Origin IGS: ttacttcacctcatcactttatagattatattttatcatctgaaaacgctttccgaaatagaaaaatgtctcaagaatatggtaaaatgttaggtaggaggtagcac .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 gtgctacctcctacctaacattttaccatattcttgagacatttttctatttcggaaagcgttttcagatgataaaatataatctataaagtgatgaggtgaagtaa Mask Tandem Repeat Region ================================================ ttacttcacctcatcactttatagattatattttatcatctgaaaacgctttccgaaatagaaaaatgtctcaagaatatggtaaaatgttaggtaggaggtagcac Find is-nt database================================================ Query_seq: SMT_1030:SMT_1031|SMT_1030:SMT_1031:alpha-galactosidase:MSM (multiple sugar metabolism) operon regulatory protein:<-->:967920..968026 107 ttacttcacctcatcactttatagattatattttatcatctgaaaacgctttccgaaatagaaaaatgtctcaagaatatggtaaaatgttaggtaggaggtagcac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_1030:SMT_1031|SMT_1030:SMT_1031:alpha-galactosidase:MSM (multiple sugar metabolism) operon regulatory protein:<-->:967920..968026 107 ttacttcacctcatcactttatagattatattttatcatctgaaaacgctttccgaaatagaaaaatgtctcaagaatatggtaaaatgttaggtaggaggtagcac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_1030:SMT_1031|SMT_1030:SMT_1031:alpha-galactosidase:MSM (multiple sugar metabolism) operon regulatory protein:<-->:967920..968026 107 ttacttcacctcatcactttatagattatattttatcatctgaaaacgctttccgaaatagaaaaatgtctcaagaatatggtaaaatgttaggtaggaggtagcac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ttacttcacctcatcactttatagattatattttatcatctgaaaacgctttccgaaatagaaaaatgtctcaagaatatggtaaaatgttaggtaggaggtagcac Predict ORF larger than 30AA ================================================ ttacttcacctcatcactttatagattatattttatcatctgaaaacgctttccgaaatagaaaaatgtctcaagaatatggtaaaatgttaggtaggaggtagcac 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================================================ ttacttcacctcatcactttatagattatattttatcatctgaaaacgctttccgaaatagaaaaatgtctcaagaatatggtaaaatgttaggtaggaggtagcac Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SMT_1030:SMT_1031|SMT_1030:SMT_1031:alpha-galactosidase:MSM (multiple sugar metabolism) operon regulatory protein:<-->:967920..968026 107 ttacttcacctcatcactttatagattatattttatcatctgaaaacgctttccgaaatagaaaaatgtctcaagaatatggtaaaatgttaggtaggaggtagcac Intra-Species Hit: Count: 2 Min: 1 Max: 107 Len: 107 Subject: smit_SMT_1037_SMT_1038|alpha-galactosidase:MSM (multiple sugar metabolism) operon regulatory protein|NEGATIVE:POSITIVE|[979700,979874]|175 HSP 1 e-value: 2.0E-54 bit: 212.0 Len: 107 Query Start:1 Query End:107 Subject Strand: POSITIVE Subject Start: 1 Subject End: 107 ttacttcacctcatcactttatagattatattttatcatctgaaaacgctttccgaaatagaaaaatgtctcaagaatatggtaaaatgttaggtaggaggtagcac ttacttcacctcatcactttatagattatattttatcatctgaaaacgctttccgaaatagaaaaatgtctcaagaatatggtaaaatgttaggtaggaggtagcac Subject: smit_SMT_1030_SMT_1031|alpha-galactosidase:MSM (multiple sugar metabolism) operon regulatory protein|NEGATIVE:POSITIVE|[967920,968026]|107 HSP 1 e-value: 2.0E-54 bit: 212.0 Len: 107 Query Start:1 Query End:107 Subject Strand: POSITIVE Subject Start: 1 Subject End: 107 