Origin IGS: attcctactcctttggtgattttcggcaattctaaaattcccgcggcatccctgccgatatgtcatttccggatcctctgtcattccgcagaagacggaagcacattaaaatttaagct .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 agcttaaattttaatgtgcttccgtcttctgcggaatgacagaggatccggaaatgacatatcggcagggatgccgcgggaattttagaattgccgaaaatcaccaaaggagtaggaat Mask Tandem Repeat Region ================================================ attcctactcctttggtgattttcggcaattctaaaattcccgcggcatccctgccgatatgtcatttccggatcctctgtcattccgcagaagacggaagcacattaaaatttaagct Find is-nt database================================================ Query_seq: TDE1004:TDE1005|TDE1004:TDE1005:flagellar filament core protein:hypothetical protein:<-->:1030227..1030345 119 attcctactcctttggtgattttcggcaattctaaaattcccgcggcatccctgccgatatgtcatttccggatcctctgtcattccgcagaagacggaagcacattaaaatttaagct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE1004:TDE1005|TDE1004:TDE1005:flagellar filament core protein:hypothetical protein:<-->:1030227..1030345 119 attcctactcctttggtgattttcggcaattctaaaattcccgcggcatccctgccgatatgtcatttccggatcctctgtcattccgcagaagacggaagcacattaaaatttaagct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE1004:TDE1005|TDE1004:TDE1005:flagellar filament core protein:hypothetical protein:<-->:1030227..1030345 119 attcctactcctttggtgattttcggcaattctaaaattcccgcggcatccctgccgatatgtcatttccggatcctctgtcattccgcagaagacggaagcacattaaaatttaagct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 attcctactcctttggtgattttcggcaattctaaaattcccgcggcatccctgccgatatgtcatttccggatcctctgtcattccgcagaagacggaagcacattaaaatttaagct Predict ORF larger than 30AA ================================================ Protein_Len: 39 Strand: + Start: 1 End: 117 M P T P L V I F G N S K I P A A S L P I C H F R I L C H S A E D G S T L K F K .. attcctactcctttggtgattttcggcaattctaaaattcccgcggcatccctgccgatatgtcatttccggatcctctgtcattccgcagaagacggaagcacattaaaatttaagct 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================================================ attcctactcctttggtgattttcggcaattctaaaattcccgcggcatccctgccgatatgtcatttccggatcctctgtcattccgcagaagacggaagcacattaaaatttaagct Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE1004:TDE1005|TDE1004:TDE1005:flagellar filament core protein:hypothetical protein:<-->:1030227..1030345 119 attcctactcctttggtgattttcggcaattctaaaattcccgcggcatccctgccgatatgtcatttccggatcctctgtcattccgcagaagacggaagcacattaaaatttaagct Intra-Species Hit: Count: 1 Min: 1 Max: 119 Len: 119 Subject: NC_002967_TDE1004_TDE1005|flagellar filament core protein:hypothetical protein|NEGATIVE:POSITIVE|[1030227,1030345]|119 HSP 1 e-value: 1.0E-61 bit: 236.0 Len: 119 Query Start:1 Query End:119 Subject Strand: POSITIVE Subject Start: 1 Subject End: 119 attcctactcctttggtgattttcggcaattctaaaattcccgcggcatccctgccgatatgtcatttccggatcctctgtcattccgcagaagacggaagcacattaaaatttaagct attcctactcctttggtgattttcggcaattctaaaattcccgcggcatccctgccgatatgtcatttccggatcctctgtcattccgcagaagacggaagcacattaaaatttaagct Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUUCCUACUCCUUUGGUGAUUUUCGGCAAUUCUAAAAUUCCCGCGGCAUCCCUGCCGAUAUGUCAUUUCCGGAUCCUCUGUCAUUCCGCAGAAGACGGAAGCACAUUAAAAUUUAAGCU ...........(((((((.....(((.((((....)))).)))(((((....)))))........((((((..((.(((((......))))).))))))))..)))))))......... (-24.70) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGCUUAAAUUUUAAUGUGCUUCCGUCUUCUGCGGAAUGACAGAGGAUCCGGAAAUGACAUAUCGGCAGGGAUGCCGCGGGAAUUUUAGAAUUGCCGAAAAUCACCAAAGGAGUAGGAAU .((((........((((..((((((((((((........)))))))..)))))...))))..(((((....)))))(((.((((....)))).))).............))))