Origin IGS: taatatagtatagatattgatggtttacaaatgtaaacatcctattaaaaagcgatagagattcgcataaacaatagaaaatcagttatgataccaatctattatttttaggtacaagtctatttacaattattttttgaaaaaggagccgtctcatatctcagcataaagagacggcttttta .........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 taaaaagccgtctctttatgctgagatatgagacggctcctttttcaaaaaataattgtaaatagacttgtacctaaaaataatagattggtatcataactgattttctattgtttatgcgaatctctatcgctttttaataggatgtttacatttgtaaaccatcaatatctatactatatta Mask Tandem Repeat Region ================================================ taatatagtatagatattgatggtttacaaatgtaaacatcctattaaaaagcgatagagattcgcataaacaatagaaaatcagttatgataccaatctattatttttaggtacaagtctatttacaattattttttgaaaaaggagccgtctcatatctcagcataaagagacggcttttta Find is-nt database================================================ Query_seq: TF0569:TF0570|TF0569:TF0570:indolepyruvate ferredoxin oxidoreductase, beta subunit:possible transcriptional regulator:->->:602439..602622 184 taatatagtatagatattgatggtttacaaatgtaaacatcctattaaaaagcgatagagattcgcataaacaatagaaaatcagttatgataccaatctattatttttaggtacaagtctatttacaattattttttgaaaaaggagccgtctcatatctcagcataaagagacggcttttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF0569:TF0570|TF0569:TF0570:indolepyruvate ferredoxin oxidoreductase, beta subunit:possible transcriptional regulator:->->:602439..602622 184 taatatagtatagatattgatggtttacaaatgtaaacatcctattaaaaagcgatagagattcgcataaacaatagaaaatcagttatgataccaatctattatttttaggtacaagtctatttacaattattttttgaaaaaggagccgtctcatatctcagcataaagagacggcttttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF0569:TF0570|TF0569:TF0570:indolepyruvate ferredoxin oxidoreductase, beta subunit:possible transcriptional regulator:->->:602439..602622 184 taatatagtatagatattgatggtttacaaatgtaaacatcctattaaaaagcgatagagattcgcataaacaatagaaaatcagttatgataccaatctattatttttaggtacaagtctatttacaattattttttgaaaaaggagccgtctcatatctcagcataaagagacggcttttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taatatagtatagatattgatggtttacaaatgtaaacatcctattaaaaagcgatagagattcgcataaacaatagaaaatcagttatgataccaatctattatttttaggtacaagtctatttacaattattttttgaaaaaggagccgtctcatatctcagcataaagagacggcttttta Predict ORF larger than 30AA ================================================ taatatagtatagatattgatggtttacaaatgtaaacatcctattaaaaagcgatagagattcgcataaacaatagaaaatcagttatgataccaatctattatttttaggtacaagtctatttacaattattttttgaaaaaggagccgtctcatatctcagcataaagagacggcttttta 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: 2 End: 31 .TTTGTAAACCATCAATATCTATACTATATT......................................................................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ taatatagtatagatattgatggtttacaaatgtaaacatcctattaaaaagcgatagagattcgcataaacaatagaaaatcagttatgataccaatctattatttttaggtacaagtctatttacaattattttttgaaaaaggagccgtctcatatctcagcataaagagacggcttttta Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TF0569:TF0570|TF0569:TF0570:indolepyruvate ferredoxin oxidoreductase, beta subunit:possible transcriptional regulator:->->:602439..602622 184 taatatagtatagatattgatggtttacaaatgtaaacatcctattaaaaagcgatagagattcgcataaacaatagaaaatcagttatgataccaatctattatttttaggtacaagtctatttacaattattttttgaaaaaggagccgtctcatatctcagcataaagagacggcttttta Intra-Species Hit: Count: 1 Min: 1 Max: 184 Len: 184 Subject: tfor_TF0569_TF0570|indolepyruvate ferredoxin oxidoreductase, beta subunit:possible transcriptional regulator|POSITIVE:POSITIVE|[602439,602622]|184 HSP 1 e-value: 1.0E-100 bit: 365.0 Len: 184 Query Start:1 Query End:184 Subject Strand: POSITIVE Subject Start: 1 Subject End: 184 taatatagtatagatattgatggtttacaaatgtaaacatcctattaaaaagcgatagagattcgcataaacaatagaaaatcagttatgataccaatctattatttttaggtacaagtctatttacaattattttttgaaaaaggagccgtctcatatctcagcataaagagacggcttttta taatatagtatagatattgatggtttacaaatgtaaacatcctattaaaaagcgatagagattcgcataaacaatagaaaatcagttatgataccaatctattatttttaggtacaagtctatttacaattattttttgaaaaaggagccgtctcatatctcagcataaagagacggcttttta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAUAUAGUAUAGAUAUUGAUGGUUUACAAAUGUAAACAUCCUAUUAAAAAGCGAUAGAGAUUCGCAUAAACAAUAGAAAAUCAGUUAUGAUACCAAUCUAUUAUUUUUAGGUACAAGUCUAUUUACAAUUAUUUUUUGAAAAAGGAGCCGUCUCAUAUCUCAGCAUAAAGAGACGGCUUUUUA .......((((((((.(((...((((((....))))))..((((..((...((((.......))))......((((((..((((....)))).....)))))).))..))))..))))))))..)))...............