Origin IGS: ctctgtaccatttattgataaaattgatgcaaagatagaaattatcaatttgacaaaaggaatttataattgtatctttgcatgcaaataagattattaacaaacacataaaaaacagttagaat .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 attctaactgttttttatgtgtttgttaataatcttatttgcatgcaaagatacaattataaattccttttgtcaaattgataatttctatctttgcatcaattttatcaataaatggtacagag Mask Tandem Repeat Region ================================================ ctctgtaccatttattgataaaattgatgcaaagatagaaattatcaatttgacaaaaggaatttataattgtatctttgcatgcaaataagattattaacaaacacataaaaaacagttagaat Find is-nt database================================================ Query_seq: TF0104:TF0105|TF0104:TF0105:redox-sensitive transcriptional activator, OxyR:DNA-binding stress protein, Dps family:->->:113369..113493 125 ctctgtaccatttattgataaaattgatgcaaagatagaaattatcaatttgacaaaaggaatttataattgtatctttgcatgcaaataagattattaacaaacacataaaaaacagttagaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF0104:TF0105|TF0104:TF0105:redox-sensitive transcriptional activator, OxyR:DNA-binding stress protein, Dps family:->->:113369..113493 125 ctctgtaccatttattgataaaattgatgcaaagatagaaattatcaatttgacaaaaggaatttataattgtatctttgcatgcaaataagattattaacaaacacataaaaaacagttagaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF0104:TF0105|TF0104:TF0105:redox-sensitive transcriptional activator, OxyR:DNA-binding stress protein, Dps family:->->:113369..113493 125 ctctgtaccatttattgataaaattgatgcaaagatagaaattatcaatttgacaaaaggaatttataattgtatctttgcatgcaaataagattattaacaaacacataaaaaacagttagaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ctctgtaccatttattgataaaattgatgcaaagatagaaattatcaatttgacaaaaggaatttataattgtatctttgcatgcaaataagattattaacaaacacataaaaaacagttagaat Predict ORF larger than 30AA ================================================ Protein_Len: 39 Strand: - Start: 2 End: 118 . R Y W K N I F N I C L Y F N D I Q C F S N I I T D K C A F L I I L L C M F F M ....... ctctgtaccatttattgataaaattgatgcaaagatagaaattatcaatttgacaaaaggaatttataattgtatctttgcatgcaaataagattattaacaaacacataaaaaacagttagaat 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: 85 Start: 96 End: 125 ...............................................................................................ATTAACAAACACATAAAAAACAGTTAGAAT PromScan Matrix: RpoD-17 Strand: + Score: 84 Start: 49 End: 78 ................................................TTTGACAAAAGGAATTTATAATTGTATCTT............................................... PromScan Matrix: RpoD-17 Strand: + Score: 83 Start: 41 End: 70 ........................................ATTATCAATTTGACAAAAGGAATTTATAAT....................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ ctctgtaccatttattgataaaattgatgcaaagatagaaattatcaatttgacaaaaggaatttataattgtatctttgcatgcaaataagattattaacaaacacataaaaaacagttagaat Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TF0104:TF0105|TF0104:TF0105:redox-sensitive transcriptional activator, OxyR:DNA-binding stress protein, Dps family:->->:113369..113493 125 ctctgtaccatttattgataaaattgatgcaaagatagaaattatcaatttgacaaaaggaatttataattgtatctttgcatgcaaataagattattaacaaacacataaaaaacagttagaat Intra-Species Hit: Count: 1 Min: 1 Max: 125 Len: 125 Subject: tfor_TF0104_TF0105|redox-sensitive transcriptional activator, OxyR:DNA-binding stress protein, Dps family|POSITIVE:POSITIVE|[113369,113493]|125 HSP 1 e-value: 4.0E-65 bit: 248.0 Len: 125 Query Start:1 Query End:125 Subject Strand: POSITIVE Subject Start: 1 Subject End: 125 ctctgtaccatttattgataaaattgatgcaaagatagaaattatcaatttgacaaaaggaatttataattgtatctttgcatgcaaataagattattaacaaacacataaaaaacagttagaat ctctgtaccatttattgataaaattgatgcaaagatagaaattatcaatttgacaaaaggaatttataattgtatctttgcatgcaaataagattattaacaaacacataaaaaacagttagaat Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUCUGUACCAUUUAUUGAUAAAAUUGAUGCAAAGAUAGAAAUUAUCAAUUUGACAAAAGGAAUUUAUAAUUGUAUCUUUGCAUGCAAAUAAGAUUAUUAACAAACACAUAAAAAACAGUUAGAAU ..((((..((.....))......((((((((((((((..((((((.(((((........))))).)))))).))))))))))).)))...........................))))