Origin IGS: attataacacaccttgtacagcggtatgtacaccgcttaaaataaatattttattattatacatcatttcctatatatttactactcattcgtaaagttagcagtattacattctctta .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 taagagaatgtaatactgctaactttacgaatgagtagtaaatatataggaaatgatgtataataataaaatatttattttaagcggtgtacataccgctgtacaaggtgtgttataat Mask Tandem Repeat Region ================================================ attataacacaccttgtacagcggtatgtacaccgcttaaaataaatattttattattatacatcatttcctatatatttactactcattcgtaaagttagcagtattacattctctta Find is-nt database================================================ Query_seq: TDE1958:TDE1959|TDE1958:TDE1959:surface protein, putative:hypothetical protein:<-<-:1973776..1973894 119 attataacacaccttgtacagcggtatgtacaccgcttaaaataaatattttattattatacatcatttcctatatatttactactcattcgtaaagttagcagtattacattctctta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE1958:TDE1959|TDE1958:TDE1959:surface protein, putative:hypothetical protein:<-<-:1973776..1973894 119 attataacacaccttgtacagcggtatgtacaccgcttaaaataaatattttattattatacatcatttcctatatatttactactcattcgtaaagttagcagtattacattctctta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE1958:TDE1959|TDE1958:TDE1959:surface protein, putative:hypothetical protein:<-<-:1973776..1973894 119 attataacacaccttgtacagcggtatgtacaccgcttaaaataaatattttattattatacatcatttcctatatatttactactcattcgtaaagttagcagtattacattctctta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 attataacacaccttgtacagcggtatgtacaccgcttaaaataaatattttattattatacatcatttcctatatatttactactcattcgtaaagttagcagtattacattctctta Predict ORF larger than 30AA ================================================ attataacacaccttgtacagcggtatgtacaccgcttaaaataaatattttattattatacatcatttcctatatatttactactcattcgtaaagttagcagtattacattctctta 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================================================ attataacacaccttgtacagcggtatgtacaccgcttaaaataaatattttattattatacatcatttcctatatatttactactcattcgtaaagttagcagtattacattctctta Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE1958:TDE1959|TDE1958:TDE1959:surface protein, putative:hypothetical protein:<-<-:1973776..1973894 119 attataacacaccttgtacagcggtatgtacaccgcttaaaataaatattttattattatacatcatttcctatatatttactactcattcgtaaagttagcagtattacattctctta Intra-Species Hit: Count: 1 Min: 1 Max: 119 Len: 119 Subject: NC_002967_TDE1958_TDE1959|surface protein, putative:hypothetical protein|NEGATIVE:NEGATIVE|[1973776,1973894]|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 attataacacaccttgtacagcggtatgtacaccgcttaaaataaatattttattattatacatcatttcctatatatttactactcattcgtaaagttagcagtattacattctctta attataacacaccttgtacagcggtatgtacaccgcttaaaataaatattttattattatacatcatttcctatatatttactactcattcgtaaagttagcagtattacattctctta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUUAUAACACACCUUGUACAGCGGUAUGUACACCGCUUAAAAUAAAUAUUUUAUUAUUAUACAUCAUUUCCUAUAUAUUUACUACUCAUUCGUAAAGUUAGCAGUAUUACAUUCUCUUA ....((((......((((.((((((......))))))((((((....))))))......))))..............(((((.........)))))))))................... (-11.70) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAGAGAAUGUAAUACUGCUAACUUUACGAAUGAGUAGUAAAUAUAUAGGAAAUGAUGUAUAAUAAUAAAAUAUUUAUUUUAAGCGGUGUACAUACCGCUGUACAAGGUGUGUUAUAAU ........((((((((.(((........(((((((((.((..((((((........))))))....))...)))))))))..(((((((....)))))))