Origin IGS: taaaaagacgttattttctcgtgtgcaaaagtaatcattgtttatgtacccaaaaagaagaggtagccgcacgagttcctgcacattccactctcaggtacaatcggatatggaggtaggcttt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aaagcctacctccatatccgattgtacctgagagtggaatgtgcaggaactcgtgcggctacctcttctttttgggtacataaacaatgattacttttgcacacgagaaaataacgtcttttta Mask Tandem Repeat Region ================================================ taaaaagacgttattttctcgtgtgcaaaagtaatcattgtttatgtacccaaaaagaagaggtagccgcacgagttcctgcacattccactctcaggtacaatcggatatggaggtaggcttt Find is-nt database================================================ Query_seq: PG0910:PG0912|PG0910:PG0912:FHA domain protein:polysaccharide transport protein, putative:<-<-:973757..973880 124 taaaaagacgttattttctcgtgtgcaaaagtaatcattgtttatgtacccaaaaagaagaggtagccgcacgagttcctgcacattccactctcaggtacaatcggatatggaggtaggcttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG0910:PG0912|PG0910:PG0912:FHA domain protein:polysaccharide transport protein, putative:<-<-:973757..973880 124 taaaaagacgttattttctcgtgtgcaaaagtaatcattgtttatgtacccaaaaagaagaggtagccgcacgagttcctgcacattccactctcaggtacaatcggatatggaggtaggcttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG0910:PG0912|PG0910:PG0912:FHA domain protein:polysaccharide transport protein, putative:<-<-:973757..973880 124 taaaaagacgttattttctcgtgtgcaaaagtaatcattgtttatgtacccaaaaagaagaggtagccgcacgagttcctgcacattccactctcaggtacaatcggatatggaggtaggcttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taaaaagacgttattttctcgtgtgcaaaagtaatcattgtttatgtacccaaaaagaagaggtagccgcacgagttcctgcacattccactctcaggtacaatcggatatggaggtaggcttt Predict ORF larger than 30AA ================================================ Protein_Len: 32 Strand: + Start: 21 End: 116 .................... M C K S N H C L C T Q K E E V A A R V P A H S T L R Y N R I W R ........ taaaaagacgttattttctcgtgtgcaaaagtaatcattgtttatgtacccaaaaagaagaggtagccgcacgagttcctgcacattccactctcaggtacaatcggatatggaggtaggcttt 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================================================ taaaaagacgttattttctcgtgtgcaaaagtaatcattgtttatgtacccaaaaagaagaggtagccgcacgagttcctgcacattccactctcaggtacaatcggatatggaggtaggcttt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PG0910:PG0912|PG0910:PG0912:FHA domain protein:polysaccharide transport protein, putative:<-<-:973757..973880 124 taaaaagacgttattttctcgtgtgcaaaagtaatcattgtttatgtacccaaaaagaagaggtagccgcacgagttcctgcacattccactctcaggtacaatcggatatggaggtaggcttt Intra-Species Hit: Count: 1 Min: 1 Max: 124 Len: 124 Subject: NC_002950_PG0910_PG0912|FHA domain protein:polysaccharide transport protein, putative|NEGATIVE:NEGATIVE|[973757,973880]|124 HSP 1 e-value: 1.0E-64 bit: 246.0 Len: 124 Query Start:1 Query End:124 Subject Strand: POSITIVE Subject Start: 1 Subject End: 124 taaaaagacgttattttctcgtgtgcaaaagtaatcattgtttatgtacccaaaaagaagaggtagccgcacgagttcctgcacattccactctcaggtacaatcggatatggaggtaggcttt taaaaagacgttattttctcgtgtgcaaaagtaatcattgtttatgtacccaaaaagaagaggtagccgcacgagttcctgcacattccactctcaggtacaatcggatatggaggtaggcttt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAAAAGACGUUAUUUUCUCGUGUGCAAAAGUAAUCAUUGUUUAUGUACCCAAAAAGAAGAGGUAGCCGCACGAGUUCCUGCACAUUCCACUCUCAGGUACAAUCGGAUAUGGAGGUAGGCUUU .................((((((((.....((((.......)))).(((((........).))))..))))))))..(((((.((((((................))).)))...))))).... (-23.09) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAGCCUACCUCCAUAUCCGAUUGUACCUGAGAGUGGAAUGUGCAGGAACUCGUGCGGCUACCUCUUCUUUUUGGGUACAUAAACAAUGAUUACUUUUGCACACGAGAAAAUAACGUCUUUUUA ........(((.((((((((.((........)).))).))))).)))..((((((..((.(((.(........)))).(((.....))).........)).))))))