Origin IGS: tgaatgactgcctcaaagctgataaagaaaagctatcacctccataaaaaatatataatggtcaagtttctccttatttgatatgataaagaaagactttttaggaggaattcgaaat .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 atttcgaattcctcctaaaaagtctttctttatcatatcaaataaggagaaacttgaccattatatattttttatggaggtgatagcttttctttatcagctttgaggcagtcattca Mask Tandem Repeat Region ================================================ tgaatgactgcctcaaagctgataaagaaaagctatcacctccataaaaaatatataatggtcaagtttctccttatttgatatgataaagaaagactttttaggaggaattcgaaat Find is-nt database================================================ Query_seq: SSA_0587:SSA_0588|SSA_0587:SSA_0588:Metal-dependent amidase/aminoacylase/carboxypeptidase, putative:L-cystine ABC transporter, substrate-binding component, putative:->->:579822..579939 118 tgaatgactgcctcaaagctgataaagaaaagctatcacctccataaaaaatatataatggtcaagtttctccttatttgatatgataaagaaagactttttaggaggaattcgaaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0587:SSA_0588|SSA_0587:SSA_0588:Metal-dependent amidase/aminoacylase/carboxypeptidase, putative:L-cystine ABC transporter, substrate-binding component, putative:->->:579822..579939 118 tgaatgactgcctcaaagctgataaagaaaagctatcacctccataaaaaatatataatggtcaagtttctccttatttgatatgataaagaaagactttttaggaggaattcgaaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0587:SSA_0588|SSA_0587:SSA_0588:Metal-dependent amidase/aminoacylase/carboxypeptidase, putative:L-cystine ABC transporter, substrate-binding component, putative:->->:579822..579939 118 tgaatgactgcctcaaagctgataaagaaaagctatcacctccataaaaaatatataatggtcaagtttctccttatttgatatgataaagaaagactttttaggaggaattcgaaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tgaatgactgcctcaaagctgataaagaaaagctatcacctccataaaaaatatataatggtcaagtttctccttatttgatatgataaagaaagactttttaggaggaattcgaaat Predict ORF larger than 30AA ================================================ Protein_Len: 32 Strand: - Start: 16 End: 111 ............... L Q Y L F A I V E M F F I Y H D L K E K N S I I F F S K K P P M ....... tgaatgactgcctcaaagctgataaagaaaagctatcacctccataaaaaatatataatggtcaagtttctccttatttgatatgataaagaaagactttttaggaggaattcgaaat 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: 81 Start: 58 End: 87 .........................................................ATGGTCAAGTTTCTCCTTATTTGATATGAT............................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tgaatgactgcctcaaagctgataaagaaaagctatcacctccataaaaaatatataatggtcaagtttctccttatttgatatgataaagaaagactttttaggaggaattcgaaat Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_0587:SSA_0588|SSA_0587:SSA_0588:Metal-dependent amidase/aminoacylase/carboxypeptidase, putative:L-cystine ABC transporter, substrate-binding component, putative:->->:579822..579939 118 tgaatgactgcctcaaagctgataaagaaaagctatcacctccataaaaaatatataatggtcaagtttctccttatttgatatgataaagaaagactttttaggaggaattcgaaat Intra-Species Hit: Count: 1 Min: 1 Max: 118 Len: 118 Subject: NC_009009_SSA_0587_SSA_0588|Metal-dependent amidase/aminoacylase/carboxypeptidase, putative:L-cystine ABC transporter, substrate-binding component, putative|POSITIVE:POSITIVE|[579822,579939]|118 HSP 1 e-value: 5.0E-61 bit: 234.0 Len: 118 Query Start:1 Query End:118 Subject Strand: POSITIVE Subject Start: 1 Subject End: 118 tgaatgactgcctcaaagctgataaagaaaagctatcacctccataaaaaatatataatggtcaagtttctccttatttgatatgataaagaaagactttttaggaggaattcgaaat tgaatgactgcctcaaagctgataaagaaaagctatcacctccataaaaaatatataatggtcaagtttctccttatttgatatgataaagaaagactttttaggaggaattcgaaat Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGAAUGACUGCCUCAAAGCUGAUAAAGAAAAGCUAUCACCUCCAUAAAAAAUAUAUAAUGGUCAAGUUUCUCCUUAUUUGAUAUGAUAAAGAAAGACUUUUUAGGAGGAAUUCGAAAU .((((...........((((..........))))....(((((.(((((..........((((...(((((..(((((......)))))))))))))))))))))))).))))..... (-19.30) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUUUCGAAUUCCUCCUAAAAAGUCUUUCUUUAUCAUAUCAAAUAAGGAGAAACUUGACCAUUAUAUAUUUUUUAUGGAGGUGAUAGCUUUUCUUUAUCAGCUUUGAGGCAGUCAUUCA .....((((..(((((...((((.(((((((((........))))))))).))))....................((((.((((((.......)))))).)))).))).))