Origin IGS: gacaacctcactttctacaagaaaaaaccttgccgcagcaaggtttcgcaaaaaacaaggcagccaattgcctcttataccgtttccccaccttgcagcctcactggacttgattaaaggttaaattgtaaacattatatcgttagcgataaggattgtcaagccataaaaaatattagaattttaagatctccgacctaccacagctttaccagtccttgtcaaattcactctttgcatccgcaagacagggcactgaa .........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 ttcagtgccctgtcttgcggatgcaaagagtgaatttgacaaggactggtaaagctgtggtaggtcggagatcttaaaattctaatattttttatggcttgacaatccttatcgctaacgatataatgtttacaatttaacctttaatcaagtccagtgaggctgcaaggtggggaaacggtataagaggcaattggctgccttgttttttgcgaaaccttgctgcggcaaggttttttcttgtagaaagtgaggttgtc Mask Tandem Repeat Region ================================================ gacaacctcactttctacaagaaaaaaccttgccgcagcaaggtttcgcaaaaaacaaggcagccaattgcctcttataccgtttccccaccttgcagcctcactggacttgattaaaggttaaattgtaaacattatatcgttagcgataaggattgtcaagccataaaaaatattagaattttaagatctccgacctaccacagctttaccagtccttgtcaaattcactctttgcatccgcaagacagggcactgaa Find is-nt database================================================ Query_seq: SSA_1243:SSA_1244|SSA_1243:SSA_1244:Dihydroorotate dehydrogenase electron transfer subunit, putative:hypothetical protein:<-<-:1268295..1268554 260 gacaacctcactttctacaagaaaaaaccttgccgcagcaaggtttcgcaaaaaacaaggcagccaattgcctcttataccgtttccccaccttgcagcctcactggacttgattaaaggttaaattgtaaacattatatcgttagcgataaggattgtcaagccataaaaaatattagaattttaagatctccgacctaccacagctttaccagtccttgtcaaattcactctttgcatccgcaagacagggcactgaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1243:SSA_1244|SSA_1243:SSA_1244:Dihydroorotate dehydrogenase electron transfer subunit, putative:hypothetical protein:<-<-:1268295..1268554 260 gacaacctcactttctacaagaaaaaaccttgccgcagcaaggtttcgcaaaaaacaaggcagccaattgcctcttataccgtttccccaccttgcagcctcactggacttgattaaaggttaaattgtaaacattatatcgttagcgataaggattgtcaagccataaaaaatattagaattttaagatctccgacctaccacagctttaccagtccttgtcaaattcactctttgcatccgcaagacagggcactgaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1243:SSA_1244|SSA_1243:SSA_1244:Dihydroorotate dehydrogenase electron transfer subunit, putative:hypothetical protein:<-<-:1268295..1268554 260 gacaacctcactttctacaagaaaaaaccttgccgcagcaaggtttcgcaaaaaacaaggcagccaattgcctcttataccgtttccccaccttgcagcctcactggacttgattaaaggttaaattgtaaacattatatcgttagcgataaggattgtcaagccataaaaaatattagaattttaagatctccgacctaccacagctttaccagtccttgtcaaattcactctttgcatccgcaagacagggcactgaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gacaacctcactttctacaagaaaaaaccttgccgcagcaaggtttcgcaaaaaacaaggcagccaattgcctcttataccgtttccccaccttgcagcctcactggacttgattaaaggttaaattgtaaacattatatcgttagcgataaggattgtcaagccataaaaaatattagaattttaagatctccgacctaccacagctttaccagtccttgtcaaattcactctttgcatccgcaagacagggcactgaa Predict ORF larger than 30AA ================================================ Protein_Len: 40 Strand: + Start: 139 End: 258 .......................................................................................................................................... M V S D K D C Q A I K N I R I L R S P T Y H S F T S P C Q I H S L H P Q D R A L .. Protein_Len: 38 Strand: - Start: 1 End: 114 V V E S E V L F F R A A A L N R L F C P L W N G R I G N G W R A A E S S K M .................................................................................................................................................. gacaacctcactttctacaagaaaaaaccttgccgcagcaaggtttcgcaaaaaacaaggcagccaattgcctcttataccgtttccccaccttgcagcctcactggacttgattaaaggttaaattgtaaacattatatcgttagcgataaggattgtcaagccataaaaaatattagaattttaagatctccgacctaccacagctttaccagtccttgtcaaattcactctttgcatccgcaagacagggcactgaa 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: 92 Start: 134 End: 163 .....................................................................................................................................CTTGACAATCCTTATCGCTAACGATATAAT................................................................................................