Origin IGS: tgaaaaatgaaagagttgcgggcagtgcttgcagctcttttttatttcatacacaattttacaagtttttcagagttatacatatctatagatgtaactctttcga .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tcgaaagagttacatctatagatatgtataactctgaaaaacttgtaaaattgtgtatgaaataaaaaagagctgcaagcactgcccgcaactctttcatttttca Mask Tandem Repeat Region ================================================ tgaaaaatgaaagagttgcgggcagtgcttgcagctcttttttatttcatacacaattttacaagtttttcagagttatacatatctatagatgtaactctttcga Find is-nt database================================================ Query_seq: TF2325:TF2326|TF2325:TF2326:conserved hypothetical protein:conserved hypothetical protein:->->:2484720..2484825 106 tgaaaaatgaaagagttgcgggcagtgcttgcagctcttttttatttcatacacaattttacaagtttttcagagttatacatatctatagatgtaactctttcga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF2325:TF2326|TF2325:TF2326:conserved hypothetical protein:conserved hypothetical protein:->->:2484720..2484825 106 tgaaaaatgaaagagttgcgggcagtgcttgcagctcttttttatttcatacacaattttacaagtttttcagagttatacatatctatagatgtaactctttcga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF2325:TF2326|TF2325:TF2326:conserved hypothetical protein:conserved hypothetical protein:->->:2484720..2484825 106 tgaaaaatgaaagagttgcgggcagtgcttgcagctcttttttatttcatacacaattttacaagtttttcagagttatacatatctatagatgtaactctttcga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tgaaaaatgaaagagttgcgggcagtgcttgcagctcttttttatttcatacacaattttacaagtttttcagagttatacatatctatagatgtaactctttcga Predict ORF larger than 30AA ================================================ Protein_Len: 33 Strand: + Start: 7 End: 105 ...... M K E L R A V L A A L F Y F I H N F T S F S E L Y I S I D V T L S . tgaaaaatgaaagagttgcgggcagtgcttgcagctcttttttatttcatacacaattttacaagtttttcagagttatacatatctatagatgtaactctttcga 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================================================ tgaaaaatgaaagagttgcgggcagtgcttgcagctcttttttatttcatacacaattttacaagtttttcagagttatacatatctatagatgtaactctttcga Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TF2325:TF2326|TF2325:TF2326:conserved hypothetical protein:conserved hypothetical protein:->->:2484720..2484825 106 tgaaaaatgaaagagttgcgggcagtgcttgcagctcttttttatttcatacacaattttacaagtttttcagagttatacatatctatagatgtaactctttcga Intra-Species Hit: Count: 1 Min: 1 Max: 106 Len: 106 Subject: tfor_TF2325_TF2326|conserved hypothetical protein:conserved hypothetical protein|POSITIVE:POSITIVE|[2484720,2484825]|106 HSP 1 e-value: 6.0E-54 bit: 210.0 Len: 106 Query Start:1 Query End:106 Subject Strand: POSITIVE Subject Start: 1 Subject End: 106 tgaaaaatgaaagagttgcgggcagtgcttgcagctcttttttatttcatacacaattttacaagtttttcagagttatacatatctatagatgtaactctttcga tgaaaaatgaaagagttgcgggcagtgcttgcagctcttttttatttcatacacaattttacaagtttttcagagttatacatatctatagatgtaactctttcga Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGAAAAAUGAAAGAGUUGCGGGCAGUGCUUGCAGCUCUUUUUUAUUUCAUACACAAUUUUACAAGUUUUUCAGAGUUAUACAUAUCUAUAGAUGUAACUCUUUCGA (((((...(((((((((((((((...)))))))))))))))...)))))......................(((((((((..((....))..)))))))))..... (-31.70) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCGAAAGAGUUACAUCUAUAGAUAUGUAUAACUCUGAAAAACUUGUAAAAUUGUGUAUGAAAUAAAAAAGAGCUGCAAGCACUGCCCGCAACUCUUUCAUUUUUCA .....((((((((((........)))))..)))))......................(((((....((((((.(((..((...))..))).))))))