Origin IGS: agcaaatcaatttgcgagacaaaaataactttattacgatcaaatggcaaataggatcacagcaatagcttgatgtaattgcattgctctcctcttactcatgaatttaatttg .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 caaattaaattcatgagtaagaggagagcaatgcaattacatcaagctattgctgtgatcctatttgccatttgatcgtaataaagttatttttgtctcgcaaattgatttgct Mask Tandem Repeat Region ================================================ agcaaatcaatttgcgagacaaaaataactttattacgatcaaatggcaaataggatcacagcaatagcttgatgtaattgcattgctctcctcttactcatgaatttaatttg Find is-nt database================================================ Query_seq: PG1563:PG1564|PG1563:PG1564:glucose-1-phosphate thymidylyltransferase:hypothetical protein:<-<-:1642557..1642670 114 agcaaatcaatttgcgagacaaaaataactttattacgatcaaatggcaaataggatcacagcaatagcttgatgtaattgcattgctctcctcttactcatgaatttaatttg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG1563:PG1564|PG1563:PG1564:glucose-1-phosphate thymidylyltransferase:hypothetical protein:<-<-:1642557..1642670 114 agcaaatcaatttgcgagacaaaaataactttattacgatcaaatggcaaataggatcacagcaatagcttgatgtaattgcattgctctcctcttactcatgaatttaatttg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG1563:PG1564|PG1563:PG1564:glucose-1-phosphate thymidylyltransferase:hypothetical protein:<-<-:1642557..1642670 114 agcaaatcaatttgcgagacaaaaataactttattacgatcaaatggcaaataggatcacagcaatagcttgatgtaattgcattgctctcctcttactcatgaatttaatttg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 agcaaatcaatttgcgagacaaaaataactttattacgatcaaatggcaaataggatcacagcaatagcttgatgtaattgcattgctctcctcttactcatgaatttaatttg Predict ORF larger than 30AA ================================================ agcaaatcaatttgcgagacaaaaataactttattacgatcaaatggcaaataggatcacagcaatagcttgatgtaattgcattgctctcctcttactcatgaatttaatttg 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: 84 Start: 22 End: 51 .....................TTTGCCATTTGATCGTAATAAAGTTATTTT............................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ agcaaatcaatttgcgagacaaaaataactttattacgatcaaatggcaaataggatcacagcaatagcttgatgtaattgcattgctctcctcttactcatgaatttaatttg Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PG1563:PG1564|PG1563:PG1564:glucose-1-phosphate thymidylyltransferase:hypothetical protein:<-<-:1642557..1642670 114 agcaaatcaatttgcgagacaaaaataactttattacgatcaaatggcaaataggatcacagcaatagcttgatgtaattgcattgctctcctcttactcatgaatttaatttg Intra-Species Hit: Count: 1 Min: 1 Max: 114 Len: 114 Subject: NC_002950_PG1563_PG1564|glucose-1-phosphate thymidylyltransferase:hypothetical protein|NEGATIVE:NEGATIVE|[1642557,1642670]|114 HSP 1 e-value: 1.0E-58 bit: 226.0 Len: 114 Query Start:1 Query End:114 Subject Strand: POSITIVE Subject Start: 1 Subject End: 114 agcaaatcaatttgcgagacaaaaataactttattacgatcaaatggcaaataggatcacagcaatagcttgatgtaattgcattgctctcctcttactcatgaatttaatttg agcaaatcaatttgcgagacaaaaataactttattacgatcaaatggcaaataggatcacagcaatagcttgatgtaattgcattgctctcctcttactcatgaatttaatttg Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGCAAAUCAAUUUGCGAGACAAAAAUAACUUUAUUACGAUCAAAUGGCAAAUAGGAUCACAGCAAUAGCUUGAUGUAAUUGCAUUGCUCUCCUCUUACUCAUGAAUUUAAUUUG .(((((....)))))(((((((...............((((..((.....))..))))...(((((.((.....)).))))).))).))))....................... (-17.40) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CAAAUUAAAUUCAUGAGUAAGAGGAGAGCAAUGCAAUUACAUCAAGCUAUUGCUGUGAUCCUAUUUGCCAUUUGAUCGUAAUAAAGUUAUUUUUGUCUCGCAAAUUGAUUUGCU ((((((((....(((.(((((((((..(((..(((((..(.....)..))))))))..)))).)))))))).....((..((((((....))))))..))