Origin IGS: taacagtcgatatattcccgattatcaatattgcacaacccgaaacttattcctaattttgccccaaaatattactactaactaacccaatgcctgtgtactatacacaccgatttagata .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tatctaaatcggtgtgtatagtacacaggcattgggttagttagtagtaatattttggggcaaaattaggaataagtttcgggttgtgcaatattgataatcgggaatatatcgactgtta Mask Tandem Repeat Region ================================================ taacagtcgatatattcccgattatcaatattgcacaacccgaaacttattcctaattttgccccaaaatattactactaactaacccaatgcctgtgtactatacacaccgatttagata Find is-nt database================================================ Query_seq: TF0272:TF0273|TF0272:TF0273:outer membrane protein:DNA polymerase III, epsilon chain:->->:299788..299908 121 taacagtcgatatattcccgattatcaatattgcacaacccgaaacttattcctaattttgccccaaaatattactactaactaacccaatgcctgtgtactatacacaccgatttagata Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF0272:TF0273|TF0272:TF0273:outer membrane protein:DNA polymerase III, epsilon chain:->->:299788..299908 121 taacagtcgatatattcccgattatcaatattgcacaacccgaaacttattcctaattttgccccaaaatattactactaactaacccaatgcctgtgtactatacacaccgatttagata Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF0272:TF0273|TF0272:TF0273:outer membrane protein:DNA polymerase III, epsilon chain:->->:299788..299908 121 taacagtcgatatattcccgattatcaatattgcacaacccgaaacttattcctaattttgccccaaaatattactactaactaacccaatgcctgtgtactatacacaccgatttagata Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taacagtcgatatattcccgattatcaatattgcacaacccgaaacttattcctaattttgccccaaaatattactactaactaacccaatgcctgtgtactatacacaccgatttagata Predict ORF larger than 30AA ================================================ taacagtcgatatattcccgattatcaatattgcacaacccgaaacttattcctaattttgccccaaaatattactactaactaacccaatgcctgtgtactatacacaccgatttagata 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================================================ taacagtcgatatattcccgattatcaatattgcacaacccgaaacttattcctaattttgccccaaaatattactactaactaacccaatgcctgtgtactatacacaccgatttagata Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TF0272:TF0273|TF0272:TF0273:outer membrane protein:DNA polymerase III, epsilon chain:->->:299788..299908 121 taacagtcgatatattcccgattatcaatattgcacaacccgaaacttattcctaattttgccccaaaatattactactaactaacccaatgcctgtgtactatacacaccgatttagata Intra-Species Hit: Count: 1 Min: 1 Max: 121 Len: 121 Subject: tfor_TF0272_TF0273|outer membrane protein:DNA polymerase III, epsilon chain|POSITIVE:POSITIVE|[299788,299908]|121 HSP 1 e-value: 8.0E-63 bit: 240.0 Len: 121 Query Start:1 Query End:121 Subject Strand: POSITIVE Subject Start: 1 Subject End: 121 taacagtcgatatattcccgattatcaatattgcacaacccgaaacttattcctaattttgccccaaaatattactactaactaacccaatgcctgtgtactatacacaccgatttagata taacagtcgatatattcccgattatcaatattgcacaacccgaaacttattcctaattttgccccaaaatattactactaactaacccaatgcctgtgtactatacacaccgatttagata Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAACAGUCGAUAUAUUCCCGAUUAUCAAUAUUGCACAACCCGAAACUUAUUCCUAAUUUUGCCCCAAAAUAUUACUACUAACUAACCCAAUGCCUGUGUACUAUACACACCGAUUUAGAUA ....(((((.........)))))....(((.((((((....(((.....)))...((((((...))))))........................)))))).)))................. ( -9.10) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAUCUAAAUCGGUGUGUAUAGUACACAGGCAUUGGGUUAGUUAGUAGUAAUAUUUUGGGGCAAAAUUAGGAAUAAGUUUCGGGUUGUGCAAUAUUGAUAAUCGGGAAUAUAUCGACUGUUA ........(((((((((...((......))....(((((.((((((...(((.((((..((..............))..)))).)))....)))))))))))....)))))))))