Origin IGS: tgagcaaatcctaaaggatttaataaaaatattttttgtcttcatacttatatatagtttttttttgtattaaatactaattttttaaatggaaatttgattttatttaaaaatatctaaaatttatctattgctgtaaataaaaaattgtgttagaatgcgccaaggagaatttcttagtt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aactaagaaattctccttggcgcattctaacacaattttttatttacagcaatagataaattttagatatttttaaataaaatcaaatttccatttaaaaaattagtatttaatacaaaaaaaaactatatataagtatgaagacaaaaaatatttttattaaatcctttaggatttgctca Mask Tandem Repeat Region ================================================ tgagcaaatcctaaaggatttaataaaaatattttttgtcttcatacttatatatagtttttttttgtattaaatactaattttttaaatggaaatttgattttatttaaaaatatctaaaatttatctattgctgtaaataaaaaattgtgttagaatgcgccaaggagaatttcttagtt Find is-nt database================================================ Query_seq: TDE1359:TDE1360|TDE1359:TDE1360:hypothetical protein:xanthine/uracil permease family protein:<-->:1399255..1399436 182 tgagcaaatcctaaaggatttaataaaaatattttttgtcttcatacttatatatagtttttttttgtattaaatactaattttttaaatggaaatttgattttatttaaaaatatctaaaatttatctattgctgtaaataaaaaattgtgttagaatgcgccaaggagaatttcttagtt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE1359:TDE1360|TDE1359:TDE1360:hypothetical protein:xanthine/uracil permease family protein:<-->:1399255..1399436 182 tgagcaaatcctaaaggatttaataaaaatattttttgtcttcatacttatatatagtttttttttgtattaaatactaattttttaaatggaaatttgattttatttaaaaatatctaaaatttatctattgctgtaaataaaaaattgtgttagaatgcgccaaggagaatttcttagtt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE1359:TDE1360|TDE1359:TDE1360:hypothetical protein:xanthine/uracil permease family protein:<-->:1399255..1399436 182 tgagcaaatcctaaaggatttaataaaaatattttttgtcttcatacttatatatagtttttttttgtattaaatactaattttttaaatggaaatttgattttatttaaaaatatctaaaatttatctattgctgtaaataaaaaattgtgttagaatgcgccaaggagaatttcttagtt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tgagcaaatcctaaaggatttaataaaaatattttttgtcttcatacttatatatagtttttttttgtattaaatactaattttttaaatggaaatttgattttatttaaaaatatctaaaatttatctattgctgtaaataaaaaattgtgttagaatgcgccaaggagaatttcttagtt Predict ORF larger than 30AA ================================================ tgagcaaatcctaaaggatttaataaaaatattttttgtcttcatacttatatatagtttttttttgtattaaatactaattttttaaatggaaatttgattttatttaaaaatatctaaaatttatctattgctgtaaataaaaaattgtgttagaatgcgccaaggagaatttcttagtt 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: 83 Start: 130 End: 159 .................................................................................................................................ATTGCTGTAAATAAAAAATTGTGTTAGAAT....................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tgagcaaatcctaaaggatttaataaaaatattttttgtcttcatacttatatatagtttttttttgtattaaatactaattttttaaatggaaatttgattttatttaaaaatatctaaaatttatctattgctgtaaataaaaaattgtgttagaatgcgccaaggagaatttcttagtt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE1359:TDE1360|TDE1359:TDE1360:hypothetical protein:xanthine/uracil permease family protein:<-->:1399255..1399436 182 tgagcaaatcctaaaggatttaataaaaatattttttgtcttcatacttatatatagtttttttttgtattaaatactaattttttaaatggaaatttgattttatttaaaaatatctaaaatttatctattgctgtaaataaaaaattgtgttagaatgcgccaaggagaatttcttagtt Intra-Species Hit: Count: 1 Min: 1 Max: 182 Len: 182 Subject: NC_002967_TDE1359_TDE1360|hypothetical protein:xanthine/uracil permease family protein|NEGATIVE:POSITIVE|[1399255,1399436]|182 HSP 1 e-value: 2.0E-24 bit: 113.0 Len: 57 Query Start:1 Query End:57 Subject Strand: POSITIVE Subject Start: 1 Subject End: 57 tgagcaaatcctaaaggatttaataaaaatattttttgtcttcatacttatatatag............................................................................................................................. tgagcaaatcctaaaggatttaataaaaatattttttgtcttcatacttatatatag............................................................................................................................. HSP 2 e-value: 4.0E-10 bit: 65.9 Len: 33 Query Start:150 Query End:182 Subject Strand: POSITIVE Subject Start: 150 Subject End: 182 .....................................................................................................................................................gtgttagaatgcgccaaggagaatttcttagtt .....................................................................................................................................................gtgttagaatgcgccaaggagaatttcttagtt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGAGCAAAUCCUAAAGGAUUUAAUAAAAAUAUUUUUUGUCUUCAUACUUAUAUAUAGUUUUUUUUUGUAUUAAAUACUAAUUUUUUAAAUGGAAAUUUGAUUUUAUUUAAAAAUAUCUAAAAUUUAUCUAUUGCUGUAAAUAAAAAAUUGUGUUAGAAUGCGCCAAGGAGAAUUUCUUAGUU ((((.