(((((((((((((...............))))))))))))). (-42.46) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAAAAGCCGUCUCUUUAUGCUGAGAUAUGAGACGGCUCCUUUUUCAAAAAAUAAUUGUAAAUAGACUUGUACCUAAAAAUAAUAGAUUGGUAUCAUAACUGAUUUUCUAUUGUUUAUGCGAAUCUCUAUCGCUUUUUAAUAGGAUGUUUACAUUUGUAAACCAUCAAUAUCUAUACUAUAUUA .....(((((((((..(((......))).))))))))).............((((.((((((((..(((((......(((((((((((..((......))..)...))))))))))..((((.......))))......))))).)))))))).)))).......................... (-40.40) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 348 179 136 106 60 tfor:TF1257|5end_hypothetical_protein_1338118..1338348_POSITIVE 348 179 136 71 25 tfor:TF1256|5end_hypothetical_protein_1338083..1338313_POSITIVE 315 180 144 115 78 tfor:TF2019|5end_dipeptidyl_peptidase_VI_2175242..2175472_POSITIVE 302 179 145 169 145 tfor:TF0090|5end_conserved_hypothetical_protein_96285..96515_POSITIVE 293 178 142 48 5 tfor:TF2750|5end_L-serine_dehydratase_2934432..2934662_POSITIVE 284 178 144 187 156 tfor:TF2774|5end_2-amino-4-hydroxy-6-hydroxymethyldihydropteridine_pyrophosphokinase_2959133..2959363_POSITIVE 280 180 133 149 103 tfor:TF0586|5end_conserved_hypothetical_protein_617313..617543_POSITIVE 273 180 143 154 119 tfor:TF2790|5end_prismane_protein,_hybrid-cluster_protein_2973397..2973627_POSITIVE 251 178 146 97 69 tfor:TF1718|5end_conserved_hypothetical_protein_1840462..1840692_POSITIVE 248 180 148 213 180 tfor:TF3027|5end_zinc_metalloprotease_3250223..3250453_POSITIVE 246 180 140 127 93 tfor:TF2652|5end_hypothetical_protein_2821803..2822033_POSITIVE 246 180 140 79 45 tfor:TF2651|5end_hypothetical_protein_2821755..2821985_POSITIVE 245 175 139 162 126 tfor:TF2585|5end_hypothetical_protein_2751264..2751494_POSITIVE 245 175 139 78 42 tfor:TF2584|5end_hypothetical_protein_2751180..2751410_POSITIVE 244 180 145 206 174 tfor:TF2596|5end_conserved_hypothetical_protein;_possible_lipoprotein_2766667..2766897_POSITIVE 241 176 133 65 22 tfor:TF2897|5end_iron(III)_ABC_transporter,_permease_component_3085898..3086128_POSITIVE 241 167 138 207 178 tfor:TF2416|5end_conserved_hypothetical_protein_2592138..2592368_POSITIVE 239 178 146 207 168 tfor:TF2291|5end_outer_membrane_protein_2446098..2446328_POSITIVE 239 178 136 218 178 tfor:TF0601|5end_aminomethyltransferase_(glycine_cleavage_system_T_protein)_631081..631311_POSITIVE 238 176 145 53 20 tfor:TF0302|5end_FKBP-type_peptidyl-prolyl_cis-trans_isomerase_328641..328871_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 348 179 136 59 13 tfor:TF1255|3end_conserved_hypothetical_protein_1338151..1338301_POSITIVE 319 180 139 42 6 tfor:TF0428|3end_methylmalonyl-CoA_mutase,_beta_subunit_450033..450183_POSITIVE 315 180 144 108 71 tfor:TF2018|3end_hypothetical_protein_2175315..2175465_POSITIVE 293 178 142 54 11 tfor:TF2749|3end_possible_hemolysin_2934518..2934668_POSITIVE 273 180 143 42 7 tfor:TF2789|3end_enoyl-[acyl-carrier-protein]_reductase_2973365..2973515_POSITIVE 268 179 141 58 29 tfor:TF2349|3end_conserved_hypothetical_protein_2514921..2515071_POSITIVE 251 178 146 49 21 tfor:TF1717|3end_DNA_mismatch_repair_protein_1840494..1840644_POSITIVE 246 180 140 50 16 tfor:TF2650|3end_succinate_dehydrogenase,_iron-sulfur_subunit_2821806..2821956_POSITIVE 246 179 134 115 64 tfor:TF0644|3end_pyruvate_phosphate_dikinase_688581..688731_POSITIVE 244 176 146 142 112 tfor:TF3055|3end_hypothetical_protein_3279034..3279184_POSITIVE 238 176 145 90 57 tfor:TF0303|3end_conserved_hypothetical_protein_328758..328908_POSITIVE 234 180 138 61 22 tfor:TF2753|3end_zinc_protease_2940448..2940598_POSITIVE 234 177 143 54 26 tfor:TF2601|3end_conserved_hypothetical_protein_2775139..2775289_POSITIVE 232 179 137 43 8 tfor:TF0018|3end_hypothetical_protein_12091..12241_POSITIVE 228 67 22 113 57 tfor:TF0990|3end_hypothetical_protein_1046662..1046812_POSITIVE 228 180 147 102 69 tfor:TF0685|3end_hypothetical_protein_731132..731282_POSITIVE 225 178 149 40 12 tfor:TF1605|3end_outer_membrane_protein,_TonB_dependent_receptor_1722414..1722564_POSITIVE 224 177 133 122 87 tfor:TF2709|3end_hypothetical_protein_2882392..2882542_POSITIVE 224 177 142 114 61 tfor:TF1047|3end_tRNA_pseudouridylate_synthetase_A_(pseudouridylate_synthase_I)_1109318..1109468_POSITIVE 222 180 145 34 2 tfor:TF2177|3end_hypothetical_protein_2349579..2349729_POSITIVE