Origin IGS: tcatcgcacgaatgacgatccgttcttccctttcttacgatcattaatagagaatggtttggggcctcggagggaaagcctgcacaattgggttttccctccggcatttcctccatccgattcatttgt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 acaaatgaatcggatggaggaaatgccggagggaaaacccaattgtgcaggctttccctccgaggccccaaaccattctctattaatgatcgtaagaaagggaagaacggatcgtcattcgtgcgatga Mask Tandem Repeat Region ================================================ tcatcgcacgaatgacgatccgttcttccctttcttacgatcattaatagagaatggtttggggcctcggagggaaagcctgcacaattgggttttccctccggcatttcctccatccgattcatttgt Find is-nt database================================================ Query_seq: PG0445:PG0446|PG0445:PG0446:peptidase T:thiF protein:->->:486610..486738 129 tcatcgcacgaatgacgatccgttcttccctttcttacgatcattaatagagaatggtttggggcctcggagggaaagcctgcacaattgggttttccctccggcatttcctccatccgattcatttgt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG0445:PG0446|PG0445:PG0446:peptidase T:thiF protein:->->:486610..486738 129 tcatcgcacgaatgacgatccgttcttccctttcttacgatcattaatagagaatggtttggggcctcggagggaaagcctgcacaattgggttttccctccggcatttcctccatccgattcatttgt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG0445:PG0446|PG0445:PG0446:peptidase T:thiF protein:->->:486610..486738 129 tcatcgcacgaatgacgatccgttcttccctttcttacgatcattaatagagaatggtttggggcctcggagggaaagcctgcacaattgggttttccctccggcatttcctccatccgattcatttgt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tcatcgcacgaatgacgatccgttcttccctttcttacgatcattaatagagaatggtttggggcctcggagggaaagcctgcacaattgggttttccctccggcatttcctccatccgattcatttgt Predict ORF larger than 30AA ================================================ Protein_Len: 30 Strand: + Start: 40 End: 129 ....................................... M I N R E W F G A S E G K P A Q L G F P S G I S S I R F I C Protein_Len: 41 Strand: - Start: 3 End: 125 .. D C S H R D T R G K R V I M L L S H N P A E S P F G A C N P K G E P M E E M R N M .... tcatcgcacgaatgacgatccgttcttccctttcttacgatcattaatagagaatggtttggggcctcggagggaaagcctgcacaattgggttttccctccggcatttcctccatccgattcatttgt 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================================================ tcatcgcacgaatgacgatccgttcttccctttcttacgatcattaatagagaatggtttggggcctcggagggaaagcctgcacaattgggttttccctccggcatttcctccatccgattcatttgt Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 62 HP_score: -5.8 Tail_Score: -3.76402 Start: 65 End: 106 Full_Region: GAGAATGGTTTGGGG CCTCGGAGGGAAAGCCTG CACAAT TGGGTTTTCCCTCCGGCA TTTCCTCCATCCGAT ................................................................CCTCGGAGGGAAAGCCTGCACAATTGGGTTTTCCCTCCGGCA....................... TransTerm Strand: + Conf: 62 HP_score: -9.3 Tail_Score: -2.8552 Start: 66 End: 105 Full_Region: AGAATGGTTTGGGGC CTCGGAGGGAAAGCCTG CACAAT TGGGTTTTCCCTCCGGC ATTTCCTCCATCCGA .................................................................CTCGGAGGGAAAGCCTGCACAATTGGGTTTTCCCTCCGGC........................ Find igs database================================================ Query_seq: PG0445:PG0446|PG0445:PG0446:peptidase T:thiF protein:->->:486610..486738 129 tcatcgcacgaatgacgatccgttcttccctttcttacgatcattaatagagaatggtttggggcctcggagggaaagcctgcacaattgggttttccctccggcatttcctccatccgattcatttgt Intra-Species Hit: Count: 1 Min: 1 Max: 129 Len: 129 Subject: NC_002950_PG0445_PG0446|peptidase T:thiF protein|POSITIVE:POSITIVE|[486610,486738]|129 HSP 1 e-value: 2.0E-67 bit: 256.0 Len: 129 Query Start:1 Query End:129 Subject Strand: POSITIVE Subject Start: 1 Subject End: 129 tcatcgcacgaatgacgatccgttcttccctttcttacgatcattaatagagaatggtttggggcctcggagggaaagcctgcacaattgggttttccctccggcatttcctccatccgattcatttgt tcatcgcacgaatgacgatccgttcttccctttcttacgatcattaatagagaatggtttggggcctcggagggaaagcctgcacaattgggttttccctccggcatttcctccatccgattcatttgt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCAUCGCACGAAUGACGAUCCGUUCUUCCCUUUCUUACGAUCAUUAAUAGAGAAUGGUUUGGGGCCUCGGAGGGAAAGCCUGCACAAUUGGGUUUUCCCUCCGGCAUUUCCUCCAUCCGAUUCAUUUGU .......((((((((((..((((((((......................))))))))..(((((..(((((((((((((((........)))))))))))))))......)))))..))