaaagtcggacaaggagtttagcaaaagcgaagtatagaacctcagcaccccttttataaaaga Mask Tandem Repeat Region ================================================ tcttttataaaaggggtgctgaggttctatacttcgcttttgctaaactccttgtccgactttgagcttcgagttttaggcggtgcacgcactgcctaaaacatctcaagaatggaaccaccgctgtttaccaatttaactttccgcctcaccctattgacaaatttaaaatatagctcaaaatacaataatgagtaaa Find is-nt database================================================ Query_seq: TDE2142:TDE2143|TDE2142:TDE2143:methyl-accepting chemotaxis protein:penicillin-binding protein:->->:2178048..2178246 199 tcttttataaaaggggtgctgaggttctatacttcgcttttgctaaactccttgtccgactttgagcttcgagttttaggcggtgcacgcactgcctaaaacatctcaagaatggaaccaccgctgtttaccaatttaactttccgcctcaccctattgacaaatttaaaatatagctcaaaatacaataatgagtaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE2142:TDE2143|TDE2142:TDE2143:methyl-accepting chemotaxis protein:penicillin-binding protein:->->:2178048..2178246 199 tcttttataaaaggggtgctgaggttctatacttcgcttttgctaaactccttgtccgactttgagcttcgagttttaggcggtgcacgcactgcctaaaacatctcaagaatggaaccaccgctgtttaccaatttaactttccgcctcaccctattgacaaatttaaaatatagctcaaaatacaataatgagtaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE2142:TDE2143|TDE2142:TDE2143:methyl-accepting chemotaxis protein:penicillin-binding protein:->->:2178048..2178246 199 tcttttataaaaggggtgctgaggttctatacttcgcttttgctaaactccttgtccgactttgagcttcgagttttaggcggtgcacgcactgcctaaaacatctcaagaatggaaccaccgctgtttaccaatttaactttccgcctcaccctattgacaaatttaaaatatagctcaaaatacaataatgagtaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tcttttataaaaggggtgctgaggttctatacttcgcttttgctaaactccttgtccgactttgagcttcgagttttaggcggtgcacgcactgcctaaaacatctcaagaatggaaccaccgctgtttaccaatttaactttccgcctcaccctattgacaaatttaaaatatagctcaaaatacaataatgagtaaa Predict ORF larger than 30AA ================================================ Protein_Len: 30 Strand: + Start: 7 End: 96 ...... M K G V L R F Y T S L L L N S L S D F E L R V L G G A R T A ....................................................................................................... Protein_Len: 32 Strand: + Start: 103 End: 195 ...................................................................................................... M S R M E P P L F T N L T F R L T L L T N L K Y S S K Y N N E * .... Protein_Len: 30 Strand: - Start: 99 End: 188 .................................................................................................. F M E L I S G G S N V L K V K R R V R N V F K F Y L E F Y M ........... Protein_Len: 38 Strand: - Start: 8 End: 121 ....... L L P A S T R Y K A K A L S R T R S Q A E L K L R H V C Q R F C R L F P V M .............................................................................. tcttttataaaaggggtgctgaggttctatacttcgcttttgctaaactccttgtccgactttgagcttcgagttttaggcggtgcacgcactgcctaaaacatctcaagaatggaaccaccgctgtttaccaatttaactttccgcctcaccctattgacaaatttaaaatatagctcaaaatacaataatgagtaaa 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================================================ tcttttataaaaggggtgctgaggttctatacttcgcttttgctaaactccttgtccgactttgagcttcgagttttaggcggtgcacgcactgcctaaaacatctcaagaatggaaccaccgctgtttaccaatttaactttccgcctcaccctattgacaaatttaaaatatagctcaaaatacaataatgagtaaa Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE2142:TDE2143|TDE2142:TDE2143:methyl-accepting chemotaxis protein:penicillin-binding protein:->->:2178048..2178246 199 tcttttataaaaggggtgctgaggttctatacttcgcttttgctaaactccttgtccgactttgagcttcgagttttaggcggtgcacgcactgcctaaaacatctcaagaatggaaccaccgctgtttaccaatttaactttccgcctcaccctattgacaaatttaaaatatagctcaaaatacaataatgagtaaa Intra-Species Hit: Count: 1 Min: 1 Max: 199 Len: 199 Subject: NC_002967_TDE2142_TDE2143|methyl-accepting chemotaxis protein:penicillin-binding protein|POSITIVE:POSITIVE|[2178048,2178246]|199 HSP 1 e-value: 1.0E-109 bit: 394.0 Len: 199 Query Start:1 Query End:199 Subject Strand: POSITIVE Subject Start: 1 Subject End: 199 tcttttataaaaggggtgctgaggttctatacttcgcttttgctaaactccttgtccgactttgagcttcgagttttaggcggtgcacgcactgcctaaaacatctcaagaatggaaccaccgctgtttaccaatttaactttccgcctcaccctattgacaaatttaaaatatagctcaaaatacaataatgagtaaa tcttttataaaaggggtgctgaggttctatacttcgcttttgctaaactccttgtccgactttgagcttcgagttttaggcggtgcacgcactgcctaaaacatctcaagaatggaaccaccgctgtttaccaatttaactttccgcctcaccctattgacaaatttaaaatatagctcaaaatacaataatgagtaaa Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCUUUUAUAAAAGGGGUGCUGAGGUUCUAUACUUCGCUUUUGCUAAACUCCUUGUCCGACUUUGAGCUUCGAGUUUUAGGCGGUGCACGCACUGCCUAAAACAUCUCAAGAAUGGAACCACCGCUGUUUACCAAUUUAACUUUCCGCCUCACCCUAUUGACAAAUUUAAAAUAUAGCUCAAAAUACAAUAAUGAGUAAA ............((((((..(((((.....)))))....(((.(((((......((((..((((((......(((((((((((((....)))))))))))))..))))))..)))).........))))).)))...............))))))....................(((((...........)))))... (-48.96) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUACUCAUUAUUGUAUUUUGAGCUAUAUUUUAAAUUUGUCAAUAGGGUGAGGCGGAAAGUUAAAUUGGUAAACAGCGGUGGUUCCAUUCUUGAGAUGUUUUAGGCAGUGCGUGCACCGCCUAAAACUCGAAGCUCAAAGUCGGACAAGGAGUUUAGCAAAAGCGAAGUAUAGAACCUCAGCACCCCUUUUAUAAAAGA ....((((...........))))............(((((.((..(((((..(.((.........(((.(((((..(....((((.(((.(((((..(((((((((.(((....))).)))))))))......)))))))).))))..)..))))).)))...(........)..)).)..)))))..)).)))))... (-46.80) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 360 105 70 43 10 NC_002967:TDE0740|5end_hypothetical_protein_775987..776217_POSITIVE 331 58 14 124 71 NC_002967:TDE2603|5end_DNA_mismatch_repair_protein_2641476..2641706_POSITIVE 328 95 56 192 146 NC_002967:TDE1604|5end_ABC_transporter,_permease_protein,_putative_1655533..1655763_NEGATIVE 323 95 58 37 1 NC_002967:TDE2425|5end_50S_ribosomal_protein_L11_2455150..2455380_NEGATIVE 321 96 52 95 39 NC_002967:TDE1362|5end_hypothetical_protein_1400992..1401222_POSITIVE 320 87 49 208 169 NC_002967:TDE1612|5end_phosphoribosyl_transferase_domain_protein_1660549..1660779_POSITIVE 319 100 56 54 1 NC_002967:TDE0138|5end_alkyldihydroxyacetonephosphate_synthase,_putative_158221..158451_POSITIVE 315 97 56 186 146 NC_002967:TDE0589|5end_acetyl-CoA_carboxylase,_carboxyl_transferase,_alpha_subunit_629044..629274_NEGATIVE 315 89 49 231 