Origin IGS: tccctaacccgtttagacatttatacccaatatttagatataacgtaggaaaaagcaaaagcgtatattggggcggttgattttttttttgaatgggtatcgccttttttcaagcagagagaaatatcctgctcgaaaactcctacctttgcctcggaaaaaagtaacatgag .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 ctcatgttacttttttccgaggcaaaggtaggagttttcgagcaggatatttctctctgcttgaaaaaaggcgatacccattcaaaaaaaaaatcaaccgccccaatatacgcttttgctttttcctacgttatatctaaatattgggtataaatgtctaaacgggttaggga Mask Tandem Repeat Region ================================================ tccctaacccgtttagacatttatacccaatatttagatataacgtaggaaaaagcaaaagcgtatattggggcggttgattttttttttgaatgggtatcgccttttttcaagcagagagaaatatcctgctcgaaaactcctacctttgcctcggaaaaaagtaacatgag Find is-nt database================================================ Query_seq: TF2902:TF2903|TF2902:TF2903:holliday junction DNA helicase:translation initiation factor SUI1:->->:3098541..3098713 173 tccctaacccgtttagacatttatacccaatatttagatataacgtaggaaaaagcaaaagcgtatattggggcggttgattttttttttgaatgggtatcgccttttttcaagcagagagaaatatcctgctcgaaaactcctacctttgcctcggaaaaaagtaacatgag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF2902:TF2903|TF2902:TF2903:holliday junction DNA helicase:translation initiation factor SUI1:->->:3098541..3098713 173 tccctaacccgtttagacatttatacccaatatttagatataacgtaggaaaaagcaaaagcgtatattggggcggttgattttttttttgaatgggtatcgccttttttcaagcagagagaaatatcctgctcgaaaactcctacctttgcctcggaaaaaagtaacatgag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF2902:TF2903|TF2902:TF2903:holliday junction DNA helicase:translation initiation factor SUI1:->->:3098541..3098713 173 tccctaacccgtttagacatttatacccaatatttagatataacgtaggaaaaagcaaaagcgtatattggggcggttgattttttttttgaatgggtatcgccttttttcaagcagagagaaatatcctgctcgaaaactcctacctttgcctcggaaaaaagtaacatgag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tccctaacccgtttagacatttatacccaatatttagatataacgtaggaaaaagcaaaagcgtatattggggcggttgattttttttttgaatgggtatcgccttttttcaagcagagagaaatatcctgctcgaaaactcctacctttgcctcggaaaaaagtaacatgag Predict ORF larger than 30AA ================================================ Protein_Len: 35 Strand: + Start: 67 End: 171 .................................................................. M G A V D F F F E W V S P F F K Q R E I S C S K T P T F A S E K S N M .. Protein_Len: 36 Strand: + Start: 65 End: 169 ................................................................ M L G R L I F F L N G Y R L F S S R E K Y P A R K L L P L P R K K V T * .... Protein_Len: 49 Strand: - Start: 24 End: 170 ....................... V W Y K S I V Y S F A F A Y I P A T S K K K S H T D G K K L C L S I D Q E F V G V K A E S F L L M ... Protein_Len: 33 Strand: - Start: 2 End: 100 . G L G N L C K Y G I N L Y L T P F L L L T Y Q P P Q N K K Q I P M ......................................................................... tccctaacccgtttagacatttatacccaatatttagatataacgtaggaaaaagcaaaagcgtatattggggcggttgattttttttttgaatgggtatcgccttttttcaagcagagagaaatatcctgctcgaaaactcctacctttgcctcggaaaaaagtaacatgag 