Origin IGS: gaattctctacttagctagagaatttttttatttttctaaatttgttgtaaaatgttaaacaaaagtaagctattaaaggagaaaatttatggtagcagcagttacagatgcaacattcgcagaagaaacaaaagatggcatggttctgattgacttttgggcaacttggtgtggtcc .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 ggaccacaccaagttgcccaaaagtcaatcagaaccatgccatcttttgtttcttctgcgaatgttgcatctgtaactgctgctaccataaattttctcctttaatagcttacttttgtttaacattttacaacaaatttagaaaaataaaaaaattctctagctaagtagagaattc Mask Tandem Repeat Region ================================================ gaattctctacttagctagagaatttttttatttttctaaatttgttgtaaaatgttaaacaaaagtaagctattaaaggagaaaatttatggtagcagcagttacagatgcaacattcgcagaagaaacaaaagatggcatggttctgattgacttttgggcaacttggtgtggtcc Find is-nt database================================================ Query_seq: SSA_0360:SSA_0362|SSA_0360:SSA_0362:Conserved uncharacterized protein:Thioredoxin, putative:->->:353252..353429 178 gaattctctacttagctagagaatttttttatttttctaaatttgttgtaaaatgttaaacaaaagtaagctattaaaggagaaaatttatggtagcagcagttacagatgcaacattcgcagaagaaacaaaagatggcatggttctgattgacttttgggcaacttggtgtggtcc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0360:SSA_0362|SSA_0360:SSA_0362:Conserved uncharacterized protein:Thioredoxin, putative:->->:353252..353429 178 gaattctctacttagctagagaatttttttatttttctaaatttgttgtaaaatgttaaacaaaagtaagctattaaaggagaaaatttatggtagcagcagttacagatgcaacattcgcagaagaaacaaaagatggcatggttctgattgacttttgggcaacttggtgtggtcc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0360:SSA_0362|SSA_0360:SSA_0362:Conserved uncharacterized protein:Thioredoxin, putative:->->:353252..353429 178 gaattctctacttagctagagaatttttttatttttctaaatttgttgtaaaatgttaaacaaaagtaagctattaaaggagaaaatttatggtagcagcagttacagatgcaacattcgcagaagaaacaaaagatggcatggttctgattgacttttgggcaacttggtgtggtcc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gaattctctacttagctagagaatttttttatttttctaaatttgttgtaaaatgttaaacaaaagtaagctattaaaggagaaaatttatggtagcagcagttacagatgcaacattcgcagaagaaacaaaagatggcatggttctgattgacttttgggcaacttggtgtggtcc Predict ORF larger than 30AA ================================================ Protein_Len: 37 Strand: + Start: 41 End: 151 ........................................ M C C K M L N K S K L L K E K I Y G S S S Y R C N I R R R N K R W H G S D ........................... Protein_Len: 41 Strand: - Start: 15 End: 137 .............. S S F K K I K R F K N Y F T L C F Y A I L P S F K H Y C C N C I C C E C F F C F M ......................................... gaattctctacttagctagagaatttttttatttttctaaatttgttgtaaaatgttaaacaaaagtaagctattaaaggagaaaatttatggtagcagcagttacagatgcaacattcgcagaagaaacaaaagatggcatggttctgattgacttttgggcaacttggtgtggtcc 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: 25 End: 54 ........................TTTTTTATTTTTCTAAATTTGTTGTAAAAT............................................................................................................................ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ gaattctctacttagctagagaatttttttatttttctaaatttgttgtaaaatgttaaacaaaagtaagctattaaaggagaaaatttatggtagcagcagttacagatgcaacattcgcagaagaaacaaaagatggcatggttctgattgacttttgggcaacttggtgtggtcc Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_0360:SSA_0362|SSA_0360:SSA_0362:Conserved uncharacterized protein:Thioredoxin, putative:->->:353252..353429 178 gaattctctacttagctagagaatttttttatttttctaaatttgttgtaaaatgttaaacaaaagtaagctattaaaggagaaaatttatggtagcagcagttacagatgcaacattcgcagaagaaacaaaagatggcatggttctgattgacttttgggcaacttggtgtggtcc Intra-Species Hit: Count: 1 Min: 37 Max: 178 Len: 142 Subject: NC_009009_SSA_0360_SSA_0362|Conserved uncharacterized protein:Thioredoxin, putative|POSITIVE:POSITIVE|[353252,353429]|178 HSP 1 e-value: 4.0E-75 bit: 281.0 Len: 142 Query Start:37 Query End:178 Subject Strand: POSITIVE Subject Start: 37 Subject End: 178 ....................................ctaaatttgttgtaaaatgttaaacaaaagtaagctattaaaggagaaaatttatggtagcagcagttacagatgcaacattcgcagaagaaacaaaagatggcatggttctgattgacttttgggcaacttggtgtggtcc ....................................ctaaatttgttgtaaaatgttaaacaaaagtaagctattaaaggagaaaatttatggtagcagcagttacagatgcaacattcgcagaagaaacaaaagatggcatggttctgattgacttttgggcaacttggtgtggtcc Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUAAAUUUGUUGUAAAAUGUUAAACAAAAGUAAGCUAUUAAAGGAGAAAAUUUAUGGUAGCAGCAGUUACAGAUGCAACAUUCGCAGAAGAAACAAAAGAUGGCAUGGUUCUGAUUGACUUUUGGGCAACUUGGUGUGGUCC (((.(((.(((((.(((.(((((.((.((.((.((((((.................(((((....)))))...(((.......)))............)))))).)).)).)).))))).)))..)))))..))).)))... (-25.00) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GGACCACACCAAGUUGCCCAAAAGUCAAUCAGAACCAUGCCAUCUUUUGUUUCUUCUGCGAAUGUUGCAUCUGUAACUGCUGCUACCAUAAAUUUUCUCCUUUAAUAGCUUACUUUUGUUUAACAUUUUACAACAAAUUUAG ((......))..((((..(((((((....((((....(((.((..(((((.......))))).)).)))))))........((((...((((........)))).))))..)))))))..)))).................. (-18.80) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 288 78 35 152 119 NC_009009:SSA_2294|5end_hypothetical_protein_2296082..2296312_POSITIVE 281 114 71 121 77 NC_009009:SSA_0045|5end_hypothetical_protein_50333..50563_POSITIVE 276 140 98 225 192 NC_009009:SSA_1694|5end_PTS_system,_lactose-specific_IIA_component,_putative_1687128..1687358_NEGATIVE 276 97 54 88 45 NC_009009:SSA_0274|5end_hypothetical_protein_269557..269787_NEGATIVE 275 107 63 70 24 NC_009009:SSA_2360|5end_tRNA_(5-methylaminomethyl-2-thiouridylate)-methyltransferase,_putative_2363779..2364009_NEGATIVE 271 139 98 205 149 NC_009009:SSA_1582|5end_Esterase,_alpha/beta_hydrolase_superfamily,_putative_1584671..1584901_POSITIVE 266 127 81 224 172 NC_009009:SSA_0433|5end_Methenyl_tetrahydrofolate_cyclohydrolase,_putative_435654..435884_NEGATIVE 256 88 41 87 45 NC_009009:SSA_1258|5end_Purine_nucleoside_phosphorylase,_family_1,_putative_1284652..1284882_NEGATIVE 256 135 98 207 153 NC_009009:SSA_0251|5end_D-tyrosyl-tRNA(Tyr)_deacylase,_putative_244455..244685_POSITIVE 252 134 96 143 108 NC_009009:SSA_1132|5end_TatC,_sec-independent_protein_translocase,_putative_1158645..1158875_POSITIVE 250 135 101 206 167 NC_009009:SSA_1509|5end_Polysaccharide_biosynthesis_protein/_rhamnosyltransferase,_putative_1514191..1514421_NEGATIVE 249 99 54 173 133 NC_009009:SSA_0643|5end_hypothetical_protein_630194..630424_NEGATIVE 