Origin IGS: atcctacctccaaaatttattttgtatatcatatcacaaagtttagaaaatatctattttttcttaaaaagaagggatttttttaggaaaacacgaacaaaatgaagaaataataaaagaagctatgaaagcttctaatcattttagatctagttttaaataaagcaactatatcaatacaaaactaccgctgataaatgt .........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 acatttatcagcggtagttttgtattgatatagttgctttatttaaaactagatctaaaatgattagaagctttcatagcttcttttattatttcttcattttgttcgtgttttcctaaaaaaatcccttctttttaagaaaaaatagatattttctaaactttgtgatatgatatacaaaataaattttggaggtaggat Mask Tandem Repeat Region ================================================ atcctacctccaaaatttattttgtatatcatatcacaaagtttagaaaatatctattttttcttaaaaagaagggatttttttaggaaaacacgaacaaaatgaagaaataataaaagaagctatgaaagcttctaatcattttagatctagttttaaataaagcaactatatcaatacaaaactaccgctgataaatgt Find is-nt database================================================ Query_seq: SSA_1715:SSA_1716|SSA_1715:SSA_1716:Phosphoserine aminotransferase, putative:Restriction endonuclease SsuRB, putative:<-<-:1702579..1702779 201 atcctacctccaaaatttattttgtatatcatatcacaaagtttagaaaatatctattttttcttaaaaagaagggatttttttaggaaaacacgaacaaaatgaagaaataataaaagaagctatgaaagcttctaatcattttagatctagttttaaataaagcaactatatcaatacaaaactaccgctgataaatgt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1715:SSA_1716|SSA_1715:SSA_1716:Phosphoserine aminotransferase, putative:Restriction endonuclease SsuRB, putative:<-<-:1702579..1702779 201 atcctacctccaaaatttattttgtatatcatatcacaaagtttagaaaatatctattttttcttaaaaagaagggatttttttaggaaaacacgaacaaaatgaagaaataataaaagaagctatgaaagcttctaatcattttagatctagttttaaataaagcaactatatcaatacaaaactaccgctgataaatgt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1715:SSA_1716|SSA_1715:SSA_1716:Phosphoserine aminotransferase, putative:Restriction endonuclease SsuRB, putative:<-<-:1702579..1702779 201 atcctacctccaaaatttattttgtatatcatatcacaaagtttagaaaatatctattttttcttaaaaagaagggatttttttaggaaaacacgaacaaaatgaagaaataataaaagaagctatgaaagcttctaatcattttagatctagttttaaataaagcaactatatcaatacaaaactaccgctgataaatgt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 atcctacctccaaaatttattttgtatatcatatcacaaagtttagaaaatatctattttttcttaaaaagaagggatttttttaggaaaacacgaacaaaatgaagaaataataaaagaagctatgaaagcttctaatcattttagatctagttttaaataaagcaactatatcaatacaaaactaccgctgataaatgt Predict ORF larger than 30AA ================================================ Protein_Len: 34 Strand: + Start: 1 End: 102 M L P P K F I L Y I I S Q S L E N I Y F F L K R R D F F R K T R T K ................................................................................................... Protein_Len: 31 Strand: - Start: 86 End: 178 ..................................................................................... S F V F L I F F Y Y F F S H F S R I M K S R T K F L A V I D M ....................... atcctacctccaaaatttattttgtatatcatatcacaaagtttagaaaatatctattttttcttaaaaagaagggatttttttaggaaaacacgaacaaaatgaagaaataataaaagaagctatgaaagcttctaatcattttagatctagttttaaataaagcaactatatcaatacaaaactaccgctgataaatgt 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: 28 End: 57 ...........................ATAGATATTTTCTAAACTTTGTGATATGAT................................................................................................................................................ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ atcctacctccaaaatttattttgtatatcatatcacaaagtttagaaaatatctattttttcttaaaaagaagggatttttttaggaaaacacgaacaaaatgaagaaataataaaagaagctatgaaagcttctaatcattttagatctagttttaaataaagcaactatatcaatacaaaactaccgctgataaatgt Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 80 HP_score: -6.6 Tail_Score: -5.08731 Start: 119 End: 135 Full_Region: gatctaaaatgatta gaagct ttcat agcttc ttttattatttcttc ......................................................................................................................gaagctttcatagcttc.................................................................. TransTerm Strand: + Conf: 41 HP_score: -2.9 Tail_Score: -3.11281 Start: 134 End: 148 Full_Region: GAAGCTATGAAAGCT TCTAA TCATT TTAGA TCTAGTTTTAAATAA .....................................................................................................................................TCTAATCATTTTAGA..................................................... Find igs database================================================ Query_seq: SSA_1715:SSA_1716|SSA_1715:SSA_1716:Phosphoserine aminotransferase, putative:Restriction endonuclease SsuRB, putative:<-<-:1702579..1702779 201 atcctacctccaaaatttattttgtatatcatatcacaaagtttagaaaatatctattttttcttaaaaagaagggatttttttaggaaaacacgaacaaaatgaagaaataataaaagaagctatgaaagcttctaatcattttagatctagttttaaataaagcaactatatcaatacaaaactaccgctgataaatgt Intra-Species Hit: Count: 1 Min: 1 Max: 201 Len: 201 Subject: NC_009009_SSA_1715_SSA_1716|Phosphoserine aminotransferase, putative:Restriction endonuclease SsuRB, putative|NEGATIVE:NEGATIVE|[1702579,1702779]|201 HSP 1 e-value: 9.0E-98 bit: 357.0 Len: 201 Query Start:1 Query End:201 Subject Strand: POSITIVE Subject Start: 1 Subject End: 201 atcctacctccaaaatttattttgtatatcatatcacaaagtttagaaaatatctattttttcttaaaaagaagggannnnnnnaggaaaacacgaacaaaatgaagaaataataaaagaagctatgaaagcttctaatcattttagatctagttttaaataaagcaactatatcaatacaaaactaccgctgataaatgt atcctacctccaaaatttattttgtatatcatatcacaaagtttagaaaatatctattttttcttaaaaagaagggatttttttaggaaaacacgaacaaaatgaagaaataataaaagaagctatgaaagcttctaatcattttagatctagttttaaataaagcaactatatcaatacaaaactaccgctgataaatgt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUCCUACCUCCAAAAUUUAUUUUGUAUAUCAUAUCACAAAGUUUAGAAAAUAUCUAUUUUUUCUUAAAAAGAAGGGAUUUUUUUAGGAAAACACGAACAAAAUGAAGAAAUAAUAAAAGAAGCUAUGAAAGCUUCUAAUCAUUUUAGAUCUAGUUUUAAAUAAAGCAACUAUAUCAAUACAAAACUACCGCUGAUAAAUGU ...............((((((((((..................((((.....))))..((((((((((((((.....)))))))))))))).....))))))))))...........(((((((.....)))))))...((((((((...(((((((.......................)))))))...))))..)))). (-31.50) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACAUUUAUCAGCGGUAGUUUUGUAUUGAUAUAGUUGCUUUAUUUAAAACUAGAUCUAAAAUGAUUAGAAGCUUUCAUAGCUUCUUUUAUUAUUUCUUCAUUUUGUUCGUGUUUUCCUAAAAAAAUCCCUUCUUUUUAAGAAAAAAUAGAUAUUUUCUAAACUUUGUGAUAUGAUAUACAAAAUAAAUUUUGGAGGUAGGAU .....(((((((((.....))))..)))))..................(((..((((((((....(((((((.....)))))))..............(((((((((((((((((.((((((.........)))))).)))....((((.....))))........)))))))...)))))))..))))))))..)))... (-32.70) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 734 140 91 231 182 NC_009009:SSA_1715|5end_Phosphoserine_aminotransferase,_putative_1702488..1702718_NEGATIVE 239 41 4 131 95 NC_009009:SSA_0365|5end_Small-conductance_mechanosensitive_efflux_channel,_putative_356621..356851_POSITIVE 226 46 2 192 145 NC_009009:SSA_2174|5end_2,3,4,5-tetrahydropyridine-2-carboxylate_N-succinyltransferase,_putative_2172689..2172919_NEGATIVE 226 79 32 151 94 NC_009009:SSA_1770|5end_hypothetical_protein_1758431..1758661_NEGATIVE 224 151 118 65 33 NC_009009:SSA_1466|5end_Prephenate_dehydrogenase,_putative_1473111..1473341_NEGATIVE 222 138 97 153 114 NC_009009:SSA_0907|5end_Fibronectin-binding_protein_A,_putative_919217..919447_NEGATIVE 217 75 32 192 143 