Origin IGS: gattatgattgatttttcgttcccgtcaaagataggaacttttcatatacatttgtacaaactaattaatagccggtttataaccctatccgattcgggattattaatggccaaagattttaggattttgcctcatcggtagtcatttcctaattatgaagagggtagtgtgtacggctgactcatagcatagaaagtctctcttcacgttagatt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aatctaacgtgaagagagactttctatgctatgagtcagccgtacacactaccctcttcataattaggaaatgactaccgatgaggcaaaatcctaaaatctttggccattaataatcccgaatcggatagggttataaaccggctattaattagtttgtacaaatgtatatgaaaagttcctatctttgacgggaacgaaaaatcaatcataatc Mask Tandem Repeat Region ================================================ gattatgattgatttttcgttcccgtcaaagataggaacttttcatatacatttgtacaaactaattaatagccggtttataaccctatccgattcgggattattaatggccaaagattttaggattttgcctcatcggtagtcatttcctaattatgaagagggtagtgtgtacggctgactcatagcatagaaagtctctcttcacgttagatt Find is-nt database================================================ Query_seq: PG0561:PG0562|PG0561:PG0562:peptidase, M20/M25/M40 family:potassium uptake protein TrkA, putative:<-->:619146..619361 216 gattatgattgatttttcgttcccgtcaaagataggaacttttcatatacatttgtacaaactaattaatagccggtttataaccctatccgattcgggattattaatggccaaagattttaggattttgcctcatcggtagtcatttcctaattatgaagagggtagtgtgtacggctgactcatagcatagaaagtctctcttcacgttagatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG0561:PG0562|PG0561:PG0562:peptidase, M20/M25/M40 family:potassium uptake protein TrkA, putative:<-->:619146..619361 216 gattatgattgatttttcgttcccgtcaaagataggaacttttcatatacatttgtacaaactaattaatagccggtttataaccctatccgattcgggattattaatggccaaagattttaggattttgcctcatcggtagtcatttcctaattatgaagagggtagtgtgtacggctgactcatagcatagaaagtctctcttcacgttagatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG0561:PG0562|PG0561:PG0562:peptidase, M20/M25/M40 family:potassium uptake protein TrkA, putative:<-->:619146..619361 216 gattatgattgatttttcgttcccgtcaaagataggaacttttcatatacatttgtacaaactaattaatagccggtttataaccctatccgattcgggattattaatggccaaagattttaggattttgcctcatcggtagtcatttcctaattatgaagagggtagtgtgtacggctgactcatagcatagaaagtctctcttcacgttagatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gattatgattgatttttcgttcccgtcaaagataggaacttttcatatacatttgtacaaactaattaatagccggtttataaccctatccgattcgggattattaatggccaaagattttaggattttgcctcatcggtagtcatttcctaattatgaagagggtagtgtgtacggctgactcatagcatagaaagtctctcttcacgttagatt Predict ORF larger than 30AA ================================================ Protein_Len: 46 Strand: + Start: 2 End: 139 . M M I D F S F P S K I G T F H I H L Y K L I N S R F I T L S D S G L L M A K D F R I L P H R ............................................................................. gattatgattgatttttcgttcccgtcaaagataggaacttttcatatacatttgtacaaactaattaatagccggtttataaccctatccgattcgggattattaatggccaaagattttaggattttgcctcatcggtagtcatttcctaattatgaagagggtagtgtgtacggctgactcatagcatagaaagtctctcttcacgttagatt 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================================================ gattatgattgatttttcgttcccgtcaaagataggaacttttcatatacatttgtacaaactaattaatagccggtttataaccctatccgattcgggattattaatggccaaagattttaggattttgcctcatcggtagtcatttcctaattatgaagagggtagtgtgtacggctgactcatagcatagaaagtctctcttcacgttagatt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PG0561:PG0562|PG0561:PG0562:peptidase, M20/M25/M40 