Origin IGS: ggaaatactatcgaaaacgatcctgtcgctttgtttgttcctctctctcttacaagatgaaatctgcagcaatagggcgaaagccccgagcaggagtaatggcgtttttgctttcatcggataaatctt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aagatttatccgatgaaagcaaaaacgccattactcctgctcggggctttcgccctattgctgcagatttcatcttgtaagagagagaggaacaaacaaagcgacaggatcgttttcgatagtatttcc Mask Tandem Repeat Region ================================================ ggaaatactatcgaaaacgatcctgtcgctttgtttgttcctctctctcttacaagatgaaatctgcagcaatagggcgaaagccccgagcaggagtaatggcgtttttgctttcatcggataaatctt Find is-nt database================================================ Query_seq: PG0466:PG0468|PG0466:PG0468:hypothetical protein:mannose-6-phosphate isomerase, class I:<-<-:510335..510463 129 ggaaatactatcgaaaacgatcctgtcgctttgtttgttcctctctctcttacaagatgaaatctgcagcaatagggcgaaagccccgagcaggagtaatggcgtttttgctttcatcggataaatctt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG0466:PG0468|PG0466:PG0468:hypothetical protein:mannose-6-phosphate isomerase, class I:<-<-:510335..510463 129 ggaaatactatcgaaaacgatcctgtcgctttgtttgttcctctctctcttacaagatgaaatctgcagcaatagggcgaaagccccgagcaggagtaatggcgtttttgctttcatcggataaatctt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG0466:PG0468|PG0466:PG0468:hypothetical protein:mannose-6-phosphate isomerase, class I:<-<-:510335..510463 129 ggaaatactatcgaaaacgatcctgtcgctttgtttgttcctctctctcttacaagatgaaatctgcagcaatagggcgaaagccccgagcaggagtaatggcgtttttgctttcatcggataaatctt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ggaaatactatcgaaaacgatcctgtcgctttgtttgttcctctctctcttacaagatgaaatctgcagcaatagggcgaaagccccgagcaggagtaatggcgtttttgctttcatcggataaatctt Predict ORF larger than 30AA ================================================ Protein_Len: 39 Strand: + Start: 5 End: 121 .... M L S K T I L S L C L F L S L L Q D E I C S N R A K A P S R S N G V F A F I G ........ Protein_Len: 42 Strand: - Start: 1 End: 126 S I S D F V I R D S Q K N R E R K C S S I Q L L L A F A G L L L L P T K A K M P Y M ... ggaaatactatcgaaaacgatcctgtcgctttgtttgttcctctctctcttacaagatgaaatctgcagcaatagggcgaaagccccgagcaggagtaatggcgtttttgctttcatcggataaatctt 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================================================ ggaaatactatcgaaaacgatcctgtcgctttgtttgttcctctctctcttacaagatgaaatctgcagcaatagggcgaaagccccgagcaggagtaatggcgtttttgctttcatcggataaatctt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PG0466:PG0468|PG0466:PG0468:hypothetical protein:mannose-6-phosphate isomerase, class I:<-<-:510335..510463 129 ggaaatactatcgaaaacgatcctgtcgctttgtttgttcctctctctcttacaagatgaaatctgcagcaatagggcgaaagccccgagcaggagtaatggcgtttttgctttcatcggataaatctt Intra-Species Hit: Count: 1 Min: 1 Max: 129 Len: 129 Subject: NC_002950_PG0466_PG0468|hypothetical protein:mannose-6-phosphate isomerase, class I|NEGATIVE:NEGATIVE|[510335,510463]|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 ggaaatactatcgaaaacgatcctgtcgctttgtttgttcctctctctcttacaagatgaaatctgcagcaatagggcgaaagccccgagcaggagtaatggcgtttttgctttcatcggataaatctt ggaaatactatcgaaaacgatcctgtcgctttgtttgttcctctctctcttacaagatgaaatctgcagcaatagggcgaaagccccgagcaggagtaatggcgtttttgctttcatcggataaatctt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GGAAAUACUAUCGAAAACGAUCCUGUCGCUUUGUUUGUUCCUCUCUCUCUUACAAGAUGAAAUCUGCAGCAAUAGGGCGAAAGCCCCGAGCAGGAGUAAUGGCGUUUUUGCUUUCAUCGGAUAAAUCUU ...........((((((((.((((((.(((..((...(((.(((..........))).)))....)))))....((((....))))...)))))).......))))))))................... (-29.70) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAGAUUUAUCCGAUGAAAGCAAAAACGCCAUUACUCCUGCUCGGGGCUUUCGCCCUAUUGCUGCAGAUUUCAUCUUGUAAGAGAGAGAGGAACAAACAAAGCGACAGGAUCGUUUUCGAUAGUAUUUCC ....(((((..((((((.((......))........((((..(((((....)))))......))))..))))))..)))))...((((.........