NC_009009:SSA_1852|5end_Metal_dependent_phosphohydrolase_(HD_motif),_putative_1848482..1848712_NEGATIVE 217 50 2 145 97 NC_009009:SSA_0820|5end_Ribosomal_protein_S21,_putative_801249..801479_POSITIVE 217 167 123 229 185 NC_009009:SSA_0049|5end_Dihydroxyacetone_kinase_(Dak1),_putative_53612..53842_POSITIVE 215 46 2 151 99 NC_009009:SSA_1723|5end_hypothetical_protein_1708926..1709156_POSITIVE 209 87 45 158 109 NC_009009:SSA_1163|5end_GMP_synthase_[glutamine-hydrolyzing],_putative_1190898..1191128_NEGATIVE 204 170 121 126 62 NC_009009:SSA_1003|5end_ABC_transporter_substrate-binding_protein-multiple_sugars,_putative_1003875..1004105_POSITIVE 204 42 6 125 95 NC_009009:SSA_0687|5end_hypothetical_protein_670467..670697_POSITIVE 203 153 118 87 57 NC_009009:SSA_1667|5end_hypothetical_protein_1667704..1667934_NEGATIVE 203 154 112 219 171 NC_009009:SSA_0855|5end_O-acetylhomoserine_sulfhydrylase,_putative_841832..842062_POSITIVE 198 153 117 172 136 NC_009009:SSA_2032|5end_Integrase/recombinase,_phage_integrase_family,_putative_2038006..2038236_POSITIVE 195 42 7 146 97 NC_009009:SSA_0747|5end_DD-carboxypeptidase,_putative_727936..728166_POSITIVE 193 49 1 147 90 NC_009009:SSA_2270|5end_Aspartyl-tRNA_synthetase,_putative_2272068..2272298_NEGATIVE 193 193 160 190 151 NC_009009:SSA_1993|5end_Conserved_uncharacterized_protein_1990790..1991020_NEGATIVE 192 156 132 123 100 NC_009009:SSA_2218|5end_Glycosyltransferase_(cell_wall_biogenesis)_Cps9G,_putative_2219941..2220171_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 226 79 32 91 34 NC_009009:SSA_1771|3end_Conserved_DNA_methyltransferase_protein,_putative_1758491..1758641_NEGATIVE 224 151 118 49 17 NC_009009:SSA_1467|3end_Chorismate_synthase,_putative_1473127..1473277_NEGATIVE 206 170 123 151 105 NC_009009:SSA_0106|3end_30S_ribosomal_protein_S10,_putative_108160..108310_POSITIVE 204 170 121 113 49 NC_009009:SSA_1002|3end_Alpha-galactosidase,_putative_1003942..1004092_POSITIVE 203 153 118 53 23 NC_009009:SSA_1668|3end_NrdI_protein,_putative_1667738..1667888_NEGATIVE 203 154 112 120 72 NC_009009:SSA_0854|3end_hypothetical_protein_841813..841963_POSITIVE 194 87 52 49 7 NC_009009:SSA_1164|3end_hypothetical_protein_1191007..1191157_NEGATIVE 193 62 23 61 22 NC_009009:SSA_2023|3end_Fructan_beta-fructosidase_precursor,_putative_2024609..2024759_NEGATIVE 193 193 160 119 80 NC_009009:SSA_1994|3end_CTP_synthase,_putative_1990861..1991011_NEGATIVE 192 156 132 97 74 NC_009009:SSA_2219|3end_UDP-glucose_4-epimerase,_putative_2219967..2220117_NEGATIVE 191 78 35 57 7 NC_009009:SSA_1485|3end_Citrulline_cluster-linked_gene,_putative_1492294..1492444_NEGATIVE 190 89 51 135 88 NC_009009:SSA_1932|3end_Biotin_carboxylase,_putative_1919507..1919657_NEGATIVE 190 39 1 131 93 NC_009009:SSA_0994|3end_Peptidase_E,_putative_995390..995540_POSITIVE 189 87 57 68 38 NC_009009:SSA_1434|3end_Conserved_uncharacterized_Firmicutes_protein_1441100..1441250_POSITIVE 187 198 165 113 83 NC_009009:SSA_1369|3end_FmtA-like_protein,_putative_1384142..1384292_NEGATIVE 187 198 165 113 83 NC_009009:SSA_1364|3end_hypothetical_protein_1380482..1380632_NEGATIVE 187 145 118 85 59 NC_009009:SSA_0686|3end_Fe2+/Zn2+_uptake_regulation_protein,_putative_670079..670229_POSITIVE 184 24 2 52 28 NC_009009:SSA_1133|3end_TatA,_sec-independent_protein_secretion_pathway_component,_putative_1159665..1159815_POSITIVE 184 156 112 105 55 NC_009009:SSA_1032|3end_30S_ribosomal_protein_subunit_S20,_putative_1048313..1048463_NEGATIVE 181 86 43 69 12 NC_009009:SSA_0886|3end_Enolase,_putative_881057..881207_POSITIVE