...... (-29.50) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 1089 90 41 181 132 NC_002967:TDE1004|5end_flagellar_filament_core_protein_1030136..1030366_NEGATIVE 383 89 41 166 104 NC_002967:TDE0957|5end_glycerophosphoryl_diester_phosphodiesterase_family_protein_980252..980482_POSITIVE 381 104 68 91 51 NC_002967:TDE1240|5end_PhoH_family_protein_1271380..1271610_POSITIVE 369 80 35 217 166 NC_002967:TDE2499|5end_hypothetical_protein_2523952..2524182_NEGATIVE 361 90 41 135 80 NC_002967:TDE1926|5end_hypothetical_protein_1942495..1942725_POSITIVE 357 89 41 228 163 NC_002967:TDE1380|5end_hypothetical_protein_1421284..1421514_NEGATIVE 354 90 43 95 43 NC_002967:TDE0544|5end_hypothetical_protein_583854..584084_POSITIVE 349 87 41 98 37 NC_002967:TDE0317|5end_hypothetical_protein_350656..350886_POSITIVE 337 90 42 188 131 NC_002967:TDE1887|5end_TPR_domain_protein_1909133..1909363_NEGATIVE 337 90 42 130 84 NC_002967:TDE0697|5end_hypothetical_protein_734372..734602_NEGATIVE 332 90 44 71 31 NC_002967:TDE0693|5end_phosphomethylpyrimidine_kinase_729942..730172_POSITIVE 330 88 41 80 39 NC_002967:TDE2554|5end_chaperonin,_33_kDa_family_2580745..2580975_POSITIVE 329 90 42 170 129 NC_002967:TDE0272|5end_hypothetical_protein_302870..303100_NEGATIVE 327 88 41 45 3 NC_002967:TDE2762|5end_flagellar_motor_switch_protein_FliY_2817744..2817974_NEGATIVE 326 47 4 182 125 NC_002967:TDE0447|5end_TPR_domain_protein_502758..502988_POSITIVE 322 89 44 73 26 NC_002967:TDE0614|5end_precorrin-4_C11-methyltransferase_647987..648217_POSITIVE 321 89 44 72 40 NC_002967:TDE2382|5end_cobinamide_kinase/cobinamide_phosphate_guanyltransferase_2412278..2412508_POSITIVE 320 90 41 67 12 NC_002967:TDE1052|5end_rubredoxin_1078870..1079100_NEGATIVE 319 85 45 165 125 NC_002967:TDE2666|5end_hydrolase,_carbon-nitrogen_family_2704394..2704624_NEGATIVE 319 85 41 156 102 NC_002967:TDE2355|5end_carbon_storage_regulator_2390838..2391068_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 427 100 51 52 9 NC_002967:TDE0740|3end_hypothetical_protein_776204..776354_POSITIVE 404 88 41 134 78 NC_002967:TDE1450|3end_MutS2_family_protein_1497856..1498006_POSITIVE 380 78 32 149 94 NC_002967:TDE0956|3end_hypothetical_protein_980330..980480_POSITIVE 354 90 41 56 5 NC_002967:TDE1347|3end_hypothetical_protein_1388032..1388182_POSITIVE 327 88 41 52 10 NC_002967:TDE2763|3end_flagellar_motor_switch_protein_2817737..2817887_NEGATIVE 315 90 41 109 36 NC_002967:TDE0833|3end_lipoprotein,_putative_854097..854247_POSITIVE 313 89 43 116 67 NC_002967:TDE2527|3end_hypothetical_protein_2555449..2555599_NEGATIVE 313 70 40 133 105 NC_002967:TDE1491|3end_chemotaxis_protein_CheA_1537294..1537444_POSITIVE 313 81 44 91 53 NC_002967:TDE0788|3end_ribosomal_protein_L36_816625..816775_POSITIVE 309 88 41 69 23 NC_002967:TDE1633|3end_citrate_lyase_acyl_carrier_protein_1682428..1682578_NEGATIVE 308 90 42 75 18 NC_002967:TDE0739|3end_hypothetical_protein_776028..776178_POSITIVE 304 100 51 151 107 NC_002967:TDE2631|3end_peptide_ABC_transporter,_permease_protein,_putative_2672733..2672883_POSITIVE 304 80 31 131 90 NC_002967:TDE0978|3end_hypothetical_protein_1002424..1002574_POSITIVE 303 89 43 134 85 NC_002967:TDE2101|3end_hypothetical_protein_2125549..2125699_NEGATIVE 303 100 52 115 78 NC_002967:TDE0898|3end_hypothetical_protein_916557..916707_POSITIVE 302 90 41 59 8 NC_002967:TDE1776|3end_hypothetical_protein_1818414..1818564_NEGATIVE 301 43 1 44 2 NC_002967:TDE0499|3end_hypothetical_protein_552517..552667_NEGATIVE 300 90 41 50 8 NC_002967:TDE1839|3end_hypothetical_protein_1870391..1870541_NEGATIVE 297 89 42 105 49 NC_002967:TDE0852|3end_50S_ribosomal_protein_L13_875527..875677_POSITIVE 295 73 37 69 23 NC_002967:TDE2460|3end_aminotransferase,_class_V_2487229..2487379_POSITIVE