Origin IGS: tactttatatgaactcttggttgtataaacaagggactagctaattacaggaagcgagactgataacatcaaattatctcgcttcctttattctaatttttaaagaaatttagaaatgttttttaaataatttaggtaatatttttgtgcaactgacattctaaagtatagagttaagacgattgatttt .........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 aaaatcaatcgtcttaactctatactttagaatgtcagttgcacaaaaatattacctaaattatttaaaaaacatttctaaatttctttaaaaattagaataaaggaagcgagataatttgatgttatcagtctcgcttcctgtaattagctagtcccttgtttatacaaccaagagttcatataaagta Mask Tandem Repeat Region ================================================ tactttatatgaactcttggttgtataaacaagggactagctaattacaggaagcgagactgataacatcaaattatctcgcttcctttattctaannnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnngtgcaactgacattctaaagtatagagttaagacgattgatttt Find is-nt database================================================ Query_seq: SMT_256:SMT_257|SMT_256:SMT_257:K02027 multiple sugar transport system substrate-binding protein:predicted integral membrane protein:->->:194343..194532 190 tactttatatgaactcttggttgtataaacaagggactagctaattacaggaagcgagactgataacatcaaattatctcgcttcctttattctaatttttaaagaaatttagaaatgttttttaaataatttaggtaatatttttgtgcaactgacattctaaagtatagagttaagacgattgatttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_256:SMT_257|SMT_256:SMT_257:K02027 multiple sugar transport system substrate-binding protein:predicted integral membrane protein:->->:194343..194532 190 tactttatatgaactcttggttgtataaacaagggactagctaattacaggaagcgagactgataacatcaaattatctcgcttcctttattctaatttttaaagaaatttagaaatgttttttaaataatttaggtaatatttttgtgcaactgacattctaaagtatagagttaagacgattgatttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_256:SMT_257|SMT_256:SMT_257:K02027 multiple sugar transport system substrate-binding protein:predicted integral membrane protein:->->:194343..194532 190 tactttatatgaactcttggttgtataaacaagggactagctaattacaggaagcgagactgataacatcaaattatctcgcttcctttattctaatttttaaagaaatttagaaatgttttttaaataatttaggtaatatttttgtgcaactgacattctaaagtatagagttaagacgattgatttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tactttatatgaactcttggttgtataaacaagggactagctaattacaggaagcgagactgataacatcaaattatctcgcttcctttattctaatttttaaagaaatttagaaatgttttttaaataatttaggtaatatttttgtgcaactgacattctaaagtatagagttaagacgattgatttt Predict ORF larger than 30AA ================================================ tactttatatgaactcttggttgtataaacaagggactagctaattacaggaagcgagactgataacatcaaattatctcgcttcctttattctaatttttaaagaaatttagaaatgttttttaaataatttaggtaatatttttgtgcaactgacattctaaagtatagagttaagacgattgatttt 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================================================ tactttatatgaactcttggttgtataaacaagggactagctaattacaggaagcgagactgataacatcaaattatctcgcttcctttattctaatttttaaagaaatttagaaatgttttttaaataatttaggtaatatttttgtgcaactgacattctaaagtatagagttaagacgattgatttt Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 76 HP_score: -6.8 Tail_Score: -4.46576 Start: 50 End: 86 Full_Region: GACTAGCTAATTACA GGAAGCGAGACTGAT AACATCAA ATTATCTCGCTTCC TTTATTCTAATTTTT .................................................GGAAGCGAGACTGATAACATCAAATTATCTCGCTTCC........................................................................................................ TransTerm Strand: - Conf: 50 HP_score: -4.6 Tail_Score: -2.92668 Start: 50 End: 86 Full_Region: aaaaattagaataaa ggaagcgagataat ttgatgtt atcagtctcgcttcc tgtaattagctagtc .................................................ggaagcgagataatttgatgttatcagtctcgcttcc........................................................................................................ Find igs database================================================ Query_seq: SMT_256:SMT_257|SMT_256:SMT_257:K02027 multiple sugar transport system substrate-binding protein:predicted integral membrane protein:->->:194343..194532 190 tactttatatgaactcttggttgtataaacaagggactagctaattacaggaagcgagactgataacatcaaattatctcgcttcctttattctaatttttaaagaaatttagaaatgttttttaaataatttaggtaatatttttgtgcaactgacattctaaagtatagagttaagacgattgatttt Intra-Species Hit: Count: 1 Min: 1 Max: 190 Len: 190 Subject: smit_SMT_256_SMT_257|K02027 multiple sugar transport system substrate-binding protein:predicted integral membrane protein|POSITIVE:POSITIVE|[194343,194532]|190 HSP 1 e-value: 1.0E-41 bit: 170.0 Len: 86 Query Start:1 Query End:86 Subject Strand: POSITIVE Subject Start: 1 Subject End: 86 tactttatatgaactcttggttgtataaacaagggactagctaattacaggaagcgagactgataacatcaaattatctcgcttcc........................................................................................................ tactttatatgaactcttggttgtataaacaagggactagctaattacaggaagcgagactgataacatcaaattatctcgcttcc........................................................................................................ HSP 2 e-value: 1.0E-16 bit: 87.7 Len: 44 Query Start:147 Query End:190 Subject Strand: POSITIVE Subject Start: 147 Subject End: 190 ..................................................................................................................................................gtgcaactgacattctaaagtatagagttaagacgattgatttt ..................................................................................................................................................gtgcaactgacattctaaagtatagagttaagacgattgatttt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UACUUUAUAUGAACUCUUGGUUGUAUAAACAAGGGACUAGCUAAUUACAGGAAGCGAGACUGAUAACAUCAAAUUAUCUCGCUUCCUUUAUUCUAAUUUUUAAAGAAAUUUAGAAAUGUUUUUUAAAUAAUUUAGGUAAUAUUUUUGUGCAACUGACAUUCUAAAGUAUAGAGUUAAGACGAUUGAUUUU (((((((...(((...(..((((((((((......(((....(((((.(((((((((((.((((........)))))))))))))))........(((((((((....)))))))))..........)))))..)))......))))))))))..)..)))))))))).((((((((.....)))))))) (-45.30) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAAUCAAUCGUCUUAACUCUAUACUUUAGAAUGUCAGUUGCACAAAAAUAUUACCUAAAUUAUUUAAAAAACAUUUCUAAAUUUCUUUAAAAAUUAGAAUAAAGGAAGCGAGAUAAUUUGAUGUUAUCAGUCUCGCUUCCUGUAAUUAGCUAGUCCCUUGUUUAUACAACCAAGAGUUCAUAUAAAGUA ...............((((((........((..(..((((((.................................((((((.(((.....))).))))))...((((((((((((....((((...))))))))))))))))))))))..)...))..((((....))))...))))))........... (-34.70) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 257 59 16 68 22 smit:SMT_1207|5end_choline_binding_protein_A_1168420..1168650_NEGATIVE 256 88 53 213 180 smit:SMT_1294|5end_K02049_sulfonate/nitrate/taurine_transport_system_ATP-binding_protein_1255983..1256213_POSITIVE 244 80 32 94 39 smit:SMT_826|5end_hypothetical_protein_750022..750252_NEGATIVE 238 66 33 69 18 smit:SMT_1754|5end_leader_peptidase_(prepilin_peptidase)_/_N-methyltransferase_1733022..1733252_NEGATIVE 234 59 14 65 16 smit:SMT_162|5end_hypothetical_protein_106593..106823_POSITIVE 233 94 53 107 53 smit:SMT_399|5end_cytochrome_c-type_biogenesis_protein_CcdA_328366..328596_POSITIVE 