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ gacaacctcactttctacaagaaaaaaccttgccgcagcaaggtttcgcaaaaaacaaggcagccaattgcctcttataccgtttccccaccttgcagcctcactggacttgattaaaggttaaattgtaaacattatatcgttagcgataaggattgtcaagccataaaaaatattagaattttaagatctccgacctaccacagctttaccagtccttgtcaaattcactctttgcatccgcaagacagggcactgaa Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 100 HP_score: -9.0 Tail_Score: -5.55769 Start: 28 End: 43 Full_Region: ttgttttttgcgaaa ccttgc tgcg gcaagg ttttttcttgtagaa ...........................ccttgctgcggcaagg......................................................................................................................................................................................................................... Find igs database================================================ Query_seq: SSA_1243:SSA_1244|SSA_1243:SSA_1244:Dihydroorotate dehydrogenase electron transfer subunit, putative:hypothetical protein:<-<-:1268295..1268554 260 gacaacctcactttctacaagaaaaaaccttgccgcagcaaggtttcgcaaaaaacaaggcagccaattgcctcttataccgtttccccaccttgcagcctcactggacttgattaaaggttaaattgtaaacattatatcgttagcgataaggattgtcaagccataaaaaatattagaattttaagatctccgacctaccacagctttaccagtccttgtcaaattcactctttgcatccgcaagacagggcactgaa Intra-Species Hit: Count: 1 Min: 1 Max: 260 Len: 260 Subject: NC_009009_SSA_1243_SSA_1244|Dihydroorotate dehydrogenase electron transfer subunit, putative:hypothetical protein|NEGATIVE:NEGATIVE|[1268295,1268554]|260 HSP 1 e-value: 1.0E-145 bit: 515.0 Len: 260 Query Start:1 Query End:260 Subject Strand: POSITIVE Subject Start: 1 Subject End: 260 gacaacctcactttctacaagaaaaaaccttgccgcagcaaggtttcgcaaaaaacaaggcagccaattgcctcttataccgtttccccaccttgcagcctcactggacttgattaaaggttaaattgtaaacattatatcgttagcgataaggattgtcaagccataaaaaatattagaattttaagatctccgacctaccacagctttaccagtccttgtcaaattcactctttgcatccgcaagacagggcactgaa gacaacctcactttctacaagaaaaaaccttgccgcagcaaggtttcgcaaaaaacaaggcagccaattgcctcttataccgtttccccaccttgcagcctcactggacttgattaaaggttaaattgtaaacattatatcgttagcgataaggattgtcaagccataaaaaatattagaattttaagatctccgacctaccacagctttaccagtccttgtcaaattcactctttgcatccgcaagacagggcactgaa Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GACAACCUCACUUUCUACAAGAAAAAACCUUGCCGCAGCAAGGUUUCGCAAAAAACAAGGCAGCCAAUUGCCUCUUAUACCGUUUCCCCACCUUGCAGCCUCACUGGACUUGAUUAAAGGUUAAAUUGUAAACAUUAUAUCGUUAGCGAUAAGGAUUGUCAAGCCAUAAAAAAUAUUAGAAUUUUAAGAUCUCCGACCUACCACAGCUUUACCAGUCCUUGUCAAAUUCACUCUUUGCAUCCGCAAGACAGGGCACUGAA ((((((((...((((.....)))).((((((((....))))))))((((........((((((....))))))....(((.((((....(((((.(((((.....)).).))....))))).)))).)))...............))))..))).)))))....................................................(((((((((((...........((((....))))))))))).)))).. (-53.80) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUCAGUGCCCUGUCUUGCGGAUGCAAAGAGUGAAUUUGACAAGGACUGGUAAAGCUGUGGUAGGUCGGAGAUCUUAAAAUUCUAAUAUUUUUUAUGGCUUGACAAUCCUUAUCGCUAACGAUAUAAUGUUUACAAUUUAACCUUUAAUCAAGUCCAGUGAGGCUGCAAGGUGGGGAAACGGUAUAAGAGGCAAUUGGCUGCCUUGUUUUUUGCGAAACCUUGCUGCGGCAAGGUUUUUUCUUGUAGAAAGUGAGGUUGUC ....((.(((..((((((.(((..((((..((((((.((((.(((.((...(((((((((.((((...(((.........)))...)))).)))))))))..)).))).(((((....)))))...))))...))))))..)))).))).((((......))))))))))..)))..))................(((.((((..((((((((((((((((((....)))))))).....))))))))))..)))).))) (-77.40) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 1039 110 61 201 152 NC_009009:SSA_1243|5end_Dihydroorotate_dehydrogenase_electron_transfer_subunit,_putative_1268204..1268434_NEGATIVE 377 105 61 74 19 NC_009009:SSA_0489|5end_Adenosylcobinamide_kinase_/_adenosylcobinamide_phosphate_guanyltransferase,_putative_489655..489885_POSITIVE 366 113 71 179 134 NC_009009:SSA_1231|5end_hypothetical_protein_1254758..1254988_NEGATIVE 361 106 62 218 166 NC_009009:SSA_0978|5end_hypothetical_protein_983736..983966_POSITIVE 354 63 23 227 186 NC_009009:SSA_1241|5end_Orotidine-5'-phosphate_decarboxylase,_putative_1266201..1266431_NEGATIVE 