Origin IGS: tgagaaaggcggctttgtgcggccttttttcttaccttgatgaacttgtaaatttaacaagattaacgcatgatttgataagaattaatcatttatgtgtttaattgcttattattttaaaatgtaaatttacatattggtctatatctttatgaaaattttcatctttttcttgttttggacagctcctatatttagcgaaaaaggaataaaaatatactgagagacacaaaatgcagtgttttctctctcatttattactaatttcagctaatgttcggttttagtaattttccgtaaggatatttgaaatttacttgaaaaagagataaaaataatgtagaatagtattatagaaaacgcttacaaatagaaaggtgattgc .........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 gcaatcacctttctatttgtaagcgttttctataatactattctacattatttttatctctttttcaagtaaatttcaaatatccttacggaaaattactaaaaccgaacattagctgaaattagtaataaatgagagagaaaacactgcattttgtgtctctcagtatatttttattcctttttcgctaaatataggagctgtccaaaacaagaaaaagatgaaaattttcataaagatatagaccaatatgtaaatttacattttaaaataataagcaattaaacacataaatgattaattcttatcaaatcatgcgttaatcttgttaaatttacaagttcatcaaggtaagaaaaaaggccgcacaaagccgcctttctca Mask Tandem Repeat Region ================================================ tgagaaaggcggctttgtgcggccttttttcttaccttgatgaacttgtaaatttaacaagattaacgcatgatttgataagaattaatcatttatgtgtttaattgcttattattttaaaatgtaaatttacatattggtctatatctttatgaaaattttcatctttttcttgttttggacagctcctatatttagcgaaaaaggaataaaaatatactgagagacacaaaatgcagtgttttctctctcatttattactaatttcagctaatgttcggttttagtaattttccgtaaggatatttgaaatttacttgaaaaagagataaaaataatgtagaatagtattatagaaaacgcttacaaatagaaaggtgattgc Find is-nt database================================================ Query_seq: SSA_0774:SSA_0775|SSA_0774:SSA_0775:NADP-dependent glyceraldehyde-3-phosphate dehydrogenase, putative:1,4-alpha-glucan branching enzyme, putative:->->:756136..756520 385 tgagaaaggcggctttgtgcggccttttttcttaccttgatgaacttgtaaatttaacaagattaacgcatgatttgataagaattaatcatttatgtgtttaattgcttattattttaaaatgtaaatttacatattggtctatatctttatgaaaattttcatctttttcttgttttggacagctcctatatttagcgaaaaaggaataaaaatatactgagagacacaaaatgcagtgttttctctctcatttattactaatttcagctaatgttcggttttagtaattttccgtaaggatatttgaaatttacttgaaaaagagataaaaataatgtagaatagtattatagaaaacgcttacaaatagaaaggtgattgc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0774:SSA_0775|SSA_0774:SSA_0775:NADP-dependent glyceraldehyde-3-phosphate dehydrogenase, putative:1,4-alpha-glucan branching enzyme, putative:->->:756136..756520 385 tgagaaaggcggctttgtgcggccttttttcttaccttgatgaacttgtaaatttaacaagattaacgcatgatttgataagaattaatcatttatgtgtttaattgcttattattttaaaatgtaaatttacatattggtctatatctttatgaaaattttcatctttttcttgttttggacagctcctatatttagcgaaaaaggaataaaaatatactgagagacacaaaatgcagtgttttctctctcatttattactaatttcagctaatgttcggttttagtaattttccgtaaggatatttgaaatttacttgaaaaagagataaaaataatgtagaatagtattatagaaaacgcttacaaatagaaaggtgattgc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0774:SSA_0775|SSA_0774:SSA_0775:NADP-dependent glyceraldehyde-3-phosphate dehydrogenase, putative:1,4-alpha-glucan branching enzyme, putative:->->:756136..756520 385 tgagaaaggcggctttgtgcggccttttttcttaccttgatgaacttgtaaatttaacaagattaacgcatgatttgataagaattaatcatttatgtgtttaattgcttattattttaaaatgtaaatttacatattggtctatatctttatgaaaattttcatctttttcttgttttggacagctcctatatttagcgaaaaaggaataaaaatatactgagagacacaaaatgcagtgttttctctctcatttattactaatttcagctaatgttcggttttagtaattttccgtaaggatatttgaaatttacttgaaaaagagataaaaataatgtagaatagtattatagaaaacgcttacaaatagaaaggtgattgc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tgagaaaggcggctttgtgcggccttttttcttaccttgatgaacttgtaaatttaacaagattaacgcatgatttgataagaattaatcatttatgtgtttaattgcttattattttaaaatgtaaatttacatattggtctatatctttatgaaaattttcatctttttcttgttttggacagctcctatatttagcgaaaaaggaataaaaatatactgagagacacaaaatgcagtgttttctctctcatttattactaatttcagctaatgttcggttttagtaattttccgtaaggatatttgaaatttacttgaaaaagagataaaaataatgtagaatagtattatagaaaacgcttacaaatagaaaggtgattgc