232 72 31 230 187 smit:SMT_758|5end_hypothetical_protein_661745..661975_POSITIVE 230 70 30 154 108 smit:SMT_765|5end_hypothetical_protein_672620..672850_NEGATIVE 227 90 48 172 124 smit:SMT_1636|5end_5-formyltetrahydrofolate_cyclo-ligase_family_protein_1622568..1622798_POSITIVE 226 78 33 106 65 smit:SMT_1797|5end_threonine_dehydratase_1772684..1772914_NEGATIVE 223 67 30 187 143 smit:SMT_1831|5end_galactose-6-phosphate_isomerase_1799912..1800142_POSITIVE 221 68 26 168 120 smit:SMT_690|5end_pyrimidine_regulatory_protein_602168..602398_NEGATIVE 220 62 29 227 192 smit:SMT_1340|5end_phosphoenolpyruvate_carboxylase_1317867..1318097_NEGATIVE 220 70 31 67 34 smit:SMT_445|5end_hypothetical_protein_384309..384539_POSITIVE 220 87 52 192 159 smit:SMT_268|5end_penicillin-binding_protein_2X_205471..205701_POSITIVE 219 179 132 42 7 smit:SMT_1528|5end_K03310_alanine_or_glycine:cation_symporter,_AGCS_family_1512667..1512897_NEGATIVE 219 63 36 133 109 smit:SMT_1327|5end_K03402_transcriptional_regulator_of_arginine_metabolism_1303746..1303976_POSITIVE 218 100 52 224 175 smit:SMT_1994|5end_phosphoglycerate_mutase_1920501..1920731_NEGATIVE 218 60 17 181 138 smit:SMT_1453|5end_K07335_basic_membrane_protein_A_and_related_proteins_1437407..1437637_NEGATIVE 218 42 13 126 96 smit:SMT_841|5end_dihydrodipicolinate_reductase_788025..788255_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 341 87 49 42 4 smit:SMT_256|3end_K02027_multiple_sugar_transport_system_substrate-binding_protein_194282..194432_POSITIVE 256 173 131 151 110 smit:SMT_1092|3end_transcription_antitermination_factor_1033160..1033310_NEGATIVE 240 56 14 129 88 smit:SMT_339|3end_K03687_molecular_chaperone_GrpE_278490..278640_POSITIVE 235 60 11 77 1 smit:SMT_1585|3end_phosphopantetheine_adenylyltransferase_1575810..1575960_POSITIVE 224 70 30 118 80 smit:SMT_1152|3end_hypothetical_protein_1096400..1096550_NEGATIVE 221 68 32 151 112 smit:SMT_1950|3end_Mn2+_and_Fe2+_transporter_of_the_NRAMP_family_1885069..1885219_POSITIVE 218 60 17 91 48 smit:SMT_1454|3end_cytidine_deaminase_1437497..1437647_NEGATIVE 217 67 30 38 4 smit:SMT_1830|3end_galactose-6-phosphate_isomerase_1799843..1799993_POSITIVE 217 95 60 115 72 smit:SMT_963|3end_K02015_iron_complex_transport_system_permease_protein_908586..908736_NEGATIVE 216 80 33 105 60 smit:SMT_1188|3end_hypothetical_protein_1146426..1146576_NEGATIVE 215 65 29 74 37 smit:SMT_236|3end_ribosomal_small_subunit_pseudouridine_synthase_A_175211..175361_POSITIVE 214 75 51 136 109 smit:SMT_559|3end_D-alanyl-D-alanine_carboxypeptidase_476801..476951_NEGATIVE 214 69 48 24 5 smit:SMT_415|3end_hypothetical_protein_359488..359638_POSITIVE 211 189 144 92 58 smit:SMT_571|3end_putative_transposase,_ISSmu1_490009..490159_POSITIVE 208 80 31 75 30 smit:SMT_1933|3end_K02006_cobalt_transport_system_ATP-binding_protein_1871986..1872136_NEGATIVE 207 96 52 99 57 smit:SMT_1604|3end_K05833_putative_ABC_transport_system_ATP-binding_protein_1595163..1595313_POSITIVE 204 58 38 56 34 smit:SMT_2057|3end_cell_division_protein_FtsH_1966897..1967047_NEGATIVE 203 90 49 101 59 smit:SMT_727|3end_phage_transcriptional_repressor_631830..631980_NEGATIVE 203 57 17 151 104 smit:SMT_183|3end_30S_ribosomal_protein_S14_121279..121429_POSITIVE 203 85 47 86 56 smit:SMT_162|3end_hypothetical_protein_107134..107284_POSITIVE