Origin IGS: aagatattcctccctggaataatgtgtttacaaagcatccttgctttgttttgaggatagaaaaccctcattatctatcttcggttttctgtttctaaaactttaggctttttttaaaaaaaaattaaaaaaaatgaggtt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aacctcattttttttaatttttttttaaaaaaagcctaaagttttagaaacagaaaaccgaagatagataatgagggttttctatcctcaaaacaaagcaaggatgctttgtaaacacattattccagggaggaatatctt Mask Tandem Repeat Region ================================================ aagatattcctccctggaataatgtgtttacaaagcatccttgctttgttttgaggatagaaaaccctcattatctatcttcggttttctgtttctaaaactttaggctttttttaaaaaaaaattaaaaaaaatgaggtt Find is-nt database================================================ Query_seq: TDE1477:TDE1478|TDE1477:TDE1478:flagellar filament core protein:hypothetical protein:<-<-:1523424..1523564 141 aagatattcctccctggaataatgtgtttacaaagcatccttgctttgttttgaggatagaaaaccctcattatctatcttcggttttctgtttctaaaactttaggctttttttaaaaaaaaattaaaaaaaatgaggtt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE1477:TDE1478|TDE1477:TDE1478:flagellar filament core protein:hypothetical protein:<-<-:1523424..1523564 141 aagatattcctccctggaataatgtgtttacaaagcatccttgctttgttttgaggatagaaaaccctcattatctatcttcggttttctgtttctaaaactttaggctttttttaaaaaaaaattaaaaaaaatgaggtt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE1477:TDE1478|TDE1477:TDE1478:flagellar filament core protein:hypothetical protein:<-<-:1523424..1523564 141 aagatattcctccctggaataatgtgtttacaaagcatccttgctttgttttgaggatagaaaaccctcattatctatcttcggttttctgtttctaaaactttaggctttttttaaaaaaaaattaaaaaaaatgaggtt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aagatattcctccctggaataatgtgtttacaaagcatccttgctttgttttgaggatagaaaaccctcattatctatcttcggttttctgtttctaaaactttaggctttttttaaaaaaaaattaaaaaaaatgaggtt Predict ORF larger than 30AA ================================================ Protein_Len: 30 Strand: + Start: 6 End: 95 ..... M P P W N N V F T K H P C F V L R I E N P H Y L S S V F C F .............................................. aagatattcctccctggaataatgtgtttacaaagcatccttgctttgttttgaggatagaaaaccctcattatctatcttcggttttctgtttctaaaactttaggctttttttaaaaaaaaattaaaaaaaatgaggtt 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================================================ aagatattcctccctggaataatgtgtttacaaagcatccttgctttgttttgaggatagaaaaccctcattatctatcttcggttttctgtttctaaaactttaggctttttttaaaaaaaaattaaaaaaaatgaggtt Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 48 HP_score: -3.1 Tail_Score: -3.49866 Start: 52 End: 83 Full_Region: ATCCTTGCTTTGTTT TGAGGATAGAAAA CCCTCA TTATCTATCTTCG GTTTTCTGTTTCTAA ...................................................TGAGGATAGAAAACCCTCATTATCTATCTTCG.......................................................... TransTerm Strand: + Conf: 48 HP_score: -4.4 Tail_Score: -2.68835 Start: 53 End: 82 Full_Region: TCCTTGCTTTGTTTT GAGGATAGAAAA CCCTCA TTATCTATCTTC GGTTTTCTGTTTCTA ....................................................GAGGATAGAAAACCCTCATTATCTATCTTC........................................................... Find igs database================================================ Query_seq: TDE1477:TDE1478|TDE1477:TDE1478:flagellar filament core protein:hypothetical protein:<-<-:1523424..1523564 141 aagatattcctccctggaataatgtgtttacaaagcatccttgctttgttttgaggatagaaaaccctcattatctatcttcggttttctgtttctaaaactttaggctttttttaaaaaaaaattaaaaaaaatgaggtt Intra-Species Hit: Count: 1 Min: 1 Max: 115 Len: 115 Subject: NC_002967_TDE1477_TDE1478|flagellar filament core protein:hypothetical protein|NEGATIVE:NEGATIVE|[1523424,1523564]|141 HSP 1 e-value: 4.0E-59 bit: 228.0 Len: 115 Query Start:1 Query End:115 Subject Strand: POSITIVE Subject Start: 1 Subject End: 115 aagatattcctccctggaataatgtgtttacaaagcatccttgctttgttttgaggatagaaaaccctcattatctatcttcggttttctgtttctaaaactttaggcttttttt.......................... aagatattcctccctggaataatgtgtttacaaagcatccttgctttgttttgaggatagaaaaccctcattatctatcttcggttttctgtttctaaaactttaggcttttttt.......................... Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAGAUAUUCCUCCCUGGAAUAAUGUGUUUACAAAGCAUCCUUGCUUUGUUUUGAGGAUAGAAAACCCUCAUUAUCUAUCUUCGGUUUUCUGUUUCUAAAACUUUAGGCUUUUUUU ....((((((.....))))))....(((((.((((((....))))))((((((..(((((((((((................)))))))))))