................. (-21.60) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 1025 110 61 201 152 NC_002950:PG0910|5end_FHA_domain_protein_973666..973896_NEGATIVE 356 102 73 231 203 NC_002950:PG1656|5end_methylmalonyl-CoA_mutase,_small_subunit_1737459..1737689_POSITIVE 342 107 68 193 144 NC_002950:PG1586|5end_batE_protein_1664054..1664284_POSITIVE 338 107 63 197 142 NC_002950:PG2154|5end_hypothetical_protein_2260945..2261175_NEGATIVE 336 104 62 53 2 NC_002950:PG1374|5end_immunoreactive_47_kDa_antigen_PG97_1456540..1456770_NEGATIVE 323 100 55 157 107 NC_002950:PG1581|5end_hypothetical_protein_1658368..1658598_POSITIVE 311 89 49 95 46 NC_002950:PG1143|5end_sugar_dehydrogenase,_UDP-glucose/GDP-mannose_dehydrogenase_family_1227198..1227428_NEGATIVE 310 108 62 64 11 NC_002950:PG2107|5end_thiamine_biosynthesis_protein_ThiH_2216658..2216888_NEGATIVE 305 97 54 126 78 NC_002950:PG1130|5end_TPR_domain_protein_1208053..1208283_POSITIVE 301 110 65 60 20 NC_002950:PG1361|5end_dipeptidyl_aminopeptidase_IV,_putative_1442108..1442338_NEGATIVE 301 95 55 231 186 NC_002950:PG0768|5end_hypothetical_protein_822381..822611_NEGATIVE 300 110 62 229 178 NC_002950:PG1784|5end_hypothetical_protein_1872566..1872796_POSITIVE 300 107 62 78 26 NC_002950:PG0246|5end_hypothetical_protein_281241..281471_NEGATIVE 293 108 65 221 179 NC_002950:PG0148|5end_sigma-54-dependent_transcriptional_regulator_170907..171137_NEGATIVE 292 110 61 106 54 NC_002950:PG0145|5end_hypothetical_protein_167831..168061_POSITIVE 291 109 62 198 157 NC_002950:PG2164|5end_peptidyl-prolyl_cis-trans_isomerase,_FKBP-type_2270125..2270355_NEGATIVE 290 119 74 217 177 NC_002950:PG0766|5end_polyribonucleotide_nucleotidyltransferase_818405..818635_NEGATIVE 289 93 56 190 146 NC_002950:PG0498|5end_S-ribosylhomocysteinase_537968..538198_POSITIVE 288 109 61 68 21 NC_002950:PG0894|5end_DNA_repair_protein_RadC_956761..956991_NEGATIVE 287 120 74 93 36 NC_002950:PG1875|5end_hemolysin_1970621..1970851_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 456 110 73 83 48 NC_002950:PG1655|3end_hypothetical_protein_1737384..1737534_POSITIVE 361 98 51 79 22 NC_002950:PG1630|3end_hypothetical_protein_1712142..1712292_POSITIVE 350 120 71 114 70 NC_002950:PG2004|3end_hypothetical_protein_2093135..2093285_NEGATIVE 349 120 73 58 12 NC_002950:PG0957|3end_riboflavin_biosynthesis_protein_RibF_1018131..1018281_POSITIVE 337 109 61 129 75 NC_002950:PG0340|3end_hypothetical_protein_376436..376586_POSITIVE 314 89 54 41 3 NC_002950:PG1274|3end_elongation_factor_P_1352489..1352639_POSITIVE 312 89 60 147 109 NC_002950:PG2155|3end_lipoprotein,_putative_2260972..2261122_NEGATIVE 310 100 55 62 12 NC_002950:PG0769|3end_fibronectin_type_III_domain_protein_822555..822705_NEGATIVE 303 106 61 129 73 NC_002950:PG1431|3end_DNA-binding_response_regulator,_LuxR_family_1515986..1516136_NEGATIVE 293 95 53 63 26 NC_002950:PG1226|3end_peptidyl-prolyl_cis-trans_isomerase,_cyclophilin-type_1304048..1304198_POSITIVE 292 109 61 148 95 NC_002950:PG1675|3end_hypothetical_protein_1760360..1760510_POSITIVE 291 90 41 137 90 NC_002950:PG0800|3end_hypothetical_protein_854719..854869_NEGATIVE 290 119 74 65 25 NC_002950:PG0767|3end_4-alpha-glucanotransferase_818557..818707_NEGATIVE 288 89 44 56 6 NC_002950:PG1332|3end_NAD(P)_transhydrogenase,_beta_subunit_1414110..1414260_POSITIVE 287 120 74 81 24 NC_002950:PG1876|3end_hypothetical_protein_1970633..1970783_NEGATIVE 286 109 61 105 57 NC_002950:PG1851|3end_phosphopantothenoylcysteine_decarboxylase/phosphopantothenate--cysteine_ligase_1949954..1950104_NEGATIVE 285 106 61 90 30 NC_002950:PG1370|3end_lysyl-tRNA_synthetase_1450493..1450643_NEGATIVE 283 99 54 54 2 NC_002950:PG2100|3end_immunoreactive_63_kDa_antigen_PG102_2208527..2208677_NEGATIVE 279 120 71 111 64 NC_002950:PG1904|3end_hypothetical_protein_2004432..2004582_NEGATIVE 279 105 62 47 2 NC_002950:PG1815|3end_3-deoxy-manno-octulosonate_cytidylyltransferase_1910669..1910819_NEGATIVE