Origin IGS: tcctcctggaacctcaaaaattgatcttgatggaggaacataccaaaattgaagcagagctgacaatcctgcagaagttgttctcctaggattgtcctcagctatcactaccatcattgaaaggaactttttgttat .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 ataacaaaaagttcctttcaatgatggtagtgatagctgaggacaatcctaggagaacaacttctgcaggattgtcagctctgcttcaattttggtatgttcctccatcaagatcaatttttgaggttccaggagga Mask Tandem Repeat Region ================================================ tcctcctggaacctcaaaaattgatcttgatggaggaacataccaaaattgaagcagagctgacaatcctgcagaagttgttctcctaggattgtcctcagctatcactaccatcattgaaaggaactttttgttat Find is-nt database================================================ Query_seq: SSA_0416:SSA_0417|SSA_0416:SSA_0417:5-methyltetrahydropteroyltriglutamate-- homocysteine methyltransferase, putative:5,10-methylenetetrahydrofolate reductase, putative:->->:414283..414419 137 tcctcctggaacctcaaaaattgatcttgatggaggaacataccaaaattgaagcagagctgacaatcctgcagaagttgttctcctaggattgtcctcagctatcactaccatcattgaaaggaactttttgttat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0416:SSA_0417|SSA_0416:SSA_0417:5-methyltetrahydropteroyltriglutamate-- homocysteine methyltransferase, putative:5,10-methylenetetrahydrofolate reductase, putative:->->:414283..414419 137 tcctcctggaacctcaaaaattgatcttgatggaggaacataccaaaattgaagcagagctgacaatcctgcagaagttgttctcctaggattgtcctcagctatcactaccatcattgaaaggaactttttgttat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0416:SSA_0417|SSA_0416:SSA_0417:5-methyltetrahydropteroyltriglutamate-- homocysteine methyltransferase, putative:5,10-methylenetetrahydrofolate reductase, putative:->->:414283..414419 137 tcctcctggaacctcaaaaattgatcttgatggaggaacataccaaaattgaagcagagctgacaatcctgcagaagttgttctcctaggattgtcctcagctatcactaccatcattgaaaggaactttttgttat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tcctcctggaacctcaaaaattgatcttgatggaggaacataccaaaattgaagcagagctgacaatcctgcagaagttgttctcctaggattgtcctcagctatcactaccatcattgaaaggaactttttgttat Predict ORF larger than 30AA ================================================ Protein_Len: 33 Strand: - Start: 3 End: 101 .. E Q F R L F Q D Q H L F M G F N F C L Q C D Q L L Q E G L I T R M .................................... Protein_Len: 39 Strand: - Start: 1 End: 117 G G P V E F I S R S P P V Y W F Q L L A S L G A S T T R R P N D E A I V V M M .................... tcctcctggaacctcaaaaattgatcttgatggaggaacataccaaaattgaagcagagctgacaatcctgcagaagttgttctcctaggattgtcctcagctatcactaccatcattgaaaggaactttttgttat 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================================================ tcctcctggaacctcaaaaattgatcttgatggaggaacataccaaaattgaagcagagctgacaatcctgcagaagttgttctcctaggattgtcctcagctatcactaccatcattgaaaggaactttttgttat Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_0416:SSA_0417|SSA_0416:SSA_0417:5-methyltetrahydropteroyltriglutamate-- homocysteine methyltransferase, putative:5,10-methylenetetrahydrofolate reductase, putative:->->:414283..414419 137 