ttacttcacctcatcactttatagattatattttatcatctgaaaacgctttccgaaatagaaaaatgtctcaagaatatggtaaaatgttaggtaggaggtagcac ttacttcacctcatcactttatagattatattttatcatctgaaaacgctttccgaaatagaaaaatgtctcaagaatatggtaaaatgttaggtaggaggtagcac Inter-species Hit: Count: 3 Min: 1 Max: 107 Len: 107 Subject: NC_008533_SPD_1678_SPD_1679|alpha-galactosidase AgaN:msm operon regulatory protein MsmR|NEGATIVE:POSITIVE|[1695563,1695669]|107 HSP 1 e-value: 6.0E-45 bit: 180.0 Len: 107 Query Start:1 Query End:107 Subject Strand: POSITIVE Subject Start: 1 Subject End: 107 ttacttcacctcatcactttatagattatattttatcatctgaaaacgctttccgaaatagaaaaatgtctcaagaatatggtaaaatgttaggtaggaggtagcac ttacttcacctcatcactttattgattatattttatcacctgaaatcgctttccaaaatagaaaaatgtctcaagaatatggtaaaatgttaggtaggaggtagcac Subject: NC_003098_spr1713_spr1714|Alpha-galactosidase (melibiase):MSM (multiple sugar metabolism) operon regulatory protein|NEGATIVE:POSITIVE|[1688032,1688138]|107 HSP 1 e-value: 6.0E-45 bit: 180.0 Len: 107 Query Start:1 Query End:107 Subject Strand: POSITIVE Subject Start: 1 Subject End: 107 ttacttcacctcatcactttatagattatattttatcatctgaaaacgctttccgaaatagaaaaatgtctcaagaatatggtaaaatgttaggtaggaggtagcac ttacttcacctcatcactttattgattatattttatcacctgaaatcgctttccaaaatagaaaaatgtctcaagaatatggtaaaatgttaggtaggaggtagcac Subject: NC_003028_SP_1898_SP_1899|alpha-galactosidase:msm operon regulatory protein|NEGATIVE:POSITIVE|[1806638,1806744]|107 HSP 1 e-value: 6.0E-45 bit: 180.0 Len: 107 Query Start:1 Query End:107 Subject Strand: POSITIVE Subject Start: 1 Subject End: 107 ttacttcacctcatcactttatagattatattttatcatctgaaaacgctttccgaaatagaaaaatgtctcaagaatatggtaaaatgttaggtaggaggtagcac ttacttcacctcatcactttattgattatattttatcacctgaaatcgctttccaaaatagaaaaatgtctcaagaatatggtaaaatgttaggtaggaggtagcac Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUACUUCACCUCAUCACUUUAUAGAUUAUAUUUUAUCAUCUGAAAACGCUUUCCGAAAUAGAAAAAUGUCUCAAGAAUAUGGUAAAAUGUUAGGUAGGAGGUAGCAC .......(((((...((((........((((((((((((((....(((.(((.(......).))).)))....)))...))))))))))).))))..)))))..... (-17.70) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GUGCUACCUCCUACCUAACAUUUUACCAUAUUCUUGAGACAUUUUUCUAUUUCGGAAAGCGUUUUCAGAUGAUAAAAUAUAAUCUAUAAAGUGAUGAGGUGAAGUAA .(((((((((.........((((((.((...(((.(((((.((((((......)))))).))))).))))).))))))...(((........))))))))..)))). (-18.90) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 779 100 51 191 142 smit:SMT_1037|5end_alpha-galactosidase_979609..979839_NEGATIVE 779 100 51 191 142 smit:SMT_1030|5end_alpha-galactosidase_967829..968059_NEGATIVE 224 42 3 46 10 smit:SMT_1541|5end_isopentenyl-diphosphate_delta-isomerase_1526093..1526323_NEGATIVE 211 70 31 62 32 smit:SMT_611|5end_aspartate-semialdehyde_dehydrogenase_522492..522722_POSITIVE 206 79 31 213 176 smit:SMT_1711|5end_Xaa-Pro_dipeptidase_1697494..1697724_NEGATIVE 202 85 46 217 175 smit:SMT_759|5end_K01992_ABC-2_type_transport_system_permease_protein_665712..665942_NEGATIVE 201 73 45 211 183 smit:SMT_960|5end_putative_esterase_906818..907048_NEGATIVE 200 85 47 215 173 smit:SMT_1526|5end_K07720_two-component_system,_response_regulator_YesN_1510554..1510784_NEGATIVE 