Origin IGS: tggtacgagaacatcagcaaatgtagttatctttgacagctgtttggattcgaacgatttgtcagaaccggcagtataatgtctcccgtagcgaggaatacctcccatttgctcttgatgagttgccgcattgcgg .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 ccgcaatgcggcaactcatcaagagcaaatgggaggtattcctcgctacgggagacattatactgccggttctgacaaatcgttcgaatccaaacagctgtcaaagataactacatttgctgatgttctcgtacca Mask Tandem Repeat Region ================================================ tggtacgagaacatcagcaaatgtagttatctttgacagctgtttggattcgaacgatttgtcagaaccggcagtataatgtctcccgtagcgaggaatacctcccatttgctcttgatgagttgccgcattgcgg Find is-nt database================================================ Query_seq: PG1750:PG1751|PG1750:PG1751:alpha-1,3/4-fucosidase, putative:aminotransferase, class V:->->:1837284..1837419 136 tggtacgagaacatcagcaaatgtagttatctttgacagctgtttggattcgaacgatttgtcagaaccggcagtataatgtctcccgtagcgaggaatacctcccatttgctcttgatgagttgccgcattgcgg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG1750:PG1751|PG1750:PG1751:alpha-1,3/4-fucosidase, putative:aminotransferase, class V:->->:1837284..1837419 136 tggtacgagaacatcagcaaatgtagttatctttgacagctgtttggattcgaacgatttgtcagaaccggcagtataatgtctcccgtagcgaggaatacctcccatttgctcttgatgagttgccgcattgcgg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG1750:PG1751|PG1750:PG1751:alpha-1,3/4-fucosidase, putative:aminotransferase, class V:->->:1837284..1837419 136 tggtacgagaacatcagcaaatgtagttatctttgacagctgtttggattcgaacgatttgtcagaaccggcagtataatgtctcccgtagcgaggaatacctcccatttgctcttgatgagttgccgcattgcgg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tggtacgagaacatcagcaaatgtagttatctttgacagctgtttggattcgaacgatttgtcagaaccggcagtataatgtctcccgtagcgaggaatacctcccatttgctcttgatgagttgccgcattgcgg Predict ORF larger than 30AA ================================================ Protein_Len: 34 Strand: + Start: 33 End: 134 ................................ M T A V W I R T I C Q N R Q Y N V S R S E E Y L P F A L D E L P H C .. Protein_Len: 32 Strand: + Start: 40 End: 135 ....................................... M F G F E R F V R T G S I M S P V A R N T S H L L L M S C R I A . Protein_Len: 34 Strand: - Start: 30 End: 131 ............................. R Q C S N P N S R N T L V P L I I D G T A L F V E W K S K I L Q R M ..... Protein_Len: 36 Strand: - Start: 1 End: 108 P V L V D A F T T I K S L Q K S E F S K D S G A T Y H R G Y R P I G G M ............................ tggtacgagaacatcagcaaatgtagttatctttgacagctgtttggattcgaacgatttgtcagaaccggcagtataatgtctcccgtagcgaggaatacctcccatttgctcttgatgagttgccgcattgcgg 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================================================ tggtacgagaacatcagcaaatgtagttatctttgacagctgtttggattcgaacgatttgtcagaaccggcagtataatgtctcccgtagcgaggaatacctcccatttgctcttgatgagttgccgcattgcgg Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PG1750:PG1751|PG1750:PG1751:alpha-1,3/4-fucosidase, putative:aminotransferase, class V:->->:1837284..1837419 136 tggtacgagaacatcagcaaatgtagttatctttgacagctgtttggattcgaacgatttgtcagaaccggcagtataatgtctcccgtagcgaggaatacctcccatttgctcttgatgagttgccgcattgcgg Intra-Species Hit: Count: 1 Min: 1 Max: 136 Len: 136 Subject: NC_002950_PG1750_PG1751|alpha-1,3/4-fucosidase, putative:aminotransferase, class V|POSITIVE:POSITIVE|[1837284,1837419]|136 HSP 1 e-value: 1.0E-71 bit: 270.0 Len: 136 Query Start:1 Query End:136 Subject Strand: POSITIVE Subject Start: 1 Subject End: 136 tggtacgagaacatcagcaaatgtagttatctttgacagctgtttggattcgaacgatttgtcagaaccggcagtataatgtctcccgtagcgaggaatacctcccatttgctcttgatgagttgccgcattgcgg tggtacgagaacatcagcaaatgtagttatctttgacagctgtttggattcgaacgatttgtcagaaccggcagtataatgtctcccgtagcgaggaatacctcccatttgctcttgatgagttgccgcattgcgg Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGGUACGAGAACAUCAGCAAAUGUAGUUAUCUUUGACAGCUGUUUGGAUUCGAACGAUUUGUCAGAACCGGCAGUAUAAUGUCUCCCGUAGCGAGGAAUACCUCCCAUUUGCUCUUGAUGAGUUGCCGCAUUGCGG ...........((((((((((((..(((((.((((((((.((((((....))))))..))))))))...((((......))))....)))))((((....)))).)))))))...))))).....((((...)))) (-35.10) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CCGCAAUGCGGCAACUCAUCAAGAGCAAAUGGGAGGUAUUCCUCGCUACGGGAGACAUUAUACUGCCGGUUCUGACAAAUCGUUCGAAUCCAAACAGCUGUCAAAGAUAACUACAUUUGCUGAUGUUCUCGUACCA ((((...)))).....(((((...(((((((.