(((((((.....)))))))........)))). (-26.33) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 1018 110 61 201 152 NC_002950:PG0466|5end_hypothetical_protein_510244..510474_NEGATIVE 392 105 62 84 35 NC_002950:PG0412|5end_DNA_mismatch_repair_protein_MutL_451440..451670_NEGATIVE 366 49 10 217 175 NC_002950:PG0333|5end_hypothetical_protein_367823..368053_POSITIVE 365 120 74 221 182 NC_002950:PG0060|5end_hypothetical_protein_71916..72146_POSITIVE 364 120 75 206 160 NC_002950:PG2163|5end_acid_phosphatase_2269571..2269801_NEGATIVE 353 110 63 61 10 NC_002950:PG1712|5end_alpha-1,2-mannosidase_family_protein_1801325..1801555_NEGATIVE 351 97 63 68 31 NC_002950:PG0434|5end_hypothetical_protein_472513..472743_NEGATIVE 348 105 66 88 43 NC_002950:PG1967|5end_TPR_domain_protein_2057168..2057398_POSITIVE 347 99 55 73 20 NC_002950:PG1773|5end_PAP2_superfamily_protein_1859815..1860045_POSITIVE 347 119 75 78 30 NC_002950:PG1620|5end_carboxyl-terminal_protease-related_protein_1700491..1700721_NEGATIVE 346 118 75 45 5 NC_002950:PG1783|5end_glycosyl_transferase,_group_2_family_protein_1871868..1872098_POSITIVE 345 118 75 165 116 NC_002950:PG0700|5end_hypothetical_protein_756595..756825_NEGATIVE 344 104 64 226 173 NC_002950:PG0360|5end_lemA_protein_393482..393712_POSITIVE 341 118 78 58 18 NC_002950:PG0493|5end_hypothetical_protein_534900..535130_NEGATIVE 341 118 78 58 18 NC_002950:PG0265|5end_hypothetical_protein_298551..298781_NEGATIVE 341 96 55 51 1 NC_002950:PG0147|5end_hypothetical_protein_169667..169897_NEGATIVE 339 98 56 60 17 NC_002950:PG2200|5end_TPR_domain_protein_2308807..2309037_NEGATIVE 339 98 56 165 106 NC_002950:PG2021|5end_hypothetical_protein_2114852..2115082_NEGATIVE 334 119 71 182 137 NC_002950:PG1254|5end_acetyltransferase,_GNAT_family_1332121..1332351_NEGATIVE 332 105 64 52 7 NC_002950:PG0782|5end_MotA/TolQ/ExbB_proton_channel_family_protein_834530..834760_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 392 105 62 87 38 NC_002950:PG0413|3end_hypothetical_protein_451437..451587_NEGATIVE 372 105 65 148 99 NC_002950:PG2214|3end_hypothetical_protein_2325301..2325451_NEGATIVE 351 120 74 138 98 NC_002950:PG1472|3end_hypothetical_protein_1549760..1549910_POSITIVE 350 110 76 48 4 NC_002950:PG0571|3end_aspartate-semialdehyde_dehydrogenase_627492..627642_POSITIVE 349 120 75 114 60 NC_002950:PG0711|3end_hypothetical_protein_766281..766431_POSITIVE 347 119 75 85 37 NC_002950:PG1621|3end_hypothetical_protein_1700484..1700634_NEGATIVE 346 118 75 58 18 NC_002950:PG1782|3end_hypothetical_protein_1871961..1872111_POSITIVE 343 105 63 84 17 NC_002950:PG0605|3end_hypothetical_protein_661165..661315_NEGATIVE 343 79 31 126 67 NC_002950:PG0129|3end_mannosyltransferase_151789..151939_POSITIVE 341 96 55 64 14 NC_002950:PG0148|3end_sigma-54-dependent_transcriptional_regulator_169654..169804_NEGATIVE 326 105 64 84 28 NC_002950:PG0226|3end_transglutaminase-related_protein_259838..259988_NEGATIVE 325 120 74 97 54 NC_002950:PG0133|3end_hypothetical_protein_154259..154409_NEGATIVE 323 57 18 98 59 NC_002950:PG1393|3end_penicillin-binding_protein_2,_putative_1474406..1474556_NEGATIVE 321 104 66 74 36 NC_002950:PG0883|3end_hypothetical_protein_946562..946712_POSITIVE 319 103 65 109 68 NC_002950:PG1559|3end_aminomethyltransferase_1637904..1638054_NEGATIVE 319 115 76 142 99 NC_002950:PG0291|3end_hypothetical_protein_326622..326772_POSITIVE 317 103 64 63 22 NC_002950:PG1593|3end_shikimate_kinase_1672143..1672293_POSITIVE 317 102 64 84 50 NC_002950:PG0164|3end_hypothetical_protein_187081..187231_NEGATIVE 315 110 66 118 59 NC_002950:PG1389|3end_DNA-binding_protein,_histone-like_family_1470870..1471020_NEGATIVE 315 118 75 76 25 NC_002950:PG0986|3end_hypothetical_protein_1048066..1048216_POSITIVE