Origin IGS: aatcccaaaaaaaccaaataaaataagcggattaattttctttctcatatctcataattttaccttaaaaatgaaaaaaaatcaaaaaaaatactcaaaaaatgggttaaggaaaggactttggagcattttttcattcaagggcgcggaatgatttgaaatatggtataataaaagggaatttctagagaaaagagaagatt .........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 aatcttctcttttctctagaaattcccttttattataccatatttcaaatcattccgcgcccttgaatgaaaaaatgctccaaagtcctttccttaacccattttttgagtattttttttgattttttttcatttttaaggtaaaattatgagatatgagaaagaaaattaatccgcttattttatttggtttttttgggatt Mask Tandem Repeat Region ================================================ aatcccaaaaaaaccaaataaaataagcggattaattttctttctcatatctcataattttaccttaaaaatgaaaaaaaatcaaaaaaaatactcaaaaaatgggttaaggaaaggactttggagcattttttcattcaagggcgcggaatgatttgaaatatggtataataaaagggaatttctagagaaaagagaagatt Find is-nt database================================================ Query_seq: SMT_598:SMT_599|SMT_598:SMT_599:K07273 lysozyme:glucosamine-1-phosphate N-acetyltransferase / UDP-N-acetylglucosamine pyrophosphorylase:<-->:514855..515057 203 aatcccaaaaaaaccaaataaaataagcggattaattttctttctcatatctcataattttaccttaaaaatgaaaaaaaatcaaaaaaaatactcaaaaaatgggttaaggaaaggactttggagcattttttcattcaagggcgcggaatgatttgaaatatggtataataaaagggaatttctagagaaaagagaagatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_598:SMT_599|SMT_598:SMT_599:K07273 lysozyme:glucosamine-1-phosphate N-acetyltransferase / UDP-N-acetylglucosamine pyrophosphorylase:<-->:514855..515057 203 aatcccaaaaaaaccaaataaaataagcggattaattttctttctcatatctcataattttaccttaaaaatgaaaaaaaatcaaaaaaaatactcaaaaaatgggttaaggaaaggactttggagcattttttcattcaagggcgcggaatgatttgaaatatggtataataaaagggaatttctagagaaaagagaagatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_598:SMT_599|SMT_598:SMT_599:K07273 lysozyme:glucosamine-1-phosphate N-acetyltransferase / UDP-N-acetylglucosamine pyrophosphorylase:<-->:514855..515057 203 aatcccaaaaaaaccaaataaaataagcggattaattttctttctcatatctcataattttaccttaaaaatgaaaaaaaatcaaaaaaaatactcaaaaaatgggttaaggaaaggactttggagcattttttcattcaagggcgcggaatgatttgaaatatggtataataaaagggaatttctagagaaaagagaagatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aatcccaaaaaaaccaaataaaataagcggattaattttctttctcatatctcataattttaccttaaaaatgaaaaaaaatcaaaaaaaatactcaaaaaatgggttaaggaaaggactttggagcattttttcattcaagggcgcggaatgatttgaaatatggtataataaaagggaatttctagagaaaagagaagatt Predict ORF larger than 30AA ================================================ Protein_Len: 50 Strand: + Start: 2 End: 151 . M P K K P N K I S G L I F F L I S H N F T L K M K K N Q K K Y S K N G L R K G L W S I F S F K G A E .................................................... aatcccaaaaaaaccaaataaaataagcggattaattttctttctcatatctcataattttaccttaaaaatgaaaaaaaatcaaaaaaaatactcaaaaaatgggttaaggaaaggactttggagcattttttcattcaagggcgcggaatgatttgaaatatggtataataaaagggaatttctagagaaaagagaagatt Predict Promoter with matrix: RpoD-15 score > 80================================================ Predict Promoter with matrix: RpoD-16 score > 80================================================ Predict Promoter with matrix: RpoD-17 score > 80================================================ PromScan Matrix: RpoD-17 Strand: - Score: 87 Start: 57 End: 86 ........................................................TTTGATTTTTTTTCATTTTTAAGGTAAAAT..................................