Origin IGS: aggagaatcctctttatttattgttcagaaggtagatatgcgtcgataggcgattcttttaaatgagacttattgcaaagaaaaacattttttttcgacaaaacaaacagaagcaactgcttatcaacccgactaatgcagcggaagag .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 ctcttccgctgcattagtcgggttgataagcagttgcttctgtttgttttgtcgaaaaaaaatgtttttctttgcaataagtctcatttaaaagaatcgcctatcgacgcatatctaccttctgaacaataaataaagaggattctcct Mask Tandem Repeat Region ================================================ aggagaatcctctttatttattgttcagaaggtagatatgcgtcgataggcgattcttttaaatgagacttattgcaaagaaaaacattttttttcgacaaaacaaacagaagcaactgcttatcaacccgactaatgcagcggaagag Find is-nt database================================================ Query_seq: PG0162:PG0163|PG0162:PG0163:RNA polymerase sigma-70 factor, ECF subfamily:diphosphate--fructose-6-phosphate 1-phosphotransferase:<-<-:185177..185325 149 aggagaatcctctttatttattgttcagaaggtagatatgcgtcgataggcgattcttttaaatgagacttattgcaaagaaaaacattttttttcgacaaaacaaacagaagcaactgcttatcaacccgactaatgcagcggaagag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG0162:PG0163|PG0162:PG0163:RNA polymerase sigma-70 factor, ECF subfamily:diphosphate--fructose-6-phosphate 1-phosphotransferase:<-<-:185177..185325 149 aggagaatcctctttatttattgttcagaaggtagatatgcgtcgataggcgattcttttaaatgagacttattgcaaagaaaaacattttttttcgacaaaacaaacagaagcaactgcttatcaacccgactaatgcagcggaagag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG0162:PG0163|PG0162:PG0163:RNA polymerase sigma-70 factor, ECF subfamily:diphosphate--fructose-6-phosphate 1-phosphotransferase:<-<-:185177..185325 149 aggagaatcctctttatttattgttcagaaggtagatatgcgtcgataggcgattcttttaaatgagacttattgcaaagaaaaacattttttttcgacaaaacaaacagaagcaactgcttatcaacccgactaatgcagcggaagag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aggagaatcctctttatttattgttcagaaggtagatatgcgtcgataggcgattcttttaaatgagacttattgcaaagaaaaacattttttttcgacaaaacaaacagaagcaactgcttatcaacccgactaatgcagcggaagag Predict ORF larger than 30AA ================================================ Protein_Len: 39 Strand: - Start: 21 End: 137 .................... Q E S P L Y A D I P S E K L H S K N C L F V N K K S L V F L L L Q K D V R S M ............ aggagaatcctctttatttattgttcagaaggtagatatgcgtcgataggcgattcttttaaatgagacttattgcaaagaaaaacattttttttcgacaaaacaaacagaagcaactgcttatcaacccgactaatgcagcggaagag 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================================================ aggagaatcctctttatttattgttcagaaggtagatatgcgtcgataggcgattcttttaaatgagacttattgcaaagaaaaacattttttttcgacaaaacaaacagaagcaactgcttatcaacccgactaatgcagcggaagag Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 53 HP_score: -3.8 Tail_Score: -3.61654 Start: 80 End: 96 Full_Region: tctgtttgttttgtc gaaaaa aaatg tttttc tttgcaataagtctc ...............................................................................gaaaaaaaatgtttttc..................................................... Find igs database================================================ Query_seq: PG0162:PG0163|PG0162:PG0163:RNA polymerase sigma-70 factor, ECF subfamily:diphosphate--fructose-6-phosphate 1-phosphotransferase:<-<-:185177..185325 149 aggagaatcctctttatttattgttcagaaggtagatatgcgtcgataggcgattcttttaaatgagacttattgcaaagaaaaacattttttttcgacaaaacaaacagaagcaactgcttatcaacccgactaatgcagcggaagag Intra-Species Hit: Count: 1 Min: 1 Max: 149 Len: 149 Subject: NC_002950_PG0162_PG0163|RNA polymerase sigma-70 factor, ECF subfamily:diphosphate--fructose-6-phosphate 1-phosphotransferase|NEGATIVE:NEGATIVE|[185177, 185325]|149 HSP 1 e-value: 4.0E-65 bit: 248.0 Len: 149 Query Start:1 Query End:149 Subject Strand: POSITIVE Subject Start: 1 Subject End: 149 aggagaatcctctttatttattgttcagaaggtagatatgcgtcgataggcgattcttttaaatgagacttattgcaaagaaaaacannnnnnnncgacaaaacaaacagaagcaactgcttatcaacccgactaatgcagcggaagag aggagaatcctctttatttattgttcagaaggtagatatgcgtcgataggcgattcttttaaatgagacttattgcaaagaaaaacattttttttcgacaaaacaaacagaagcaactgcttatcaacccgactaatgcagcggaagag Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGGAGAAUCCUCUUUAUUUAUUGUUCAGAAGGUAGAUAUGCGUCGAUAGGCGAUUCUUUUAAAUGAGACUUAUUGCAAAGAAAAACAUUUUUUUUCGACAAAACAAACAGAAGCAACUGCUUAUCAACCCGACUAAUGCAGCGGAAGAG .......(((.((.((((..(((....((((((((...(((.((.....(((((((((......))))...)))))...((((((.....)))))).............)).))).)))))).))....)))