Predict ORF larger than 30AA ================================================ Protein_Len: 31 Strand: + Start: 128 End: 220 ............................................................................................................................... M Y I L V Y I F M K I F I F F L F W T A P I F S E K G I K I Y ..................................................................................................................................................................... Protein_Len: 42 Strand: - Start: 145 End: 270 ................................................................................................................................................ I K I F I K M K K K N Q V A G I N L S F P I F I Y Q S V C F A T N E R E N I V L K M ................................................................................................................... Protein_Len: 44 Strand: - Start: 104 End: 235 ....................................................................................................... N S I I K F H L N V Y Q D I D K H F N E D K E Q K P C S R Y K A F F S Y F Y V S L C L M ...................................................................................................................................................... tgagaaaggcggctttgtgcggccttttttcttaccttgatgaacttgtaaatttaacaagattaacgcatgatttgataagaattaatcatttatgtgtttaattgcttattattttaaaatgtaaatttacatattggtctatatctttatgaaaattttcatctttttcttgttttggacagctcctatatttagcgaaaaaggaataaaaatatactgagagacacaaaatgcagtgttttctctctcatttattactaatttcagctaatgttcggttttagtaattttccgtaaggatatttgaaatttacttgaaaaagagataaaaataatgtagaatagtattatagaaaacgcttacaaatagaaaggtgattgc 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: 85 Start: 317 End: 346 ............................................................................................................................................................................................................................................................................................................................CTTGAAAAAGAGATAAAAATAATGTAGAAT....................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tgagaaaggcggctttgtgcggccttttttcttaccttgatgaacttgtaaatttaacaagattaacgcatgatttgataagaattaatcatttatgtgtttaattgcttattattttaaaatgtaaatttacatattggtctatatctttatgaaaattttcatctttttcttgttttggacagctcctatatttagcgaaaaaggaataaaaatatactgagagacacaaaatgcagtgttttctctctcatttattactaatttcagctaatgttcggttttagtaattttccgtaaggatatttgaaatttacttgaaaaagagataaaaataatgtagaatagtattatagaaaacgcttacaaatagaaaggtgattgc Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_0774:SSA_0775|SSA_0774:SSA_0775:NADP-dependent glyceraldehyde-3-phosphate dehydrogenase, putative:1,4-alpha-glucan branching enzyme, putative:->->:756136..756520 385 tgagaaaggcggctttgtgcggccttttttcttaccttgatgaacttgtaaatttaacaagattaacgcatgatttgataagaattaatcatttatgtgtttaattgcttattattttaaaatgtaaatttacatattggtctatatctttatgaaaattttcatctttttcttgttttggacagctcctatatttagcgaaaaaggaataaaaatatactgagagacacaaaatgcagtgttttctctctcatttattactaatttcagctaatgttcggttttagtaattttccgtaaggatatttgaaatttacttgaaaaagagataaaaataatgtagaatagtattatagaaaacgcttacaaatagaaaggtgattgc Intra-Species Hit: Count: 1 Min: 1 Max: 385 Len: 385 Subject: NC_009009_SSA_0774_SSA_0775|NADP-dependent