Origin IGS: aattttgtctgagctgaagcagctcgtcctttcttgaaaagcaggcaggaatctcacctgcgattatgttttatacctcattatatgaaaaatttaacaatttttcaagatgggatccattcttgatttgctttttcccttttgaaaacgaattaaattttcaaaaaatctgtattttctgaaatttgttagtttattaaaaataaaagttcggaatttttgtaaaatcgtagcggaaatttgttttctttttccgtttgtaatagactaaaattactaccataggacggtgaa .........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 ttcaccgtcctatggtagtaattttagtctattacaaacggaaaaagaaaacaaatttccgctacgattttacaaaaattccgaacttttatttttaataaactaacaaatttcagaaaatacagattttttgaaaatttaattcgttttcaaaagggaaaaagcaaatcaagaatggatcccatcttgaaaaattgttaaatttttcatataatgaggtataaaacataatcgcaggtgagattcctgcctgcttttcaagaaaggacgagctgcttcagctcagacaaaatt Mask Tandem Repeat Region ================================================ aattttgtctgagctgaagcagctcgtcctttcttgaaaagcaggcaggaatctcacctgcgattatgttttatacctcattatatgaaaaatttaacaatttttcaagatgggatccattcttgatttgctttttcccttttgaaaacgaattaaattttcaaaaaatctgtattttctgaaatttgttagtttattaaaaataaaagttcggaatttttgtaaaatcgtagcggaaatttgttttctttttccgtttgtaatagactaaaattactaccataggacggtgaa Find is-nt database================================================ Query_seq: SSA_2185:SSA_2186|SSA_2185:SSA_2186:Adenylosuccinate synthetase, putative:Glutathione biosynthesis bifunctional protein gshAB (Gamma-GCS-GS) (GCS-GS), putative:<-->:2185381..2185674 294 aattttgtctgagctgaagcagctcgtcctttcttgaaaagcaggcaggaatctcacctgcgattatgttttatacctcattatatgaaaaatttaacaatttttcaagatgggatccattcttgatttgctttttcccttttgaaaacgaattaaattttcaaaaaatctgtattttctgaaatttgttagtttattaaaaataaaagttcggaatttttgtaaaatcgtagcggaaatttgttttctttttccgtttgtaatagactaaaattactaccataggacggtgaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_2185:SSA_2186|SSA_2185:SSA_2186:Adenylosuccinate synthetase, putative:Glutathione biosynthesis bifunctional protein gshAB (Gamma-GCS-GS) (GCS-GS), putative:<-->:2185381..2185674 294 aattttgtctgagctgaagcagctcgtcctttcttgaaaagcaggcaggaatctcacctgcgattatgttttatacctcattatatgaaaaatttaacaatttttcaagatgggatccattcttgatttgctttttcccttttgaaaacgaattaaattttcaaaaaatctgtattttctgaaatttgttagtttattaaaaataaaagttcggaatttttgtaaaatcgtagcggaaatttgttttctttttccgtttgtaatagactaaaattactaccataggacggtgaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_2185:SSA_2186|SSA_2185:SSA_2186:Adenylosuccinate synthetase, putative:Glutathione biosynthesis bifunctional protein gshAB (Gamma-GCS-GS) (GCS-GS), putative:<-->:2185381..2185674 294 aattttgtctgagctgaagcagctcgtcctttcttgaaaagcaggcaggaatctcacctgcgattatgttttatacctcattatatgaaaaatttaacaatttttcaagatgggatccattcttgatttgctttttcccttttgaaaacgaattaaattttcaaaaaatctgtattttctgaaatttgttagtttattaaaaataaaagttcggaatttttgtaaaatcgtagcggaaatttgttttctttttccgtttgtaatagactaaaattactaccataggacggtgaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aattttgtctgagctgaagcagctcgtcctttcttgaaaagcaggcaggaatctcacctgcgattatgttttatacctcattatatgaaaaatttaacaatttttcaagatgggatccattcttgatttgctttttcccttttgaaaacgaattaaattttcaaaaaatctgtattttctgaaatttgttagtttattaaaaataaaagttcggaatttttgtaaaatcgtagcggaaatttgttttctttttccgtttgtaatagactaaaattactaccataggacggtgaa Predict ORF larger than 30AA ================================================ Protein_Len: 30 Strand: + Start: 34 End: 123 ................................. M K S R Q E S H L R L C F I P H Y M K N L T I F Q D G I H S ........................................................................................................................................................................... Protein_Len: 