...... (-19.84) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 247 46 18 225 191 tfor:TF2772|5end_tRNA_pseudouridine_synthase_B_2957383..2957613_POSITIVE 238 100 51 183 145 tfor:TF0120|5end_hexouronate_transporter_131307..131537_POSITIVE 234 45 5 227 188 tfor:TF0179|5end_pyrophosphate-energized_proton_pump_188413..188643_POSITIVE 229 47 1 193 149 tfor:TF2177|5end_hypothetical_protein_2349281..2349511_POSITIVE 224 99 52 126 82 tfor:TF2892|5end_seryl-tRNA_synthetase_3079309..3079539_POSITIVE 224 50 3 160 103 tfor:TF0231|5end_conserved_hypothetical_protein_257804..258034_POSITIVE 223 44 4 155 117 tfor:TF1818|5end_conserved_hypothetical_protein_1957967..1958197_POSITIVE 223 79 31 112 62 tfor:TF1573|5end_ATP_synthase,_subunit_E_1680955..1681185_POSITIVE 222 65 25 64 18 tfor:TF0389|5end_conserved_hypothetical_protein;_possible_integral_membrane_protein_408774..409004_POSITIVE 218 42 4 139 89 tfor:TF2502|5end_conserved_hypothetical_protein_2678103..2678333_POSITIVE 218 65 22 188 140 tfor:TF0302|5end_FKBP-type_peptidyl-prolyl_cis-trans_isomerase_328641..328871_POSITIVE 213 66 25 179 136 tfor:TF1854|5end_competence-damage_protein_CinA_2007469..2007699_POSITIVE 211 50 4 185 137 tfor:TF0449|5end_transposase_467891..468121_POSITIVE 210 52 17 150 113 tfor:TF0156|5end_conserved_hypothetical_protein_164973..165203_POSITIVE 209 112 71 65 14 tfor:TF0790|5end_conserved_hypothetical_protein_843920..844150_POSITIVE 208 43 1 59 30 tfor:TF2108|5end_hypothetical_protein_2277385..2277615_POSITIVE 208 101 61 170 118 tfor:TF1406|5end_transposase_1481758..1481988_POSITIVE 207 44 7 193 165 tfor:TF2977|5end_candidate_b-glycosyltransferase,_Glycosyltransferase_Family_2_protein_3185228..3185458_POSITIVE 206 79 32 166 119 tfor:TF0403|5end_TPR_repeat_protein_422600..422830_POSITIVE 206 97 51 53 8 tfor:TF0402|5end_conserved_hypothetical_protein_422107..422337_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 243 107 61 94 46 tfor:TF2615|3end_conserved_hypothetical_protein_2791209..2791359_POSITIVE 238 100 51 130 92 tfor:TF0119|3end_gluconate_aldolase_131334..131484_POSITIVE 234 104 62 91 50 tfor:TF2366|3end_conserved_hypothetical_protein_2531892..2532042_POSITIVE 224 99 52 118 74 tfor:TF2891|3end_lipoprotein_3079381..3079531_POSITIVE 224 50 3 138 81 tfor:TF0230|3end_hydrolase,_haloacid_dehalogenase-like_family_257862..258012_POSITIVE 223 44 4 82 44 tfor:TF1816|3end_hypothetical_protein_1957974..1958124_POSITIVE 223 44 4 99 61 tfor:TF1817|3end_hypothetical_protein_1957991..1958141_POSITIVE 223 79 31 109 59 tfor:TF1571|3end_conserved_hypothetical_protein_1681032..1681182_POSITIVE 222 65 25 56 10 tfor:TF0388|3end_conserved_hypothetical_protein;_possible_integral_membrane_protein_408846..408996_POSITIVE 218 42 4 139 89 tfor:TF2501|3end_DNA_mismatch_repair_protein_2678183..2678333_POSITIVE 217 50 8 46 7 tfor:TF2603|3end_transcriptional_regulator,_AraC_family_2777272..2777422_POSITIVE 213 66 25 124 81 tfor:TF1853|3end_homoserine_O-succinyltransferase_2007494..2007644_POSITIVE 211 50 4 125 77 tfor:TF0448|3end_hypothetical_protein_467911..468061_POSITIVE 209 43 8 134 105 tfor:TF1540|3end_possible_ATPase_1645987..1646137_POSITIVE 208 43 1 30 1 tfor:TF2107|3end_hypothetical_protein_2277436..2277586_POSITIVE 208 101 61 151 99 tfor:TF1405|3end_conserved_hypothetical_protein_1481819..1481969_POSITIVE 206 79 32 95 48 tfor:TF0402|3end_conserved_hypothetical_protein_422609..422759_POSITIVE 205 112 88 97 73 tfor:TF0429|3end_ABC_transporter,_ATP-binding_protein_452227..452377_POSITIVE 204 45 4 71 25 tfor:TF3088|3end_conserved_hypothetical_protein_3323791..3323941_POSITIVE 203 114 86 82 64 tfor:TF2793|3end_possible_L-lysine_2,3-aminomutase_2979888..2980038_POSITIVE