Origin IGS: gatgcggaggcgttaaaaaaacgactgaaaaataggaactgggcgatggattctatgaatccaagtccagttctcttttttccgagtttttagccgaagcttgatttagctgagctaacctagactgaatagatctattcacagcaaaaatagacgaagaagcgacagcttctaggagattttatcttttttgccaagagcttaggtcgagtttagtttagctgaataccaagagtttaaataagtccaaaagaaacagaacctctctaaacggggttcttttgcttgctacaattttttatatgttacaaacaaatctccatattacagggggcagacagttttgttaaataggtcgaaaaaggcttttttcttagaagatttatggtaagatggttttcgtatcatgaatgattaggaaggtgcattttgcat .........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.........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 atgcaaaatgcaccttcctaatcattcatgatacgaaaaccatcttaccataaatcttctaagaaaaaagcctttttcgacctatttaacaaaactgtctgccccctgtaatatggagatttgtttgtaacatataaaaaattgtagcaagcaaaagaaccccgtttagagaggttctgtttcttttggacttatttaaactcttggtattcagctaaactaaactcgacctaagctcttggcaaaaaagataaaatctcctagaagctgtcgcttcttcgtctatttttgctgtgaatagatctattcagtctaggttagctcagctaaatcaagcttcggctaaaaactcggaaaaaagagaactggacttggattcatagaatccatcgcccagttcctatttttcagtcgtttttttaacgcctccgcatc Mask Tandem Repeat Region ================================================ gatgcggaggcgttaaaaaaacgactgaaaaataggaactgggcgatggattctatgaatccaagtccagttctcttttttccgagtttttagccgaagcttgatttagctgagctaacctagactgaatagatctattcacagcaaaaatagacgaagaagcgacagcttctaggagattttatcttttttgccaagagcttaggtcgagtttagtttagctgaataccaagagtttaaataagtccaaaagaaacagaacctctctaaacggggttcttttgcttgctacaattttttatatgttacaaacaaatctccatattacagggggcagacagttttgttaaataggtcgaaaaaggcttttttcttagaagatttatggtaagatggttttcgtatcatgaatgattaggaaggtgcattttgcat Find is-nt database================================================ Query_seq: SSA_0093:SSA_0094|SSA_0093:SSA_0094:V-type sodium ATPase, subunit D, putative:Cell wall metabolism, LysM type protein, putative:->->:95050..95484 435 gatgcggaggcgttaaaaaaacgactgaaaaataggaactgggcgatggattctatgaatccaagtccagttctcttttttccgagtttttagccgaagcttgatttagctgagctaacctagactgaatagatctattcacagcaaaaatagacgaagaagcgacagcttctaggagattttatcttttttgccaagagcttaggtcgagtttagtttagctgaataccaagagtttaaataagtccaaaagaaacagaacctctctaaacggggttcttttgcttgctacaattttttatatgttacaaacaaatctccatattacagggggcagacagttttgttaaataggtcgaaaaaggcttttttcttagaagatttatggtaagatggttttcgtatcatgaatgattaggaaggtgcattttgcat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0093:SSA_0094|SSA_0093:SSA_0094:V-type sodium ATPase, subunit D, putative:Cell wall metabolism, LysM type protein, putative:->->:95050..95484 435 gatgcggaggcgttaaaaaaacgactgaaaaataggaactgggcgatggattctatgaatccaagtccagttctcttttttccgagtttttagccgaagcttgatttagctgagctaacctagactgaatagatctattcacagcaaaaatagacgaagaagcgacagcttctaggagattttatcttttttgccaagagcttaggtcgagtttagtttagctgaataccaagagtttaaataagtccaaaagaaacagaacctctctaaacggggttcttttgcttgctacaattttttatatgttacaaacaaatctccatattacagggggcagacagttttgttaaataggtcgaaaaaggcttttttcttagaagatttatggtaagatggttttcgtatcatgaatgattaggaaggtgcattttgcat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0093:SSA_0094|SSA_0093:SSA_0094:V-type sodium ATPase, subunit D, putative:Cell wall metabolism, LysM type protein, putative:->->:95050..95484 435 gatgcggaggcgttaaaaaaacgactgaaaaataggaactgggcgatggattctatgaatccaagtccagttctcttttttccgagtttttagccgaagcttgatttagctgagctaacctagactgaatagatctattcacagcaaaaatagacgaagaagcgacagcttctaggagattttatcttttttgccaagagcttaggtcgagtttagtttagctgaataccaagagtttaaataagtccaaaagaaacagaacctctctaaacggggttcttttgcttgctacaattttttatatgttacaaacaaatctccatattacagggggcagacagttttgttaaataggtcgaaaaaggcttttttcttagaagatttatggtaagatggttttcgtatcatgaatgattaggaaggtgcattttgcat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gatgcggaggcgttaaaaaaacgactgaaaaataggaactgggcgatggattctatgaatccaagtccagttctcttttttccgagtttttagccgaagcttgatttagctgagctaacctagactgaatagatctattcacagcaaaaatagacgaagaagcgacagcttctaggagattttatcttttttgccaagagcttaggtcgagtttagtttagctgaataccaagagtttaaataagtccaaaagaaacagaacctctctaaacggggttcttttgcttgctacaattttttatatgttacaaacaaatctccatattacagggggcagacagttttgttaaataggtcgaaaaaggcttttttcttagaagatttatggtaagatggttttcgtatcatgaatgattaggaaggtgcattttgcat