Origin IGS: ataacgaacactcctctttagtattttgttatattatacatcttttttgcttaaaaaggaactaaaccactactattttaacaaacattcgttttttcagaaaattactagaaaattttctgtgttaaaaaagaccctgaaattcatcagagtctaatctgca .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tgcagattagactctgatgaatttcagggtcttttttaacacagaaaattttctagtaattttctgaaaaaacgaatgtttgttaaaatagtagtggtttagttcctttttaagcaaaaaagatgtataatataacaaaatactaaagaggagtgttcgttat Mask Tandem Repeat Region ================================================ ataacgaacactcctctttagtattttgttatattatacatcttttttgcttaaaaaggaactaaaccactactattttaacaaacattcgttttttcagaaaattactagaaaattttctgtgttaaaaaagaccctgaaattcatcagagtctaatctgca Find is-nt database================================================ Query_seq: SSA_1234:SSA_1235|SSA_1234:SSA_1235:5'-nucleotidase, putative:Dihydroorotase, putative:<-<-:1259886..1260048 163 ataacgaacactcctctttagtattttgttatattatacatcttttttgcttaaaaaggaactaaaccactactattttaacaaacattcgttttttcagaaaattactagaaaattttctgtgttaaaaaagaccctgaaattcatcagagtctaatctgca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1234:SSA_1235|SSA_1234:SSA_1235:5'-nucleotidase, putative:Dihydroorotase, putative:<-<-:1259886..1260048 163 ataacgaacactcctctttagtattttgttatattatacatcttttttgcttaaaaaggaactaaaccactactattttaacaaacattcgttttttcagaaaattactagaaaattttctgtgttaaaaaagaccctgaaattcatcagagtctaatctgca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1234:SSA_1235|SSA_1234:SSA_1235:5'-nucleotidase, putative:Dihydroorotase, putative:<-<-:1259886..1260048 163 ataacgaacactcctctttagtattttgttatattatacatcttttttgcttaaaaaggaactaaaccactactattttaacaaacattcgttttttcagaaaattactagaaaattttctgtgttaaaaaagaccctgaaattcatcagagtctaatctgca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ataacgaacactcctctttagtattttgttatattatacatcttttttgcttaaaaaggaactaaaccactactattttaacaaacattcgttttttcagaaaattactagaaaattttctgtgttaaaaaagaccctgaaattcatcagagtctaatctgca Predict ORF larger than 30AA ================================================ Protein_Len: 44 Strand: + Start: 23 End: 154 ...................... M L L Y Y T S F L L K K E L N H Y Y F N K H S F F Q K I T R K F S V L K K T L K F I R V ......... ataacgaacactcctctttagtattttgttatattatacatcttttttgcttaaaaaggaactaaaccactactattttaacaaacattcgttttttcagaaaattactagaaaattttctgtgttaaaaaagaccctgaaattcatcagagtctaatctgca 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: 75 End: 104 ..........................................................................TTTTCTGAAAAAACGAATGTTTGTTAAAAT........................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ ataacgaacactcctctttagtattttgttatattatacatcttttttgcttaaaaaggaactaaaccactactattttaacaaacattcgttttttcagaaaattactagaaaattttctgtgttaaaaaagaccctgaaattcatcagagtctaatctgca Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 57 HP_score: -5.9 Tail_Score: -3.01712 Start: 98 End: 122 Full_Region: AAACATTCGTTTTTT CAGAAAATT ACTAGAA AATTTTCTG TGTTAAAAAAGACCC .................................................................................................CAGAAAATTACTAGAAAATTTTCTG......................................... TransTerm Strand: + Conf: 42 HP_score: -2.7 Tail_Score: -3.06696 Start: 100 