Origin IGS: gcaattttcctttctcacaatattcagttttaaatgtacaatgtaattgtatactaactgagcttccccatcttgtcagtgcccactttctaaaaagcgaacatttatagatacattacatctacattttatcatactataagaaaaatggctatacacaaaaggagatttttttaacatttgtttacctttttgtcatttagaaaagatggaaaacttacatcgttcattcgcaaatcaaaccactattgttagggtcaattgcgtctgacaatcaatgtcctcaataacatagaaaaaccggaaacaaagtccggttcttctgat .........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 atcagaagaaccggactttgtttccggtttttctatgttattgaggacattgattgtcagacgcaattgaccctaacaatagtggtttgatttgcgaatgaacgatgtaagttttccatcttttctaaatgacaaaaaggtaaacaaatgttaaaaaaatctccttttgtgtatagccatttttcttatagtatgataaaatgtagatgtaatgtatctataaatgttcgctttttagaaagtgggcactgacaagatggggaagctcagttagtatacaattacattgtacatttaaaactgaatattgtgagaaaggaaaattgc Mask Tandem Repeat Region ================================================ gcaattttcctttctcacaatattcagttttaaatgtacaatgtaattgtatactaactgagcttccccatcttgtcagtgcccactttctaaaaagcgaacatttatagatacattacatctacattttatcatactataagaaaaatggctatacacaaaaggagatttttttaacatttgtttacctttttgtcatttagaaaagatggaaaacttacatcgttcattcgcaaatcaaaccactattgttagggtcaattgcgtctgacaatcaatgtcctcaataacatagaaaaaccggaaacaaagtccggttcttctgat Find is-nt database================================================ Query_seq: SSA_1663:SSA_1664|SSA_1663:SSA_1664:Collagen-binding protein A:Phosphatidylethanolamine N-methyltransferase, putative:<-<-:1664212..1664538 327 gcaattttcctttctcacaatattcagttttaaatgtacaatgtaattgtatactaactgagcttccccatcttgtcagtgcccactttctaaaaagcgaacatttatagatacattacatctacattttatcatactataagaaaaatggctatacacaaaaggagatttttttaacatttgtttacctttttgtcatttagaaaagatggaaaacttacatcgttcattcgcaaatcaaaccactattgttagggtcaattgcgtctgacaatcaatgtcctcaataacatagaaaaaccggaaacaaagtccggttcttctgat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1663:SSA_1664|SSA_1663:SSA_1664:Collagen-binding protein A:Phosphatidylethanolamine N-methyltransferase, putative:<-<-:1664212..1664538 327 gcaattttcctttctcacaatattcagttttaaatgtacaatgtaattgtatactaactgagcttccccatcttgtcagtgcccactttctaaaaagcgaacatttatagatacattacatctacattttatcatactataagaaaaatggctatacacaaaaggagatttttttaacatttgtttacctttttgtcatttagaaaagatggaaaacttacatcgttcattcgcaaatcaaaccactattgttagggtcaattgcgtctgacaatcaatgtcctcaataacatagaaaaaccggaaacaaagtccggttcttctgat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1663:SSA_1664|SSA_1663:SSA_1664:Collagen-binding protein A:Phosphatidylethanolamine N-methyltransferase, putative:<-<-:1664212..1664538 327 gcaattttcctttctcacaatattcagttttaaatgtacaatgtaattgtatactaactgagcttccccatcttgtcagtgcccactttctaaaaagcgaacatttatagatacattacatctacattttatcatactataagaaaaatggctatacacaaaaggagatttttttaacatttgtttacctttttgtcatttagaaaagatggaaaacttacatcgttcattcgcaaatcaaaccactattgttagggtcaattgcgtctgacaatcaatgtcctcaataacatagaaaaaccggaaacaaagtccggttcttctgat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gcaattttcctttctcacaatattcagttttaaatgtacaatgtaattgtatactaactgagcttccccatcttgtcagtgcccactttctaaaaagcgaacatttatagatacattacatctacattttatcatactataagaaaaatggctatacacaaaaggagatttttttaacatttgtttacctttttgtcatttagaaaagatggaaaacttacatcgttcattcgcaaatcaaaccactattgttagggtcaattgcgtctgacaatcaatgtcctcaataacatagaaaaaccggaaacaaagtccggttcttctgat Predict ORF larger than 30AA ================================================ Protein_Len: 30 Strand: + Start: 111 End: 200 .............................................................................................................. M