..))))))..)))))....... (-29.69) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAAAAAGCCUAAAGUUUUAGAAACAGAAAACCGAAGAUAGAUAAUGAGGGUUUUCUAUCCUCAAAACAAAGCAAGGAUGCUUUGUAAACACAUUAUUCCAGGGAGGAAUAUCUU ..............(((((........)))))..((((((.....(((((((.....)))))))..((((((((....))))))))..........((((.....)))))))))) (-23.70) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 848 60 11 151 102 NC_002967:TDE1477|5end_flagellar_filament_core_protein_1523333..1523563_NEGATIVE 299 50 5 108 50 NC_002967:TDE0609|5end_hypothetical_protein_646166..646396_NEGATIVE 292 45 4 131 90 NC_002967:TDE1475|5end_flagellar_filament_core_protein_1522191..1522421_NEGATIVE 289 47 2 36 2 NC_002967:TDE1659|5end_alanyl-tRNA_synthetase_1710633..1710863_NEGATIVE 274 80 37 138 95 NC_002967:TDE1246|5end_lipoprotein,_putative_1279039..1279269_POSITIVE 273 87 43 77 27 NC_002967:TDE0118|5end_hypothetical_protein_137047..137277_NEGATIVE 262 70 24 229 184 NC_002967:TDE1309|5end_modulator_of_DNA_gyrase_family_protein_1344535..1344765_POSITIVE 259 57 13 153 102 NC_002967:TDE0978|5end_hypothetical_protein_1001868..1002098_POSITIVE 255 59 13 81 30 NC_002967:TDE0216|5end_hypothetical_protein_251305..251535_POSITIVE 253 43 2 50 5 NC_002967:TDE0333|5end_MATE_efflux_family_protein_371648..371878_POSITIVE 252 108 74 89 50 NC_002967:TDE0366|5end_type_I_restriction-modification_system,_R_subunit_415541..415771_NEGATIVE 250 88 66 156 133 NC_002967:TDE1874|5end_hypothetical_protein_1895762..1895992_NEGATIVE 249 78 32 142 95 NC_002967:TDE1075|5end_oligopeptide/dipeptide_ABC_transporter,_ATP-binding_protein_1105962..1106192_POSITIVE 245 56 11 207 165 NC_002967:TDE0873|5end_hypothetical_protein_896143..896373_POSITIVE 242 69 22 101 56 NC_002967:TDE2297|5end_TPR_domain_protein_2337019..2337249_NEGATIVE 242 108 68 122 88 NC_002967:TDE1327|5end_hypothetical_protein_1362949..1363179_NEGATIVE 240 90 44 150 101 NC_002967:TDE1089|5end_hypothetical_protein_1120944..1121174_NEGATIVE 238 110 66 198 150 NC_002967:TDE1300|5end_hypothetical_protein_1337419..1337649_NEGATIVE 234 55 15 51 11 NC_002967:TDE1944|5end_hypothetical_protein_1960434..1960664_POSITIVE 232 110 65 169 124 NC_002967:TDE1165|5end_hypothetical_protein_1198390..1198620_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 319 60 11 115 56 NC_002967:TDE0944|3end_hypothetical_protein_967037..967187_POSITIVE 273 87 43 66 16 NC_002967:TDE0119|3end_flagellar_protein_FliS_137058..137208_NEGATIVE 262 80 39 125 77 NC_002967:TDE1913|3end_hypothetical_protein_1930897..1931047_POSITIVE 253 96 55 50 8 NC_002967:TDE2329|3end_hypothetical_protein_2366347..2366497_NEGATIVE 252 108 74 96 57 NC_002967:TDE0367|3end_hypothetical_protein_415534..415684_NEGATIVE 250 88 66 112 89 NC_002967:TDE1875|3end_hypothetical_protein_1895806..1895956_NEGATIVE 249 78 32 129 82 NC_002967:TDE1074|3end_oligopeptide/dipeptide_ABC_transporter,_permease_protein_1106029..1106179_POSITIVE 247 93 60 147 108 NC_002967:TDE2441|3end_hypothetical_protein_2472356..2472506_NEGATIVE 245 110 64 84 37 NC_002967:TDE1955|3end_hypothetical_protein_1970190..1970340_NEGATIVE 245 56 11 149 107 NC_002967:TDE0872|3end_recA_protein_896165..896315_POSITIVE 244 96 68 37 1 NC_002967:TDE2442|3end_surface_protein,_putative_2472471..2472621_NEGATIVE 242 108 68 109 75 NC_002967:TDE1328|3end_hypothetical_protein_1362962..1363112_NEGATIVE 231 49 9 130 89 NC_002967:TDE0111|3end_hypothetical_protein_132114..132264_POSITIVE 228 46 4 111 54 NC_002967:TDE0499|3end_hypothetical_protein_552517..552667_NEGATIVE 224 89 43 88 35 NC_002967:TDE0473|3end_heavy_metal_translocating_P-type_ATPase_530800..530950_POSITIVE 223 80 31 109 57 NC_002967:TDE2763|3end_flagellar_motor_switch_protein_2817737..2817887_NEGATIVE 223 71 31 56 11 NC_002967:TDE2477|3end_selenocysteine_synthase_2500949..2501099_POSITIVE 222 110 65 124 85 NC_002967:TDE1344|3end_hypothetical_protein_1383350..1383500_POSITIVE 222 80 34 76 10 NC_002967:TDE0602|3end_3-oxoacyl-(acyl-carrier-protein)_synthase_III_639836..639986_NEGATIVE 221 93 54 56 20 NC_002967:TDE0592|3end_acetyl-CoA_carboxylase,_biotin_carboxyl_carrier_protein_631363..631513_NEGATIVE