43 Strand: + Start: 51 End: 179 .................................................. M S P A I M F Y T S L Y E K F N N F S R W D P F L I C F F P F E N E L N F Q K I C I F ................................................................................................................... Protein_Len: 39 Strand: + Start: 152 End: 268 ....................................................................................................................................................... M K F S K N L Y F L K F V S L L K I K V R N F C K I V A E I C F L F P F V I D .......................... Protein_Len: 56 Strand: - Start: 97 End: 264 ................................................................................................ C N K L I P D M R S K S K G K Q F R I L N E F F R Y K R F N T L K N F I F T R F K Q L I T A S I Q K R K G N T M .............................. aattttgtctgagctgaagcagctcgtcctttcttgaaaagcaggcaggaatctcacctgcgattatgttttatacctcattatatgaaaaatttaacaatttttcaagatgggatccattcttgatttgctttttcccttttgaaaacgaattaaattttcaaaaaatctgtattttctgaaatttgttagtttattaaaaataaaagttcggaatttttgtaaaatcgtagcggaaatttgttttctttttccgtttgtaatagactaaaattactaccataggacggtgaa 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: 80 End: 109 ...............................................................................CTTGAAAAATTGTTAAATTTTTCATATAAT......................................................................................................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aattttgtctgagctgaagcagctcgtcctttcttgaaaagcaggcaggaatctcacctgcgattatgttttatacctcattatatgaaaaatttaacaatttttcaagatgggatccattcttgatttgctttttcccttttgaaaacgaattaaattttcaaaaaatctgtattttctgaaatttgttagtttattaaaaataaaagttcggaatttttgtaaaatcgtagcggaaatttgttttctttttccgtttgtaatagactaaaattactaccataggacggtgaa Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 74 HP_score: -6.7 Tail_Score: -4.34557 Start: 105 End: 126 Full_Region: AAATTTAACAATTTT TCAAGATGG GAT CCATTCTTGA TTTGCTTTTTCCCTT ........................................................................................................TCAAGATGGGATCCATTCTTGA........................................................................................................................................................................ Find igs database================================================ Query_seq: SSA_2185:SSA_2186|SSA_2185:SSA_2186:Adenylosuccinate synthetase, putative:Glutathione biosynthesis bifunctional protein gshAB (Gamma-GCS-GS) (GCS-GS), putative:<-->:2185381..2185674 294 aattttgtctgagctgaagcagctcgtcctttcttgaaaagcaggcaggaatctcacctgcgattatgttttatacctcattatatgaaaaatttaacaatttttcaagatgggatccattcttgatttgctttttcccttttgaaaacgaattaaattttcaaaaaatctgtattttctgaaatttgttagtttattaaaaataaaagttcggaatttttgtaaaatcgtagcggaaatttgttttctttttccgtttgtaatagactaaaattactaccataggacggtgaa Intra-Species Hit: Count: 1 Min: 1 Max: 294 Len: 294 Subject: NC_009009_SSA_2185_SSA_2186|Adenylosuccinate synthetase, putative:Glutathione biosynthesis bifunctional protein gshAB (Gamma-GCS-GS) (GCS-GS), putative|NEGATIVE:POSITIVE|[2185381,2185674]|294 HSP 1 e-value: 4.0E-76 bit: 285.0 Len: 144 Query Start:1 Query End:144 Subject Strand: POSITIVE Subject Start: 1 Subject End: 144 