337 100 58 229 172 NC_009009:SSA_0607|5end_ABC_transporter,_permease_component,_putative_596926..597156_NEGATIVE 332 110 61 142 83 NC_009009:SSA_2228|5end_Acetyltransferase_(GNAT)_family,_putative_2228768..2228998_NEGATIVE 332 244 205 178 134 NC_009009:SSA_1451|5end_Exonuclease_RexA,_putative_1456418..1456648_NEGATIVE 324 120 77 209 164 NC_009009:SSA_2070|5end_Zinc_metalloprotease,_putative_2074574..2074804_NEGATIVE 322 66 22 52 17 NC_009009:SSA_1107|5end_Lipid/multidrug/protein-type_ABC_exporter,_ATP_binding/membrane-spanning_protein,_putative_1131968..1132198_POSITIVE 316 99 55 217 168 NC_009009:SSA_1972|5end_Two-component_system_transcriptional_regulator_(CheY_domain_and_HTH-like_DNA-binding_domain),_putative_1968410..1968640_NEGATIVE 314 110 63 187 129 NC_009009:SSA_0939|5end_Inositol_monophosphatase_(Mg++_dependent),_putative_946810..947040_POSITIVE 313 92 58 73 39 NC_009009:SSA_1074|5end_Pyrroline-5-carboxylate_reductase,_putative_1092151..1092381_POSITIVE 313 76 36 84 37 NC_009009:SSA_0554|5end_hypothetical_protein_549265..549495_POSITIVE 311 110 65 228 182 NC_009009:SSA_1540|5end_hypothetical_protein_1545268..1545498_NEGATIVE 311 119 72 60 4 NC_009009:SSA_1452|5end_Second_subunit_of_major_exonuclease,_putative_1459696..1459926_NEGATIVE 310 120 71 149 96 NC_009009:SSA_2131|5end_DNA-binding_protein,_putative_2133949..2134179_POSITIVE 310 255 211 224 182 NC_009009:SSA_1770|5end_hypothetical_protein_1758431..1758661_NEGATIVE 309 45 4 209 165 NC_009009:SSA_1866|5end_hypothetical_protein_1862182..1862412_NEGATIVE 308 110 62 46 5 NC_009009:SSA_1459|5end_RNA_methyltransferase,_putative_1467481..1467711_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 377 105 61 81 26 NC_009009:SSA_0488|3end_Glutamate-1-semialdehyde_2,1-aminotransferase,_putative_489742..489892_POSITIVE 366 113 71 131 86 NC_009009:SSA_1232|3end_Topoisomerase_IV_subunit_B,_putative_1254806..1254956_NEGATIVE 358 110 61 147 92 NC_009009:SSA_1960|3end_hypothetical_protein_1956571..1956721_NEGATIVE 332 110 61 89 30 NC_009009:SSA_2229|3end_hypothetical_protein_2228821..2228971_NEGATIVE 322 107 61 58 5 NC_009009:SSA_1602|3end_Exoribonuclease,_VacB/Rnb_family,_putative_1607022..1607172_NEGATIVE 321 122 90 36 3 NC_009009:SSA_1242|3end_Dihydroorotate_dehydrogenase_B,_putative_1266448..1266598_NEGATIVE 313 92 58 70 36 NC_009009:SSA_1073|3end_Gamma-glutamyl_phosphate_reductase,_putative_1092228..1092378_POSITIVE 313 76 36 80 33 NC_009009:SSA_0553|3end_hypothetical_protein_549341..549491_POSITIVE 310 120 71 140 87 NC_009009:SSA_2130|3end_hypothetical_protein_2134020..2134170_POSITIVE 307 70 24 68 11 NC_009009:SSA_1867|3end_ABC-type_polar_amino_acid_transport_system,_ATPase_component,_putative_1862353..1862503_NEGATIVE 306 259 213 66 27 NC_009009:SSA_0688|3end_2,3-bisphosphoglycerate-dependent_phosphoglycerate_mutase,_putative_672132..672282_POSITIVE 301 50 3 86 31 NC_009009:SSA_0812|3end_hypothetical_protein_794434..794584_POSITIVE 299 238 191 125 62 NC_009009:SSA_1153|3end_HemK_protein,_putative_1182748..1182898_POSITIVE 299 113 73 94 64 NC_009009:SSA_0532|3end_Propanediol_utilization_protein_PduB,_putative_529028..529178_POSITIVE 298 106 67 83 47 NC_009009:SSA_1343|3end_Aspartate_carbamoyltransferase,_putative_1361042..1361192_NEGATIVE 297 96 58 90 47 NC_009009:SSA_0297|3end_Malolactic_enzyme,_putative_291411..291561_POSITIVE 293 76 31 146 101 NC_009009:SSA_0489|3end_Adenosylcobinamide_kinase_/_adenosylcobinamide_phosphate_guanyltransferase,_putative_490319..490469_POSITIVE 290 240 192 60 5 NC_009009:SSA_1806|3end_Replication_initiation/membrane_attachment_protein_DnaB,_putative_1789565..1789715_NEGATIVE 290 72 31 65 30 NC_009009:SSA_0110|3end_50S_ribosomal_protein_L2,_putative_110666..110816_POSITIVE 289 238 191 135 82 NC_009009:SSA_1058|3end_Thiamine_biosynthesis_protein,_putative_1076211..1076361_POSITIVE