Origin IGS: aattatcctgataattttatcttgaaactttaagttttatcataagaaggttaaaaactcctatggatgtttttaacctttttttattactcagggctgtaaatcgataaaagagctttaat .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 attaaagctcttttatcgatttacagccctgagtaataaaaaaaggttaaaaacatccataggagtttttaaccttcttatgataaaacttaaagtttcaagataaaattatcaggataatt Mask Tandem Repeat Region ================================================ aattatcctgataattttatcttgaaactttaagttttatcataagaaggttaaaaactcctatggatgtttttaacctttttttattactcagggctgtaaatcgataaaagagctttaat Find is-nt database================================================ Query_seq: TDE1409:TDE1410|TDE1409:TDE1410:flagellar filament outer layer protein FlaA, putative:hypothetical protein:-><-:1452442..1452563 122 aattatcctgataattttatcttgaaactttaagttttatcataagaaggttaaaaactcctatggatgtttttaacctttttttattactcagggctgtaaatcgataaaagagctttaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE1409:TDE1410|TDE1409:TDE1410:flagellar filament outer layer protein FlaA, putative:hypothetical protein:-><-:1452442..1452563 122 aattatcctgataattttatcttgaaactttaagttttatcataagaaggttaaaaactcctatggatgtttttaacctttttttattactcagggctgtaaatcgataaaagagctttaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE1409:TDE1410|TDE1409:TDE1410:flagellar filament outer layer protein FlaA, putative:hypothetical protein:-><-:1452442..1452563 122 aattatcctgataattttatcttgaaactttaagttttatcataagaaggttaaaaactcctatggatgtttttaacctttttttattactcagggctgtaaatcgataaaagagctttaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aattatcctgataattttatcttgaaactttaagttttatcataagaaggttaaaaactcctatggatgtttttaacctttttttattactcagggctgtaaatcgataaaagagctttaat Predict ORF larger than 30AA ================================================ aattatcctgataattttatcttgaaactttaagttttatcataagaaggttaaaaactcctatggatgtttttaacctttttttattactcagggctgtaaatcgataaaagagctttaat 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================================================ aattatcctgataattttatcttgaaactttaagttttatcataagaaggttaaaaactcctatggatgtttttaacctttttttattactcagggctgtaaatcgataaaagagctttaat Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 100 HP_score: -11.7 Tail_Score: -5.84381 Start: 49 End: 78 Full_Region: GTTTTATCATAAGAA GGTTAAAAACTCC TAT GGATGTTTTTAACC TTTTTTTATTACTCA ................................................GGTTAAAAACTCCTATGGATGTTTTTAACC............................................ TransTerm Strand: - Conf: 100 HP_score: -11.7 Tail_Score: -3.84406 Start: 49 End: 78 Full_Region: tgagtaataaaaaaa ggttaaaaacatcc ata ggagtttttaacc ttcttatgataaaac ................................................ggttaaaaacatccataggagtttttaacc............................................ Find igs database================================================ Query_seq: TDE1409:TDE1410|TDE1409:TDE1410:flagellar filament outer layer protein FlaA, putative:hypothetical protein:-><-:1452442..1452563 122 aattatcctgataattttatcttgaaactttaagttttatcataagaaggttaaaaactcctatggatgtttttaacctttttttattactcagggctgtaaatcgataaaagagctttaat Intra-Species Hit: Count: 1 Min: 1 Max: 122 Len: 122 Subject: NC_002967_TDE1409_TDE1410|flagellar filament outer layer protein FlaA, putative:hypothetical protein|POSITIVE:NEGATIVE|[1452442,1452563]|122 HSP 1 e-value: 7.0E-51 bit: 200.0 Len: 122 Query Start:1 Query End:122 Subject Strand: POSITIVE Subject Start: 1 Subject End: 122 aattatcctgataattttatcttgaaactttaagttttatcataagaaggttaaaaactcctatggatgtttttaaccnnnnnnnattactcagggctgtaaatcgataaaagagctttaat aattatcctgataattttatcttgaaactttaagttttatcataagaaggttaaaaactcctatggatgtttttaacctttttttattactcagggctgtaaatcgataaaagagctttaat Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUUAUCCUGAUAAUUUUAUCUUGAAACUUUAAGUUUUAUCAUAAGAAGGUUAAAAACUCCUAUGGAUGUUUUUAACCUUUUUUUAUUACUCAGGGCUGUAAAUCGAUAAAAGAGCUUUAAU .....((((((((((.......((((((.....))))))....((((((((((((((((((...))).)))))))))))))))..)))).)))))).......................... (-27.60) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUUAAAGCUCUUUUAUCGAUUUACAGCCCUGAGUAAUAAAAAAAGGUUAAAAACAUCCAUAGGAGUUUUUAACCUUCUUAUGAUAAAACUUAAAGUUUCAAGAUAAAAUUAUCAGGAUAAUU ...........................