199 76 34 146 100 smit:SMT_1262|5end_ribosomal_protein_L11_methyltransferase_1227152..1227382_POSITIVE 195 42 3 133 95 smit:SMT_1257|5end_acetolactate_synthase_small_subunit_1223173..1223403_NEGATIVE 195 37 2 119 91 smit:SMT_260|5end_phage_transcriptional_repressor_199470..199700_POSITIVE 194 100 51 133 86 smit:SMT_813|5end_acetyltransferase,_GNAT_family_722322..722552_NEGATIVE 189 98 52 95 47 smit:SMT_889|5end_K02029_polar_amino_acid_transport_system_permease_protein_836266..836496_POSITIVE 189 98 54 203 159 smit:SMT_846|5end_hypothetical_protein_792769..792999_NEGATIVE 188 49 7 140 98 smit:SMT_1141|5end_4-alpha-glucanotransferase_1085117..1085347_NEGATIVE 185 56 14 143 98 smit:SMT_1409|5end_hypothetical_protein_1388514..1388744_NEGATIVE 184 53 14 133 97 smit:SMT_794|5end_hypothetical_protein_703487..703717_NEGATIVE 180 99 70 177 139 smit:SMT_399|5end_cytochrome_c-type_biogenesis_protein_CcdA_328366..328596_POSITIVE 179 45 1 140 95 smit:SMT_1965|5end_hypothetical_protein_1897044..1897274_POSITIVE 179 45 1 140 95 smit:SMT_74|5end_hypothetical_protein_2197..2427_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 224 42 3 62 26 smit:SMT_1542|3end_phosphomevalonate_kinase_1526077..1526227_NEGATIVE 204 94 51 77 27 smit:SMT_1511|3end_hypothetical_protein_1493902..1494052_POSITIVE 195 42 3 140 102 smit:SMT_1258|3end_acetolactate_synthase_large_subunit_1223166..1223316_NEGATIVE 194 100 51 123 76 smit:SMT_814|3end_UDP-N-acetyl_muramate-alanine_ligase_722332..722482_NEGATIVE 189 76 37 41 1 smit:SMT_1034|3end_K05896_segregation_and_condensation_protein_A_976768..976918_NEGATIVE 189 98 52 82 34 smit:SMT_888|3end_K02030_polar_amino_acid_transport_system_substrate-binding_protein_836333..836483_POSITIVE 185 56 14 125 80 smit:SMT_1410|3end_exonuclease_RexA_1388532..1388682_NEGATIVE 184 53 14 120 84 smit:SMT_795|3end_similar_to_O6-alkylguanine-DNA-alkyltransferase_703500..703650_NEGATIVE 179 68 31 83 51 smit:SMT_337|3end_hypothetical_protein_276197..276347_POSITIVE 177 76 36 73 31 smit:SMT_360|3end_K07742_hypothetical_protein_296001..296151_POSITIVE 175 57 13 61 4 smit:SMT_1564|3end_transcriptional_antiterminator,_BglG_family_1557697..1557847_POSITIVE 175 90 47 87 48 smit:SMT_545|3end_hypothetical_protein_predicted_by_Glimmer/Critica_461424..461574_POSITIVE 172 100 68 57 29 smit:SMT_1370|3end_K06217_phosphate_starvation-inducible_protein_PhoH_and_related_proteins_1349499..1349649_NEGATIVE 172 70 21 145 85 smit:SMT_211|3end_hypothetical_protein_predicted_by_Glimmer/Critica_144316..144466_POSITIVE 171 98 52 72 11 smit:SMT_1059|3end_NAD(P)H-flavin_oxidoreductase_998172..998322_POSITIVE 170 50 6 51 8 smit:SMT_328|3end_23S_rRNA_methyltransferase_264863..265013_POSITIVE 168 100 54 74 27 smit:SMT_2017|3end_exonuclease_RexA_1935862..1936012_NEGATIVE 168 98 51 145 102 smit:SMT_1139|3end_rRNA_(guanine-N1-)-methyltransferase_1080683..1080833_POSITIVE 167 68 23 72 29 smit:SMT_1101|3end_K03210_preprotein_translocase_YajC_subunit_1042614..1042764_NEGATIVE 162 49 6 143 96 smit:SMT_379|3end_acetyltransferase,_GNAT_family_316456..316606_POSITIVE