H Y I Y I L S Y Y K K N G Y T Q K E I F L T F V Y L F V I ............................................................................................................................... Protein_Len: 30 Strand: + Start: 179 End: 268 .................................................................................................................................................................................. M C L P F C H L E K M E N L H R S F A N Q T T I V R V N C V ........................................................... Protein_Len: 34 Strand: - Start: 79 End: 180 .............................................................................. H G S E L F R V N I S V N C R C K I M S Y S F H S Y V F P S K K L M ................................................................................................................................................... Protein_Len: 37 Strand: - Start: 2 End: 112 . L K G K E C Y E T K F T C H L Q I S V S S G W R T L A W K R F L S C K Y M ....................................................................................................................................................................................................................... gcaattttcctttctcacaatattcagttttaaatgtacaatgtaattgtatactaactgagcttccccatcttgtcagtgcccactttctaaaaagcgaacatttatagatacattacatctacattttatcatactataagaaaaatggctatacacaaaaggagatttttttaacatttgtttacctttttgtcatttagaaaagatggaaaacttacatcgttcattcgcaaatcaaaccactattgttagggtcaattgcgtctgacaatcaatgtcctcaataacatagaaaaaccggaaacaaagtccggttcttctgat 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: 82 Start: 126 End: 155 .............................................................................................................................ATAGCCATTTTTCTTATAGTATGATAAAAT............................................................................................................................................................................ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ gcaattttcctttctcacaatattcagttttaaatgtacaatgtaattgtatactaactgagcttccccatcttgtcagtgcccactttctaaaaagcgaacatttatagatacattacatctacattttatcatactataagaaaaatggctatacacaaaaggagatttttttaacatttgtttacctttttgtcatttagaaaagatggaaaacttacatcgttcattcgcaaatcaaaccactattgttagggtcaattgcgtctgacaatcaatgtcctcaataacatagaaaaaccggaaacaaagtccggttcttctgat Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_1663:SSA_1664|SSA_1663:SSA_1664:Collagen-binding protein A:Phosphatidylethanolamine N-methyltransferase, putative:<-<-:1664212..1664538 327 gcaattttcctttctcacaatattcagttttaaatgtacaatgtaattgtatactaactgagcttccccatcttgtcagtgcccactttctaaaaagcgaacatttatagatacattacatctacattttatcatactataagaaaaatggctatacacaaaaggagatttttttaacatttgtttacctttttgtcatttagaaaagatggaaaacttacatcgttcattcgcaaatcaaaccactattgttagggtcaattgcgtctgacaatcaatgtcctcaataacatagaaaaaccggaaacaaagtccggttcttctgat Intra-Species Hit: Count: 1 Min: 1 Max: 327 Len: 327 Subject: NC_009009_SSA_1663_SSA_1664|Collagen-binding protein A:Phosphatidylethanolamine N-methyltransferase, putative|NEGATIVE:NEGATIVE|[1664212,1664538]|327 HSP 1 e-value: 1.0E-172 bit: 607.0 Len: 327 Query Start:1 Query End:327 Subject Strand: POSITIVE Subject Start: 1 Subject End: 327 