....))))) (-18.70) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 358 52 11 155 114 tfor:TF1327|5end_L-fucose_permease_1405790..1406020_POSITIVE 333 43 12 219 188 tfor:TF1797|5end_SNF_family_transporter_1937136..1937366_POSITIVE 305 35 1 206 172 tfor:TF1634|5end_hypothetical_protein_1746831..1747061_POSITIVE 297 55 17 151 119 tfor:TF0302|5end_FKBP-type_peptidyl-prolyl_cis-trans_isomerase_328641..328871_POSITIVE 293 50 11 91 44 tfor:TF2804|5end_conserved_hypothetical_protein_2993494..2993724_POSITIVE 288 54 11 143 89 tfor:TF1948|5end_conserved_hypothetical_protein_2095942..2096172_POSITIVE 282 39 13 182 158 tfor:TF1187|5end_hypothetical_protein_1269625..1269855_POSITIVE 282 39 13 125 101 tfor:TF1186|5end_hypothetical_protein_1269568..1269798_POSITIVE 282 39 13 148 124 tfor:TF1184|5end_hypothetical_protein_1269004..1269234_POSITIVE 280 42 12 153 121 tfor:TF1610|5end_peptide_chain_release_factor_RF-2_1728635..1728865_POSITIVE 280 42 12 87 55 tfor:TF1612|5end_conserved_hypothetical_protein_1728569..1728799_POSITIVE 279 33 13 219 194 tfor:TF1543|5end_conserved_hypothetical_protein_1649429..1649659_POSITIVE 278 53 15 85 27 tfor:TF0424|5end_outer_membrane_receptor,_TonB-linked_440028..440258_POSITIVE 277 38 1 148 113 tfor:TF3136|5end_Na+-translocating_NADH-quinone_reductase,_subunit_F_3369994..3370224_POSITIVE 276 41 1 141 99 tfor:TF0457|5end_beta-glucanase_precursor_474099..474329_POSITIVE 269 37 8 175 143 tfor:TF1730|5end_diaminopimelate_decarboxylase_1854670..1854900_POSITIVE 269 37 8 124 92 tfor:TF1732|5end_conserved_hypothetical_protein_1854619..1854849_POSITIVE 269 38 12 158 127 tfor:TF0023|5end_possible_response_element_in_two_component_regulation_19446..19676_POSITIVE 268 55 12 71 25 tfor:TF2876|5end_cytosine_deaminase_3065144..3065374_POSITIVE 267 39 11 67 27 tfor:TF1868|5end_conserved_hypothetical_protein;_possible_transposase_2022598..2022828_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 455 49 1 90 42 tfor:TF2325|3end_conserved_hypothetical_protein_2484659..2484809_POSITIVE 305 35 1 126 92 tfor:TF1635|3end_conserved_hypothetical_protein;_possible_helicase_1746831..1746981_POSITIVE 293 43 11 146 114 tfor:TF1325|3end_L-fucose_isomerase_1405870..1406020_POSITIVE 288 54 11 144 90 tfor:TF1947|3end_conserved_hypothetical_protein_2096023..2096173_POSITIVE 282 39 13 40 16 tfor:TF1185|3end_hypothetical_protein_1269563..1269713_POSITIVE 280 42 12 58 26 tfor:TF1609|3end_hypothetical_protein_1728620..1728770_POSITIVE 277 38 1 148 113 tfor:TF3135|3end_hypothetical_protein_3370074..3370224_POSITIVE 277 43 15 44 11 tfor:TF2260|3end_transfer_region-related_protein,_TraL_2430592..2430742_POSITIVE 276 41 1 134 92 tfor:TF0456|3end_conserved_hypothetical_protein_474172..474322_POSITIVE 269 37 8 143 111 tfor:TF1729|3end_aspartokinase_1854718..1854868_POSITIVE 268 55 12 71 25 tfor:TF2874|3end_conserved_hypothetical_protein_3065224..3065374_POSITIVE 268 48 1 68 19 tfor:TF2349|3end_conserved_hypothetical_protein_2514921..2515071_POSITIVE 266 50 9 72 23 tfor:TF2662|3end_hypothetical_protein_2837131..2837281_POSITIVE 266 35 8 96 66 tfor:TF0528|3end_two-component_system_sensor_histidine_kinase_554779..554929_POSITIVE 265 39 6 98 72 tfor:TF3106|3end_hypothetical_protein_3338608..3338758_POSITIVE 259 48 2 62 21 tfor:TF2654|3end_arginyl-tRNA_synthetase_2824559..2824709_POSITIVE 259 48 11 94 63 tfor:TF1026|3end_beta-N-acetylglucosaminidase;_beta_lactamase_1085639..1085789_POSITIVE 256 38 6 137 112 tfor:TF0678|3end_hypothetical_protein_721335..721485_POSITIVE 256 49 11 36 2 tfor:TF0189|3end_phosphatidate_cytidylytransferase_(CDP-diglyceride_synthetase)_204090..204240_POSITIVE 255 43 6 74 34 tfor:TF0541|3end_conserved_hypothetical_protein_571858..572008_POSITIVE