aattttgtctgagctgaagcagctcgtcctttcttgaaaagcaggcaggaatctcacctgcgattatgttttatacctcattatatgaaaaatttaacaatttttcaagatgggatccattcttgatttgctttttcccttttg...................................................................................................................................................... aattttgtctgagctgaagcagctcgtcctttcttgaaaagcaggcaggaatctcacctgcgattatgttttatacctcattatatgaaaaatttaacaatttttcaagatgggatccattcttgatttgctttttcccttttg...................................................................................................................................................... HSP 2 e-value: 2.0E-41 bit: 170.0 Len: 86 Query Start:209 Query End:294 Subject Strand: POSITIVE Subject Start: 209 Subject End: 294 ................................................................................................................................................................................................................gttcggaatttttgtaaaatcgtagcggaaatttgttttctttttccgtttgtaatagactaaaattactaccataggacggtgaa ................................................................................................................................................................................................................gttcggaatttttgtaaaatcgtagcggaaatttgttttctttttccgtttgtaatagactaaaattactaccataggacggtgaa Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUUUUGUCUGAGCUGAAGCAGCUCGUCCUUUCUUGAAAAGCAGGCAGGAAUCUCACCUGCGAUUAUGUUUUAUACCUCAUUAUAUGAAAAAUUUAACAAUUUUUCAAGAUGGGAUCCAUUCUUGAUUUGCUUUUUCCCUUUUGAAAACGAAUUAAAUUUUCAAAAAAUCUGUAUUUUCUGAAAUUUGUUAGUUUAUUAAAAAUAAAAGUUCGGAAUUUUUGUAAAAUCGUAGCGGAAAUUUGUUUUCUUUUUCCGUUUGUAAUAGACUAAAAUUACUACCAUAGGACGGUGAA ..........((((((...))))))((((((((..((((((((((((((.......)))))........................((((((.(((((....(((((((((.((((....................)))))))))))))....)))))))))))......)))).))))).))).....(((((((((((...((((((((.....))))))))........((((((((...........))))))))..)))))))))))............)))))...... (-63.05) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUCACCGUCCUAUGGUAGUAAUUUUAGUCUAUUACAAACGGAAAAAGAAAACAAAUUUCCGCUACGAUUUUACAAAAAUUCCGAACUUUUAUUUUUAAUAAACUAACAAAUUUCAGAAAAUACAGAUUUUUUGAAAAUUUAAUUCGUUUUCAAAAGGGAAAAAGCAAAUCAAGAAUGGAUCCCAUCUUGAAAAAUUGUUAAAUUUUUCAUAUAAUGAGGUAUAAAACAUAAUCGCAGGUGAGAUUCCUGCCUGCUUUUCAAGAAAGGACGAGCUGCUUCAGCUCAGACAAAAUU ......(((((...............(((((((.....((((((...........))))))....(((((...........((((..(((((.....)))))........(((((((((((....)))))))))))......))))(((((......)))))...)))))...)))))))....((((((((...((((.....((((((...)))))).....)))).....((((((.((....)))))))).)))))))).)))))((((((...)))))).......... (-56.60) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 1012 60 11 151 102 NC_009009:SSA_2185|5end_Adenylosuccinate_synthetase,_putative_2185290..2185520_NEGATIVE 396 48 7 148 102 NC_009009:SSA_2024|5end_hypothetical_protein_2029272..2029502_NEGATIVE 352 288 243 174 120 NC_009009:SSA_2218|5end_Glycosyltransferase_(cell_wall_biogenesis)_Cps9G,_putative_2219941..2220171_NEGATIVE 340 46 2 210 154 NC_009009:SSA_0486|5end_Uroporphyrinogen-III_synthase,_putative_486637..486867_POSITIVE 334 58 12 75 20 NC_009009:SSA_1106|5end_IgA-specific_metalloendopeptidase_1125974..1126204_POSITIVE 327 46 5 146 112 NC_009009:SSA_2080|5end_hypothetical_protein_2085341..2085571_NEGATIVE 327 67 28 219 176 NC_009009:SSA_0832|5end_SecY-like_protein,_putative_816708..816938_POSITIVE 326 60 11 212 152 NC_009009:SSA_0090|5end_Acetyltransferase,_GNAT_family,_putative_90258..90488_POSITIVE 