Origin IGS: gatgtagactctttctctcttattttctacttacaaacgaaaaaccaccctcacaaaaaggcgagggtggttcatccgttacaatgcttggggatttcctagcaagttccccctcaaaaggactttatgctattctatcacaaagaccgaccatctgcaagatggactggattagacaggatagcgtgagggagtttcc .........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 ggaaactccctcacgctatcctgtctaatccagtccatcttgcagatggtcggtctttgtgatagaatagcataaagtccttttgagggggaacttgctaggaaatccccaagcattgtaacggatgaaccaccctcgcctttttgtgagggtggtttttcgtttgtaagtagaaaataagagagaaagagtctacatc Mask Tandem Repeat Region ================================================ gatgtagactctttctctcttattttctacttacaaacgaaaaaccaccctcacaaaaaggcgagggtggttcatccgttacaatgcttggggatttcctagcaagttccccctcaaaaggactttatgctattctatcacaaagaccgaccatctgcaagatggactggattagacaggatagcgtgagggagtttcc Find is-nt database================================================ Query_seq: SMT_1176:SMT_1177|SMT_1176:SMT_1177:hypothetical protein predicted by Glimmer/Critica:immunoglobulin A1 protease:<-<-:1129084..1129282 199 gatgtagactctttctctcttattttctacttacaaacgaaaaaccaccctcacaaaaaggcgagggtggttcatccgttacaatgcttggggatttcctagcaagttccccctcaaaaggactttatgctattctatcacaaagaccgaccatctgcaagatggactggattagacaggatagcgtgagggagtttcc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_1176:SMT_1177|SMT_1176:SMT_1177:hypothetical protein predicted by Glimmer/Critica:immunoglobulin A1 protease:<-<-:1129084..1129282 199 gatgtagactctttctctcttattttctacttacaaacgaaaaaccaccctcacaaaaaggcgagggtggttcatccgttacaatgcttggggatttcctagcaagttccccctcaaaaggactttatgctattctatcacaaagaccgaccatctgcaagatggactggattagacaggatagcgtgagggagtttcc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_1176:SMT_1177|SMT_1176:SMT_1177:hypothetical protein predicted by Glimmer/Critica:immunoglobulin A1 protease:<-<-:1129084..1129282 199 gatgtagactctttctctcttattttctacttacaaacgaaaaaccaccctcacaaaaaggcgagggtggttcatccgttacaatgcttggggatttcctagcaagttccccctcaaaaggactttatgctattctatcacaaagaccgaccatctgcaagatggactggattagacaggatagcgtgagggagtttcc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gatgtagactctttctctcttattttctacttacaaacgaaaaaccaccctcacaaaaaggcgagggtggttcatccgttacaatgcttggggatttcctagcaagttccccctcaaaaggactttatgctattctatcacaaagaccgaccatctgcaagatggactggattagacaggatagcgtgagggagtttcc Predict ORF larger than 30AA ================================================ Protein_Len: 33 Strand: + Start: 74 End: 172 ......................................................................... M R Y N A W G F P S K F P L K R T L C Y S I T K T D H L Q D G L D ........................... Protein_Len: 38 Strand: + Start: 84 End: 197 ................................................................................... M L G D F L A S S P S K G L Y A I L S Q R P T I C K M D W I R Q D S V R E F .. gatgtagactctttctctcttattttctacttacaaacgaaaaaccaccctcacaaaaaggcgagggtggttcatccgttacaatgcttggggatttcctagcaagttccccctcaaaaggactttatgctattctatcacaaagaccgaccatctgcaagatggactggattagacaggatagcgtgagggagtttcc 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: 81 Start: 132 End: 161 ...................................................................................................................................CTTGCAGATGGTCGGTCTTTGTGATAGAAT...................