..)))))))) (-43.85) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACAAAUGAAUCGGAUGGAGGAAAUGCCGGAGGGAAAACCCAAUUGUGCAGGCUUUCCCUCCGAGGCCCCAAACCAUUCUCUAUUAAUGAUCGUAAGAAAGGGAAGAACGGAUCGUCAUUCGUGCGAUGA ............(((((((((.....((((((((((.((..........)).)))))))))).((.......)).)))))))))....((((((.(((...((.((.....)).)).))).)))))).. (-36.70) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 396 110 61 185 129 NC_002950:PG0735|5end_aminotransferase,_class_V_784383..784613_POSITIVE 388 97 54 73 18 NC_002950:PG1305|5end_glycine_dehydrogenase_1386538..1386768_NEGATIVE 379 120 72 194 141 NC_002950:PG1296|5end_hypothetical_protein_1374794..1375024_POSITIVE 375 119 73 207 140 NC_002950:PG0987|5end_hypothetical_protein_1048002..1048232_POSITIVE 370 110 67 175 135 NC_002950:PG1964|5end_bacterial_sugar_transferase_2052910..2053140_POSITIVE 369 106 62 177 134 NC_002950:PG0888|5end_hypothetical_protein_949910..950140_POSITIVE 367 118 73 225 164 NC_002950:PG1163|5end_cobyrinic_acid_a,c-diamide_synthase_1243381..1243611_NEGATIVE 362 110 61 229 173 NC_002950:PG0159|5end_endopeptidase_PepO_183164..183394_NEGATIVE 359 94 51 224 173 NC_002950:PG0844|5end_hypothetical_protein_905289..905519_POSITIVE 350 120 73 85 41 NC_002950:PG0606|5end_hypothetical_protein_662558..662788_NEGATIVE 346 109 61 104 44 NC_002950:PG0787|5end_hypothetical_protein_837675..837905_POSITIVE 345 120 72 187 140 NC_002950:PG1719|5end_ABC_transporter,_ATP-binding_protein,_MsbA_family_1806749..1806979_POSITIVE 345 119 71 167 128 NC_002950:PG0253|5end_hypothetical_protein_284607..284837_POSITIVE 340 106 63 103 62 NC_002950:PG2145|5end_polysaccharide_deacetylase_2253253..2253483_POSITIVE 339 110 63 108 61 NC_002950:PG1388|5end_hypothetical_protein_1470889..1471119_NEGATIVE 338 106 61 51 6 NC_002950:PG1374|5end_immunoreactive_47_kDa_antigen_PG97_1456540..1456770_NEGATIVE 337 102 65 222 177 NC_002950:PG0006|5end_MATE_efflux_family_protein_6332..6562_NEGATIVE 333 107 61 163 107 NC_002950:PG1542|5end_collagenase_1620788..1621018_POSITIVE 332 120 71 69 6 NC_002950:PG0802|5end_alpha_keto_acid_dehydrogenase_complex,_E3_component,_lipoamide_dehydrogenase_859722..859952_NEGATIVE 328 90 47 96 46 NC_002950:PG1594|5end_ComEC/Rec2-related_protein_1673587..1673817_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 407 105 61 121 72 NC_002950:PG2036|3end_ion_transporter_2137552..2137702_POSITIVE 396 110 61 126 70 NC_002950:PG0734|3end_nitroreductase_family_protein_784404..784554_POSITIVE 388 97 54 68 13 NC_002950:PG1306|3end_metallo-beta-lactamase_family_protein_1386543..1386693_NEGATIVE 372 103 61 67 21 NC_002950:PG1226|3end_peptidyl-prolyl_cis-trans_isomerase,_cyclophilin-type_1304048..1304198_POSITIVE 360 94 51 59 14 NC_002950:PG0627|3end_RNA-binding_protein_681142..681292_NEGATIVE 349 104 61 87 30 NC_002950:PG1117|3end_MATE_efflux_family_protein_1191541..1191691_POSITIVE 349 110 61 97 28 NC_002950:PG1004|3end_prolyl_oligopeptidase_family_protein_1060433..1060583_NEGATIVE 340 106 63 60 19 NC_002950:PG2144|3end_hypothetical_protein_2253290..2253440_POSITIVE 339 110 63 127 80 NC_002950:PG1389|3end_DNA-binding_protein,_histone-like_family_1470870..1471020_NEGATIVE 336 83 47 144 98 NC_002950:PG0199|3end_TatD_family_protein_237424..237574_NEGATIVE 333 107 61 150 94 NC_002950:PG1541|3end_2-amino-4-hydroxy-6-_hydroxymethyldihydropteridine_pyrophosphokinase_1620855..1621005_POSITIVE 333 110 61 134 82 NC_002950:PG0278|3end_hypothetical_protein_310477..310627_POSITIVE 332 120 71 64 1 NC_002950:PG0803|3end_glucosamine-6-phosphate_deaminase_859727..859877_NEGATIVE 328 90 47 89 39 NC_002950:PG1595|3end_ribulose-phosphate_3-epimerase_1673594..1673744_NEGATIVE 327 120 71 72 22 NC_002950:PG0481|3end_2-amino-3-ketobutyrate_coenzyme_A_ligase_521432..521582_NEGATIVE 325 120 77 109 61 NC_002950:PG0132|3end_hypothetical_protein_153054..153204_POSITIVE 324 43 6 98 64 NC_002950:PG2004|3end_hypothetical_protein_2093135..2093285_NEGATIVE 324 106 61 53 1 NC_002950:PG1638|3end_thioredoxin_family_protein_1718664..1718814_NEGATIVE 323 98 51 140 88 NC_002950:PG2031|3end_hypothetical_protein_2130871..2131021_POSITIVE 323 110 61 141 86 NC_002950:PG1677|3end_phosphoglycerate_kinase_1763678..1763828_POSITIVE