Origin IGS: ctttggttttttaatgaaacaaggtaaaagagaaattgccgaattcggttaacgatctgtgtgtcatatcttcatatccataccaaagaaataaagaaatctaccggttcctgctaaaccattcactctgcattactgctttcactggacgcaaaggaaatcaaataaactgattggacaagcaggcagcatacctgaaatgacgaaaaacagctataaggcaccgacaaacggcaggtgcagcgaag .........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 cttcgctgcacctgccgtttgtcggtgccttatagctgtttttcgtcatttcaggtatgctgcctgcttgtccaatcagtttatttgatttcctttgcgtccagtgaaagcagtaatgcagagtgaatggtttagcaggaaccggtagatttctttatttctttggtatggatatgaagatatgacacacagatcgttaaccgaattcggcaatttctcttttaccttgtttcattaaaaaaccaaag Mask Tandem Repeat Region ================================================ ctttggttttttaatgaaacaaggtaaaagagaaattgccgaattcggttaacgatctgtgtgtcatatcttcatatccataccaaagaaataaagaaatctaccggttcctgctaaaccattcactctgcattactgctttcactggacgcaaaggaaatcaaataaactgattggacaagcaggcagcatacctgaaatgacgaaaaacagctataaggcaccgacaaacggcaggtgcagcgaag Find is-nt database================================================ Query_seq: PG0627:PG0628|PG0627:PG0628:RNA-binding protein:ABC transporter, ATP-binding protein:<-<-:681526..681773 248 ctttggttttttaatgaaacaaggtaaaagagaaattgccgaattcggttaacgatctgtgtgtcatatcttcatatccataccaaagaaataaagaaatctaccggttcctgctaaaccattcactctgcattactgctttcactggacgcaaaggaaatcaaataaactgattggacaagcaggcagcatacctgaaatgacgaaaaacagctataaggcaccgacaaacggcaggtgcagcgaag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG0627:PG0628|PG0627:PG0628:RNA-binding protein:ABC transporter, ATP-binding protein:<-<-:681526..681773 248 ctttggttttttaatgaaacaaggtaaaagagaaattgccgaattcggttaacgatctgtgtgtcatatcttcatatccataccaaagaaataaagaaatctaccggttcctgctaaaccattcactctgcattactgctttcactggacgcaaaggaaatcaaataaactgattggacaagcaggcagcatacctgaaatgacgaaaaacagctataaggcaccgacaaacggcaggtgcagcgaag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG0627:PG0628|PG0627:PG0628:RNA-binding protein:ABC transporter, ATP-binding protein:<-<-:681526..681773 248 ctttggttttttaatgaaacaaggtaaaagagaaattgccgaattcggttaacgatctgtgtgtcatatcttcatatccataccaaagaaataaagaaatctaccggttcctgctaaaccattcactctgcattactgctttcactggacgcaaaggaaatcaaataaactgattggacaagcaggcagcatacctgaaatgacgaaaaacagctataaggcaccgacaaacggcaggtgcagcgaag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ctttggttttttaatgaaacaaggtaaaagagaaattgccgaattcggttaacgatctgtgtgtcatatcttcatatccataccaaagaaataaagaaatctaccggttcctgctaaaccattcactctgcattactgctttcactggacgcaaaggaaatcaaataaactgattggacaagcaggcagcatacctgaaatgacgaaaaacagctataaggcaccgacaaacggcaggtgcagcgaag Predict ORF larger than 30AA ================================================ Protein_Len: 45 Strand: + Start: 36 End: 170 ................................... M P N S V N D L C V I S S Y P Y Q R N K E I Y R F L L N H S L C I T A F T G R K G N Q I N .............................................................................. Protein_Len: 40 Strand: + Start: 128 End: 247 ............................................................................................................................... M H Y C F H W T Q R K S N K L I G Q A G S I P E M T K N S Y K A P T N G R C S E . Protein_Len: 35 Strand: - Start: 126 End: 230 ............................................................................................................................. E A N S S E S S A F S I L Y V S Q V L L C C V Q F S S F C S Y P V S M .................. ctttggttttttaatgaaacaaggtaaaagagaaattgccgaattcggttaacgatctgtgtgtcatatcttcatatccataccaaagaaataaagaaatctaccggttcctgctaaaccattcactctgcattactgctttcactggacgcaaaggaaatcaaataaactgattggacaagcaggcagcatacctgaaatgacgaaaaacagctataaggcaccgacaaacggcaggtgcagcgaag 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================================================ ctttggttttttaatgaaacaaggtaaaagagaaattgccgaattcggttaacgatctgtgtgtcatatcttcatatccataccaaagaaataaagaaatctaccggttcctgctaaaccattcactctgcattactgctttcactggacgcaaaggaaatcaaataaactgattggacaagcaggcagcatacctgaaatgacgaaaaacagctataaggcaccgacaaacggcaggtgcagcgaag Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PG0627:PG0628|PG0627:PG0628:RNA-binding protein:ABC transporter, ATP-binding protein:<-<-:681526..681773 248 ctttggttttttaatgaaacaaggtaaaagagaaattgccgaattcggttaacgatctgtgtgtcatatcttcatatccataccaaagaaataaagaaatctaccggttcctgctaaaccattcactctgcattactgctttcactggacgcaaaggaaatcaaataaactgattggacaagcaggcagcatacctgaaatgacgaaaaacagctataaggcaccgacaaacggcaggtgcagcgaag Intra-Species Hit: Count: 1 Min: 1 Max: 248 Len: 248 Subject: NC_002950_PG0627_PG0628|RNA-binding protein:ABC transporter, ATP-binding protein|NEGATIVE:NEGATIVE|[681526,681773]|248 HSP 1 e-value: 1.0E-138 bit: 492.0 Len: 248 Query Start:1 Query End:248 Subject Strand: POSITIVE Subject Start: 1 Subject End: 248 ctttggttttttaatgaaacaaggtaaaagagaaattgccgaattcggttaacgatctgtgtgtcatatcttcatatccataccaaagaaataaagaaatctaccggttcctgctaaaccattcactctgcattactgctttcactggacgcaaaggaaatcaaataaactgattggacaagcaggcagcatacctgaaatgacgaaaaacagctataaggcaccgacaaacggcaggtgcagcgaag ctttggttttttaatgaaacaaggtaaaagagaaattgccgaattcggttaacgatctgtgtgtcatatcttcatatccataccaaagaaataaagaaatctaccggttcctgctaaaccattcactctgcattactgctttcactggacgcaaaggaaatcaaataaactgattggacaagcaggcagcatacctgaaatgacgaaaaacagctataaggcaccgacaaacggcaggtgcagcgaag Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUUUGGUUUUUUAAUGAAACAAGGUAAAAGAGAAAUUGCCGAAUUCGGUUAACGAUCUGUGUGUCAUAUCUUCAUAUCCAUACCAAAGAAAUAAAGAAAUCUACCGGUUCCUGCUAAACCAUUCACUCUGCAUUACUGCUUUCACUGGACGCAAAGGAAAUCAAAUAAACUGAUUGGACAAGCAGGCAGCAUACCUGAAAUGACGAAAAACAGCUAUAAGGCACCGACAAACGGCAGGUGCAGCGAAG (((((((......(((((....(..(..(((......((((....))))......)))...)..).....)))))......)))))))..................(((((((((...(((.(((....(((....))).(((.((........)))))...........))).)))...)))))).))).((((((...............(((....))).(((.....)))))))))........ (-50.70) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUUCGCUGCACCUGCCGUUUGUCGGUGCCUUAUAGCUGUUUUUCGUCAUUUCAGGUAUGCUGCCUGCUUGUCCAAUCAGUUUAUUUGAUUUCCUUUGCGUCCAGUGAAAGCAGUAAUGCAGAGUGAAUGGUUUAGCAGGAACCGGUAGAUUUCUUUAUUUCUUUGGUAUGGAUAUGAAGAUAUGACACACAGAUCGUUAACCGAAUUCGGCAAUUUCUCUUUUACCUUGUUUCAUUAAAAAACCAAAG ............(((((....(((((.........((((.....(((((........(((((((((((...((.(((((.....)))))(((((((((((...((....))....)))))))).))).))...))))))...)))))....(((((((.(((.......))).))))))).)))))..)))).......)))))...))))).................................... (-58.79) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 887 140 91 231 182 NC_002950:PG0627|5end_RNA-binding_protein_681435..681665_NEGATIVE 413 150 101 88 40 NC_002950:PG0362|5end_hypothetical_protein_395301..395531_POSITIVE 363 190 146 67 27 NC_002950:PG1385|5end_TPR_domain_protein_1466335..1466565_NEGATIVE 359 216 175 39 7 NC_002950:PG1947|5end_TPR_domain_protein_2032932..2033162_POSITIVE 339 229 181 202 154 NC_002950:PG1393|5end_penicillin-binding_protein_2,_putative_1476271..1476501_NEGATIVE 