Origin IGS: tagggattatggtctattgtatcgaaaatccctcggcaaataaaatagttaattatactggtagggtatagccgaaaactattgctagcgcttaatgtgtatttccttataataaaaactgctttttcttgacaaatgaaacagacaagtgtagaatataagtataaactacaaatgtagaaaaaggagaaagcgat .........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 atcgctttctcctttttctacatttgtagtttatacttatattctacacttgtctgtttcatttgtcaagaaaaagcagtttttattataaggaaatacacattaagcgctagcaatagttttcggctataccctaccagtataattaactattttatttgccgagggattttcgatacaatagaccataatcccta Mask Tandem Repeat Region ================================================ tagggattatggtctattgtatcgaaaatccctcggcaaataaaatagttaattatactggtagggtatagccgaaaactattgctagcgcttaatgtgtatttccttataataaaaactgctttttcttgacaaatgaaacagacaagtgtagaatataagtataaactacaaatgtagaaaaaggagaaagcgat Find is-nt database================================================ Query_seq: SSA_0917:SSA_0918|SSA_0917:SSA_0918:Cobalamin-independent methionine synthase II, putative:Conserved uncharacterized protein:<-->:930341..930537 197 tagggattatggtctattgtatcgaaaatccctcggcaaataaaatagttaattatactggtagggtatagccgaaaactattgctagcgcttaatgtgtatttccttataataaaaactgctttttcttgacaaatgaaacagacaagtgtagaatataagtataaactacaaatgtagaaaaaggagaaagcgat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0917:SSA_0918|SSA_0917:SSA_0918:Cobalamin-independent methionine synthase II, putative:Conserved uncharacterized protein:<-->:930341..930537 197 tagggattatggtctattgtatcgaaaatccctcggcaaataaaatagttaattatactggtagggtatagccgaaaactattgctagcgcttaatgtgtatttccttataataaaaactgctttttcttgacaaatgaaacagacaagtgtagaatataagtataaactacaaatgtagaaaaaggagaaagcgat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0917:SSA_0918|SSA_0917:SSA_0918:Cobalamin-independent methionine synthase II, putative:Conserved uncharacterized protein:<-->:930341..930537 197 tagggattatggtctattgtatcgaaaatccctcggcaaataaaatagttaattatactggtagggtatagccgaaaactattgctagcgcttaatgtgtatttccttataataaaaactgctttttcttgacaaatgaaacagacaagtgtagaatataagtataaactacaaatgtagaaaaaggagaaagcgat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tagggattatggtctattgtatcgaaaatccctcggcaaataaaatagttaattatactggtagggtatagccgaaaactattgctagcgcttaatgtgtatttccttataataaaaactgctttttcttgacaaatgaaacagacaagtgtagaatataagtataaactacaaatgtagaaaaaggagaaagcgat Predict ORF larger than 30AA ================================================ Protein_Len: 60 Strand: - Start: 3 End: 197 .. T D F I G R C I F Y N I I S T P Y L R F S N S A S L T Y K R I I F V A K E Q C I F C V L T S Y L Y L S C I Y F F S F A M tagggattatggtctattgtatcgaaaatccctcggcaaataaaatagttaattatactggtagggtatagccgaaaactattgctagcgcttaatgtgtatttccttataataaaaactgctttttcttgacaaatgaaacagacaagtgtagaatataagtataaactacaaatgtagaaaaaggagaaagcgat 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: 90 Start: 128 End: 157 ...............................................................................................................................CTTGACAAATGAAACAGACAAGTGTAGAAT........................................ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tagggattatggtctattgtatcgaaaatccctcggcaaataaaatagttaattatactggtagggtatagccgaaaactattgctagcgcttaatgtgtatttccttataataaaaactgctttttcttgacaaatgaaacagacaagtgtagaatataagtataaactacaaatgtagaaaaaggagaaagcgat Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_0917:SSA_0918|SSA_0917:SSA_0918:Cobalamin-independent methionine synthase II, putative:Conserved uncharacterized protein:<-->:930341..930537 197 tagggattatggtctattgtatcgaaaatccctcggcaaataaaatagttaattatactggtagggtatagccgaaaactattgctagcgcttaatgtgtatttccttataataaaaactgctttttcttgacaaatgaaacagacaagtgtagaatataagtataaactacaaatgtagaaaaaggagaaagcgat Intra-Species Hit: Count: 1 Min: 1 Max: 197 Len: 197 Subject: NC_009009_SSA_0917_SSA_0918|Cobalamin-independent methionine synthase II, putative:Conserved uncharacterized protein|NEGATIVE:POSITIVE|[930341,930537]|197 HSP 1 e-value: 1.0E-108 bit: 391.0 Len: 197 Query Start:1 Query End:197 Subject Strand: POSITIVE Subject Start: 1 Subject End: 197 tagggattatggtctattgtatcgaaaatccctcggcaaataaaatagttaattatactggtagggtatagccgaaaactattgctagcgcttaatgtgtatttccttataataaaaactgctttttcttgacaaatgaaacagacaagtgtagaatataagtataaactacaaatgtagaaaaaggagaaagcgat tagggattatggtctattgtatcgaaaatccctcggcaaataaaatagttaattatactggtagggtatagccgaaaactattgctagcgcttaatgtgtatttccttataataaaaactgctttttcttgacaaatgaaacagacaagtgtagaatataagtataaactacaaatgtagaaaaaggagaaagcgat Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAGGGAUUAUGGUCUAUUGUAUCGAAAAUCCCUCGGCAAAUAAAAUAGUUAAUUAUACUGGUAGGGUAUAGCCGAAAACUAUUGCUAGCGCUUAAUGUGUAUUUCCUUAUAAUAAAAACUGCUUUUUCUUGACAAAUGAAACAGACAAGUGUAGAAUAUAAGUAUAAACUACAAAUGUAGAAAAAGGAGAAAGCGAU .(((((((.(((((....).))))..)))))))((((.(((......)))...((((((.....))))))))))......((((((.((((.....)))).(((((((...........(((((.((((..(((..((.......))..)))))))...)))))....((((....))))...))))))).)))))) (-39.00) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUCGCUUUCUCCUUUUUCUACAUUUGUAGUUUAUACUUAUAUUCUACACUUGUCUGUUUCAUUUGUCAAGAAAAAGCAGUUUUUAUUAUAAGGAAAUACACAUUAAGCGCUAGCAAUAGUUUUCGGCUAUACCCUACCAGUAUAAUUAACUAUUUUAUUUGCCGAGGGAUUUUCGAUACAAUAGACCAUAAUCCCUA ..(((((.......((((((((..(((((..(((....)))..)))))..)))((((((..(((....)))..))))))............)))))........)))))(((....)))...((((((((((.......)))))................)))))((((((.((.........))....)))))).. (-32.25) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 872 100 51 191 142 NC_009009:SSA_0917|5end_Cobalamin-independent_methionine_synthase_II,_putative_930250..930480_NEGATIVE 285 93 58 37 7 NC_009009:SSA_2023|5end_Fructan_beta-fructosidase_precursor,_putative_2028826..2029056_NEGATIVE 277 93 58 84 39 NC_009009:SSA_0475|5end_CbiK_protein,_putative_477723..477953_POSITIVE 269 99 52 178 115 NC_009009:SSA_0626|5end_hypothetical_protein_616089..616319_POSITIVE 267 110 61 105 52 NC_009009:SSA_0098|5end_Hydrolase,_haloacid_dehalogenase-like_family,_putative_99422..99652_POSITIVE 259 110 65 215 166 NC_009009:SSA_0334|5end_Diphosphomevalonate_decarboxylase,_putative_327855..328085_POSITIVE 256 154 119 225 193 NC_009009:SSA_1771|5end_Conserved_DNA_methyltransferase_protein,_putative_1758799..1759029_NEGATIVE 256 88 52 164 126 NC_009009:SSA_1172|5end_hypothetical_protein_1199926..1200156_NEGATIVE 254 109 64 98 61 NC_009009:SSA_1941|5end_hypothetical_protein_1927452..1927682_NEGATIVE 254 91 53 73 37 NC_009009:SSA_1661|5end_hypothetical_protein_1658004..1658234_NEGATIVE 254 99 55 207 157 