glyceraldehyde-3-phosphate dehydrogenase, putative:1,4-alpha-glucan branching enzyme, putative|POSITIVE:POSITIVE|[756136,756520]|385 HSP 1 e-value: 0.0 bit: 763.0 Len: 385 Query Start:1 Query End:385 Subject Strand: POSITIVE Subject Start: 1 Subject End: 385 tgagaaaggcggctttgtgcggccttttttcttaccttgatgaacttgtaaatttaacaagattaacgcatgatttgataagaattaatcatttatgtgtttaattgcttattattttaaaatgtaaatttacatattggtctatatctttatgaaaattttcatctttttcttgttttggacagctcctatatttagcgaaaaaggaataaaaatatactgagagacacaaaatgcagtgttttctctctcatttattactaatttcagctaatgttcggttttagtaattttccgtaaggatatttgaaatttacttgaaaaagagataaaaataatgtagaatagtattatagaaaacgcttacaaatagaaaggtgattgc tgagaaaggcggctttgtgcggccttttttcttaccttgatgaacttgtaaatttaacaagattaacgcatgatttgataagaattaatcatttatgtgtttaattgcttattattttaaaatgtaaatttacatattggtctatatctttatgaaaattttcatctttttcttgttttggacagctcctatatttagcgaaaaaggaataaaaatatactgagagacacaaaatgcagtgttttctctctcatttattactaatttcagctaatgttcggttttagtaattttccgtaaggatatttgaaatttacttgaaaaagagataaaaataatgtagaatagtattatagaaaacgcttacaaatagaaaggtgattgc Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGAGAAAGGCGGCUUUGUGCGGCCUUUUUUCUUACCUUGAUGAACUUGUAAAUUUAACAAGAUUAACGCAUGAUUUGAUAAGAAUUAAUCAUUUAUGUGUUUAAUUGCUUAUUAUUUUAAAAUGUAAAUUUACAUAUUGGUCUAUAUCUUUAUGAAAAUUUUCAUCUUUUUCUUGUUUUGGACAGCUCCUAUAUUUAGCGAAAAAGGAAUAAAAAUAUACUGAGAGACACAAAAUGCAGUGUUUUCUCUCUCAUUUAUUACUAAUUUCAGCUAAUGUUCGGUUUUAGUAAUUUUCCGUAAGGAUAUUUGAAAUUUACUUGAAAAAGAGAUAAAAAUAAUGUAGAAUAGUAUUAUAGAAAACGCUUACAAAUAGAAAGGUGAUUGC .(((((((((.((.....)).))))))))).(((((((..((...((((((......(((....(((((((((..((((........)))).)))))))))...)))..((((((((((...((.((((((.((((..(((....)))..)))).)))))).))((((((((..((...(((((..........(((((((((..((((((((.......((((((((((........))).....))))))))))))).))..)))).)))))))))).(((((((......(((....)))...)))))))..))..)))))))).............)))))))))).............)))))).))..))))))).... (-84.01) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GCAAUCACCUUUCUAUUUGUAAGCGUUUUCUAUAAUACUAUUCUACAUUAUUUUUAUCUCUUUUUCAAGUAAAUUUCAAAUAUCCUUACGGAAAAUUACUAAAACCGAACAUUAGCUGAAAUUAGUAAUAAAUGAGAGAGAAAACACUGCAUUUUGUGUCUCUCAGUAUAUUUUUAUUCCUUUUUCGCUAAAUAUAGGAGCUGUCCAAAACAAGAAAAAGAUGAAAAUUUUCAUAAAGAUAUAGACCAAUAUGUAAAUUUACAUUUUAAAAUAAUAAGCAAUUAAACACAUAAAUGAUUAAUUCUUAUCAAAUCAUGCGUUAAUCUUGUUAAAUUUACAAGUUCAUCAAGGUAAGAAAAAAGGCCGCACAAAGCCGCCUUUCUCA ......(((((...(((((((((((.((((((((.................................(((((.((((...((....))..)))).)))))...........(((((.((((..((.(((((((((((((.....(((........)))))))))).......)))))).)).))))))))).)))))))).)))....(((((((..((((((.((((((.((((..(........)..)))).)))))).))))))......(((((.((((((.((......)).)))))))))))...............)))))))....)))))))).....)))))..((..((((((.((.....)).)))))).)). (-68.41) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 370 46 3 98 47 NC_009009:SSA_0956|5end_surface_protein_D_961223..961453_POSITIVE 336 44 7 39 4 NC_009009:SSA_1190|5end_Conserved_uncharacterized_protein_1218137..1218367_NEGATIVE 323 31 1 193 155 NC_009009:SSA_0206|5end_hypothetical_protein_204256..204486_POSITIVE 295 48 7 184 143 NC_009009:SSA_1439|5end_hypothetical_protein_1444373..1444603_NEGATIVE 291 199 162 134 97 NC_009009:SSA_1059|5end_hypothetical_protein_1076153..1076383_POSITIVE 286 271 233 124 75 NC_009009:SSA_0660|5end_Cell_division_protein_DivIVA,_putative_643798..644028_POSITIVE 283 49 1 63 4 NC_009009:SSA_1783|5end_Xanthosine_triphosphate_pyrophosphatase_(NTPase/HAM1_family),_putative_1769106..1769336_NEGATIVE 