..)))).)).))).... (-25.30) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUCUUCCGCUGCAUUAGUCGGGUUGAUAAGCAGUUGCUUCUGUUUGUUUUGUCGAAAAAAAAUGUUUUUCUUUGCAAUAAGUCUCAUUUAAAAGAAUCGCCUAUCGACGCAUAUCUACCUUCUGAACAAUAAAUAAAGAGGAUUCUCCU ....(((.((...(((.(((((..(((((((((......)))))))))..(((((........((..((((((.................))))))..))...)))))............)))))....)))....)).)))....... (-23.43) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 863 70 21 161 112 NC_002950:PG0162|5end_RNA_polymerase_sigma-70_factor,_ECF_subfamily_185086..185316_NEGATIVE 305 140 95 47 3 NC_002950:PG1247|5end_3-dehydroquinate_synthase_1324444..1324674_POSITIVE 299 69 26 88 34 NC_002950:PG0265|5end_hypothetical_protein_298551..298781_NEGATIVE 288 76 31 227 181 NC_002950:PG1694|5end_hypothetical_protein_1779010..1779240_NEGATIVE 277 66 21 222 171 NC_002950:PG2043|5end_conserved_hypothetical_protein_TIGR00486_2142218..2142448_POSITIVE 273 52 19 202 156 NC_002950:PG1752|5end_hypothetical_protein_1838394..1838624_POSITIVE 272 69 26 88 36 NC_002950:PG1426|5end_hypothetical_protein_1511310..1511540_NEGATIVE 268 58 20 166 132 NC_002950:PG1851|5end_phosphopantothenoylcysteine_decarboxylase/phosphopantothenate--cysteine_ligase_1951168..1951398_NEGATIVE 268 80 31 60 13 NC_002950:PG1210|5end_peptidase,_M24_family_1289044..1289274_POSITIVE 260 67 21 213 164 NC_002950:PG1393|5end_penicillin-binding_protein_2,_putative_1476271..1476501_NEGATIVE 257 46 2 156 121 NC_002950:PG1252|5end_hypothetical_protein_1329584..1329814_NEGATIVE 256 80 32 219 177 NC_002950:PG0729|5end_D-alanylalanine_synthetase_780818..781048_NEGATIVE 255 51 11 123 82 NC_002950:PG0750|5end_glycosyl_transferase,_group_2_family_protein_796692..796922_NEGATIVE 253 50 3 230 180 NC_002950:PG1726|5end_PDZ_domain_protein_1815281..1815511_POSITIVE 247 59 11 65 27 NC_002950:PG0062|5end_TPR_domain_protein_73688..73918_POSITIVE 245 57 15 158 117 NC_002950:PG0307|5end_NADH-ubiquinone_oxidoreductase_342560..342790_POSITIVE 244 69 25 151 91 NC_002950:PG2087|5end_hypothetical_protein_2186990..2187220_POSITIVE 243 68 31 127 84 NC_002950:PG2027|5end_hypothetical_protein_2125494..2125724_POSITIVE 242 136 103 43 6 NC_002950:PG2037|5end_hypothetical_protein_2137812..2138042_NEGATIVE 242 132 94 146 102 NC_002950:PG1479|5end_conjugative_transposon_protein_TraJ_1555234..1555464_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 350 53 11 126 81 NC_002950:PG1378|3end_A/G-specific_adenine_glycosylase_1457715..1457865_NEGATIVE 276 139 95 119 65 NC_002950:PG0530|3end_carbamoyl-phosphate_synthase,_large_subunit_579036..579186_POSITIVE 268 58 20 140 106 NC_002950:PG1852|3end_exonuclease_1951194..1951344_NEGATIVE 262 70 21 138 85 NC_002950:PG2159|3end_protoporphyrinogen_oxidase_2265874..2266024_POSITIVE 258 68 21 143 95 NC_002950:PG0090|3end_Dps_family_protein_106083..106233_POSITIVE 257 46 2 143 108 NC_002950:PG1253|3end_DNA_ligase,_NAD-dependent_1329597..1329747_NEGATIVE 248 76 31 78 38 NC_002950:PG2062|3end_histidyl-tRNA_synthetase_2160415..2160565_POSITIVE 247 70 23 122 78 NC_002950:PG2024|3end_hemagglutinin_protein_HagE_2119083..2119233_NEGATIVE 247 59 11 60 22 NC_002950:PG0061|3end_yngK_protein_73763..73913_POSITIVE 244 69 25 151 91 NC_002950:PG2086|3end_hypothetical_protein_2187070..2187220_POSITIVE 244 62 26 144 106 NC_002950:PG0085|3end_alpha-galactosidase_100556..100706_POSITIVE 243 68 31 98 55 NC_002950:PG2026|3end_phosphoglycerate_mutase_family_protein_2125545..2125695_POSITIVE 243 44 1 91 45 NC_002950:PG1374|3end_immunoreactive_47_kDa_antigen_PG97_1455254..1455404_NEGATIVE 242 136 103 46 9 NC_002950:PG2038|3end_N-acetylmuramoyl-L-alanine_amidase,_putative_2137809..2137959_NEGATIVE 242 132 94 114 70 NC_002950:PG1480|3end_conjugative_transposon_protein_TraI_1555266..1555416_NEGATIVE 241 52 17 132 90 NC_002950:PG1605|3end_aminopeptidase_C_1686602..1686752_POSITIVE 239 57 26 55 23 NC_002950:PG0505|3end_hypothetical_protein_545397..545547_POSITIVE 237 46 1 141 85 NC_002950:PG2163|3end_acid_phosphatase_2268801..2268951_NEGATIVE 237 49 2 110 74 NC_002950:PG1808|3end_guanosine-3',5'-bis(diphosphate)_3'-pyrophosphohydrolase_1902955..1903105_NEGATIVE 228 52 25 121 91 NC_002950:PG1366|3end_UDP-N-acetylglucosamine_1-carboxyvinyltransferase_1446076..1446226_NEGATIVE