319 190 142 68 21 NC_002950:PG1872|5end_urocanate_hydratase_1968911..1969141_NEGATIVE 309 148 104 216 157 NC_002950:PG0498|5end_S-ribosylhomocysteinase_537968..538198_POSITIVE 302 237 193 201 148 NC_002950:PG0589|5end_bifunctional_GMP_synthase/glutamine_amidotransferase_protein_647708..647938_NEGATIVE 299 228 183 60 11 NC_002950:PG1763|5end_ribonuclease_III_1851712..1851942_NEGATIVE 298 67 21 91 33 NC_002950:PG1706|5end_hypothetical_protein_1794211..1794441_NEGATIVE 298 150 104 210 152 NC_002950:PG0064|5end_heavy_metal_efflux_pump,_CzcA_family_80193..80423_NEGATIVE 290 150 109 60 23 NC_002950:PG1037|5end_hypothetical_protein_1101365..1101595_POSITIVE 288 228 181 54 3 NC_002950:PG0280|5end_ABC_transporter,_permease_protein,_putative_314625..314855_NEGATIVE 285 214 174 122 83 NC_002950:PG2030|5end_hypothetical_protein_2129747..2129977_POSITIVE 285 206 170 67 25 NC_002950:PG1634|5end_hypothetical_protein_1715148..1715378_NEGATIVE 281 240 202 176 135 NC_002950:PG0829|5end_hypothetical_protein_886746..886976_NEGATIVE 280 148 103 95 48 NC_002950:PG1619|5end_biotin_synthesis_protein_BioC,_putative_1698568..1698798_POSITIVE 280 215 173 214 169 NC_002950:PG0593|5end_htrA_protein_650362..650592_POSITIVE 280 140 101 189 157 NC_002950:PG0242|5end_conserved_hypothetical_protein_TIGR00096_278960..279190_NEGATIVE 278 149 104 45 4 NC_002950:PG0434|5end_hypothetical_protein_472513..472743_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 359 216 175 46 14 NC_002950:PG1946|3end_ABC_3_transporter_family_protein_2033019..2033169_POSITIVE 303 198 170 142 110 NC_002950:PG1129|3end_ribonucleotide_reductase_1208030..1208180_POSITIVE 298 67 21 70 12 NC_002950:PG1707|3end_hypothetical_protein_1794232..1794382_NEGATIVE 298 149 101 138 98 NC_002950:PG0361|3end_hypothetical_protein_395481..395631_POSITIVE 280 148 103 116 69 NC_002950:PG1618|3end_hypothetical_protein_1698669..1698819_POSITIVE 277 219 171 96 41 NC_002950:PG1389|3end_DNA-binding_protein,_histone-like_family_1470870..1471020_NEGATIVE 273 240 212 139 108 NC_002950:PG0316|3end_seryl-tRNA_synthetase_349788..349938_POSITIVE 272 150 101 151 97 NC_002950:PG0347|3end_UDP-glucose_4-epimerase_382382..382532_POSITIVE 271 144 102 43 2 NC_002950:PG1079|3end_enoyl-CoA_hydratase/isomerase_family_protein_1147399..1147549_POSITIVE 268 73 31 120 65 NC_002950:PG1609|3end_methylmalonyl-CoA_decarboxylase,_gamma_subunit_1689841..1689991_NEGATIVE 268 229 182 100 48 NC_002950:PG0509|3end_hypothetical_protein_548728..548878_NEGATIVE 267 227 182 60 19 NC_002950:PG0439|3end_hypothetical_protein_478810..478960_POSITIVE 265 148 101 104 66 NC_002950:PG0267|3end_arginyl-tRNA_synthetase_300973..301123_POSITIVE 263 150 104 69 23 NC_002950:PG1115|3end_signal_recognition_particle_protein_1188887..1189037_POSITIVE 263 240 200 85 49 NC_002950:PG0226|3end_transglutaminase-related_protein_259838..259988_NEGATIVE 262 67 37 74 42 NC_002950:PG1459|3end_hypothetical_protein_1539632..1539782_NEGATIVE 262 213 175 90 46 NC_002950:PG0265|3end_hypothetical_protein_298393..298543_NEGATIVE 261 149 103 145 97 NC_002950:PG0603|3end_cytidylate_kinase_660345..660495_POSITIVE 259 237 211 140 111 NC_002950:PG1897|3end_thiamin_pyrophosphokinase_catalytic_domain_protein_1996053..1996203_NEGATIVE 258 225 181 52 9 NC_002950:PG1678|3end_hypothetical_protein_1763755..1763905_NEGATIVE