family:potassium uptake protein TrkA, putative:<-->:619146..619361 216 gattatgattgatttttcgttcccgtcaaagataggaacttttcatatacatttgtacaaactaattaatagccggtttataaccctatccgattcgggattattaatggccaaagattttaggattttgcctcatcggtagtcatttcctaattatgaagagggtagtgtgtacggctgactcatagcatagaaagtctctcttcacgttagatt Intra-Species Hit: Count: 1 Min: 1 Max: 216 Len: 216 Subject: NC_002950_PG0561_PG0562|peptidase, M20/M25/M40 family:potassium uptake protein TrkA, putative|NEGATIVE:POSITIVE|[619146,619361]|216 HSP 1 e-value: 1.0E-119 bit: 428.0 Len: 216 Query Start:1 Query End:216 Subject Strand: POSITIVE Subject Start: 1 Subject End: 216 gattatgattgatttttcgttcccgtcaaagataggaacttttcatatacatttgtacaaactaattaatagccggtttataaccctatccgattcgggattattaatggccaaagattttaggattttgcctcatcggtagtcatttcctaattatgaagagggtagtgtgtacggctgactcatagcatagaaagtctctcttcacgttagatt gattatgattgatttttcgttcccgtcaaagataggaacttttcatatacatttgtacaaactaattaatagccggtttataaccctatccgattcgggattattaatggccaaagattttaggattttgcctcatcggtagtcatttcctaattatgaagagggtagtgtgtacggctgactcatagcatagaaagtctctcttcacgttagatt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAUUAUGAUUGAUUUUUCGUUCCCGUCAAAGAUAGGAACUUUUCAUAUACAUUUGUACAAACUAAUUAAUAGCCGGUUUAUAACCCUAUCCGAUUCGGGAUUAUUAAUGGCCAAAGAUUUUAGGAUUUUGCCUCAUCGGUAGUCAUUUCCUAAUUAUGAAGAGGGUAGUGUGUACGGCUGACUCAUAGCAUAGAAAGUCUCUCUUCACGUUAGAUU ..(((((..(((......(((((..((...))..)))))..............................((((((.......((.((((((..((((.(((((..((((((.(..(((...(((......))).)))..).))))))...))))).))))..)))))).))...))))))..)))...)))))..(((((..(.....)..))))) (-47.20) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUCUAACGUGAAGAGAGACUUUCUAUGCUAUGAGUCAGCCGUACACACUACCCUCUUCAUAAUUAGGAAAUGACUACCGAUGAGGCAAAAUCCUAAAAUCUUUGGCCAUUAAUAAUCCCGAAUCGGAUAGGGUUAUAAACCGGCUAUUAAUUAGUUUGUACAAAUGUAUAUGAAAAGUUCCUAUCUUUGACGGGAACGAAAAAUCAAUCAUAAUC ..(((((.((((((((.(((((..........)))))....(((.....))).))))))))..))))).((((.(((..(((.(((......)))...)))..))).)))).....(((((....((((((((.........(((((.....)))))(((((....)))))........))))))))....))))).................... (-45.40) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 883 120 71 211 162 NC_002950:PG0561|5end_peptidase,_M20/M25/M40_family_619055..619285_NEGATIVE 331 117 71 77 35 NC_002950:PG1763|5end_ribonuclease_III_1851712..1851942_NEGATIVE 321 139 91 117 71 NC_002950:PG0559|5end_chlorohydrolase_family_protein_617496..617726_NEGATIVE 314 179 138 59 17 NC_002950:PG1571|5end_metallo-beta-lactamase_superfamily_protein_1650353..1650583_NEGATIVE 313 114 71 216 168 NC_002950:PG1095|5end_RNA_methyltransferase,_TrmA_family_1160225..1160455_POSITIVE 310 200 158 82 45 NC_002950:PG1790|5end_hypothetical_protein_1880954..1881184_NEGATIVE 298 181 144 40 1 NC_002950:PG1730|5end_O-methyltransferase_family_protein_1819577..1819807_NEGATIVE 297 99 54 132 87 NC_002950:PG1639|5end_hypothetical_protein_1719919..1720149_NEGATIVE 297 178 131 213 171 