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================================================ tccctaacccgtttagacatttatacccaatatttagatataacgtaggaaaaagcaaaagcgtatattggggcggttgattttttttttgaatgggtatcgccttttttcaagcagagagaaatatcctgctcgaaaactcctacctttgcctcggaaaaaagtaacatgag Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TF2902:TF2903|TF2902:TF2903:holliday junction DNA helicase:translation initiation factor SUI1:->->:3098541..3098713 173 tccctaacccgtttagacatttatacccaatatttagatataacgtaggaaaaagcaaaagcgtatattggggcggttgattttttttttgaatgggtatcgccttttttcaagcagagagaaatatcctgctcgaaaactcctacctttgcctcggaaaaaagtaacatgag Intra-Species Hit: Count: 1 Min: 1 Max: 173 Len: 173 Subject: tfor_TF2902_TF2903|holliday junction DNA helicase:translation initiation factor SUI1|POSITIVE:POSITIVE|[3098541,3098713]|173 HSP 1 e-value: 9.0E-76 bit: 283.0 Len: 173 Query Start:1 Query End:173 Subject Strand: POSITIVE Subject Start: 1 Subject End: 173 tccctaacccgtttagacatttatacccaatatttagatataacgtaggaaaaagcaaaagcgtatattggggcggttgannnnnnnnnngaatgggtatcgccttttttcaagcagagagaaatatcctgctcgaaaactcctacctttgcctcggaaaaaagtaacatgag tccctaacccgtttagacatttatacccaatatttagatataacgtaggaaaaagcaaaagcgtatattggggcggttgattttttttttgaatgggtatcgccttttttcaagcagagagaaatatcctgctcgaaaactcctacctttgcctcggaaaaaagtaacatgag Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCCCUAACCCGUUUAGACAUUUAUACCCAAUAUUUAGAUAUAACGUAGGAAAAAGCAAAAGCGUAUAUUGGGGCGGUUGAUUUUUUUUUUGAAUGGGUAUCGCCUUUUUUCAAGCAGAGAGAAAUAUCCUGCUCGAAAACUCCUACCUUUGCCUCGGAAAAAAGUAACAUGAG ....(((((.((....)).......((((((((.........((((..............))))))))))))..)))))..(((((((((((..(((((.......(((((.(((((.((......))))))).)))))....))))).....)))))))))))......... (-34.24) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUCAUGUUACUUUUUUCCGAGGCAAAGGUAGGAGUUUUCGAGCAGGAUAUUUCUCUCUGCUUGAAAAAAGGCGAUACCCAUUCAAAAAAAAAAUCAACCGCCCCAAUAUACGCUUUUGCUUUUUCCUACGUUAUAUCUAAAUAUUGGGUAUAAAUGUCUAAACGGGUUAGGGA .........((((..((((.((.((((((((((((((((((((((((......)).))))))))))...((((.........................)))).........)))))))))))).)).((((((((((((.....))))))).))))).....))))..)))). (-45.71) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 322 120 71 210 149 tfor:TF2242|5end_hypothetical_protein_2416947..2417177_POSITIVE 321 157 114 216 165 tfor:TF1857|5end_conserved_hypothetical_protein_2014366..2014596_POSITIVE 310 135 101 220 189 tfor:TF2647|5end_transcriptional_regulator,_possible_arylsulfatase_regulator_2816796..2817026_POSITIVE 305 104 61 64 15 tfor:TF2006|5end_uracil_permease_2157279..2157509_POSITIVE 302 120 71 171 116 tfor:TF1255|5end_conserved_hypothetical_protein_1336635..1336865_POSITIVE 301 79 36 43 1 tfor:TF1671|5end_ATP_synthase,_delta_subunit_1786080..1786310_POSITIVE 291 170 121 102 35 tfor:TF1548|5end_thiophene_and_furan_oxidation_protein_1652501..1652731_POSITIVE 288 160 113 223 158 tfor:TF0909|5end_Tn5520-like_integrase_(transfer_factor)_951217..951447_POSITIVE 287 115 71 166 117 