((((....))))....(((.((........)).)))....(((((..(.(((.(....).))))..)))))..........))))))))))))........... (-31.30) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 382 97 51 226 183 NC_002950:PG1752|5end_hypothetical_protein_1838394..1838624_POSITIVE 374 128 90 71 29 NC_002950:PG0629|5end_inorganic_polyphosphate/ATP-NAD_kinase_683364..683594_NEGATIVE 357 98 51 127 73 NC_002950:PG2087|5end_hypothetical_protein_2186990..2187220_POSITIVE 349 106 68 197 152 NC_002950:PG1655|5end_hypothetical_protein_1737095..1737325_POSITIVE 348 96 58 197 159 NC_002950:PG0705|5end_glutamate_racemase_759529..759759_POSITIVE 346 130 88 226 170 NC_002950:PG1332|5end_NAD(P)_transhydrogenase,_beta_subunit_1412042..1412272_POSITIVE 345 128 82 223 172 NC_002950:PG1758|5end_ribosomal_protein_S15_1845185..1845415_POSITIVE 342 78 34 197 158 NC_002950:PG0434|5end_hypothetical_protein_472513..472743_NEGATIVE 340 96 51 48 4 NC_002950:PG2187|5end_1,4-dihydroxy-2-naphthoate_octaprenyltransferase_2294643..2294873_NEGATIVE 336 77 31 207 166 NC_002950:PG0523|5end_inositol-5-monophosphate_dehydrogenase_568394..568624_NEGATIVE 327 128 81 80 32 NC_002950:PG1608|5end_methylmalonyl-CoA_decarboxylase,_beta_subunit_1689836..1690066_NEGATIVE 322 127 83 224 175 NC_002950:PG1565|5end_3-deoxy-D-manno-octulosonic-acid_transferase,_putative_1645859..1646089_NEGATIVE 322 98 51 112 54 NC_002950:PG1402|5end_AP_endonuclease_domain_protein_1485963..1486193_NEGATIVE 322 106 64 201 162 NC_002950:PG0071|5end_UDP-3-O-acyl-GlcNAc_deacetylase/beta-hydroxyacyl-[acyl_carrier_protein]_dehydratase_FabZ_86119..86349_NEGATIVE 319 130 81 210 148 NC_002950:PG2173|5end_outer_membrane_lipoprotein_Omp28_2280813..2281043_NEGATIVE 318 129 81 231 177 NC_002950:PG0977|5end_ubiquinone/menaquinone_biosynthesis_methyltransferase_1039299..1039529_POSITIVE 318 129 84 55 3 NC_002950:PG0858|5end_hypothetical_protein_917540..917770_POSITIVE 314 130 81 73 16 NC_002950:PG1338|5end_umuC_protein_1418246..1418476_POSITIVE 313 128 85 225 185 NC_002950:PG1392|5end_rod_shape-determining_protein_RodA,_putative_1474416..1474646_NEGATIVE 313 128 84 56 1 NC_002950:PG0368|5end_DNA_topoisomerase_IV_subunit_B_401245..401475_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 370 130 85 59 15 NC_002950:PG1162|3end_ATP:cob(I)alamin_adenosyltransferase,_putative_1241473..1241623_NEGATIVE 357 98 51 127 73 NC_002950:PG2086|3end_hypothetical_protein_2187070..2187220_POSITIVE 352 130 82 137 83 NC_002950:PG0403|3end_hypothetical_protein_439453..439603_NEGATIVE 348 96 58 135 97 NC_002950:PG0704|3end_phosphoglycerate_mutase_family_protein_759547..759697_POSITIVE 340 96 51 58 14 NC_002950:PG2188|3end_diaminopimelate_decarboxylase_2294633..2294783_NEGATIVE 334 66 21 90 48 NC_002950:PG2031|3end_hypothetical_protein_2130871..2131021_POSITIVE 331 129 81 125 71 NC_002950:PG0566|3end_DNA-binding_protein,_histone-like_family_622935..623085_NEGATIVE 327 130 82 144 102 NC_002950:PG2065|3end_conserved_hypothetical_protein_TIGR00048_2162105..2162255_POSITIVE 327 128 81 75 27 NC_002950:PG1609|3end_methylmalonyl-CoA_decarboxylase,_gamma_subunit_1689841..1689991_NEGATIVE 324 105 67 42 5 NC_002950:PG2037|3end_hypothetical_protein_2137591..2137741_NEGATIVE 318 129 84 58 6 NC_002950:PG0857|3end_transcriptional_regulator,_putative_917623..917773_POSITIVE 314 130 81 65 8 NC_002950:PG1337|3end_umuD_protein_1418318..1418468_POSITIVE 307 126 86 109 70 NC_002950:PG1761|3end_acetyltransferase,_GNAT_family_1847739..1847889_POSITIVE 304 78 31 59 4 NC_002950:PG1395|3end_cell_shape-determining_protein_MreC,_putative_1476782..1476932_NEGATIVE 301 128 81 79 25 NC_002950:PG2004|3end_hypothetical_protein_2093135..2093285_NEGATIVE 300 114 80 65 21 NC_002950:PG0503|3end_dipeptidyl_aminopeptidase_IV_544211..544361_POSITIVE 298 103 68 73 42 NC_002950:PG1522|3end_mandelate_racemase/muconate_lactonizing_enzyme_family_protein_1599100..1599250_NEGATIVE 298 95 51 107 41 NC_002950:PG1235|3end_epimerase/reductase,_putative_1310300..1310450_NEGATIVE 297 75 36 118 73 NC_002950:PG1899|3end_TonB-dependent_receptor,_putative_1997340..1997490_NEGATIVE 297 130 86 67 29 NC_002950:PG0523|3end_inositol-5-monophosphate_dehydrogenase_566898..567048_NEGATIVE