Predict ORF larger than 30AA ================================================ Protein_Len: 30 Strand: + Start: 129 End: 218 ................................................................................................................................ M D L F T A K I D E E A T A S R R F Y L F C Q E L R S S L V ......................................................................................................................................................................................................................... Protein_Len: 42 Strand: + Start: 222 End: 347 ............................................................................................................................................................................................................................. M N T K S L N K S K R N R T S L N G V L L L A T I F Y M L Q T N L H I T G G R Q F C ........................................................................................ Protein_Len: 32 Strand: - Start: 56 End: 151 ....................................................... S D L D L E R K E S N K A S A Q N L Q A L R S Q I S R N V A F M ............................................................................................................................................................................................................................................................................................ Protein_Len: 30 Strand: - Start: 16 End: 105 ............... F F S Q F I P V P R H I R H I W T W N E K K R T K L R L K M .......................................................................................................................................................................................................................................................................................................................................... gatgcggaggcgttaaaaaaacgactgaaaaataggaactgggcgatggattctatgaatccaagtccagttctcttttttccgagtttttagccgaagcttgatttagctgagctaacctagactgaatagatctattcacagcaaaaatagacgaagaagcgacagcttctaggagattttatcttttttgccaagagcttaggtcgagtttagtttagctgaataccaagagtttaaataagtccaaaagaaacagaacctctctaaacggggttcttttgcttgctacaattttttatatgttacaaacaaatctccatattacagggggcagacagttttgttaaataggtcgaaaaaggcttttttcttagaagatttatggtaagatggttttcgtatcatgaatgattaggaaggtgcattttgcat 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: 83 Start: 322 End: 351 .................................................................................................................................................................................................................................................................................................................................TTTAACAAAACTGTCTGCCCCCTGTAATAT.................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ gatgcggaggcgttaaaaaaacgactgaaaaataggaactgggcgatggattctatgaatccaagtccagttctcttttttccgagtttttagccgaagcttgatttagctgagctaacctagactgaatagatctattcacagcaaaaatagacgaagaagcgacagcttctaggagattttatcttttttgccaagagcttaggtcgagtttagtttagctgaataccaagagtttaaataagtccaaaagaaacagaacctctctaaacggggttcttttgcttgctacaattttttatatgttacaaacaaatctccatattacagggggcagacagttttgttaaataggtcgaaaaaggcttttttcttagaagatttatggtaagatggttttcgtatcatgaatgattaggaaggtgcattttgcat Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 71 HP_score: -4.4 Tail_Score: -4.7329 Start: 33 End: 77 Full_Region: taaaaactcggaaaa aagagaactggacttggattc ata gaatccatcgcccagttccta tttttcagtcgtttt ................................aagagaactggacttggattcatagaatccatcgcccagttccta...................................................................................................................................................................................................................................................................................................................................................................... TransTerm