tcctcctggaacctcaaaaattgatcttgatggaggaacataccaaaattgaagcagagctgacaatcctgcagaagttgttctcctaggattgtcctcagctatcactaccatcattgaaaggaactttttgttat Intra-Species Hit: Count: 1 Min: 1 Max: 137 Len: 137 Subject: NC_009009_SSA_0416_SSA_0417|5-methyltetrahydropteroyltriglutamate-- homocysteine methyltransferase, putative:5,10-methylenetetrahydrofolate reductase, putative|POSITIVE:POSITIVE|[414283,414419]|137 HSP 1 e-value: 3.0E-72 bit: 272.0 Len: 137 Query Start:1 Query End:137 Subject Strand: POSITIVE Subject Start: 1 Subject End: 137 tcctcctggaacctcaaaaattgatcttgatggaggaacataccaaaattgaagcagagctgacaatcctgcagaagttgttctcctaggattgtcctcagctatcactaccatcattgaaaggaactttttgttat tcctcctggaacctcaaaaattgatcttgatggaggaacataccaaaattgaagcagagctgacaatcctgcagaagttgttctcctaggattgtcctcagctatcactaccatcattgaaaggaactttttgttat Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCCUCCUGGAACCUCAAAAAUUGAUCUUGAUGGAGGAACAUACCAAAAUUGAAGCAGAGCUGACAAUCCUGCAGAAGUUGUUCUCCUAGGAUUGUCCUCAGCUAUCACUACCAUCAUUGAAAGGAACUUUUUGUUAU ...((((......(((.....)))...((((((.((......)).....((((((.(((..((((((((((.((((....)))).).)))))))))))).))).)))...)))))).....))))............ (-34.10) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUAACAAAAAGUUCCUUUCAAUGAUGGUAGUGAUAGCUGAGGACAAUCCUAGGAGAACAACUUCUGCAGGAUUGUCAGCUCUGCUUCAAUUUUGGUAUGUUCCUCCAUCAAGAUCAAUUUUUGAGGUUCCAGGAGGA ....(((((....((..........))...(((.(((.((((((((((((.(.((((....)))).))))))))))..))).)))))).)))))......((((((.((((((.....))))))(....).)))))) (-38.10) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 340 93 54 53 12 NC_009009:SSA_0433|5end_Methenyl_tetrahydrofolate_cyclohydrolase,_putative_435654..435884_NEGATIVE 339 90 43 200 161 NC_009009:SSA_0486|5end_Uroporphyrinogen-III_synthase,_putative_486637..486867_POSITIVE 334 97 55 74 28 NC_009009:SSA_0551|5end_L-asparaginase,_putative_547293..547523_NEGATIVE 331 70 25 66 18 NC_009009:SSA_2219|5end_UDP-glucose_4-epimerase,_putative_2220827..2221057_NEGATIVE 320 105 61 91 47 NC_009009:SSA_1175|5end_Acetoin_dehydrogenase_complex,_E2_component,_dihydrolipoamide_acetyltransferase,_putative_1203976..1204206_NEGATIVE 318 99 53 100 48 NC_009009:SSA_2165|5end_ABC-type_oligopeptide_transporter,_periplasmic_component,_putative_2161734..2161964_POSITIVE 313 87 41 148 94 NC_009009:SSA_1068|5end_Transcriptional_regulator,_LysR_family_(capsular_polysaccharide_biosynthesis_regulation),_putative_1087355..1087585_POSITIVE 312 119 71 218 167 NC_009009:SSA_0807|5end_GTP-binding_protein,_putative_789449..789679_POSITIVE 312 99 55 216 170 NC_009009:SSA_0336|5end_Isopentenyl-diphosphate_delta-isomerase,_putative_329792..330022_POSITIVE 299 103 64 229 179 NC_009009:SSA_0220|5end_PTS_system,_mannose-specific_IIB_component,_putative_215848..216078_POSITIVE 295 99 53 180 114 NC_009009:SSA_0210|5end_hypothetical_protein_207757..207987_POSITIVE 294 75 31 46 2 NC_009009:SSA_1949|5end_AliA_protein,_putative_1944373..1944603_NEGATIVE 293 97 53 190 140 