......))))))))))).. (-22.90) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 792 50 1 141 92 NC_002967:TDE1958|5end_surface_protein,_putative_1973685..1973915_NEGATIVE 270 73 31 103 64 NC_002967:TDE1629|5end_dihydrolipoamide_dehydrogenase_1678514..1678744_NEGATIVE 267 37 9 169 142 NC_002967:TDE1935|5end_hypothetical_protein_1952994..1953224_POSITIVE 255 106 63 150 108 NC_002967:TDE0662|5end_hypothetical_protein_697835..698065_NEGATIVE 250 108 71 182 139 NC_002967:TDE0349|5end_phosphoenolpyruvate_synthase,_putative_391093..391323_POSITIVE 229 35 8 69 41 NC_002967:TDE2584|5end_dipeptidase_2616413..2616643_POSITIVE 226 42 11 211 181 NC_002967:TDE2550|5end_hypothetical_protein_2576215..2576445_NEGATIVE 225 73 33 187 150 NC_002967:TDE0116|5end_hypothetical_protein_134709..134939_POSITIVE 223 54 13 85 50 NC_002967:TDE0838|5end_Na(+)-translocating_NADH-quinone_reductase,_A_subunit_858551..858781_NEGATIVE 220 71 32 101 62 NC_002967:TDE1655|5end_hypothetical_protein_1704958..1705188_POSITIVE 217 49 21 59 27 NC_002967:TDE0594|5end_cysteine_protease_domain,_YopT-type_634805..635035_NEGATIVE 210 38 8 142 102 NC_002967:TDE1978|5end_hypothetical_protein_1991758..1991988_NEGATIVE 210 37 3 198 152 NC_002967:TDE1245|5end_hypothetical_protein_1278894..1279124_NEGATIVE 205 38 12 35 12 NC_002967:TDE0535|5end_ABC_transporter,_ATP-binding_protein_577323..577553_POSITIVE 202 38 9 71 41 NC_002967:TDE1540|5end_hypothetical_protein_1584422..1584652_POSITIVE 200 49 7 216 161 NC_002967:TDE2140|5end_protease_II_2175140..2175370_NEGATIVE 199 37 12 47 16 NC_002967:TDE2003|5end_internalin-related_protein_2022277..2022507_POSITIVE 197 37 16 35 12 NC_002967:TDE1720|5end_radical_SAM_domain_protein_1774463..1774693_POSITIVE 196 36 12 110 82 NC_002967:TDE2309|5end_sigma-54_dependent_transcriptional_regulator,_putative_2348099..2348329_NEGATIVE 196 37 10 188 159 NC_002967:TDE0945|5end_hypothetical_protein_967128..967358_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 255 106 63 145 103 NC_002967:TDE0663|3end_hypothetical_protein_697840..697990_NEGATIVE 250 108 71 142 99 NC_002967:TDE0348|3end_transcriptional_regulator,_TetR_family_391133..391283_POSITIVE 238 38 7 38 4 NC_002967:TDE0210|3end_cob(I)yrinic_acid_a,c-diamide_adenosyltransferase_246146..246296_POSITIVE 229 35 8 76 48 NC_002967:TDE2583|3end_hypothetical_protein_2616500..2616650_POSITIVE 217 38 1 143 106 NC_002967:TDE2268|3end_hypothetical_protein_2304822..2304972_NEGATIVE 210 38 8 145 105 NC_002967:TDE1979|3end_hypothetical_protein_1991755..1991905_NEGATIVE 204 37 8 38 2 NC_002967:TDE1719|3end_transcriptional_regulator,_MarR_family_1774546..1774696_POSITIVE 203 36 7 70 39 NC_002967:TDE1003|3end_hypothetical_protein_1029325..1029475_POSITIVE 201 37 13 144 120 NC_002967:TDE0609|3end_hypothetical_protein_645276..645426_NEGATIVE 194 105 65 75 36 NC_002967:TDE1304|3end_hypothetical_protein_1339948..1340098_POSITIVE 194 59 12 87 37 NC_002967:TDE0689|3end_5-methylthioribose_kinase_726972..727122_POSITIVE 193 38 9 151 122 NC_002967:TDE1361|3end_hypothetical_protein_1401106..1401256_POSITIVE 190 38 8 34 4 NC_002967:TDE2269|3end_hypothetical_protein_2304931..2305081_NEGATIVE 189 39 2 104 65 NC_002967:TDE2745|3end_fic_family_protein_2799881..2800031_NEGATIVE 189 59 11 127 61 NC_002967:TDE0710|3end_hypothetical_protein_745667..745817_POSITIVE 189 58 13 82 35 NC_002967:TDE0221|3end_hypothetical_protein_254046..254196_NEGATIVE 188 57 14 78 40 NC_002967:TDE2769|3end_flagellar_hook_assembly_protein_2822523..2822673_NEGATIVE 188 36 1 150 116 NC_002967:TDE1402|3end_hypothetical_protein_1444515..1444665_POSITIVE 185 38 13 141 106 NC_002967:TDE0772|3end_50S_ribosomal_protein_L22_809520..809670_POSITIVE 185 43 5 52 4 NC_002967:TDE0236|3end_PIN_domain_protein_269647..269797_POSITIVE