tfor:TF1940|5end_TPR-repeat-containing_protein_2086953..2087183_POSITIVE 287 130 89 187 137 tfor:TF1768|5end_conserved_hypothetical_protein;_possible_transposase_1906526..1906756_POSITIVE 287 166 127 71 29 tfor:TF0190|5end_cell_division_protein_FtsH_204029..204259_POSITIVE 287 80 35 147 100 tfor:TF0141|5end_exodeoxyribonuclease_VII,_large_subunit_148422..148652_POSITIVE 284 159 124 64 21 tfor:TF2151|5end_uridine_kinase_2323033..2323263_POSITIVE 284 160 115 211 159 tfor:TF0809|5end_cation_efflux_protein_865358..865588_POSITIVE 284 159 116 60 1 tfor:TF0336|5end_Xaa-Pro_aminopeptidase_360613..360843_POSITIVE 279 156 116 155 111 tfor:TF3025|5end_hypothetical_protein_3248772..3249002_POSITIVE 278 110 61 229 175 tfor:TF1404|5end_conserved_hypothetical_protein_1479074..1479304_POSITIVE 277 108 61 181 124 tfor:TF1465|5end_modulator_of_DNA_gyrase_1554148..1554378_POSITIVE 276 160 126 119 87 tfor:TF1730|5end_diaminopimelate_decarboxylase_1854670..1854900_POSITIVE 276 160 126 68 36 tfor:TF1732|5end_conserved_hypothetical_protein_1854619..1854849_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 312 157 111 138 83 tfor:TF2653|3end_hypothetical_protein_2822460..2822610_POSITIVE 310 135 101 41 10 tfor:TF2646|3end_conserved_hypothetical_protein_2816697..2816847_POSITIVE 300 159 113 78 10 tfor:TF0337|3end_hypothetical_protein_360711..360861_POSITIVE 287 115 71 87 38 tfor:TF1939|3end_hypothetical_protein_2086954..2087104_POSITIVE 287 166 127 52 10 tfor:TF0189|3end_phosphatidate_cytidylytransferase_(CDP-diglyceride_synthetase)_204090..204240_POSITIVE 287 80 35 128 81 tfor:TF0140|3end_exodeoxyribonuclease_VII,_small_subunit_148483..148633_POSITIVE 284 159 124 61 18 tfor:TF2149|3end_deoxyribose-phosphate_aldolase_2323110..2323260_POSITIVE 277 108 61 69 12 tfor:TF1464|3end_conserved_hypothetical_protein_1554116..1554266_POSITIVE 276 160 126 87 55 tfor:TF1729|3end_aspartokinase_1854718..1854868_POSITIVE 273 160 124 54 5 tfor:TF2918|3end_hypothetical_protein_3114382..3114532_POSITIVE 272 102 61 148 104 tfor:TF2308|3end_conserved_hypothetical_protein_2468859..2469009_POSITIVE 271 102 61 45 1 tfor:TF1670|3end_ATP_synthase,_alpha_subunit_1786133..1786283_POSITIVE 269 159 116 61 16 tfor:TF0761|3end_conserved_hypothetical_protein_809080..809230_POSITIVE 266 97 51 150 104 tfor:TF2245|3end_conserved_hypothetical_protein_2421291..2421441_POSITIVE 264 155 113 111 45 tfor:TF1914|3end_conserved_hypothetical_protein_2067656..2067806_POSITIVE 261 158 124 35 1 tfor:TF0183|3end_conserved_hypothetical_protein_196567..196717_POSITIVE 260 109 61 56 6 tfor:TF2490|3end_4-hydroxyphenylacetate-3-hydroxylase/4-hydroxybut_yryl_dehydratase_2666755..2666905_POSITIVE 259 104 65 48 10 tfor:TF1854|3end_competence-damage_protein_CinA_2008808..2008958_POSITIVE 258 160 112 63 17 tfor:TF0408|3end_possible_gliding_motility-related_lipoprotein_426324..426474_POSITIVE 257 156 114 44 4 tfor:TF0930|3end_conserved_hypothetical_protein;_possible_prophage_protein_969965..970115_POSITIVE