Origin IGS: catttactttggaatcagtataaaaaatcctctcttgtccatgggacaagggaggatttccgtgagacttacatttttatatattatcatactgtgttggagccctgttttcagcttgtggctgaagtgagcgattcccatcttgattgaaaaaagtatttctacgtttaaatctgcttcccgctattaagaaagggagataaccatccact .........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 agtggatggttatctccctttcttaatagcgggaagcagatttaaacgtagaaatacttttttcaatcaagatgggaatcgctcacttcagccacaagctgaaaacagggctccaacacagtatgataatatataaaaatgtaagtctcacggaaatcctcccttgtcccatggacaagagaggattttttatactgattccaaagtaaatg Mask Tandem Repeat Region ================================================ catttactttggaatcagtataaaaaatcctctcttgtccatgggacaagggaggatttccgtgagacttacatttttatatattatcatactgtgttggagccctgttttcagcttgtggctgaagtgagcgattcccatcttgattgaaaaaagtatttctacgtttaaatctgcttcccgctattaagaaagggagataaccatccact Find is-nt database================================================ Query_seq: SSA_0778:SSA_0779|SSA_0778:SSA_0779:Glycogen synthase, putative:Glycogen phosphorylase, putative:->->:762137..762348 212 catttactttggaatcagtataaaaaatcctctcttgtccatgggacaagggaggatttccgtgagacttacatttttatatattatcatactgtgttggagccctgttttcagcttgtggctgaagtgagcgattcccatcttgattgaaaaaagtatttctacgtttaaatctgcttcccgctattaagaaagggagataaccatccact Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0778:SSA_0779|SSA_0778:SSA_0779:Glycogen synthase, putative:Glycogen phosphorylase, putative:->->:762137..762348 212 catttactttggaatcagtataaaaaatcctctcttgtccatgggacaagggaggatttccgtgagacttacatttttatatattatcatactgtgttggagccctgttttcagcttgtggctgaagtgagcgattcccatcttgattgaaaaaagtatttctacgtttaaatctgcttcccgctattaagaaagggagataaccatccact Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0778:SSA_0779|SSA_0778:SSA_0779:Glycogen synthase, putative:Glycogen phosphorylase, putative:->->:762137..762348 212 catttactttggaatcagtataaaaaatcctctcttgtccatgggacaagggaggatttccgtgagacttacatttttatatattatcatactgtgttggagccctgttttcagcttgtggctgaagtgagcgattcccatcttgattgaaaaaagtatttctacgtttaaatctgcttcccgctattaagaaagggagataaccatccact Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 catttactttggaatcagtataaaaaatcctctcttgtccatgggacaagggaggatttccgtgagacttacatttttatatattatcatactgtgttggagccctgttttcagcttgtggctgaagtgagcgattcccatcttgattgaaaaaagtatttctacgtttaaatctgcttcccgctattaagaaagggagataaccatccact Predict ORF larger than 30AA ================================================ Protein_Len: 42 Strand: + Start: 2 End: 127 . M Y F G I S I K N P L L S M G Q G R I S V R L T F L Y I I I L C W S P V F S L W L K ..................................................................................... Protein_Len: 44 Strand: - Start: 80 End: 211 ............................................................................... I N D Y Q T P A R N E A Q P Q L S R N G D Q N F F T N R R K F R S G A I L F P L Y G D M . Protein_Len: 51 Strand: - Start: 7 End: 159 ...... K P I L I F F G R K D M P C P L I E T L S V N K Y I I M S H Q L G T K L K H S F H A I G M K I S F L M ..................................................... catttactttggaatcagtataaaaaatcctctcttgtccatgggacaagggaggatttccgtgagacttacatttttatatattatcatactgtgttggagccctgttttcagcttgtggctgaagtgagcgattcccatcttgattgaaaaaagtatttctacgtttaaatctgcttcccgctattaagaaagggagataaccatccact 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: 61 End: 90 ............................................................CGTGAGACTTACATTTTTATATATTATCAT.......................................