248 108 62 216 167 NC_009009:SSA_1013|5end_Phosphatidylserine_synthase,_putative_1017221..1017451_POSITIVE 248 140 109 133 100 NC_009009:SSA_0496|5end_Succinylglutamate_desuccinylase_/_Aspartoacylase_family,_putative_495946..496176_POSITIVE 248 135 101 211 176 NC_009009:SSA_0431|5end_hypothetical_protein_433275..433505_NEGATIVE 247 129 83 87 38 NC_009009:SSA_1673|5end_hypothetical_protein_1670353..1670583_POSITIVE 244 140 97 60 6 NC_009009:SSA_0710|5end_Exopolysaccharide_biosynthesis_protein,_acetyltransferase,_putative_695639..695869_NEGATIVE 243 76 31 185 140 NC_009009:SSA_1393|5end_hypothetical_protein_1408773..1409003_NEGATIVE 243 138 96 189 148 NC_009009:SSA_0468|5end_Precorrin-6y_C5,15-methyltransferase-like,_putative_471706..471936_POSITIVE 239 140 94 143 104 NC_009009:SSA_1361|5end_ORFA,_transposon_ISSsa2_1377168..1377398_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 285 73 33 134 93 NC_009009:SSA_1162|3end_Possible_fimbrial_assembly_protein_fimC,_putative_1188489..1188639_NEGATIVE 272 140 101 146 102 NC_009009:SSA_0047|3end_NAD(P)H_dehydrogenase_(Quinone),_putative_52284..52434_NEGATIVE 256 135 98 138 84 NC_009009:SSA_0250|3end_GTP_pyrophosphokinase,_putative_244466..244616_POSITIVE 250 86 57 140 104 NC_009009:SSA_0599|3end_hypothetical_protein_589007..589157_POSITIVE 248 140 109 143 110 NC_009009:SSA_0495|3end_ABC-type_oligopeptide/nickel_transport_system,_ATPase_component,_putative_496036..496186_POSITIVE 246 136 96 135 93 NC_009009:SSA_0183|3end_hypothetical_protein_188106..188256_POSITIVE 244 140 97 67 13 NC_009009:SSA_0709|3end_hypothetical_protein_695632..695782_NEGATIVE 239 140 94 65 26 NC_009009:SSA_1360|3end_Arginine/histidine_ABC_transporter,_ATPase_component,_putative_1377170..1377320_POSITIVE 239 140 94 74 35 NC_009009:SSA_0574|3end_YdjX_protein,_putative_568801..568951_NEGATIVE 239 140 94 48 9 NC_009009:SSA_0264|3end_PEP_phosphonomutase-like_protein,_putative_259376..259526_POSITIVE 238 97 54 77 43 NC_009009:SSA_1565|3end_Two-component_response_transcriptional_regulator_(CheY-like_receiver_and_winged-helix_DNA-binding_domains),_putative_1568608..1568758_NEGATIVE 236 115 71 46 1 NC_009009:SSA_0197|3end_Dihydropteroate_synthase,_putative_196979..197129_POSITIVE 234 139 101 58 1 NC_009009:SSA_1464|3end_3-phosphoshikimate_1-carboxyvinyltransferase,_putative_1470233..1470383_NEGATIVE 232 88 41 55 13 NC_009009:SSA_1268|3end_Chorismate_mutase/prephenate_dehydratase,_putative_1291347..1291497_NEGATIVE 230 76 42 65 30 NC_009009:SSA_0739|3end_Carbamate_kinase,_putative_722114..722264_POSITIVE 229 86 41 86 45 NC_009009:SSA_2207|3end_hypothetical_protein_2206868..2207018_NEGATIVE 228 91 51 116 67 NC_009009:SSA_2101|3end_Amino_acid_ABC_transporter,_periplasmic_amino_acid-binding_protein,_putative_2104509..2104659_NEGATIVE 227 139 94 148 105 NC_009009:SSA_1615|3end_Alanine_dehydrogenase,_putative_1619318..1619468_POSITIVE 226 100 55 51 7 NC_009009:SSA_1308|3end_hypothetical_protein_1326267..1326417_NEGATIVE 226 110 61 91 42 NC_009009:SSA_0341|3end_hypothetical_protein_333955..334105_NEGATIVE