Origin IGS: tcgcgtacgattttcccctcaaaaaataaataagacatactcgtttaatggtcatcttcgcctttttttgcaaatgccggttacggatacatatagttctatccgcta .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tagcggatagaactatatgtatccgtaaccggcatttgcaaaaaaaggcgaagatgaccattaaacgagtatgtcttatttattttttgaggggaaaatcgtacgcga Mask Tandem Repeat Region ================================================ tcgcgtacgattttcccctcaaaaaataaataagacatactcgtttaatggtcatcttcgcctttttttgcaaatgccggttacggatacatatagttctatccgcta Find is-nt database================================================ Query_seq: TF1938:TF1939|TF1938:TF1939:hypothetical protein:hypothetical protein:->->:2086331..2086438 108 tcgcgtacgattttcccctcaaaaaataaataagacatactcgtttaatggtcatcttcgcctttttttgcaaatgccggttacggatacatatagttctatccgcta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF1938:TF1939|TF1938:TF1939:hypothetical protein:hypothetical protein:->->:2086331..2086438 108 tcgcgtacgattttcccctcaaaaaataaataagacatactcgtttaatggtcatcttcgcctttttttgcaaatgccggttacggatacatatagttctatccgcta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF1938:TF1939|TF1938:TF1939:hypothetical protein:hypothetical protein:->->:2086331..2086438 108 tcgcgtacgattttcccctcaaaaaataaataagacatactcgtttaatggtcatcttcgcctttttttgcaaatgccggttacggatacatatagttctatccgcta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tcgcgtacgattttcccctcaaaaaataaataagacatactcgtttaatggtcatcttcgcctttttttgcaaatgccggttacggatacatatagttctatccgcta Predict ORF larger than 30AA ================================================ Protein_Len: 31 Strand: - Start: 2 End: 94 . A Y S K G R L F Y I L C V R K I T M K A K K Q L H R N R I C M .............. tcgcgtacgattttcccctcaaaaaataaataagacatactcgtttaatggtcatcttcgcctttttttgcaaatgccggttacggatacatatagttctatccgcta 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================================================ tcgcgtacgattttcccctcaaaaaataaataagacatactcgtttaatggtcatcttcgcctttttttgcaaatgccggttacggatacatatagttctatccgcta Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TF1938:TF1939|TF1938:TF1939:hypothetical protein:hypothetical protein:->->:2086331..2086438 108 tcgcgtacgattttcccctcaaaaaataaataagacatactcgtttaatggtcatcttcgcctttttttgcaaatgccggttacggatacatatagttctatccgcta Intra-Species Hit: Count: 1 Min: 1 Max: 108 Len: 108 Subject: tfor_TF1938_TF1939|hypothetical protein:hypothetical protein|POSITIVE:POSITIVE|[2086331,2086438]|108 HSP 1 e-value: 1.0E-42 bit: 172.0 Len: 108 Query Start:1 Query End:108 Subject Strand: POSITIVE Subject Start: 1 Subject End: 108 tcgcgtacgattttcccctcaaaaaataaataagacatactcgtttaatggtcatcttcgccnnnnnnngcaaatgccggttacggatacatatagttctatccgcta tcgcgtacgattttcccctcaaaaaataaataagacatactcgtttaatggtcatcttcgcctttttttgcaaatgccggttacggatacatatagttctatccgcta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCGCGUACGAUUUUCCCCUCAAAAAAUAAAUAAGACAUACUCGUUUAAUGGUCAUCUUCGCCUUUUUUUGCAAAUGCCGGUUACGGAUACAUAUAGUUCUAUCCGCUA ..(((..............(((((((......((((......))))...(((.......))).)))))))......(((....))).................))).. (-11.90) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAGCGGAUAGAACUAUAUGUAUCCGUAACCGGCAUUUGCAAAAAAAGGCGAAGAUGACCAUUAAACGAGUAUGUCUUAUUUAUUUUUUGAGGGGAAAAUCGUACGCGA ..(((((((.(......).)))))))....(((((((((........)))..)))).))......((.((((((((..((........))..)))