282 44 3 117 77 NC_009009:SSA_1764|5end_hypothetical_protein_1750868..1751098_POSITIVE 281 41 1 201 155 NC_009009:SSA_0973|5end_hypothetical_protein_980296..980526_POSITIVE 273 39 1 174 125 NC_009009:SSA_0279|5end_Sugar-binding_transcriptional_repressor_(DeoR),_putative_272319..272549_POSITIVE 272 47 8 88 50 NC_009009:SSA_0485|5end_Porphobilinogen_deaminase,_putative_485732..485962_POSITIVE 265 25 10 20 4 NC_009009:SSA_1792|5end_Preprotein_translocase_subunit_YidC,_putative_1774036..1774266_POSITIVE 265 27 4 196 168 NC_009009:SSA_1031|5end_DNA_topology_modulation_protein_FlaR,_putative_1048255..1048485_NEGATIVE 265 44 5 164 117 NC_009009:SSA_0611|5end_HtpX_protease,_putative_599539..599769_POSITIVE 262 289 245 80 35 NC_009009:SSA_1289|5end_hypothetical_protein_1308385..1308615_NEGATIVE 258 303 265 142 104 NC_009009:SSA_2071|5end_hypothetical_protein_2074766..2074996_NEGATIVE 257 32 2 171 146 NC_009009:SSA_0678|5end_Transcriptional_regulator,_ArgR_family,_putative_660274..660504_POSITIVE 254 32 4 221 192 NC_009009:SSA_0397|5end_hypothetical_protein_394657..394887_NEGATIVE 253 31 8 71 45 NC_009009:SSA_1626|5end_DNA_translocase_ftsK,_putative_1629377..1629607_NEGATIVE 252 47 3 222 178 NC_009009:SSA_1269|5end_hypothetical_protein_1293352..1293582_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 295 48 7 150 109 NC_009009:SSA_1440|3end_Phosphoribosyl-ATP_pyrophosphohydrolase,_putative_1444407..1444557_NEGATIVE 295 29 2 76 46 NC_009009:SSA_0564|3end_Potential_aminotransferase,_putative_556988..557138_POSITIVE 291 199 162 112 75 NC_009009:SSA_1058|3end_Thiamine_biosynthesis_protein,_putative_1076211..1076361_POSITIVE 286 271 233 114 65 NC_009009:SSA_0659|3end_hypothetical_protein_643868..644018_POSITIVE 283 49 1 66 7 NC_009009:SSA_1784|3end_Glutamate_racemase,_putative_1769103..1769253_NEGATIVE 282 44 3 120 80 NC_009009:SSA_1763|3end_ABC-type_molybdenum_transport_system,_ATPase_component,_putative_1750951..1751101_POSITIVE 278 40 2 77 44 NC_009009:SSA_1661|3end_hypothetical_protein_1657759..1657909_NEGATIVE 277 34 3 93 64 NC_009009:SSA_1739|3end_UDP-N-acetylmuramoylalanyl-D-glutamate--2,_6-diaminopimelate_ligase,_putative_1727065..1727215_POSITIVE 272 47 8 101 63 NC_009009:SSA_0484|3end_Glutamyl-tRNA_reductase,_putative_485825..485975_POSITIVE 270 47 10 147 113 NC_009009:SSA_0929|3end_ABC-type_multidrug_transporter,_ATPase_and_permease_components,_putative_940263..940413_POSITIVE 266 46 1 106 54 NC_009009:SSA_0395|3end_6-phospho-beta-glucosidase,_putative_392580..392730_POSITIVE 265 27 4 138 110 NC_009009:SSA_1032|3end_30S_ribosomal_protein_subunit_S20,_putative_1048313..1048463_NEGATIVE 263 34 1 93 63 NC_009009:SSA_1707|3end_Conserved_uncharacterized_protein_1698248..1698398_POSITIVE 262 50 1 114 48 NC_009009:SSA_1554|3end_hypothetical_protein_1556847..1556997_POSITIVE 258 303 265 108 70 NC_009009:SSA_2072|3end_Phosphatidate_cytidylyltransferase,_putative_2074800..2074950_NEGATIVE 252 47 3 98 54 NC_009009:SSA_1270|3end_Flavodoxin_1293476..1293626_NEGATIVE 246 44 10 106 70 NC_009009:SSA_2048|3end_Serine_acetyltransferase,_putative_2049984..2050134_NEGATIVE 244 29 1 34 2 NC_009009:SSA_0922|3end_hypothetical_protein_932225..932375_NEGATIVE 243 49 6 51 6 NC_009009:SSA_1210|3end_GTP_pyrophosphokinase,_putative_1233984..1234134_NEGATIVE 242 201 161 71 32 NC_009009:SSA_1690|3end_hypothetical_protein_1683348..1683498_POSITIVE