End: 120 Full_Region: ACATTCGTTTTTTCA GAAAATT ACTAGAA AATTTTC TGTGTTAAAAAAGAC ...................................................................................................GAAAATTACTAGAAAATTTTC........................................... Find igs database================================================ Query_seq: SSA_1234:SSA_1235|SSA_1234:SSA_1235:5'-nucleotidase, putative:Dihydroorotase, putative:<-<-:1259886..1260048 163 ataacgaacactcctctttagtattttgttatattatacatcttttttgcttaaaaaggaactaaaccactactattttaacaaacattcgttttttcagaaaattactagaaaattttctgtgttaaaaaagaccctgaaattcatcagagtctaatctgca Intra-Species Hit: Count: 1 Min: 1 Max: 163 Len: 163 Subject: NC_009009_SSA_1234_SSA_1235|5'-nucleotidase, putative:Dihydroorotase, putative|NEGATIVE:NEGATIVE|[1259886,1260048]|163 HSP 1 e-value: 1.0E-87 bit: 323.0 Len: 163 Query Start:1 Query End:163 Subject Strand: POSITIVE Subject Start: 1 Subject End: 163 ataacgaacactcctctttagtattttgttatattatacatcttttttgcttaaaaaggaactaaaccactactattttaacaaacattcgttttttcagaaaattactagaaaattttctgtgttaaaaaagaccctgaaattcatcagagtctaatctgca ataacgaacactcctctttagtattttgttatattatacatcttttttgcttaaaaaggaactaaaccactactattttaacaaacattcgttttttcagaaaattactagaaaattttctgtgttaaaaaagaccctgaaattcatcagagtctaatctgca Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUAACGAACACUCCUCUUUAGUAUUUUGUUAUAUUAUACAUCUUUUUUGCUUAAAAAGGAACUAAACCACUACUAUUUUAACAAACAUUCGUUUUUUCAGAAAAUUACUAGAAAAUUUUCUGUGUUAAAAAAGACCCUGAAAUUCAUCAGAGUCUAAUCUGCA ((((((((.(((.......)))..))))))))........((((((((....))))))))...............(((((((.(((....)))....(((((((((.......))))))))).))))))).((((.((((......)))).))))........ (-26.00) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGCAGAUUAGACUCUGAUGAAUUUCAGGGUCUUUUUUAACACAGAAAAUUUUCUAGUAAUUUUCUGAAAAAACGAAUGUUUGUUAAAAUAGUAGUGGUUUAGUUCCUUUUUAAGCAAAAAAGAUGUAUAAUAUAACAAAAUACUAAAGAGGAGUGUUCGUUAU ...(((..(((((((((......)))))))))..)))....(((((((((.......)))))))))....((((((..(((.((....(((((...((((((.......))))))........(((........)))...)))))..)).)))..)))))).. (-38.10) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 713 50 1 141 92 NC_009009:SSA_1234|5end_5'-nucleotidase,_putative_1259795..1260025_NEGATIVE 256 160 117 213 167 NC_009009:SSA_2166|5end_ABC-type_multidrug_transporter,_ATPase_and_permease_components,_putative_2165642..2165872_NEGATIVE 253 160 116 88 36 NC_009009:SSA_1086|5end_TRNA_nucleotidyltransferase,_putative_1103328..1103558_POSITIVE 221 155 118 209 169 NC_009009:SSA_1489|5end_hypothetical_protein_1495788..1496018_NEGATIVE 215 155 115 164 121 NC_009009:SSA_1293|5end_hypothetical_protein_1312249..1312479_NEGATIVE 211 155 111 45 3 NC_009009:SSA_0026|5end_Fatty_acid/phospholipid_synthesis_protein_plsX,_putative_30473..30703_POSITIVE 209 51 12 155 96 NC_009009:SSA_2154|5end_Conserved_uncharacterized_protein_2155259..2155489_NEGATIVE 205 51 13 59 14 NC_009009:SSA_0360|5end_Conserved_uncharacterized_protein_352704..352934_POSITIVE 203 52 11 145 98 NC_009009:SSA_2189|5end_hypothetical_protein_2191097..2191327_NEGATIVE 203 159 135 213 191 NC_009009:SSA_1822|5end_hypothetical_protein_1811125..1811355_NEGATIVE 200 107 69 166 