....))))).)). (-21.80) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 371 81 47 133 97 tfor:TF0265|5end_conserved_hypothetical_protein,_Rhs_family_293279..293509_POSITIVE 327 90 42 222 177 tfor:TF2560|5end_30S_ribosomal_protein_S3_2737897..2738127_POSITIVE 314 89 48 203 152 tfor:TF2932|5end_capsule_biosynthesis_protein_3135514..3135744_POSITIVE 310 85 49 124 85 tfor:TF1730|5end_diaminopimelate_decarboxylase_1854670..1854900_POSITIVE 310 85 49 73 34 tfor:TF1732|5end_conserved_hypothetical_protein_1854619..1854849_POSITIVE 307 89 43 224 181 tfor:TF2412|5end_outer_membrane_protein_2587017..2587247_POSITIVE 306 86 41 220 182 tfor:TF2822|5end_arginine_repressor_3011793..3012023_POSITIVE 296 96 53 84 37 tfor:TF2378|5end_peptide_chain_release_factor_1_2542682..2542912_POSITIVE 294 84 41 55 13 tfor:TF2035|5end_conserved_hypothetical_protein_2194665..2194895_POSITIVE 290 97 52 62 9 tfor:TF2214|5end_peptidyl-prolyl_cis-trans_isomerase_2386897..2387127_POSITIVE 290 83 49 51 1 tfor:TF1602|5end_L-aspartate_oxidase_1715579..1715809_POSITIVE 286 87 41 186 138 tfor:TF0305|5end_peptidyl-prolyl_cis-trans_isomerase_330280..330510_POSITIVE 284 88 42 67 20 tfor:TF0249|5end_3-hydroxymyristoyl/3-hydroxydecanoyl-(acyl_carrier_protein)_dehydratase_278808..279038_POSITIVE 283 99 56 46 1 tfor:TF2979|5end_possible_outer_membrane__protein_3190778..3191008_POSITIVE 280 79 31 58 10 tfor:TF0827|5end_conserved_hypothetical_protein_886240..886470_POSITIVE 277 86 42 143 99 tfor:TF0292|5end_conserved_hypothetical_protein_320087..320317_POSITIVE 276 100 60 50 12 tfor:TF1864|5end_conserved_hypothetical_protein_2020289..2020519_POSITIVE 275 88 41 180 126 tfor:TF1886|5end_auxin-regulated_protein_2038720..2038950_POSITIVE 274 99 51 62 12 tfor:TF1577|5end_hypothetical_protein_1685960..1686190_POSITIVE 271 86 49 49 6 tfor:TF2696|5end_oxidoreductase,_short_chain_dehydrogenase/reductase_family_2870752..2870982_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 333 90 57 149 110 tfor:TF2674|3end_conserved_hypothetical_protein;_possible_phosphoesterase_2848777..2848927_POSITIVE 310 85 49 92 53 tfor:TF1729|3end_aspartokinase_1854718..1854868_POSITIVE 294 84 41 48 6 tfor:TF2034|3end_arabinose-proton_symporter_2194738..2194888_POSITIVE 290 99 53 50 3 tfor:TF2978|3end_conserved_hypothetical_protein_3190862..3191012_POSITIVE 285 86 41 80 27 tfor:TF2694|3end_hypothetical_protein_2870863..2871013_POSITIVE 284 88 42 74 27 tfor:TF0248|3end_hypothetical_protein_278895..279045_POSITIVE 283 81 41 148 104 tfor:TF0525|3end_conserved_hypothetical_protein_549584..549734_POSITIVE 277 86 42 107 63 tfor:TF0291|3end_triose-phosphate_isomerase_320131..320281_POSITIVE 276 87 42 150 97 tfor:TF1174|3end_ABC_transporter,_permease_component_1257896..1258046_POSITIVE 275 88 41 131 77 tfor:TF1885|3end_conserved_hypothetical_protein_2038751..2038901_POSITIVE 267 90 50 150 103 tfor:TF1576|3end_hypothetical_protein_1686135..1686285_POSITIVE 266 90 49 144 96 tfor:TF0569|3end_indolepyruvate_ferredoxin_oxidoreductase,_beta_subunit_602378..602528_POSITIVE 265 82 41 61 23 tfor:TF1713|3end_hypothetical_protein_1833716..1833866_POSITIVE 264 86 41 143 101 tfor:TF3143|3end_conserved_hypothetical_protein;_possible_membrane_protein_3379227..3379377_POSITIVE 263 99 53 63 3 tfor:TF0235|3end_hypothetical_protein_261849..261999_POSITIVE 255 96 52 127 88 tfor:TF3154|3end_conserved_hypothetical_protein_3390489..3390639_POSITIVE 253 88 52 58 22 tfor:TF1930|3end_two-component_response_regulator_2078203..2078353_POSITIVE 253 85 41 147 96 tfor:TF1743|3end_conserved_hypothetical_protein_1877909..1878059_POSITIVE 253 89 50 59 25 tfor:TF1537|3end_hypothetical_protein_1643336..1643486_POSITIVE 252 86 41 146 96 tfor:TF2686|3end_ABC_transporter,_ATP-binding_protein_2863576..2863726_POSITIVE