....)))))))).. (-23.20) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 893 100 51 191 142 NC_002950:PG1563|5end_glucose-1-phosphate_thymidylyltransferase_1642466..1642696_NEGATIVE 313 90 46 56 14 NC_002950:PG1018|5end_hypothetical_protein_1078894..1079124_POSITIVE 282 100 60 195 152 NC_002950:PG0657|5end_Maf-like_protein_707782..708012_NEGATIVE 278 102 61 184 135 NC_002950:PG1369|5end_glycerol-3-phosphate_dehydrogenase_(NAD(P)+)_1450407..1450637_NEGATIVE 274 96 61 208 164 NC_002950:PG1113|5end_integrase_1186746..1186976_NEGATIVE 260 93 58 123 87 NC_002950:PG0438|5end_hypothetical_protein_476884..477114_POSITIVE 256 95 51 133 88 NC_002950:PG2101|5end_hypothetical_protein_2211273..2211503_NEGATIVE 255 103 68 92 44 NC_002950:PG1721|5end_ribonuclease_R_1810284..1810514_POSITIVE 253 76 32 80 27 NC_002950:PG1582|5end_batA_protein_1659321..1659551_POSITIVE 251 90 41 68 25 NC_002950:PG0834|5end_hypothetical_protein_893260..893490_NEGATIVE 249 73 37 231 175 NC_002950:PG1052|5end_transcriptional_regulator,_putative_1119690..1119920_POSITIVE 248 100 54 46 5 NC_002950:PG1783|5end_glycosyl_transferase,_group_2_family_protein_1871868..1872098_POSITIVE 246 89 45 183 138 NC_002950:PG1983|5end_CRISPR-associated_TM1791_family_protein_2073442..2073672_NEGATIVE 244 88 45 56 22 NC_002950:PG1019|5end_lipoprotein,_putative_1079215..1079445_POSITIVE 240 75 36 77 30 NC_002950:PG0383|5end_membrane-associated_zinc_metalloprotease,_putative_414766..414996_POSITIVE 239 100 54 226 168 NC_002950:PG1880|5end_glycosyl_transferase,_group_2_family_protein_1975481..1975711_POSITIVE 239 104 61 208 170 NC_002950:PG0704|5end_phosphoglycerate_mutase_family_protein_758928..759158_POSITIVE 238 69 29 46 5 NC_002950:PG2050|5end_hypothetical_protein_2149434..2149664_NEGATIVE 238 89 44 216 161 NC_002950:PG1254|5end_acetyltransferase,_GNAT_family_1332121..1332351_NEGATIVE 237 89 53 50 3 NC_002950:PG0084|5end_L-serine_dehydratase,_iron-sulfur-dependent,_single_chain_form_97832..98062_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 278 102 61 98 49 NC_002950:PG1370|3end_lysyl-tRNA_synthetase_1450493..1450643_NEGATIVE 253 76 32 83 30 NC_002950:PG1581|3end_hypothetical_protein_1659404..1659554_POSITIVE 252 99 53 113 63 NC_002950:PG0097|3end_hypothetical_protein_115056..115206_NEGATIVE 248 100 54 59 18 NC_002950:PG1782|3end_hypothetical_protein_1871961..1872111_POSITIVE 244 88 45 43 9 NC_002950:PG1018|3end_hypothetical_protein_1079282..1079432_POSITIVE 231 95 62 86 48 NC_002950:PG0753|3end_protease_800288..800438_POSITIVE 228 100 53 149 97 NC_002950:PG0123|3end_hypothetical_protein_145585..145735_POSITIVE 224 87 41 56 12 NC_002950:PG1015|3end_hypothetical_protein_1075877..1076027_NEGATIVE 224 89 43 123 77 NC_002950:PG0226|3end_transglutaminase-related_protein_259838..259988_NEGATIVE 222 108 63 90 46 NC_002950:PG0702|3end_nicotinate-nucleotide--dimethylbenzimidazole_phosphoribosyltransferase,_putative_758217..758367_POSITIVE 222 98 53 39 3 NC_002950:PG0205|3end_peptide_chain_release_factor_3_240513..240663_NEGATIVE 219 99 51 105 49 NC_002950:PG0998|3end_hypothetical_protein_1057104..1057254_POSITIVE 218 93 51 118 82 NC_002950:PG0790|3end_GTP-binding_protein_Obg_841399..841549_NEGATIVE 218 99 56 41 3 NC_002950:PG0516|3end_hypothetical_protein_557937..558087_NEGATIVE 217 72 34 131 85 NC_002950:PG2170|3end_sugar_transporter_2276685..2276835_NEGATIVE 217 88 47 143 104 NC_002950:PG0196|3end_peptidase,_M16_family_235808..235958_POSITIVE 216 94 67 31 3 NC_002950:PG1017|3end_pyruvate_phosphate_dikinase_1078944..1079094_POSITIVE 215 69 22 78 26 NC_002950:PG1229|3end_hypothetical_protein_1305559..1305709_NEGATIVE 213 104 67 47 3 NC_002950:PG0768|3end_hypothetical_protein_821275..821425_NEGATIVE 213 83 46 131 99 NC_002950:PG0524|3end_hypothetical_protein_568963..569113_POSITIVE