Strand: + Conf: 100 HP_score: -9.2 Tail_Score: -5.08011 Start: 35 End: 75 Full_Region: AACGACTGAAAAATA GGAACTGGGCGATGGATTC TAT GAATCCAAGTCCAGTTCTC TTTTTTCCGAGTTTT ..................................GGAACTGGGCGATGGATTCTATGAATCCAAGTCCAGTTCTC........................................................................................................................................................................................................................................................................................................................................................................ TransTerm Strand: - Conf: 71 HP_score: -7.2 Tail_Score: -3.96486 Start: 35 End: 74 Full_Region: aaactcggaaaaaag agaactggacttggattc ata gaatccatcgcccagttcc tatttttcagtcgtt ..................................agaactggacttggattcatagaatccatcgcccagttcc......................................................................................................................................................................................................................................................................................................................................................................... TransTerm Strand: + Conf: 95 HP_score: -12.9 Tail_Score: -4.15235 Start: 36 End: 73 Full_Region: ACGACTGAAAAATAG GAACTGGGCGATGGATTC TAT GAATCCAAGTCCAGTTC TCTTTTTTCCGAGTT ...................................GAACTGGGCGATGGATTCTATGAATCCAAGTCCAGTTC.......................................................................................................................................................................................................................................................................................................................................................................... TransTerm Strand: - Conf: 78 HP_score: -10.7 Tail_Score: -2.96807 Start: 36 End: 73 Full_Region: aactcggaaaaaaga gaactggacttggattc ata gaatccatcgcccagttc ctatttttcagtcgt ...................................gaactggacttggattcatagaatccatcgcccagttc.......................................................................................................................................................................................................................................................................................................................................................................... TransTerm Strand: + Conf: 68 HP_score: -4.7 Tail_Score: -4.45544 Start: 259 End: 279 Full_Region: AGTCCAAAAGAAACA GAACCTC TCTAAAC GGGGTTC TTTTGCTTGCTACAA ..................................................................................................................................................................................................................................................................GAACCTCTCTAAACGGGGTTC............................................................................................................................................................ TransTerm Strand: - Conf: 52 HP_score: -2.5 Tail_Score: -3.94471 Start: 259 End: 279 Full_Region: ttgtagcaagcaaaa gaacccc gtttaga gaggttc tgtttcttttggact ..................................................................................................................................................................................................................................................................gaaccccgtttagagaggttc............................................................................................................................................................ Find igs database================================================ Query_seq: SSA_0093:SSA_0094|SSA_0093:SSA_0094:V-type sodium ATPase, subunit D, putative:Cell wall metabolism, LysM type protein, putative:->->:95050..95484 435 