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ catttactttggaatcagtataaaaaatcctctcttgtccatgggacaagggaggatttccgtgagacttacatttttatatattatcatactgtgttggagccctgttttcagcttgtggctgaagtgagcgattcccatcttgattgaaaaaagtatttctacgtttaaatctgcttcccgctattaagaaagggagataaccatccact Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 100 HP_score: -16.1 Tail_Score: -5.33785 Start: 28 End: 56 Full_Region: taagtctcacggaaa tcctcccttgtcc cat ggacaagagagga ttttttatactgatt ...........................tcctcccttgtcccatggacaagagagga............................................................................................................................................................ Find igs database================================================ Query_seq: SSA_0778:SSA_0779|SSA_0778:SSA_0779:Glycogen synthase, putative:Glycogen phosphorylase, putative:->->:762137..762348 212 catttactttggaatcagtataaaaaatcctctcttgtccatgggacaagggaggatttccgtgagacttacatttttatatattatcatactgtgttggagccctgttttcagcttgtggctgaagtgagcgattcccatcttgattgaaaaaagtatttctacgtttaaatctgcttcccgctattaagaaagggagataaccatccact Intra-Species Hit: Count: 1 Min: 1 Max: 212 Len: 212 Subject: NC_009009_SSA_0778_SSA_0779|Glycogen synthase, putative:Glycogen phosphorylase, putative|POSITIVE:POSITIVE|[762137,762348]|212 HSP 1 e-value: 1.0E-117 bit: 420.0 Len: 212 Query Start:1 Query End:212 Subject Strand: POSITIVE Subject Start: 1 Subject End: 212 catttactttggaatcagtataaaaaatcctctcttgtccatgggacaagggaggatttccgtgagacttacatttttatatattatcatactgtgttggagccctgttttcagcttgtggctgaagtgagcgattcccatcttgattgaaaaaagtatttctacgtttaaatctgcttcccgctattaagaaagggagataaccatccact catttactttggaatcagtataaaaaatcctctcttgtccatgggacaagggaggatttccgtgagacttacatttttatatattatcatactgtgttggagccctgttttcagcttgtggctgaagtgagcgattcccatcttgattgaaaaaagtatttctacgtttaaatctgcttcccgctattaagaaagggagataaccatccact Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CAUUUACUUUGGAAUCAGUAUAAAAAAUCCUCUCUUGUCCAUGGGACAAGGGAGGAUUUCCGUGAGACUUACAUUUUUAUAUAUUAUCAUACUGUGUUGGAGCCCUGUUUUCAGCUUGUGGCUGAAGUGAGCGAUUCCCAUCUUGAUUGAAAAAAGUAUUUCUACGUUUAAAUCUGCUUCCCGCUAUUAAGAAAGGGAGAUAACCAUCCACU .........((((..((((((...((((((((((((((((...)))))))))))))))).(....)......................))))))...(((.((.(...(((((((.....))))))).).))..(((((.(((((((.(....(((((................)))))....).)))))))..)))))....))))))).. (-59.09) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGUGGAUGGUUAUCUCCCUUUCUUAAUAGCGGGAAGCAGAUUUAAACGUAGAAAUACUUUUUUCAAUCAAGAUGGGAAUCGCUCACUUCAGCCACAAGCUGAAAACAGGGCUCCAACACAGUAUGAUAAUAUAUAAAAAUGUAAGUCUCACGGAAAUCCUCCCUUGUCCCAUGGACAAGAGAGGAUUUUUUAUACUGAUUCCAAAGUAAAUG ..(((((((.....((((..((((....((.....)).((...(((.(((....))).))).))....)))).))))...((((..((((((.....))))))....)))).)))...((((((((...(((((....))))).........(((((((((.(((((((...))))))).)))))))))))))))))..))))......... (-59.70) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 418 140 92 210 158 NC_009009:SSA_0883|5end_Glycerate_kinase,_putative_877560..877790_POSITIVE 348 140 92 53 1 NC_009009:SSA_0274|5end_hypothetical_protein_269557..269787_NEGATIVE 345 67 25 182 141 NC_009009:SSA_1790|5end_SpoU_rRNA_Methylase_family_protein,_putative_1773641..1773871_NEGATIVE 343 150 102 221 167 NC_009009:SSA_1530|5end_ABC-type_antimicrobial_peptide_transport_system,_permease_component,_putative_1538778..1539008_NEGATIVE 334 145 101 44 3 NC_009009:SSA_1183|5end_hypothetical_protein_1211453..1211683_NEGATIVE 326 69 28 146 101 NC_009009:SSA_0604|5end_hypothetical_protein_592451..592681_POSITIVE 325 140 95 214 170 NC_009009:SSA_0475|5end_CbiK_protein,_putative_477723..477953_POSITIVE 318 140 101 64 26 