(((((.((((.....((((((((((((.(((...)))))))))))))))....(((...(((.....)))))).......)))))))))...... (-22.60) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 234 120 93 158 134 NC_002967:TDE1340|5end_ribosomal_5S_rRNA_E-loop_binding_protein_Ctc/L25/TL5_1376317..1376547_POSITIVE 233 99 57 122 83 NC_002967:TDE0447|5end_TPR_domain_protein_502758..502988_POSITIVE 232 79 39 190 151 NC_002967:TDE0756|5end_iron_compound_ABC_transporter,_ATP-binding_protein,_putative_796859..797089_NEGATIVE 230 117 78 97 53 NC_002967:TDE1027|5end_ribonuclease_III_1057562..1057792_POSITIVE 229 119 78 223 188 NC_002967:TDE1225|5end_zinc_ABC_transporter,_ATP-binding_protein_1259518..1259748_NEGATIVE 226 97 58 102 62 NC_002967:TDE1039|5end_riboflavin_biosynthesis_protein,_putative_1067072..1067302_POSITIVE 225 119 77 222 182 NC_002967:TDE0551|5end_hypothetical_protein_588273..588503_NEGATIVE 224 118 77 147 102 NC_002967:TDE1631|5end_citrate_lyase,_alpha_subunit_1681556..1681786_NEGATIVE 219 118 77 51 6 NC_002967:TDE0884|5end_tRNA_(guanine-N(1)-)-methyltransferase_902221..902451_POSITIVE 219 106 63 174 132 NC_002967:TDE0203|5end_hypothetical_protein_236670..236900_POSITIVE 215 118 75 125 69 NC_002967:TDE1539|5end_hypothetical_protein_1583508..1583738_POSITIVE 215 97 57 119 86 NC_002967:TDE1155|5end_hypothetical_protein_1191455..1191685_NEGATIVE 212 99 59 118 75 NC_002967:TDE0860|5end_ribosomal_small_subunit_pseudouridine_synthase_A_881023..881253_POSITIVE 211 98 59 202 173 NC_002967:TDE1450|5end_MutS2_family_protein_1495320..1495550_POSITIVE 208 116 77 69 29 NC_002967:TDE2095|5end_hypothetical_protein_2121749..2121979_POSITIVE 207 110 61 70 9 NC_002967:TDE2709|5end_BNR_domain_protein_2766358..2766588_NEGATIVE 206 99 64 223 184 NC_002967:TDE2680|5end_hypothetical_protein_2721072..2721302_NEGATIVE 206 118 72 115 74 NC_002967:TDE2306|5end_hypothetical_protein_2344251..2344481_NEGATIVE 205 117 77 144 101 NC_002967:TDE1021|5end_lipoprotein,_putative_1053564..1053794_NEGATIVE 205 97 58 165 135 NC_002967:TDE0857|5end_lipoprotein,_putative_878313..878543_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 335 83 44 47 8 NC_002967:TDE1409|3end_flagellar_filament_outer_layer_protein_FlaA,_putative_1452381..1452531_POSITIVE 242 100 55 88 41 NC_002967:TDE2081|3end_hypothetical_protein_2112529..2112679_POSITIVE 239 99 53 99 58 NC_002967:TDE1056|3end_hypothetical_protein_1085895..1086045_POSITIVE 238 109 63 63 22 NC_002967:TDE0114|3end_iron-dependent_transcriptional_regulator_133581..133731_NEGATIVE 233 99 57 132 93 NC_002967:TDE0446|3end_fibronectin_type_III_domain_protein_502848..502998_POSITIVE 230 117 78 73 29 NC_002967:TDE1026|3end_acyl_carrier_protein_1057618..1057768_POSITIVE 224 118 77 134 89 NC_002967:TDE1632|3end_citrate_lyase,_beta_subunit_1681569..1681719_NEGATIVE 221 120 90 85 51 NC_002967:TDE1443|3end_RNA_methyltransferase,_TrmH_family,_group_3_1488809..1488959_NEGATIVE 219 118 77 54 9 NC_002967:TDE0883|3end_16S_rRNA_processing_protein_RimM_902304..902454_POSITIVE 215 118 75 122 66 NC_002967:TDE1538|3end_DNA_ligase,_NAD-dependent_1583585..1583735_POSITIVE 212 99 59 121 78 NC_002967:TDE0859|3end_hypothetical_protein_881106..881256_POSITIVE 209 100 66 103 65 NC_002967:TDE2261|3end_hypothetical_protein_2297915..2298065_NEGATIVE 209 85 42 104 66 NC_002967:TDE1495|3end_hypothetical_protein_1539596..1539746_NEGATIVE 206 118 72 131 90 NC_002967:TDE2307|3end_seryl-tRNA_synthetase_2344235..2344385_NEGATIVE 206 118 73 72 14 NC_002967:TDE0479|3end_hydroxylamine_reductase_535029..535179_NEGATIVE 205 97 58 150 120 NC_002967:TDE0856|3end_L-fuculose_phosphate_aldolase,_putative_878378..878528_POSITIVE 202 99 58 135 88 NC_002967:TDE2366|3end_high-affinity_branched-chain_amino_acid_ABC_transporter,_permease_protein_2399959..2400109_NEGATIVE 202 45 6 89 44 NC_002967:TDE0725|3end_exopolysaccharide_biosynthesis_protein_764720..764870_POSITIVE 202 99 57 144 107 NC_002967:TDE0119|3end_flagellar_protein_FliS_137058..137208_NEGATIVE 198 106 62 112 59 NC_002967:TDE2407|3end_amidophosphoribosyltransferase_2433644..2433794_NEGATIVE