118 NC_009009:SSA_0806|5end_hypothetical_protein_789270..789500_POSITIVE 198 50 4 138 92 NC_009009:SSA_0574|5end_YdjX_protein,_putative_569427..569657_NEGATIVE 196 150 105 173 119 NC_009009:SSA_1244|5end_hypothetical_protein_1268704..1268934_NEGATIVE 196 109 64 226 178 NC_009009:SSA_1230|5end_Conserved_uncharacterized_protein_1253358..1253588_NEGATIVE 194 75 32 96 46 NC_009009:SSA_1683|5end_NrdI_protein,_putative_1677405..1677635_NEGATIVE 194 154 116 165 128 NC_009009:SSA_0435|5end_Urocanate_hydratase,_putative_438719..438949_NEGATIVE 193 35 4 127 90 NC_009009:SSA_2008|5end_Molecular_chaperone_GrpE_(HSP-70_cofactor),_putative_2010062..2010292_NEGATIVE 193 155 120 206 166 NC_009009:SSA_0101|5end_Conserved_uncharacterized_protein_103596..103826_POSITIVE 189 60 11 114 64 NC_009009:SSA_1747|5end_hypothetical_protein_1733450..1733680_NEGATIVE 188 40 10 124 92 NC_009009:SSA_1330|5end_hypothetical_protein_1346368..1346598_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 253 160 116 91 39 NC_009009:SSA_1085|3end_Dihydrodipicolinate_reductase,_putative_1103411..1103561_POSITIVE 228 52 11 64 27 NC_009009:SSA_1736|3end_L-cysteine_desulfhydrase,_putative_1721453..1721603_NEGATIVE 198 50 9 145 103 NC_009009:SSA_0263|3end_Zinc_metalloproteinase_in_scaA_5'region,_putative_258246..258396_POSITIVE 194 75 32 75 25 NC_009009:SSA_1684|3end_Histidine_kinase,_putative_1677426..1677576_NEGATIVE 193 52 16 89 45 NC_009009:SSA_2022|3end_Transcriptional_regulator,_MerR_family_(multidrug-efflux_transporter_genes),_putative_2024488..2024638_POSITIVE 193 35 4 91 54 NC_009009:SSA_2009|3end_Heat_shock_transcription_repressor_HrcA,_putative_2010098..2010248_NEGATIVE 193 151 123 86 54 NC_009009:SSA_0585|3end_hypothetical_protein_577286..577436_POSITIVE 189 69 43 37 6 NC_009009:SSA_0798|3end_ABC_transporter_membrane-spanning_permease-macrolide_efflux,_putative_781724..781874_POSITIVE 186 151 128 45 17 NC_009009:SSA_0327|3end_Glycosyltransferase,_putative_320436..320586_POSITIVE 184 107 70 48 1 NC_009009:SSA_0805|3end_Collagen-binding_surface_protein,_putative_789232..789382_POSITIVE 183 126 82 109 55 NC_009009:SSA_2261|3end_Transcriptional_repressor_(arginine_synthesis),_putative_2258229..2258379_NEGATIVE 181 155 115 59 11 NC_009009:SSA_2128|3end_hypothetical_protein_2130851..2131001_NEGATIVE 181 50 4 69 24 NC_009009:SSA_0665|3end_NTP_pyrophosphohydrolases_including_oxidative_damage_repair_enzymes_(MutT/NUDIX_family)_649154..649304_NEGATIVE 180 83 46 127 86 NC_009009:SSA_1191|3end_hypothetical_protein_1218222..1218372_NEGATIVE 178 157 115 60 7 NC_009009:SSA_0555|3end_Conserved_hypothetical_cytosolic_protein_551446..551596_POSITIVE 174 97 67 130 102 NC_009009:SSA_1358|3end_hypothetical_protein_1373104..1373254_NEGATIVE 173 160 132 37 6 NC_009009:SSA_0926|3end_Histone_acetyltransferase_HPA2,_putative_935961..936111_POSITIVE 172 98 59 106 73 NC_009009:SSA_2275|3end_hypothetical_protein_2275225..2275375_NEGATIVE 172 48 4 73 28 NC_009009:SSA_1388|3end_hypothetical_protein_1403828..1403978_NEGATIVE 171 122 83 71 39 NC_009009:SSA_0153|3end_hypothetical_protein_149503..149653_POSITIVE