NC_009009:SSA_1149|5end_Glycosyl_hydrolase,_family_1,_putative_1178399..1178629_POSITIVE 310 150 103 187 131 NC_009009:SSA_1764|5end_hypothetical_protein_1750868..1751098_POSITIVE 310 55 14 228 185 NC_009009:SSA_1001|5end_Arabinose_(multiple_sugar_metabolism)_operon_transcriptional_regulator,_putative_1001689..1001919_NEGATIVE 309 134 92 48 8 NC_009009:SSA_0567|5end_Isochorismitase_family_protein,_putative_560805..561035_POSITIVE 305 138 96 76 21 NC_009009:SSA_1687|5end_NADH-binding_ferric-oxidoreductase,_putative_1680547..1680777_POSITIVE 304 133 93 53 7 NC_009009:SSA_2296|5end_Transcriptional_regulator,_XRE_family,_putative_2298773..2299003_NEGATIVE 304 139 101 173 135 NC_009009:SSA_1922|5end_hypothetical_protein_1912106..1912336_NEGATIVE 304 70 26 201 155 NC_009009:SSA_1439|5end_hypothetical_protein_1444373..1444603_NEGATIVE 304 78 32 51 19 NC_009009:SSA_0286|5end_Transaldolase-like_protein,_putative_278814..279044_POSITIVE 302 140 94 203 169 NC_009009:SSA_1438|5end_Acetyltransferase,_putative_1443612..1443842_NEGATIVE 301 149 101 207 144 NC_009009:SSA_0964|5end_DEAD_RNA_helicase,_putative_974114..974344_NEGATIVE 301 139 93 223 153 NC_009009:SSA_0363|5end_D-alanine/glycine/Na_permease,_putative_353858..354088_POSITIVE 300 140 94 59 9 NC_009009:SSA_2016|5end_Phosphoglycerate_mutase,_putative_2016293..2016523_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 477 59 25 66 32 NC_009009:SSA_0778|3end_Glycogen_synthase,_putative_762076..762226_POSITIVE 326 69 28 127 82 NC_009009:SSA_0603|3end_Cobalt_transporter,_putative_592512..592662_POSITIVE 318 140 101 58 20 NC_009009:SSA_1148|3end_Beta-glucosides_PTS,_EIIC,_putative_1178473..1178623_POSITIVE 314 138 91 78 42 NC_009009:SSA_2179|3end_Conserved_uncharacterized_protein_2178104..2178254_NEGATIVE 310 140 95 149 95 NC_009009:SSA_1621|3end_Amino_acid_transporter,_putative_1623172..1623322_NEGATIVE 309 67 31 133 99 NC_009009:SSA_1932|3end_Biotin_carboxylase,_putative_1919507..1919657_NEGATIVE 309 134 92 48 8 NC_009009:SSA_0566|3end_GTP-sensing_transcriptional_pleiotropic_repressor,_putative_560885..561035_POSITIVE 306 135 99 135 98 NC_009009:SSA_2285|3end_hypothetical_protein_2287825..2287975_POSITIVE 304 133 93 50 4 NC_009009:SSA_2297|3end_hypothetical_protein_2298776..2298926_NEGATIVE 304 78 32 36 4 NC_009009:SSA_0285|3end_Formate_acetyltransferase_3,_putative_278879..279029_POSITIVE 295 149 106 136 105 NC_009009:SSA_1916|3end_hypothetical_protein_1906379..1906529_POSITIVE 295 140 96 129 60 NC_009009:SSA_0833|3end_Accessory_secretory_protein_Asp1,_putative_819600..819750_POSITIVE 293 140 91 67 5 NC_009009:SSA_0057|3end_Phosphotransferase_system_sugar-specific_EII_component,_putative_61246..61396_POSITIVE 287 134 92 149 96 NC_009009:SSA_1569|3end_ABC_transporter_membrane-spanning_permease,_arginine/histidine_transport,_putative_1572630..1572780_POSITIVE 278 138 102 54 10 NC_009009:SSA_0454|3end_Lactose_operon_transcriptional_repressor,_LacI_family,_putative_456050..456200_NEGATIVE 276 146 101 60 3 NC_009009:SSA_1375|3end_Multidrug_ABC_transporter,_ATPase_and_permease_components,_putative_1393085..1393235_NEGATIVE 274 135 96 150 116 NC_009009:SSA_0621|3end_SOS_responce_UmuC_protein,_putative_612322..612472_NEGATIVE 270 70 30 92 41 NC_009009:SSA_1493|3end_hypothetical_protein_1498929..1499079_NEGATIVE 269 144 103 70 9 NC_009009:SSA_1384|3end_hypothetical_protein_1401715..1401865_NEGATIVE 267 143 104 142 102 NC_009009:SSA_1267|3end_crcB-like_protein_2,_putative_1290973..1291123_NEGATIVE