NC_002950:PG1467|5end_methlytransferase,_UbiE/COQ5_family_1543210..1543440_POSITIVE 296 118 75 41 2 NC_002950:PG1289|5end_GDP-fucose_synthetase_1367041..1367271_POSITIVE 295 113 71 48 8 NC_002950:PG0046|5end_phosphatidate_cytidylyltransferase_57200..57430_NEGATIVE 293 210 161 153 95 NC_002950:PG0139|5end_membrane-bound_lytic_murein_transglycosylase_D,_putative_163141..163371_NEGATIVE 288 180 132 221 175 NC_002950:PG1848|5end_RNA_methyltransferase,_TrmH_family_1947382..1947612_NEGATIVE 288 190 145 169 122 NC_002950:PG0524|5end_hypothetical_protein_568599..568829_POSITIVE 286 178 132 58 16 NC_002950:PG0607|5end_hypothetical_protein_662552..662782_POSITIVE 280 136 91 91 54 NC_002950:PG0594|5end_RNA_polymerase_sigma-70_factor_652048..652278_POSITIVE 278 111 72 150 112 NC_002950:PG0328|5end_imidazolonepropionase_363426..363656_NEGATIVE 277 209 163 85 25 NC_002950:PG0986|5end_hypothetical_protein_1047426..1047656_POSITIVE 276 118 72 102 63 NC_002950:PG1783|5end_glycosyl_transferase,_group_2_family_protein_1871868..1872098_POSITIVE 276 210 161 96 32 NC_002950:PG0171|5end_5'-nucleotidase_family_protein_191724..191954_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 328 98 69 49 12 NC_002950:PG1085|3end_hypothetical_protein_1153531..1153681_POSITIVE 316 118 75 48 5 NC_002950:PG1288|3end_GDP-mannose_4,6-dehydratase_1367128..1367278_POSITIVE 313 114 71 132 84 NC_002950:PG1094|3end_phosphomannomutase_1160221..1160371_POSITIVE 310 200 158 85 48 NC_002950:PG1791|3end_hypothetical_protein_1880951..1881101_NEGATIVE 297 99 54 116 71 NC_002950:PG1640|3end_DNA-damage-inducible_protein_F_1719935..1720085_NEGATIVE 293 210 161 143 85 NC_002950:PG0140|3end_hypothetical_protein_163151..163301_NEGATIVE 285 179 131 150 100 NC_002950:PG0354|3end_hypothetical_protein_389131..389281_NEGATIVE 284 133 91 110 65 NC_002950:PG2227|3end_hypothetical_protein_2342744..2342894_POSITIVE 281 185 141 130 72 NC_002950:PG1773|3end_PAP2_superfamily_protein_1861232..1861382_POSITIVE 280 208 168 45 4 NC_002950:PG1416|3end_enoyl-(acyl-carrier-protein)_reductase_II_1501078..1501228_POSITIVE 280 118 72 88 47 NC_002950:PG0046|3end_phosphatidate_cytidylyltransferase_56346..56496_NEGATIVE 278 111 72 49 11 NC_002950:PG0329|3end_formiminotransferase-cyclodeaminase-related_protein_363527..363677_NEGATIVE 277 209 163 95 35 NC_002950:PG0985|3end_RNA_polymerase_sigma-70_factor,_ECF_subfamily_1047516..1047666_POSITIVE 276 118 72 115 76 NC_002950:PG1782|3end_hypothetical_protein_1871961..1872111_POSITIVE 276 210 161 66 2 NC_002950:PG0170|3end_methionyl-tRNA_synthetase_191774..191924_POSITIVE 273 193 156 64 22 NC_002950:PG1741|3end_aspartate_ammonia-lyase_1825856..1826006_NEGATIVE 272 139 97 135 86 NC_002950:PG0802|3end_alpha_keto_acid_dehydrogenase_complex,_E3_component,_lipoamide_dehydrogenase_858373..858523_NEGATIVE 272 180 136 86 33 NC_002950:PG0347|3end_UDP-glucose_4-epimerase_382382..382532_POSITIVE 270 179 131 92 35 NC_002950:PG2041|3end_hypothetical_protein_2139235..2139385_NEGATIVE 270 204 162 130 85 NC_002950:PG0246|3end_hypothetical_protein_281050..281200_NEGATIVE