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aatcccaaaaaaaccaaataaaataagcggattaattttctttctcatatctcataattttaccttaaaaatgaaaaaaaatcaaaaaaaatactcaaaaaatgggttaaggaaaggactttggagcattttttcattcaagggcgcggaatgatttgaaatatggtataataaaagggaatttctagagaaaagagaagatt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SMT_598:SMT_599|SMT_598:SMT_599:K07273 lysozyme:glucosamine-1-phosphate N-acetyltransferase / UDP-N-acetylglucosamine pyrophosphorylase:<-->:514855..515057 203 aatcccaaaaaaaccaaataaaataagcggattaattttctttctcatatctcataattttaccttaaaaatgaaaaaaaatcaaaaaaaatactcaaaaaatgggttaaggaaaggactttggagcattttttcattcaagggcgcggaatgatttgaaatatggtataataaaagggaatttctagagaaaagagaagatt Intra-Species Hit: Count: 1 Min: 14 Max: 203 Len: 190 Subject: smit_SMT_598_SMT_599|K07273 lysozyme:glucosamine-1-phosphate N-acetyltransferase / UDP-N-acetylglucosamine pyrophosphorylase|NEGATIVE:POSITIVE|[514855,515057]|203 HSP 1 e-value: 1.0E-50 bit: 200.0 Len: 101 Query Start:103 Query End:203 Subject Strand: POSITIVE Subject Start: 103 Subject End: 203 ......................................................................................................tgggttaaggaaaggactttggagcattttttcattcaagggcgcggaatgatttgaaatatggtataataaaagggaatttctagagaaaagagaagatt ......................................................................................................tgggttaaggaaaggactttggagcattttttcattcaagggcgcggaatgatttgaaatatggtataataaaagggaatttctagagaaaagagaagatt HSP 2 e-value: 6.0E-22 bit: 105.0 Len: 53 Query Start:14 Query End:66 Subject Strand: POSITIVE Subject Start: 14 Subject End: 66 .............ccaaataaaataagcggattaattttctttctcatatctcataattttacctt......................................................................................................................................... .............ccaaataaaataagcggattaattttctttctcatatctcataattttacctt......................................................................................................................................... Inter-species Hit: Count: 2 Min: 103 Max: 203 Len: 101 Subject: NC_008533_SPD_0873_SPD_0874|hypothetical protein:UDP-N-acetylglucosamine pyrophosphorylase|NEGATIVE:POSITIVE|[887754,887896]|143 HSP 1 e-value: 3.0E-36 bit: 153.0 Len: 101 Query Start:103 Query End:203 Subject Strand: POSITIVE Subject Start: 43 Subject End: 143 ......................................................................................................tgggttaaggaaaggactttggagcattttttcattcaagggcgcggaatgatttgaaatatggtataataaaagggaatttctagagaaaagagaagatt ......................................................................................................tgggttaaggaagagactttagagcattttttcattcaagagtgcggaatgatttgaaatatggtataataaaagggaatttctacagaaaagagaagatt Subject: NC_003028_SP_0987_SP_0988|hypothetical protein:UDP-N-acetylglucosamine pyrophosphorylase|NEGATIVE:POSITIVE|[932116,932258]|143 HSP 1 e-value: 3.0E-36 bit: 153.0 Len: 101 Query Start:103 Query End:203 Subject Strand: POSITIVE Subject Start: 43 Subject End: 143 ......................................................................................................tgggttaaggaaaggactttggagcattttttcattcaagggcgcggaatgatttgaaatatggtataataaaagggaatttctagagaaaagagaagatt ......................................................................................................tgggttaaggaagagactttagagcattttttcattcaagagtgcggaatgatttgaaatatggtataataaaagggaatttctacagaaaagagaagatt Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGGGUUAAGGAAAGGACUUUGGAGCAUUUUUUCAUUCAAGGGCGCGGAAUGAUUUGAAAUAUGGUAUAAUAAAAGGGAAUUUCUAGAGAAAAGAGAAGAUU ................((((((((.((((((((((((.........)))))).......(((......)))...))))))))))))))............. (-11.70) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUCUUCUCUUUUCUCUAGAAAUUCCCUUUUAUUAUACCAUAUUUCAAAUCAUUCCGCGCCCUUGAAUGAAAAAAUGCUCCAAAGUCCUUUCCUUAACCCA ..................(((((..................)))))...((((((.........))))))