gatgcggaggcgttaaaaaaacgactgaaaaataggaactgggcgatggattctatgaatccaagtccagttctcttttttccgagtttttagccgaagcttgatttagctgagctaacctagactgaatagatctattcacagcaaaaatagacgaagaagcgacagcttctaggagattttatcttttttgccaagagcttaggtcgagtttagtttagctgaataccaagagtttaaataagtccaaaagaaacagaacctctctaaacggggttcttttgcttgctacaattttttatatgttacaaacaaatctccatattacagggggcagacagttttgttaaataggtcgaaaaaggcttttttcttagaagatttatggtaagatggttttcgtatcatgaatgattaggaaggtgcattttgcat Intra-Species Hit: Count: 1 Min: 22 Max: 435 Len: 414 Subject: NC_009009_SSA_0093_SSA_0094|V-type sodium ATPase, subunit D, putative:Cell wall metabolism, LysM type protein, putative|POSITIVE:POSITIVE|[95050,95484]|435 HSP 1 e-value: 0.0 bit: 821.0 Len: 414 Query Start:22 Query End:435 Subject Strand: POSITIVE Subject Start: 22 Subject End: 435 .....................cgactgaaaaataggaactgggcgatggattctatgaatccaagtccagttctcttttttccgagtttttagccgaagcttgatttagctgagctaacctagactgaatagatctattcacagcaaaaatagacgaagaagcgacagcttctaggagattttatcttttttgccaagagcttaggtcgagtttagtttagctgaataccaagagtttaaataagtccaaaagaaacagaacctctctaaacggggttcttttgcttgctacaattttttatatgttacaaacaaatctccatattacagggggcagacagttttgttaaataggtcgaaaaaggcttttttcttagaagatttatggtaagatggttttcgtatcatgaatgattaggaaggtgcattttgcat .....................cgactgaaaaataggaactgggcgatggattctatgaatccaagtccagttctcttttttccgagtttttagccgaagcttgatttagctgagctaacctagactgaatagatctattcacagcaaaaatagacgaagaagcgacagcttctaggagattttatcttttttgccaagagcttaggtcgagtttagtttagctgaataccaagagtttaaataagtccaaaagaaacagaacctctctaaacggggttcttttgcttgctacaattttttatatgttacaaacaaatctccatattacagggggcagacagttttgttaaataggtcgaaaaaggcttttttcttagaagatttatggtaagatggttttcgtatcatgaatgattaggaaggtgcattttgcat Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CGACUGAAAAAUAGGAACUGGGCGAUGGAUUCUAUGAAUCCAAGUCCAGUUCUCUUUUUUCCGAGUUUUUAGCCGAAGCUUGAUUUAGCUGAGCUAACCUAGACUGAAUAGAUCUAUUCACAGCAAAAAUAGACGAAGAAGCGACAGCUUCUAGGAGAUUUUAUCUUUUUUGCCAAGAGCUUAGGUCGAGUUUAGUUUAGCUGAAUACCAAGAGUUUAAAUAAGUCCAAAAGAAACAGAACCUCUCUAAACGGGGUUCUUUUGCUUGCUACAAUUUUUUAUAUGUUACAAACAAAUCUCCAUAUUACAGGGGGCAGACAGUUUUGUUAAAUAGGUCGAAAAAGGCUUUUUUCUUAGAAGAUUUAUGGUAAGAUGGUUUUCGUAUCAUGAAUGAUUAGGAAGGUGCAUUUUGCAU (((((((((((..((((((((((..(((((((...))))))).))))))))))..))))))......((((((..((((((.(((((((((((((((.((.(((((((((....)))))...(((((((.(((..(((((((....))))))........)..))))))))))..........)))).)).))))))))))))))).....))))))......(((..........((((((((.......))))))))((((.(((..(((..........)))..))).)))).((((........))))...)))......))))))..))))).((((.((..(((((((((...((((((((((.((......)).))))))))))..))))))))).)).)))).... (-119.10) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUGCAAAAUGCACCUUCCUAAUCAUUCAUGAUACGAAAACCAUCUUACCAUAAAUCUUCUAAGAAAAAAGCCUUUUUCGACCUAUUUAACAAAACUGUCUGCCCCCUGUAAUAUGGAGAUUUGUUUGUAACAUAUAAAAAAUUGUAGCAAGCAAAAGAACCCCGUUUAGAGAGGUUCUGUUUCUUUUGGACUUAUUUAAACUCUUGGUAUUCAGCUAAACUAAACUCGACCUAAGCUCUUGGCAAAAAAGAUAAAAUCUCCUAGAAGCUGUCGCUUCUUCGUCUAUUUUUGCUGUGAAUAGAUCUAUUCAGUCUAGGUUAGCUCAGCUAAAUCAAGCUUCGGCUAAAAACUCGGAAAAAAGAGAACUGGACUUGGAUUCAUAGAAUCCAUCGCCCAGUUCCUAUUUUUCAGUCG ..((.....((.........((((....))))..(((.((((.......((((.(((...((((((..(((((((((.(((.......................((........))...(((((((((.(((..........))).)))))))))........))).)))))))))...))))))..))).)))).........)))).))).))............((((((..(....((((((((((((..........((((((....))))))..)))).))))))))..(((((....))))).)..))))))......)).......(((....)))....(((.((((((.((.(((((((...(((((((...)))))))