Origin IGS: ttccaattacccccttagtttggtacgtatatctctattttcaatcattttcattgtaaagtcaagtagtaaaatcggctttttctacttttaagtctatttttaggtctta .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 taagacctaaaaatagacttaaaagtagaaaaagccgattttactacttgactttacaatgaaaatgattgaaaatagagatatacgtaccaaactaagggggtaattggaa Mask Tandem Repeat Region ================================================ ttccaattacccccttagtttggtacgtatatctctattttcaatcattttcattgtaaagtcaagtagtaaaatcggctttttctacttttaagtctatttttaggtctta Find is-nt database================================================ Query_seq: TDE2349:TDE2350|TDE2349:TDE2350:hypothetical protein:lipoprotein, putative:<-<-:2386031..2386142 112 ttccaattacccccttagtttggtacgtatatctctattttcaatcattttcattgtaaagtcaagtagtaaaatcggctttttctacttttaagtctatttttaggtctta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE2349:TDE2350|TDE2349:TDE2350:hypothetical protein:lipoprotein, putative:<-<-:2386031..2386142 112 ttccaattacccccttagtttggtacgtatatctctattttcaatcattttcattgtaaagtcaagtagtaaaatcggctttttctacttttaagtctatttttaggtctta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE2349:TDE2350|TDE2349:TDE2350:hypothetical protein:lipoprotein, putative:<-<-:2386031..2386142 112 ttccaattacccccttagtttggtacgtatatctctattttcaatcattttcattgtaaagtcaagtagtaaaatcggctttttctacttttaagtctatttttaggtctta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ttccaattacccccttagtttggtacgtatatctctattttcaatcattttcattgtaaagtcaagtagtaaaatcggctttttctacttttaagtctatttttaggtctta Predict ORF larger than 30AA ================================================ ttccaattacccccttagtttggtacgtatatctctattttcaatcattttcattgtaaagtcaagtagtaaaatcggctttttctacttttaagtctatttttaggtctta Predict Promoter with matrix: RpoD-15 score > 80================================================ Predict Promoter with matrix: RpoD-16 score > 80================================================ Predict Promoter with matrix: RpoD-17 score > 80================================================ PromScan Matrix: RpoD-17 Strand: - Score: 81 Start: 37 End: 66 ....................................CTTGACTTTACAATGAAAATGATTGAAAAT.............................................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ ttccaattacccccttagtttggtacgtatatctctattttcaatcattttcattgtaaagtcaagtagtaaaatcggctttttctacttttaagtctatttttaggtctta Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 58 HP_score: -3.5 Tail_Score: -4.30885 Start: 66 End: 88 Full_Region: TCATTGTAAAGTCAA GTAGTAAAA TCGGC TTTTTCTAC TTTTAAGTCTATTTT .................................................................GTAGTAAAATCGGCTTTTTCTAC........................ Find igs database================================================ Query_seq: TDE2349:TDE2350|TDE2349:TDE2350:hypothetical protein:lipoprotein, putative:<-<-:2386031..2386142 112 ttccaattacccccttagtttggtacgtatatctctattttcaatcattttcattgtaaagtcaagtagtaaaatcggctttttctacttttaagtctatttttaggtctta Intra-Species Hit: Count: 1 Min: 1 Max: 112 Len: 112 Subject: NC_002967_TDE2349_TDE2350|hypothetical protein:lipoprotein, putative|NEGATIVE:NEGATIVE|[2386031,2386142]|112 HSP 1 e-value: 2.0E-57 bit: 222.0 Len: 112 Query Start:1 Query End:112 Subject Strand: POSITIVE Subject Start: 1 Subject End: 112 ttccaattacccccttagtttggtacgtatatctctattttcaatcattttcattgtaaagtcaagtagtaaaatcggctttttctacttttaagtctatttttaggtctta ttccaattacccccttagtttggtacgtatatctctattttcaatcattttcattgtaaagtcaagtagtaaaatcggctttttctacttttaagtctatttttaggtctta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUCCAAUUACCCCCUUAGUUUGGUACGUAUAUCUCUAUUUUCAAUCAUUUUCAUUGUAAAGUCAAGUAGUAAAAUCGGCUUUUUCUACUUUUAAGUCUAUUUUUAGGUCUUA ............(((.((..(((.((..........(((((((((.......)))).))))).((((((.((((......))))))))))....)))))..)).)))..... (-11.60) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAGACCUAAAAAUAGACUUAAAAGUAGAAAAAGCCGAUUUUACUACUUGACUUUACAAUGAAAAUGAUUGAAAAUAGAGAUAUACGUACCAAACUAAGGGGGUAAUUGGAA ....