NC_009009:SSA_0238|5end_hypothetical_protein_232481..232711_POSITIVE 251 37 1 218 182 NC_009009:SSA_1086|5end_TRNA_nucleotidyltransferase,_putative_1103328..1103558_POSITIVE 250 90 54 145 110 NC_009009:SSA_0320|5end_hypothetical_protein_313406..313636_POSITIVE 249 37 3 41 10 NC_009009:SSA_1196|5end_Acetyltransferase,_GNAT_family,_putative_1222052..1222282_NEGATIVE 249 106 63 179 130 NC_009009:SSA_0204|5end_Nisin_biosynthesis_two-component_response_transcriptional_regulator_nisR,_putative_202057..202287_POSITIVE 246 76 52 196 175 NC_009009:SSA_1292|5end_hypothetical_protein_1311578..1311808_NEGATIVE 244 92 61 226 198 NC_009009:SSA_0472|5end_Precorrin-3B_C17-methyltransferase,_putative_474780..475010_POSITIVE 242 93 58 50 14 NC_009009:SSA_0927|5end_Transcriptional_regulator,_TetR/AcrR_family,_putative_936049..936279_POSITIVE 241 86 55 68 33 NC_009009:SSA_1384|5end_hypothetical_protein_1402203..1402433_NEGATIVE 238 73 32 45 2 NC_009009:SSA_1216|5end_AT-rich_DNA-binding_protein,_possible_redox-sensing_transcriptional_repressor,_putative_1238292..1238522_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 293 94 58 63 29 NC_009009:SSA_2323|3end_Transporter,_putative_2328850..2329000_POSITIVE 293 96 57 41 3 NC_009009:SSA_1122|3end_Thioredoxin_family_protein,_putative_1148526..1148676_POSITIVE 278 91 57 150 117 NC_009009:SSA_1371|3end_FmtA-like_protein,_putative_1387051..1387201_NEGATIVE 277 93 58 70 25 NC_009009:SSA_0474|3end_Uroporphyrin-III_C-methyltransferase/uroporphyrinogen-III_synthase,_putative_477789..477939_POSITIVE 267 110 61 108 55 NC_009009:SSA_0097|3end_Multi_antimicrobial_extrusion_(MATE)_family_transporter,_putative_99505..99655_POSITIVE 256 154 119 129 97 NC_009009:SSA_1772|3end_hypothetical_protein_1758895..1759045_NEGATIVE 249 37 3 44 13 NC_009009:SSA_1197|3end_DNA_alkylation_repair_enzyme,_putative_1222049..1222199_NEGATIVE 244 92 61 149 121 NC_009009:SSA_0471|3end_CbiG_protein,_putative_474783..474933_POSITIVE 234 91 57 57 19 NC_009009:SSA_2125|3end_Small_primase-like_protein_(Toprim_domain),_putative_2129423..2129573_NEGATIVE 232 112 71 70 29 NC_009009:SSA_1354|3end_hypothetical_protein_1368555..1368705_NEGATIVE 230 87 59 81 52 NC_009009:SSA_2046|3end_Uridine_phosphorylase,_putative_2048957..2049107_NEGATIVE 228 99 58 129 86 NC_009009:SSA_2008|3end_Molecular_chaperone_GrpE_(HSP-70_cofactor),_putative_2009526..2009676_NEGATIVE 227 38 1 130 96 NC_009009:SSA_0355|3end_DNA_mismatch_repair_protein,_putative_349260..349410_POSITIVE 226 38 4 128 88 NC_009009:SSA_0250|3end_GTP_pyrophosphokinase,_putative_244466..244616_POSITIVE 224 109 69 93 62 NC_009009:SSA_1405|3end_Copper_homeostasis_protein_CutC,_putative_1418758..1418908_NEGATIVE 222 89 57 150 127 NC_009009:SSA_1865|3end_Thioredoxin_reductase,_putative_1860978..1861128_NEGATIVE 219 91 59 134 98 NC_009009:SSA_1326|3end_Peptidase_T,_putative_1343735..1343885_POSITIVE 219 69 29 49 22 NC_009009:SSA_0089|3end_V-type_sodium_ATPase,_subunit_F,_putative_90330..90480_POSITIVE 216 92 64 140 114 NC_009009:SSA_2131|3end_DNA-binding_protein,_putative_2134247..2134397_POSITIVE 215 37 4 66 38 NC_009009:SSA_0035|3end_Bifunctional_purine_biosynthesis_protein_purH,_putative_41957..42107_POSITIVE