gcaattttcctttctcacaatattcagttttaaatgtacaatgtaattgtatactaactgagcttccccatcttgtcagtgcccactttctaaaaagcgaacatttatagatacattacatctacattttatcatactataagaaaaatggctatacacaaaaggagannnnnnnaacatttgtttacctttttgtcatttagaaaagatggaaaacttacatcgttcattcgcaaatcaaaccactattgttagggtcaattgcgtctgacaatcaatgtcctcaataacatagaaaaaccggaaacaaagtccggttcttctgat gcaattttcctttctcacaatattcagttttaaatgtacaatgtaattgtatactaactgagcttccccatcttgtcagtgcccactttctaaaaagcgaacatttatagatacattacatctacattttatcatactataagaaaaatggctatacacaaaaggagatttttttaacatttgtttacctttttgtcatttagaaaagatggaaaacttacatcgttcattcgcaaatcaaaccactattgttagggtcaattgcgtctgacaatcaatgtcctcaataacatagaaaaaccggaaacaaagtccggttcttctgat Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GCAAUUUUCCUUUCUCACAAUAUUCAGUUUUAAAUGUACAAUGUAAUUGUAUACUAACUGAGCUUCCCCAUCUUGUCAGUGCCCACUUUCUAAAAAGCGAACAUUUAUAGAUACAUUACAUCUACAUUUUAUCAUACUAUAAGAAAAAUGGCUAUACACAAAAGGAGAUUUUUUUAACAUUUGUUUACCUUUUUGUCAUUUAGAAAAGAUGGAAAACUUACAUCGUUCAUUCGCAAAUCAAACCACUAUUGUUAGGGUCAAUUGCGUCUGACAAUCAAUGUCCUCAAUAACAUAGAAAAACCGGAAACAAAGUCCGGUUCUUCUGAU ((((((..((((....((((((.((((((.....((((((((...))))))))..))))))((..........(((.(((..((((((((((((.(((...(((((.(((((.......)))))..((((((......)))))).))))))))..(((.((((((((((.............)))).)))))))))..))))).)))).)))...))).)))..........))............)))))).))))..))))))....((((.....))))..........(((((.(((((((.......))))))).))))).. (-63.57) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUCAGAAGAACCGGACUUUGUUUCCGGUUUUUCUAUGUUAUUGAGGACAUUGAUUGUCAGACGCAAUUGACCCUAACAAUAGUGGUUUGAUUUGCGAAUGAACGAUGUAAGUUUUCCAUCUUUUCUAAAUGACAAAAAGGUAAACAAAUGUUAAAAAAAUCUCCUUUUGUGUAUAGCCAUUUUUCUUAUAGUAUGAUAAAAUGUAGAUGUAAUGUAUCUAUAAAUGUUCGCUUUUUAGAAAGUGGGCACUGACAAGAUGGGGAAGCUCAGUUAGUAUACAAUUACAUUGUACAUUUAAAACUGAAUAUUGUGAGAAAGGAAAAUUGC ...((((((((((((.......))))))))))))............((((((....(((..(((((..(((((((....))).))))....)))))..))).)))))).((((((((..............(((((((((......................)))))).))).........(((((((((((((....((((((((((((((((((((((....((((((((((....)))))))))).........((((....))))..))).)))).)))))))).)))))))........))))))))))))))))))))).. (-87.35) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 928 100 51 191 142 NC_009009:SSA_1663|5end_Collagen-binding_protein_A_1664121..1664351_NEGATIVE 314 283 242 89 47 NC_009009:SSA_1903|5end_hypothetical_protein_1898182..1898412_NEGATIVE 304 99 52 59 11 NC_009009:SSA_0210|5end_hypothetical_protein_207757..207987_POSITIVE 301 49 1 57 8 NC_009009:SSA_1666|5end_Collagen-binding_surface_protein,_putative_1667312..1667542_NEGATIVE 298 284 244 195 160 NC_009009:SSA_1217|5end_Conserved_uncharacterized_protein_1238964..1239194_POSITIVE 290 90 42 174 111 NC_009009:SSA_1521|5end_Phosphoenolpyruvate_carboxylase,_putative_1530683..1530913_NEGATIVE 282 99 55 201 155 NC_009009:SSA_0079|5end_ROK_family_protein,_putative_82855..83085_POSITIVE 279 120 71 68 12 NC_009009:SSA_1681|5end_ABC-type_bacitracin_resistance_protein_A,_ATPase_component,_putative_1675960..1676190_NEGATIVE 277 87 51 230 195 NC_009009:SSA_0212|5end_Phenylalanyl-tRNA_synthetase,_beta_subunit,_putative_208373..208603_POSITIVE 273 320 272 72 19 NC_009009:SSA_0069|5end_Hypothetical_protein,_possibly_membrane-associated_73037..73267_POSITIVE 270 290 244 87 27 NC_009009:SSA_1630|5end_hypothetical_protein_1631192..1631422_POSITIVE 269 87 57 196 170 