191 NC_002967:TDE0178|5end_methyl-accepting_chemotaxis_protein_212628..212858_NEGATIVE 312 100 52 137 82 NC_002967:TDE2521|5end_hypothetical_protein_2548074..2548304_NEGATIVE 312 97 57 227 192 NC_002967:TDE1309|5end_modulator_of_DNA_gyrase_family_protein_1344535..1344765_POSITIVE 311 95 52 209 169 NC_002967:TDE1345|5end_DNA_primase_1383439..1383669_POSITIVE 311 60 12 120 71 NC_002967:TDE0773|5end_30S_ribosomal_protein_S3_809443..809673_POSITIVE 310 96 51 226 174 NC_002967:TDE2259|5end_hypothetical_protein_2297237..2297467_NEGATIVE 309 90 48 153 98 NC_002967:TDE0118|5end_hypothetical_protein_137047..137277_NEGATIVE 308 85 52 195 160 NC_002967:TDE2646|5end_ABC_transporter,_ATP-binding_protein,_putative_2685348..2685578_POSITIVE 308 133 94 215 181 NC_002967:TDE1095|5end_alanine_racemase_1129826..1130056_POSITIVE 308 98 56 60 9 NC_002967:TDE0351|5end_L-lactate_dehydrogenase_395998..396228_NEGATIVE 307 97 51 75 31 NC_002967:TDE1914|5end_Holliday_junction_DNA_helicase_RuvB_1931920..1932150_NEGATIVE 307 60 12 186 135 NC_002967:TDE1415|5end_nucleotidyl_transferase/aminotransferase,_class_V_1457941..1458171_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 382 130 91 146 103 NC_002967:TDE2238|3end_hypothetical_protein_2276545..2276695_POSITIVE 373 109 61 65 9 NC_002967:TDE2735|3end_surface_antigen,_putative_2791616..2791766_POSITIVE 367 105 61 46 9 NC_002967:TDE2736|3end_hypothetical_protein_2791702..2791852_NEGATIVE 345 95 51 71 20 NC_002967:TDE2714|3end_hypothetical_protein_2770627..2770777_NEGATIVE 331 58 14 131 78 NC_002967:TDE2602|3end_outer_membrane_protein,_putative_2641563..2641713_POSITIVE 328 90 41 81 32 NC_002967:TDE1770|3end_hypothetical_protein_1814468..1814618_POSITIVE 321 96 52 129 73 NC_002967:TDE1361|3end_hypothetical_protein_1401106..1401256_POSITIVE 315 89 49 88 48 NC_002967:TDE0179|3end_hypothetical_protein_212771..212921_NEGATIVE 312 80 31 74 24 NC_002967:TDE2719|3end_hypothetical_protein_2777015..2777165_POSITIVE 311 60 12 117 68 NC_002967:TDE0772|3end_50S_ribosomal_protein_L22_809520..809670_POSITIVE 309 90 48 142 87 NC_002967:TDE0119|3end_flagellar_protein_FliS_137058..137208_NEGATIVE 307 97 51 67 23 NC_002967:TDE1915|3end_alcohol_dehydrogenase,_iron-containing_1931928..1932078_NEGATIVE 305 95 64 40 8 NC_002967:TDE1344|3end_hypothetical_protein_1383350..1383500_POSITIVE 296 92 54 43 14 NC_002967:TDE2543|3end_hypothetical_protein_2570753..2570903_NEGATIVE 296 67 21 106 55 NC_002967:TDE0860|3end_ribosomal_small_subunit_pseudouridine_synthase_A_881840..881990_POSITIVE 295 127 91 66 22 NC_002967:TDE2547|3end_hypothetical_protein_2573184..2573334_POSITIVE 293 107 69 98 50 NC_002967:TDE0992|3end_5-formyltetrahydrofolate_cyclo-ligase_family_protein_1018321..1018471_NEGATIVE 291 60 12 90 31 NC_002967:TDE2582|3end_GGDEF_domain_protein_2616164..2616314_POSITIVE 291 130 81 93 46 NC_002967:TDE1963|3end_selenocysteine-specific_translation_elongation_factor_1977141..1977291_POSITIVE 291 147 105 149 105 NC_002967:TDE1254|3end_Smr_domain_protein_1289003..1289153_POSITIVE