NC_009009:SSA_1012|5end_Phosphoenolpyruvate_synthase,_putative_1014739..1014969_POSITIVE 290 98 52 184 127 NC_009009:SSA_2017|5end_Hypothetical_protein_(possibly_membrane-associated)_2017331..2017561_NEGATIVE 290 98 53 193 144 NC_009009:SSA_0496|5end_Succinylglutamate_desuccinylase_/_Aspartoacylase_family,_putative_495946..496176_POSITIVE 288 100 54 73 21 NC_009009:SSA_2259|5end_hypothetical_protein_2255422..2255652_NEGATIVE 281 99 54 68 20 NC_009009:SSA_0481|5end_Cobyric_acid_synthase,_putative_481962..482192_POSITIVE 281 47 2 97 51 NC_009009:SSA_0062|5end_Aldose_1-epimerase,_putative_63732..63962_POSITIVE 280 92 53 188 137 NC_009009:SSA_0204|5end_Nisin_biosynthesis_two-component_response_transcriptional_regulator_nisR,_putative_202057..202287_POSITIVE 278 98 59 86 37 NC_009009:SSA_0390|5end_hypothetical_protein_385002..385232_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 331 70 25 59 11 NC_009009:SSA_2220|3end_Galactosyltransferase,_putative_2220834..2220984_NEGATIVE 313 87 41 58 4 NC_009009:SSA_1067|3end_hypothetical_protein_1087345..1087495_POSITIVE 303 102 65 62 25 NC_009009:SSA_2126|3end_hypothetical_protein_2129985..2130135_NEGATIVE 297 94 51 78 29 NC_009009:SSA_2242|3end_hypothetical_protein_2238121..2238271_NEGATIVE 293 97 59 134 100 NC_009009:SSA_0781|3end_Mannose-6-phosphate_isomerase,_putative_766394..766544_POSITIVE 287 98 51 149 95 NC_009009:SSA_1126|3end_Thiamine_biosynthesis_lipoprotein,_putative_1150587..1150737_NEGATIVE 286 125 81 61 20 NC_009009:SSA_0631|3end_Tryptophan_synthase_beta_chain,_putative_621133..621283_POSITIVE 281 99 54 83 35 NC_009009:SSA_0480|3end_Cobalt_ABC_transporter,_ATP-binding_protein,_putative_482057..482207_POSITIVE 281 47 2 72 26 NC_009009:SSA_0061|3end_Tagatose_1,6-diphosphate_aldolase,_putative_63787..63937_POSITIVE 280 100 59 67 23 NC_009009:SSA_1008|3end_Galactokinase,_putative_1011114..1011264_POSITIVE 278 98 59 86 37 NC_009009:SSA_0389|3end_hypothetical_protein_385082..385232_POSITIVE 277 110 68 141 95 NC_009009:SSA_0346|3end_hypothetical_protein_340322..340472_POSITIVE 276 96 55 77 31 NC_009009:SSA_0502|3end_Peptide_ABC_transporter,_permease_protein,_putative_502323..502473_POSITIVE 275 80 31 63 18 NC_009009:SSA_0287|3end_Glycerol_dehydrogenase,_NAD+_dependent,_putative_280702..280852_POSITIVE 273 118 71 117 59 NC_009009:SSA_0680|3end_Serine/threonine_protein_phosphatase,_putative_663233..663383_POSITIVE 272 98 55 36 2 NC_009009:SSA_0575|3end_Hydrolase,_HAD_superfamily,_putative_570116..570266_POSITIVE 268 100 54 83 18 NC_009009:SSA_0546|3end_Phospho-2-dehydro-3-deoxyheptonate_aldolase_(DAHP_synthatase),_possibly_tyr-sensitive,_putative_541963..542113_POSITIVE 267 99 59 76 34 NC_009009:SSA_1926|3end_hypothetical_protein_1915034..1915184_POSITIVE 267 100 53 60 11 NC_009009:SSA_1248|3end_hypothetical_protein_1272355..1272505_NEGATIVE 267 96 58 91 52 NC_009009:SSA_0486|3end_Uroporphyrinogen-III_synthase,_putative_487442..487592_POSITIVE