....... (-21.80) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUUCUAACUGUUUUUUAUGUGUUUGUUAAUAAUCUUAUUUGCAUGCAAAGAUACAAUUAUAAAUUCCUUUUGUCAAAUUGAUAAUUUCUAUCUUUGCAUCAAUUUUAUCAAUAAAUGGUACAGAG .......((((.........(((((((.((((......(((.(((((((((((.((((((.((((..........)))).))))))..))))))))))))))..)))).)))))))...)))).. (-21.20) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 275 119 71 216 161 tfor:TF0108|5end_thiamine_biosynthesis_protein,_ThiF_family_115168..115398_POSITIVE 232 85 41 173 126 tfor:TF0902|5end_methyltransferase_947237..947467_POSITIVE 217 70 28 79 40 tfor:TF1644|5end_conserved_hypothetical_protein_1752625..1752855_POSITIVE 207 37 2 170 133 tfor:TF1538|5end_conserved_hypothetical_protein_1643531..1643761_POSITIVE 195 85 70 60 45 tfor:TF1888|5end_RNA_polymerase_ECF-type_sigma_factor_2040940..2041170_POSITIVE 193 93 63 93 63 tfor:TF0852|5end_transcriptional_regulator,_TetR_family_903246..903476_POSITIVE 186 67 24 202 161 tfor:TF2409|5end_hypothetical_protein_2582972..2583202_POSITIVE 186 62 28 46 8 tfor:TF1270|5end_hypothetical_protein_1355273..1355503_POSITIVE 184 62 28 179 133 tfor:TF1766|5end_alanyl-tRNA_synthetase_1902858..1903088_POSITIVE 184 56 14 160 114 tfor:TF1211|5end_phosphoserine_aminotransferase_1298700..1298930_POSITIVE 182 119 73 63 12 tfor:TF1253|5end_hypothetical_protein_1335982..1336212_POSITIVE 182 83 49 55 14 tfor:TF0520|5end_tetraacyldisaccharide_4'-kinase_544752..544982_POSITIVE 177 67 33 212 177 tfor:TF0870|5end_conserved_hypothetical_protein_922126..922356_POSITIVE 175 89 51 199 159 tfor:TF1578|5end_hypothetical_protein_1686187..1686417_POSITIVE 175 41 24 182 165 tfor:TF0378|5end_aspartyl-tRNA_synthetase_397641..397871_POSITIVE 174 98 58 152 118 tfor:TF1861|5end_conserved_hypothetical_protein;_possible_membrane_protein_2017220..2017450_POSITIVE 173 48 2 121 73 tfor:TF1241|5end_prolyl-tRNA_synthetase_1324711..1324941_POSITIVE 172 34 3 52 24 tfor:TF0586|5end_conserved_hypothetical_protein_617313..617543_POSITIVE 170 94 59 142 100 tfor:TF2740|5end_conserved_hypothetical_protein_2920657..2920887_POSITIVE 169 118 71 189 137 tfor:TF0703|5end_conserved_hypothetical_protein_747252..747482_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 275 119 71 61 6 tfor:TF0107|3end_ion_channel_protein_115093..115243_POSITIVE 232 85 41 129 82 tfor:TF0901|3end_conserved_hypothetical_protein_947273..947423_POSITIVE 217 70 28 92 53 tfor:TF1643|3end_conserved_hypothetical_protein_1752718..1752868_POSITIVE 207 37 2 42 5 tfor:TF1536|3end_hypothetical_protein_1643483..1643633_POSITIVE 193 50 8 45 2 tfor:TF1195|3end_hypothetical_protein_1278845..1278995_POSITIVE 186 67 24 122 81 tfor:TF2408|3end_conserved_hypothetical_protein;_possible_sugar_transferase_2582972..2583122_POSITIVE 185 84 63 73 49 tfor:TF0748|3end_ATP-dependent_protease_La_795435..795585_POSITIVE 184 62 28 80 34 tfor:TF1765|3end_possible_peptidase_1902839..1902989_POSITIVE 182 119 73 85 34 tfor:TF1252|3end_phosphofructokinase;_pyrophosphate-fructose_6-phosphate_1-phosphotransferase_(probable_beta_subunit)_1336084..1336234_POSITIVE 177 46 1 70 13 tfor:TF2952|3end_transposase_3160989..3161139_POSITIVE 175 89 51 67 27 tfor:TF1576|3end_hypothetical_protein_1686135..1686285_POSITIVE 174 98 58 76 42 tfor:TF1860|3end_aspartate_carbamoyltransferase,_catalytic_subunit_2017224..2017374_POSITIVE 173 48 2 67 19 tfor:TF1240|3end_conserved_hypothetical_protein_1324737..1324887_POSITIVE 170 94 59 63 21 tfor:TF2739|3end_thioredoxin_2920658..2920808_POSITIVE 169 118 71 85 33 tfor:TF0702|3end_possible_peptidyl-prolyl_isomerase_747228..747378_POSITIVE 168 69 24 77 37 tfor:TF0785|3end_biopolymer_transport_protein,_MotA/TolQ/ExbB_proton_channel_family_838600..838750_POSITIVE 164 106 68 82 47 tfor:TF2583|3end_possible_ABC_transporter,__permease_component_2751026..2751176_POSITIVE 162 110 66 119 78 tfor:TF2204|3end_conserved_hypothetical_protein_2379122..2379272_POSITIVE 162 82 60 66 46 tfor:TF1733|3end_conserved_hypothetical_protein_1856562..1856712_POSITIVE 162 87 56 52 19 tfor:TF1108|3end_conserved_hypothetical_protein;_possible_lipoprotein_1178851..1179001_POSITIVE