((((((....)))))).................(((((....((((.((((((........((((...))))....(((((((((((((......)))))))))))))...................)))))).))))......((((......))))...)))))....))))... (-25.00) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AACUAAGAAAUUCUCCUUGGCGCAUUCUAACACAAUUUUUUAUUUACAGCAAUAGAUAAAUUUUAGAUAUUUUUAAAUAAAAUCAAAUUUCCAUUUAAAAAAUUAGUAUUUAAUACAAAAAAAAACUAUAUAUAAGUAUGAAGACAAAAAAUAUUUUUAUUAAAUCCUUUAGGAUUUGCUCA .....((((((.....(((...(((.((..........((((((((......))))))))..((((((((((((((((..((......))..)))))))).....)))))))).....................)).)))....))).....))))))..(((((((....))))))).... (-17.40) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 669 50 1 141 92 NC_002967:TDE1359|5end_hypothetical_protein_1399164..1399394_NEGATIVE 271 169 121 162 95 NC_002967:TDE0234|5end_ABC_transporter,_ATP-binding_protein,_HlyB_family_267053..267283_POSITIVE 248 175 147 165 135 NC_002967:TDE1357|5end_aldose_1-epimerase_1396695..1396925_POSITIVE 222 169 127 229 179 NC_002967:TDE0819|5end_ABC_transporter,_ATP-binding/permease_protein_843385..843615_NEGATIVE 217 169 129 208 160 NC_002967:TDE0471|5end_BNR_domain_protein_528288..528518_NEGATIVE 214 169 123 186 143 NC_002967:TDE0379|5end_hypothetical_protein_432458..432688_POSITIVE 210 176 131 99 54 NC_002967:TDE1358|5end_hypothetical_protein_1397732..1397962_POSITIVE 200 172 133 98 60 NC_002967:TDE2070|5end_hypothetical_protein_2097035..2097265_POSITIVE 191 50 3 99 45 NC_002967:TDE1045|5end_hypothetical_protein_1073240..1073470_POSITIVE 188 49 1 67 11 NC_002967:TDE0086|5end_hypothetical_protein_103876..104106_NEGATIVE 187 81 47 120 83 NC_002967:TDE1685|5end_GGDEF_domain_protein_1740315..1740545_NEGATIVE 180 68 28 105 71 NC_002967:TDE0823|5end_(3R)-hydroxymyristoyl-(acyl-carrier-protein)_dehydratase,_putative_844741..844971_POSITIVE 179 165 127 102 54 NC_002967:TDE1396|5end_hypothetical_protein_1435661..1435891_POSITIVE 178 47 4 58 16 NC_002967:TDE1249|5end_hypothetical_protein_1283525..1283755_POSITIVE 177 28 1 39 12 NC_002967:TDE1984|5end_hypothetical_protein_1997565..1997795_NEGATIVE 175 70 30 108 70 NC_002967:TDE0937|5end_RNA_polymerase_sigma-70_factor_family_protein_959951..960181_POSITIVE 175 167 133 92 52 NC_002967:TDE0649|5end_hypothetical_protein_684363..684593_NEGATIVE 174 170 122 149 107 NC_002967:TDE2545|5end_hypothetical_protein_2571814..2572044_NEGATIVE 173 169 146 138 118 NC_002967:TDE2734|5end_hypothetical_protein_2789071..2789301_POSITIVE 173 78 56 198 176 NC_002967:TDE1768|5end_hypothetical_protein_1813947..1814177_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 210 176 131 117 72 NC_002967:TDE1357|3end_aldose_1-epimerase_1397830..1397980_POSITIVE 200 172 133 72 34 NC_002967:TDE2069|3end_endoribonuclease_L-PSP,_putative_2097089..2097239_POSITIVE 197 126 87 93 45 NC_002967:TDE0305|3end_GTP-binding_protein_YchF_335645..335795_NEGATIVE 185 157 116 48 5 NC_002967:TDE1741|3end_penicillin-binding_protein_1795412..1795562_POSITIVE 178 47 4 73 31 NC_002967:TDE1248|3end_hypothetical_protein_1283620..1283770_POSITIVE 177 28 1 49 22 NC_002967:TDE1985|3end_hypothetical_protein_1997555..1997705_NEGATIVE 174 170 122 86 44 NC_002967:TDE2546|3end_hypothetical_protein_2571877..2572027_NEGATIVE 174 179 131 50 5 NC_002967:TDE1278|3end_conserved_hypothetical_protein_TIGR01440_1312228..1312378_NEGATIVE 173 169 146 113 93 NC_002967:TDE2733|3end_hypothetical_protein_2789126..2789276_POSITIVE 173 136 96 146 100 NC_002967:TDE1557|3end_hypothetical_protein_1600770..1600920_POSITIVE 173 169 146 79 59 NC_002967:TDE0943|3end_hypothetical_protein_966272..966422_POSITIVE 171 167 124 104 64 NC_002967:TDE0572|3end_hypothetical_protein_604734..604884_POSITIVE 170 174 133 58 17 NC_002967:TDE1855|3end_hypothetical_protein_1883213..1883363_POSITIVE 168 171 161 128 118 NC_002967:TDE2784|3end_hypothetical_protein_2838627..2838777_POSITIVE 168 169 146 147 127 NC_002967:TDE0976|3end_hypothetical_protein_1000498..1000648_POSITIVE 166 138 111 74 49 NC_002967:TDE2157|3end_ABC_transporter,_permease_protein,_putative_2191732..2191882_POSITIVE 166 169 129 129 82 NC_002967:TDE0089|3end_transglutaminase-like_domain_protein_106875..107025_NEGATIVE 165 179 155 48 26 NC_002967:TDE2436|3end_hypothetical_protein_2467446..2467596_POSITIVE 165 167 127 104 55 NC_002967:TDE0977|3end_hypothetical_protein_1001640..1001790_POSITIVE 164 172 135 149 114 NC_002967:TDE2128|3end_hypothetical_protein_2161558..2161708_POSITIVE