............................... ( -4.77) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 605 38 1 231 194 smit:SMT_598|5end_K07273_lysozyme_514764..514994_NEGATIVE 287 56 12 135 84 smit:SMT_1013|5end_galactose-1-phosphate_uridylyltransferase_950626..950856_NEGATIVE 269 63 21 225 177 smit:SMT_405|5end_zinc_metalloprotease_ZmpB,_truncated_333952..334182_POSITIVE 263 70 22 170 121 smit:SMT_499|5end_hypothetical_protein_432572..432802_POSITIVE 262 46 1 103 41 smit:SMT_2064|5end_amino_acid_ABC_transporter,_ATP-binding_protein_1972182..1972412_POSITIVE 262 58 14 183 146 smit:SMT_1296|5end_K03696_ATP-dependent_Clp_protease_ATP-binding_subunit_ClpC_1257290..1257520_POSITIVE 258 51 14 204 162 smit:SMT_1631|5end_phosphopantothenoylcysteine_synthase/decarboxylase_1618359..1618589_NEGATIVE 253 45 3 221 178 smit:SMT_1682|5end_K07282_poly-gamma-glutamate_synthesis_protein_(capsule_biosynthesis_protein)_1665337..1665567_POSITIVE 252 56 12 55 1 smit:SMT_594|5end_lysyl-tRNA_synthetase_511838..512068_NEGATIVE 250 48 21 63 35 smit:SMT_1541|5end_isopentenyl-diphosphate_delta-isomerase_1526093..1526323_NEGATIVE 246 46 3 79 25 smit:SMT_1581|5end_transcriptional_regulator,_biotin_repressor_family_1573635..1573865_NEGATIVE 242 45 1 50 12 smit:SMT_679|5end_LicC_protein_589072..589302_NEGATIVE 242 48 1 205 145 smit:SMT_178|5end_50S_ribosomal_protein_L29_119161..119391_POSITIVE 239 41 1 33 1 smit:SMT_1462|5end_phosphate_ABC_transporter,_ATP-binding_protein,_putative_1443140..1443370_POSITIVE 234 50 4 51 3 smit:SMT_975|5end_hypothetical_protein_922953..923183_POSITIVE 234 66 23 208 158 smit:SMT_360|5end_K07742_hypothetical_protein_295628..295858_POSITIVE 233 65 21 179 143 smit:SMT_726|5end_ImpB/MucB/SamB_family_protein_631827..632057_NEGATIVE 230 47 7 197 165 smit:SMT_841|5end_dihydrodipicolinate_reductase_788025..788255_NEGATIVE 229 52 16 216 185 smit:SMT_391|5end_PTS_system,_galactose-specific_IIC_component_322647..322877_POSITIVE 228 49 15 124 80 smit:SMT_1993|5end_hypothetical_protein_1919800..1920030_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 287 56 12 116 65 smit:SMT_1014|3end_galactokinase_950645..950795_NEGATIVE 250 48 21 79 51 smit:SMT_1542|3end_phosphomevalonate_kinase_1526077..1526227_NEGATIVE 246 43 1 102 67 smit:SMT_973|3end_signal_transduction_histidine_kinase_921203..921353_NEGATIVE 240 47 1 72 18 smit:SMT_559|3end_D-alanyl-D-alanine_carboxypeptidase_476801..476951_NEGATIVE 237 47 2 107 58 smit:SMT_1476|3end_thiol_peroxidase_1458728..1458878_NEGATIVE 237 47 8 44 6 smit:SMT_478|3end_hypothetical_protein_predicted_by_Glimmer/Critica_415257..415407_POSITIVE 236 47 8 128 95 smit:SMT_1467|3end_hydroxyacylglutathione_hydrolase_1448004..1448154_NEGATIVE 229 45 1 90 27 smit:SMT_1570|3end_hypothetical_protein_1563250..1563400_NEGATIVE 229 41 5 139 98 smit:SMT_1327|3end_K03402_transcriptional_regulator_of_arginine_metabolism_1304296..1304446_POSITIVE 228 59 13 69 8 smit:SMT_917|3end_hydroxymethylglutaryl-CoA_synthase_870004..870154_NEGATIVE 227 47 3 83 40 smit:SMT_780|3end_peptidase_family_U32_688752..688902_NEGATIVE 226 96 53 61 29 smit:SMT_1004|3end_thioredoxin_945824..945974_POSITIVE 226 47 1 62 6 smit:SMT_994|3end_nicotinate-nucleotide_adenylyltransferase_935476..935626_NEGATIVE 226 49 2 73 15 smit:SMT_397|3end_NAD(+)_synthetase_327423..327573_POSITIVE 225 47 1 142 96 smit:SMT_997|3end_integral_membrane_protein_939243..939393_POSITIVE 225 45 2 38 1 smit:SMT_680|3end_choline_transport_protein_589084..589234_NEGATIVE 225 47 5 78 34 smit:SMT_116|3end_beta-N-acetylhexosaminidase_68356..68506_POSITIVE 218 49 1 137 79 smit:SMT_1902|3end_proton-translocating_NADH-quinone_oxidoreductase,_chain_L_1852028..1852178_NEGATIVE 218 52 20 145 110 smit:SMT_212|3end_Holliday_junction_DNA_helicase_RuvB_145299..145449_POSITIVE 217 78 31 114 66 smit:SMT_863|3end_K07485_transposase_814447..814597_POSITIVE