322 144 103 113 70 NC_009009:SSA_0651|5end_hypothetical_protein_634548..634778_POSITIVE 320 60 11 134 80 NC_009009:SSA_0838|5end_GtfB,_putative_825406..825636_POSITIVE 315 50 4 52 7 NC_009009:SSA_0078|5end_N-acetylneuraminate_lyase,_putative_81904..82134_POSITIVE 312 60 18 197 145 NC_009009:SSA_1013|5end_Phosphatidylserine_synthase,_putative_1017221..1017451_POSITIVE 308 65 22 57 11 NC_009009:SSA_0452|5end_Nitrogen_utilization_substance_protein_B,_putative_451534..451764_POSITIVE 304 51 12 51 10 NC_009009:SSA_0505|5end_Conserved_protein/domain_typically_associated_with_flavoprotein_oxygenases,_DIM6/NTAB_family,_putative_503772..504002_POSITIVE 302 135 94 74 30 NC_009009:SSA_1954|5end_Aminotransferase,_class-V,_putative_1951298..1951528_NEGATIVE 299 49 2 62 10 NC_009009:SSA_1251|5end_Hydrolase,_HD_superfamily,_putative_1276790..1277020_NEGATIVE 297 66 21 185 123 NC_009009:SSA_1363|5end_FmtA-like_protein,_putative_1380417..1380647_NEGATIVE 296 50 5 214 157 NC_009009:SSA_2044|5end_Cysteinyl-tRNA_synthetase,_putative_2048409..2048639_NEGATIVE 295 46 7 172 133 NC_009009:SSA_0366|5end_hypothetical_protein_357506..357736_POSITIVE 294 61 22 133 95 NC_009009:SSA_1681|5end_ABC-type_bacitracin_resistance_protein_A,_ATPase_component,_putative_1675960..1676190_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 352 288 243 148 94 NC_009009:SSA_2219|3end_UDP-glucose_4-epimerase,_putative_2219967..2220117_NEGATIVE 336 45 9 145 104 NC_009009:SSA_0815|3end_hypothetical_protein_797411..797561_POSITIVE 328 46 7 52 1 NC_009009:SSA_0585|3end_hypothetical_protein_577286..577436_POSITIVE 327 46 5 136 102 NC_009009:SSA_2082|3end_Carbohydrate_kinase,_FGGY_family,_putative_2085351..2085501_NEGATIVE 322 144 103 89 46 NC_009009:SSA_0650|3end_GTP-binding_protein_TypA/BipA,_putative_634604..634754_POSITIVE 320 60 11 150 96 NC_009009:SSA_0837|3end_Glucosyltransferase,_putative_825502..825652_POSITIVE 311 70 22 58 14 NC_009009:SSA_0480|3end_Cobalt_ABC_transporter,_ATP-binding_protein,_putative_482057..482207_POSITIVE 308 65 22 79 33 NC_009009:SSA_0451|3end_Conserved_uncharacterized_protein_451636..451786_POSITIVE 299 49 2 81 29 NC_009009:SSA_1252|3end_hypothetical_protein_1276771..1276921_NEGATIVE 297 66 21 120 58 NC_009009:SSA_1364|3end_hypothetical_protein_1380482..1380632_NEGATIVE 295 46 7 150 111 NC_009009:SSA_0365|3end_Small-conductance_mechanosensitive_efflux_channel,_putative_357564..357714_POSITIVE 293 48 5 61 7 NC_009009:SSA_0569|3end_Aspartyl/glutamyl-tRNA(Asn/Gln)_amidotransferase_subunit_C,_putative_563995..564145_POSITIVE 292 67 23 70 26 NC_009009:SSA_1790|3end_SpoU_rRNA_Methylase_family_protein,_putative_1772901..1773051_NEGATIVE 291 58 13 147 96 NC_009009:SSA_1621|3end_Amino_acid_transporter,_putative_1623172..1623322_NEGATIVE 288 59 11 72 1 NC_009009:SSA_2108|3end_Glyceraldehyde_3-phosphate_dehydrogenase,_putative_2111457..2111607_NEGATIVE 285 50 10 148 114 NC_009009:SSA_0861|3end_hypothetical_protein_851742..851892_NEGATIVE 285 50 7 54 4 NC_009009:SSA_0086|3end_V-type_sodium_ATPase,_subunit_K,_putative_88398..88548_POSITIVE 284 51 13 71 27 NC_009009:SSA_1801|3end_hypothetical_protein_1782652..1782802_NEGATIVE 282 48 4 141 101 NC_009009:SSA_1497|3end_DCMP_deaminase,_putative_1503068..1503218_NEGATIVE 281 47 3 73 27 NC_009009:SSA_0912|3end_Phenylalanyl-tRNA_synthetase_alpha_chain,_putative_924229..924379_POSITIVE