NC_009009:SSA_1243|5end_Dihydroorotate_dehydrogenase_electron_transfer_subunit,_putative_1268204..1268434_NEGATIVE 267 285 245 54 15 NC_009009:SSA_0524|5end_Microcompartment_protein,_putative_523150..523380_POSITIVE 265 89 57 199 166 NC_009009:SSA_2070|5end_Zinc_metalloprotease,_putative_2074574..2074804_NEGATIVE 265 93 64 82 51 NC_009009:SSA_1254|5end_hypothetical_protein_1281484..1281714_NEGATIVE 265 98 58 219 163 NC_009009:SSA_0759|5end_Acetylglutamate_kinase,_putative_741841..742071_POSITIVE 261 85 61 38 14 NC_009009:SSA_0377|5end_ABC-type_methionine_transporter,_permease_component,_putative_366446..366676_POSITIVE 260 98 57 53 5 NC_009009:SSA_1448|5end_ATP_phosphoribosyltransferase_regulatory_subunit,_putative_1450817..1451047_NEGATIVE 258 320 278 193 144 NC_009009:SSA_2032|5end_Integrase/recombinase,_phage_integrase_family,_putative_2038006..2038236_POSITIVE 256 269 221 206 160 NC_009009:SSA_0778|5end_Glycogen_synthase,_putative_760566..760796_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 307 100 61 77 38 NC_009009:SSA_2239|3end_Conserved_uncharacterized_cytosolic_protein_2236922..2237072_NEGATIVE 290 90 42 127 64 NC_009009:SSA_1522|3end_Cell_division_protein_FtsW,_putative_1530730..1530880_NEGATIVE 279 270 221 128 74 NC_009009:SSA_1140|3end_Dihydrolipoamide_acetyl_transferase,_E2_component,_putative_1169207..1169357_POSITIVE 277 88 46 149 93 NC_009009:SSA_0593|3end_Rhodanese-like_sulfurtransferase,_putative_585551..585701_POSITIVE 271 318 276 65 18 NC_009009:SSA_0380|3end_Enzyme_of_poly-gamma-glutamate_biosynthesis_(capsule_formation),_putative_372378..372528_POSITIVE 265 93 64 110 79 NC_009009:SSA_1255|3end_hypothetical_protein_1281456..1281606_NEGATIVE 264 283 246 38 1 NC_009009:SSA_1904|3end_ABC-type_multidrug_transport_system,_permease_component,_putative_1898233..1898383_NEGATIVE 261 270 226 137 90 NC_009009:SSA_0422|3end_Phosphoglycerate_mutase_family_protein,_putative_420839..420989_POSITIVE 261 85 61 38 14 NC_009009:SSA_0376|3end_ABC-type_methionine_transporter,_ATPase_component,_putative_366526..366676_POSITIVE 248 110 64 146 99 NC_009009:SSA_0653|3end_UDP-N-acetylglucosamine--N-acetylmuramyl-_(pentapeptide)_pyrophosphoryl-undecaprenol_N-acetylglucosamine_transferase,_putative_637540..637690_POSITIVE 247 240 195 51 1 NC_009009:SSA_1949|3end_AliA_protein,_putative_1942403..1942553_NEGATIVE 245 100 55 100 56 NC_009009:SSA_0235|3end_Integrase/recombinase,_phage_associated,_putative_230780..230930_POSITIVE 243 99 55 51 12 NC_009009:SSA_2367|3end_ABC-type_cobalt_transport_system,_ATPase_component,_putative_2368845..2368995_NEGATIVE 243 98 51 63 9 NC_009009:SSA_0978|3end_hypothetical_protein_984082..984232_POSITIVE 243 105 71 70 31 NC_009009:SSA_0679|3end_DNA_repair_and_genetic_recombination,_putative_662452..662602_POSITIVE 241 104 63 138 87 NC_009009:SSA_2213|3end_Nucleotide_sugar_dehydratase,_putative_2214047..2214197_NEGATIVE 241 99 58 69 35 NC_009009:SSA_0627|3end_hypothetical_protein_617975..618125_POSITIVE 239 319 280 78 35 NC_009009:SSA_1521|3end_Phosphoenolpyruvate_carboxylase,_putative_1527837..1527987_NEGATIVE 239 88 51 111 74 NC_009009:SSA_1454|3end_hypothetical_protein_1460255..1460405_NEGATIVE 238 82 57 139 111 NC_009009:SSA_2001|3end_Hydroxymethylpyrimidine/phosphomethylpyrimidine_kinase,_putative_1997450..1997600_NEGATIVE