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ gatgtagactctttctctcttattttctacttacaaacgaaaaaccaccctcacaaaaaggcgagggtggttcatccgttacaatgcttggggatttcctagcaagttccccctcaaaaggactttatgctattctatcacaaagaccgaccatctgcaagatggactggattagacaggatagcgtgagggagtttcc Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 95 HP_score: -12.8 Tail_Score: -2.94924 Start: 39 End: 76 Full_Region: ccaagcattgtaacg gatgaaccaccctcgc cttttt gtgagggtggtttttc gtttgtaagtagaaa ......................................gatgaaccaccctcgcctttttgtgagggtggtttttc........................................................................................................................... TransTerm Strand: + Conf: 77 HP_score: -10.4 Tail_Score: -3.22091 Start: 45 End: 70 Full_Region: CTTACAAACGAAAAA CCACCCTCAC AAAAAG GCGAGGGTGG TTCATCCGTTACAAT ............................................CCACCCTCACAAAAAGGCGAGGGTGG................................................................................................................................. TransTerm Strand: - Conf: 100 HP_score: -12.6 Tail_Score: -5.04601 Start: 45 End: 70 Full_Region: attgtaacggatgaa ccaccctcgc cttttt gtgagggtgg tttttcgtttgtaag ............................................ccaccctcgcctttttgtgagggtgg................................................................................................................................. Find igs database================================================ Query_seq: SMT_1176:SMT_1177|SMT_1176:SMT_1177:hypothetical protein predicted by Glimmer/Critica:immunoglobulin A1 protease:<-<-:1129084..1129282 199 gatgtagactctttctctcttattttctacttacaaacgaaaaaccaccctcacaaaaaggcgagggtggttcatccgttacaatgcttggggatttcctagcaagttccccctcaaaaggactttatgctattctatcacaaagaccgaccatctgcaagatggactggattagacaggatagcgtgagggagtttcc Intra-Species Hit: Count: 1 Min: 1 Max: 199 Len: 199 Subject: smit_SMT_1176_SMT_1177|hypothetical protein predicted by Glimmer/Critica:immunoglobulin A1 protease|NEGATIVE:NEGATIVE|[1129084,1129282]|199 HSP 1 e-value: 1.0E-109 bit: 394.0 Len: 199 Query Start:1 Query End:199 Subject Strand: POSITIVE Subject Start: 1 Subject End: 199 gatgtagactctttctctcttattttctacttacaaacgaaaaaccaccctcacaaaaaggcgagggtggttcatccgttacaatgcttggggatttcctagcaagttccccctcaaaaggactttatgctattctatcacaaagaccgaccatctgcaagatggactggattagacaggatagcgtgagggagtttcc gatgtagactctttctctcttattttctacttacaaacgaaaaaccaccctcacaaaaaggcgagggtggttcatccgttacaatgcttggggatttcctagcaagttccccctcaaaaggactttatgctattctatcacaaagaccgaccatctgcaagatggactggattagacaggatagcgtgagggagtttcc Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAUGUAGACUCUUUCUCUCUUAUUUUCUACUUACAAACGAAAAACCACCCUCACAAAAAGGCGAGGGUGGUUCAUCCGUUACAAUGCUUGGGGAUUUCCUAGCAAGUUCCCCCUCAAAAGGACUUUAUGCUAUUCUAUCACAAAGACCGACCAUCUGCAAGAUGGACUGGAUUAGACAGGAUAGCGUGAGGGAGUUUCC .....((((((((((..((((..............((((...((((((((((.(......).))))))))))....)))).........((((((((......)))))))).......))))....((((((((((.((.......(((.(((((.....)))))..)))....)).)))))))))))))))))))).. (-58.90) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GGAAACUCCCUCACGCUAUCCUGUCUAAUCCAGUCCAUCUUGCAGAUGGUCGGUCUUUGUGAUAGAAUAGCAUAAAGUCCUUUUGAGGGGGAACUUGCUAGGAAAUCCCCAAGCAUUGUAACGGAUGAACCACCCUCGCCUUUUUGUGAGGGUGGUUUUUCGUUUGUAAGUAGAAAAUAAGAGAGAAAGAGUCUACAUC .....((((((((.(((((.((((((((.((.(.(((((.....))))).)))...))).))))).)))))..(((....)))))))))))....((((.((......)).))))....((((((.(((((((((((((......))))))))))))))))))).....(((((.................)))))