....))))))))).))))))))).. (-97.59) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 420 200 151 203 153 NC_009009:SSA_0241|5end_Ribosomal_protein_L11_methyltransferase,_putative_234021..234251_POSITIVE 398 65 21 180 137 NC_009009:SSA_2005|5end_Chaperone_protein_dnaJ,_putative_2006384..2006614_NEGATIVE 335 90 43 217 161 NC_009009:SSA_2139|5end_Membrane_protein_(preprotein_translocase)_oxaA_1_precursor,_putative_2140324..2140554_NEGATIVE 328 80 41 59 7 NC_009009:SSA_1855|5end_hypothetical_protein_1852051..1852281_NEGATIVE 325 188 141 210 163 NC_009009:SSA_1313|5end_hypothetical_protein_1330548..1330778_NEGATIVE 322 158 119 66 22 NC_009009:SSA_1792|5end_Preprotein_translocase_subunit_YidC,_putative_1774036..1774266_POSITIVE 321 46 1 167 118 NC_009009:SSA_0914|5end_Phenylalanyl-tRNA_synthetase_beta_chain,_putative_924952..925182_POSITIVE 320 180 131 174 135 NC_009009:SSA_2277|5end_DNA_segregation_ATPase_FtsK/SpoIIIE_family_protein,_putative_2280407..2280637_NEGATIVE 320 178 131 153 103 NC_009009:SSA_1941|5end_hypothetical_protein_1927452..1927682_NEGATIVE 319 86 45 141 101 NC_009009:SSA_2145|5end_Tributyrin_esterase,_putative_2146658..2146888_NEGATIVE 317 90 43 177 115 NC_009009:SSA_1712|5end_Arsenate_reductase_(ArsC),_glutaredoxin_family,_putative_1700084..1700314_NEGATIVE 315 90 45 137 95 NC_009009:SSA_1451|5end_Exonuclease_RexA,_putative_1456418..1456648_NEGATIVE 311 118 71 197 149 NC_009009:SSA_0204|5end_Nisin_biosynthesis_two-component_response_transcriptional_regulator_nisR,_putative_202057..202287_POSITIVE 307 189 147 199 156 NC_009009:SSA_1366|5end_Alkaline_D-stereospecific_endopeptidase_precursor,_putative_1383663..1383893_NEGATIVE 306 49 8 225 178 NC_009009:SSA_1237|5end_Uracil-DNA_glycosylase,_putative_1262366..1262596_NEGATIVE 303 111 71 227 190 NC_009009:SSA_2338|5end_Conserved_uncharacterized_protein_2339272..2339502_POSITIVE 299 339 295 69 17 NC_009009:SSA_0159|5end_hypothetical_protein_155000..155230_POSITIVE 296 107 61 205 153 NC_009009:SSA_1446|5end_Histidinol_dehydrogenase,_putative_1449190..1449420_NEGATIVE 294 198 157 186 148 NC_009009:SSA_1153|5end_HemK_protein,_putative_1181838..1182068_POSITIVE 290 217 176 201 158 NC_009009:SSA_0940|5end_NOL1/NOP2/sun_family_protein,_putative_947626..947856_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 420 200 151 62 12 NC_009009:SSA_0240|3end_Acetyltransferase,_GNAT_family,_putative_233960..234110_POSITIVE 420 60 13 63 15 NC_009009:SSA_0093|3end_V-type_sodium_ATPase,_subunit_D,_putative_94989..95139_POSITIVE 320 107 61 58 7 NC_009009:SSA_0468|3end_Precorrin-6y_C5,15-methyltransferase-like,_putative_472418..472568_POSITIVE 319 86 45 67 27 NC_009009:SSA_2146|3end_Metallo-beta-lactamase,_putative_2146732..2146882_NEGATIVE 315 90 45 140 98 NC_009009:SSA_1452|3end_Second_subunit_of_major_exonuclease,_putative_1456415..1456565_NEGATIVE 307 189 147 114 71 NC_009009:SSA_1368|3end_hypothetical_protein_1383748..1383898_NEGATIVE 299 339 295 63 11 NC_009009:SSA_0158|3end_hypothetical_protein_155074..155224_POSITIVE 297 105 61 54 2 NC_009009:SSA_2380|3end_hypothetical_protein_2385665..2385815_NEGATIVE 290 80 38 119 83 NC_009009:SSA_0466|3end_Precorrin-8X_methylmutase_/_precorrin_isomerase,_putative_470668..470818_POSITIVE 289 80 31 133 76 NC_009009:SSA_0123|3end_50S_ribosomal_protein_L18P,_putative_116484..116634_POSITIVE 287 53 12 63 21 NC_009009:SSA_0319|3end_Branched-chain_amino_acid_permease_(L-methionine,_L-isoleucine,_leucine_and_valine),_putative_313496..313646_POSITIVE 281 198 152 129 64 NC_009009:SSA_1830|3end_Aminoglycoside_phosphotransferase,_putative_1821191..1821341_POSITIVE 281 58 13 67 10 NC_009009:SSA_0205|3end_NisK_(sensor-receptor_histidine_kinase_domain),_putative_203839..203989_POSITIVE 280 180 132 91 42 NC_009009:SSA_1525|3end_Lyzozyme_M1_(1,4-beta-N-acetylmuramidase),_putative_1533683..1533833_POSITIVE 280 55 13 148 94 NC_009009:SSA_1009|3end_Galactose-1-phosphate-uridylyltransferase,_putative_1012815..1012965_POSITIVE 279 198 152 135 82 NC_009009:SSA_1611|3end_Era-like_GTP-binding_protein,_putative_1615133..1615283_NEGATIVE 279 175 137 44 5 NC_009009:SSA_0079|3end_ROK_family_protein,_putative_83819..83969_POSITIVE 274 59 11 89 44 NC_009009:SSA_0154|3end_hypothetical_protein_150950..151100_POSITIVE 272 59 13 92 45 NC_009009:SSA_1633|3end_FimA_fimbrial_subunit-like_protein,_putative_1634106..1634256_NEGATIVE 271 49 14 134 96 NC_009009:SSA_0980|3end_3-isopropylmalate_dehydratase_large_subunit,_putative_985466..985616_POSITIVE