..)))). (-23.20) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 285 108 61 130 87 NC_009009:SSA_1299|5end_Maltose/maltodextrin_ABC_transport_system,_putative_1316629..1316859_POSITIVE 260 43 2 41 1 NC_009009:SSA_1746|5end_hypothetical_protein_1732945..1733175_NEGATIVE 259 44 3 160 122 NC_009009:SSA_0512|5end_Nicotinate-nucleotide--dimethylbenzimidazole_phosphoribosyltransferase,_putative_510439..510669_POSITIVE 254 43 5 231 190 NC_009009:SSA_1447|5end_ATP_phosphoribosyltransferase,_putative_1449831..1450061_NEGATIVE 248 47 2 231 181 NC_009009:SSA_0940|5end_NOL1/NOP2/sun_family_protein,_putative_947626..947856_POSITIVE 248 44 4 96 59 NC_009009:SSA_0037|5end_Phosphoribosylamine-glycine_ligase;_phosphoribosyl_glycinamide_synthetase_(GARS),_putative_44272..44502_POSITIVE 245 47 12 107 56 NC_009009:SSA_1554|5end_hypothetical_protein_1555949..1556179_POSITIVE 240 19 4 190 175 NC_009009:SSA_2041|5end_Leucine-rich_protein,_putative_2046682..2046912_NEGATIVE 240 44 7 100 54 NC_009009:SSA_0548|5end_Alanine_racemase,_putative_542340..542570_POSITIVE 238 48 8 63 17 NC_009009:SSA_1026|5end_ABC-type_multidrug_transporter,_ATPase_component,_putative_1042794..1043024_POSITIVE 232 41 14 157 129 NC_009009:SSA_1495|5end_S-adenosylmethionine_synthetase,_putative_1502209..1502439_NEGATIVE 230 45 7 40 1 NC_009009:SSA_1937|5end_Malonyl-CoA:ACP_transacylase,_putative_1924771..1925001_NEGATIVE 229 99 53 202 156 NC_009009:SSA_0908|5end_ABC-type_uncharacterized_transport_system,_periplasmic_component,_putative_919700..919930_POSITIVE 227 42 8 102 66 NC_009009:SSA_0374|5end_Peptide_methionine_sulfoxide_reductase_msrA/msrB,_putative_363163..363393_POSITIVE 225 107 65 142 103 NC_009009:SSA_0741|5end_Acetylornithine_deacetylase/Succinyl-diaminopimelate_desuccinylase,_putative_723773..724003_POSITIVE 225 45 3 217 179 NC_009009:SSA_0516|5end_AmiR_two-component_response_regulator_with_transcriptional_antiterminator_output_domain,_putative_514485..514715_POSITIVE 220 44 1 204 171 NC_009009:SSA_1841|5end_Cof_family_protein/peptidyl-prolyl_cis-trans_isomerase,_cyclophilin_type,_putative_1835822..1836052_NEGATIVE 219 41 8 215 162 NC_009009:SSA_0703|5end_Citrate_synthase,_putative_688154..688384_POSITIVE 218 109 65 63 22 NC_009009:SSA_2215|5end_Oligosaccharide_repeat_unit_polymerase_Wzy,_putative_2217157..2217387_NEGATIVE 218 44 5 172 127 NC_009009:SSA_1751|5end_Dextran_glucosidase,_alpha_amylase_family,_putative_1739801..1740031_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 285 108 61 48 5 NC_009009:SSA_1298|3end_Maltose/maltodextrin_ABC_transporter,_sugar-binding_protein_MalX,_putative_1316627..1316777_POSITIVE 284 41 7 142 112 NC_009009:SSA_1960|3end_hypothetical_protein_1956571..1956721_NEGATIVE 260 43 2 48 8 NC_009009:SSA_1747|3end_hypothetical_protein_1732938..1733088_NEGATIVE 250 45 5 47 6 NC_009009:SSA_1938|3end_Enoyl-acyl_carrier_protein(ACP)_reductase,_putative_1924764..1924914_NEGATIVE 245 47 12 110 59 NC_009009:SSA_1553|3end_Permease,_putative_1556032..1556182_POSITIVE 240 44 7 113 67 NC_009009:SSA_0547|3end_Acyl_carrier_protein_synthase,_putative_542433..542583_POSITIVE 225 107 65 120 81 NC_009009:SSA_0740|3end_C4-dicarboxylate_anaerobic_carrier,_possible_arginine_transporter,_putative_723831..723981_POSITIVE 223 33 2 150 120 NC_009009:SSA_2018|3end_hypothetical_protein_2017464..2017614_NEGATIVE 223 41 4 60 13 NC_009009:SSA_0039|3end_Phosphoribosylaminoimidazole_carboxylase,_catalytic_subunit,_putative_46401..46551_POSITIVE 220 109 65 122 77 NC_009009:SSA_2027|3end_P-type_ATPase-metal/cation_transport_(probably_copper),_putative_2033109..2033259_NEGATIVE 218 109 65 63 22 NC_009009:SSA_2216|3end_LPS_biosynthesis_protein,_putative_2217157..2217307_NEGATIVE 217 95 57 45 8 NC_009009:SSA_1610|3end_hypothetical_protein_1614004..1614154_NEGATIVE 216 43 1 63 16 NC_009009:SSA_2220|3end_Galactosyltransferase,_putative_2220834..2220984_NEGATIVE 215 45 5 120 58 NC_009009:SSA_0893|3end_ATP-binding_cassette_transporter-like_protein,_putative_885872..886022_POSITIVE 213 37 8 71 39 NC_009009:SSA_1268|3end_Chorismate_mutase/prephenate_dehydratase,_putative_1291347..1291497_NEGATIVE 211 80 39 97 55 NC_009009:SSA_2331|3end_D-alanine_transfer_protein,_putative_2333696..2333846_NEGATIVE 209 46 4 151 104 NC_009009:SSA_1627|3end_hypothetical_protein_1629508..1629658_NEGATIVE 205 42 9 90 52 NC_009009:SSA_1420|3end_Homoserine_O-succinyltransferase,_putative_1429684..1429834_NEGATIVE 204 44 10 145 104 NC_009009:SSA_1959|3end_Undecaprenyl-diphosphatase,_putative_1955589..1955739_NEGATIVE 203 47 7 116 63 NC_009009:SSA_1660|3end_ABC-type_antimicrobial_peptide_transport_system,_ATPase_component,_putative_1656819..1656969_NEGATIVE