... (-68.73) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 1001 110 61 201 152 smit:SMT_1176|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1128993..1129223_NEGATIVE 342 78 38 153 105 smit:SMT_216|5end_Holliday_junction_DNA_helicase_RuvB_148257..148487_POSITIVE 342 78 38 153 105 smit:SMT_212|5end_Holliday_junction_DNA_helicase_RuvB_144830..145060_POSITIVE 326 130 86 50 7 smit:SMT_2126|5end_indole-3-glycerol_phosphate_synthase_2009107..2009337_POSITIVE 326 130 86 50 7 smit:SMT_1751|5end_indole-3-glycerol_phosphate_synthase_1729012..1729242_POSITIVE 314 176 131 212 163 smit:SMT_485|5end_hypothetical_protein_421401..421631_NEGATIVE 306 169 127 87 41 smit:SMT_1783|5end_peptide_methionine_sulfoxide_reductase_1759756..1759986_POSITIVE 306 190 148 63 17 smit:SMT_301|5end_hypothetical_protein_244086..244316_POSITIVE 300 126 82 78 26 smit:SMT_676|5end_DNA_helicase_II_585266..585496_NEGATIVE 292 182 141 169 117 smit:SMT_395|5end_hypothetical_protein_324459..324689_POSITIVE 292 82 45 131 88 smit:SMT_358|5end_hypothetical_protein_293947..294177_POSITIVE 290 99 54 56 4 smit:SMT_344|5end_K02503_Hit-like_protein_involved_in_cell-cycle_regulation_283974..284204_NEGATIVE 289 149 102 135 92 smit:SMT_919|5end_hypothetical_protein_872499..872729_NEGATIVE 287 190 149 152 101 smit:SMT_928|5end_hypothetical_protein_883218..883448_NEGATIVE 287 190 144 61 14 smit:SMT_155|5end_hypothetical_protein_102704..102934_NEGATIVE 284 92 55 63 29 smit:SMT_2167|5end_hypothetical_protein_2039927..2040157_POSITIVE 284 92 55 63 29 smit:SMT_2157|5end_hypothetical_protein_2030615..2030845_POSITIVE 284 92 55 63 29 smit:SMT_1706|5end_hypothetical_protein_1690026..1690256_POSITIVE 284 92 55 63 29 smit:SMT_1546|5end_hypothetical_protein_1530068..1530298_POSITIVE 283 76 33 163 114 smit:SMT_1554|5end_isoleucyl-tRNA_synthetase_1537040..1537270_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 346 120 73 151 94 smit:SMT_269|3end_phospho-N-acetylmuramoyl-pentapeptide-transferas_e_208785..208935_POSITIVE 326 130 86 53 10 smit:SMT_1750|3end_anthranilate_phosphoribosyltransferase_1729095..1729245_POSITIVE 289 149 102 46 3 smit:SMT_920|3end_serine/threonine_protein_kinase_872588..872738_NEGATIVE 277 188 142 109 57 smit:SMT_1900|3end_K03710_GntR_family_transcriptional_regulator_1850620..1850770_POSITIVE 277 177 131 149 104 smit:SMT_486|3end_hypothetical_protein_421460..421610_NEGATIVE 274 122 84 67 27 smit:SMT_958|3end_hypothetical_protein_predicted_by_Glimmer/Critica_905239..905389_POSITIVE 270 57 13 136 78 smit:SMT_1200|3end_K06148_ATP-binding_cassette,_subfamily_C,_bacterial_1161076..1161226_NEGATIVE 269 122 84 78 38 smit:SMT_2024|3end_hypothetical_protein_1940690..1940840_POSITIVE 269 122 84 67 27 smit:SMT_2002|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1924145..1924295_NEGATIVE 269 122 84 78 38 smit:SMT_1981|3end_K03696_ATP-dependent_Clp_protease_ATP-binding_subunit_ClpC_1912868..1913018_POSITIVE 269 122 84 83 43 smit:SMT_1971|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1903526..1903676_POSITIVE 269 122 84 67 27 smit:SMT_1966|3end_DNA_polymerase_III_alpha_subunit_1898328..1898478_POSITIVE 269 122 84 78 38 smit:SMT_1942|3end_zinc_metalloprotease_ZmpB,_truncated_1878384..1878534_POSITIVE 269 122 84 67 27 smit:SMT_1927|3end_cell_division_protein_FtsH_1868408..1868558_NEGATIVE 269 122 84 78 38 smit:SMT_1926|3end_mevalonate_kinase_1868062..1868212_POSITIVE 269 122 84 78 38 smit:SMT_1887|3end_LicC_protein_1841740..1841890_POSITIVE 269 122 84 67 27 smit:SMT_1885|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1839830..1839980_NEGATIVE 269 122 84 67 27 smit:SMT_1873|3end_K02006_cobalt_transport_system_ATP-binding_protein_1832351..1832501_POSITIVE 269 122 84 83 43 smit:SMT_1852|3end_1,4-alpha-glucan_branching_enzyme_1816467..1816617_NEGATIVE 269 122 84 83 43 smit:SMT_326|3end_K02029_polar_amino_acid_transport_system_permease_protein_263217..263367_NEGATIVE