((((.....(((......((((((.((((.....)))).))))))..(((((((((.......))))....)))))..............)))...))))........ (-12.90) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 786 50 1 141 92 NC_002967:TDE2349|5end_hypothetical_protein_2385940..2386170_NEGATIVE 250 80 31 139 84 NC_002967:TDE0900|5end_ABC_transporter,_ATP-binding_protein_917188..917418_POSITIVE 241 98 55 157 117 NC_002967:TDE1499|5end_adenylosuccinate_lyase,_putative_1545266..1545496_POSITIVE 225 41 2 139 91 NC_002967:TDE1165|5end_hypothetical_protein_1198390..1198620_NEGATIVE 222 60 12 105 61 NC_002967:TDE2778|5end_PspC_domain_protein_2829604..2829834_NEGATIVE 220 96 64 184 150 NC_002967:TDE2551|5end_hypothetical_protein_2577282..2577512_NEGATIVE 219 110 66 74 12 NC_002967:TDE0604|5end_hypothetical_protein_642631..642861_NEGATIVE 216 45 2 83 31 NC_002967:TDE0248|5end_hypothetical_protein_282068..282298_POSITIVE 214 68 25 231 183 NC_002967:TDE2678|5end_alpha-amylase_family_protein_2719390..2719620_NEGATIVE 213 82 42 59 19 NC_002967:TDE0166|5end_hypothetical_protein_195871..196101_NEGATIVE 212 59 19 200 156 NC_002967:TDE1524|5end_hypothetical_protein_1570292..1570522_POSITIVE 212 110 61 99 41 NC_002967:TDE0080|5end_betaine_aldehyde_dehydrogenase_92212..92442_NEGATIVE 210 36 1 116 86 NC_002967:TDE2048|5end_hypothetical_protein_2076411..2076641_POSITIVE 206 50 8 144 96 NC_002967:TDE1996|5end_hypothetical_protein_2014243..2014473_POSITIVE 204 43 3 205 155 NC_002967:TDE1342|5end_hypothetical_protein_1378442..1378672_POSITIVE 202 110 76 197 161 NC_002967:TDE1013|5end_hemerythrin-related_protein_1044390..1044620_NEGATIVE 201 110 66 115 66 NC_002967:TDE2348|5end_maf_protein_2385219..2385449_NEGATIVE 201 43 3 212 164 NC_002967:TDE0973|5end_DNA_repair_protein_RadC_998617..998847_NEGATIVE 198 78 43 226 188 NC_002967:TDE1282|5end_hypothetical_protein_1316801..1317031_POSITIVE 197 58 11 119 78 NC_002967:TDE0472|5end_hypothetical_protein_528376..528606_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 250 80 31 148 93 NC_002967:TDE0899|3end_ABC_transporter,_permease_protein,_putative_917277..917427_POSITIVE 241 98 55 65 25 NC_002967:TDE1498|3end_hypothetical_protein_1545254..1545404_POSITIVE 232 46 3 95 54 NC_002967:TDE0157|3end_KHG/KDPG_family_aldolase/carbohydrate_kinase,_PfkB_family_185711..185861_POSITIVE 225 41 2 135 87 NC_002967:TDE1166|3end_hypothetical_protein_1198394..1198544_NEGATIVE 222 60 12 81 37 NC_002967:TDE2779|3end_hypothetical_protein_2829628..2829778_NEGATIVE 220 96 64 96 62 NC_002967:TDE2552|3end_ABC_transporter,_ATP-binding/permease_protein_2577370..2577520_NEGATIVE 219 110 66 74 12 NC_002967:TDE0605|3end_hypothetical_protein_642631..642781_NEGATIVE 214 86 52 145 112 NC_002967:TDE0022|3end_hypothetical_protein_28521..28671_POSITIVE 213 82 42 57 17 NC_002967:TDE0167|3end_ABC_transporter,_ATP-binding_protein_195873..196023_NEGATIVE 212 59 19 149 105 NC_002967:TDE1523|3end_citXG_protein,_putative_1570321..1570471_POSITIVE 210 83 41 130 104 NC_002967:TDE0608|3end_DNA-binding_protein,_putative_644994..645144_NEGATIVE 206 50 8 65 17 NC_002967:TDE1995|3end_magnesium_chelatase_family_protein_2014244..2014394_POSITIVE 205 39 3 111 73 NC_002967:TDE1933|3end_hypothetical_protein_1949600..1949750_NEGATIVE 202 110 76 140 104 NC_002967:TDE1014|3end_hypothetical_protein_1044447..1044597_NEGATIVE 202 108 72 101 65 NC_002967:TDE0139|3end_hypothetical_protein_160121..160271_NEGATIVE 201 110 66 98 49 NC_002967:TDE2349|3end_hypothetical_protein_2385236..2385386_NEGATIVE 200 80 33 131 83 NC_002967:TDE1191|3end_hypothetical_protein_1219218..1219368_POSITIVE 197 108 66 96 55 NC_002967:TDE1323|3end_hypothetical_protein_1360968..1361118_POSITIVE 197 45 1 115 62 NC_002967:TDE0659|3end_hypothetical_protein_695690..695840_NEGATIVE 195 37 1 69 13 NC_002967:TDE1881|3end_methyltransferase,_putative_1903631..1903781_POSITIVE