Origin IGS: atctgcctcctagattggttgctaaatgtcactttatttcaagacaaatcttttggacatctgttctatattttaccataaagcgattgcaatagctatccttgaagagactaaatctcagaaaaattaaaaaaccagcctcctaaaggctggcggataactctctctgaataagagga .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tcctcttattcagagagagttatccgccagcctttaggaggctggttttttaatttttctgagatttagtctcttcaaggatagctattgcaatcgctttatggtaaaatatagaacagatgtccaaaagatttgtcttgaaataaagtgacatttagcaaccaatctaggaggcagat Mask Tandem Repeat Region ================================================ atctgcctcctagattggttgctaaatgtcactttatttcaagacaaatcttttggacatctgttctatattttaccataaagcgattgcaatagctatccttgaagagactaaatctcagaaaaattaaaaaaccagcctcctaaaggctggcggataactctctctgaataagagga Find is-nt database================================================ Query_seq: SSA_1378:SSA_1379|SSA_1378:SSA_1379:hypothetical protein:hypothetical protein:<-<-:1398089..1398267 179 atctgcctcctagattggttgctaaatgtcactttatttcaagacaaatcttttggacatctgttctatattttaccataaagcgattgcaatagctatccttgaagagactaaatctcagaaaaattaaaaaaccagcctcctaaaggctggcggataactctctctgaataagagga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1378:SSA_1379|SSA_1378:SSA_1379:hypothetical protein:hypothetical protein:<-<-:1398089..1398267 179 atctgcctcctagattggttgctaaatgtcactttatttcaagacaaatcttttggacatctgttctatattttaccataaagcgattgcaatagctatccttgaagagactaaatctcagaaaaattaaaaaaccagcctcctaaaggctggcggataactctctctgaataagagga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1378:SSA_1379|SSA_1378:SSA_1379:hypothetical protein:hypothetical protein:<-<-:1398089..1398267 179 atctgcctcctagattggttgctaaatgtcactttatttcaagacaaatcttttggacatctgttctatattttaccataaagcgattgcaatagctatccttgaagagactaaatctcagaaaaattaaaaaaccagcctcctaaaggctggcggataactctctctgaataagagga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 atctgcctcctagattggttgctaaatgtcactttatttcaagacaaatcttttggacatctgttctatattttaccataaagcgattgcaatagctatccttgaagagactaaatctcagaaaaattaaaaaaccagcctcctaaaggctggcggataactctctctgaataagagga Predict ORF larger than 30AA ================================================ Protein_Len: 30 Strand: + Start: 3 End: 92 .. M P P R L V A K C H F I S R Q I F W T S V L Y F T I K R L Q ....................................................................................... Protein_Len: 34 Strand: + Start: 26 End: 127 ......................... M S L Y F K T N L L D I C S I F Y H K A I A I A I L E E T K S Q K N .................................................... Protein_Len: 32 Strand: - Start: 32 End: 127 ............................... K I E L C I K Q V D T R Y K V M F R N C Y S D K F L S F R L F M .................................................... atctgcctcctagattggttgctaaatgtcactttatttcaagacaaatcttttggacatctgttctatattttaccataaagcgattgcaatagctatccttgaagagactaaatctcagaaaaattaaaaaaccagcctcctaaaggctggcggataactctctctgaataagagga Predict Promoter with matrix: RpoD-15 score > 80================================================ Predict Promoter with matrix: RpoD-16 score > 80================================================ Predict Promoter with matrix: RpoD-17 score > 80================================================ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ atctgcctcctagattggttgctaaatgtcactttatttcaagacaaatcttttggacatctgttctatattttaccataaagcgattgcaatagctatccttgaagagactaaatctcagaaaaattaaaaaaccagcctcctaaaggctggcggataactctctctgaataagagga Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_1378:SSA_1379|SSA_1378:SSA_1379:hypothetical protein:hypothetical protein:<-<-:1398089..1398267 179 atctgcctcctagattggttgctaaatgtcactttatttcaagacaaatcttttggacatctgttctatattttaccataaagcgattgcaatagctatccttgaagagactaaatctcagaaaaattaaaaaaccagcctcctaaaggctggcggataactctctctgaataagagga Intra-Species Hit: Count: 1 Min: 1 Max: 179 Len: 179 Subject: NC_009009_SSA_1378_SSA_1379|hypothetical protein:hypothetical protein|NEGATIVE:NEGATIVE|[1398089,1398267]|179 HSP 1 e-value: 1.0E-62 bit: 240.0 Len: 121 Query Start:1 Query End:121 Subject Strand: POSITIVE Subject Start: 1 Subject End: 121 atctgcctcctagattggttgctaaatgtcactttatttcaagacaaatcttttggacatctgttctatattttaccataaagcgattgcaatagctatccttgaagagactaaatctcag.......................................................... atctgcctcctagattggttgctaaatgtcactttatttcaagacaaatcttttggacatctgttctatattttaccataaagcgattgcaatagctatccttgaagagactaaatctcag.......................................................... HSP 2 e-value: 3.0E-17 bit: 89.7 Len: 45 Query Start:135 Query End:179 Subject Strand: POSITIVE Subject Start: 135 Subject End: 179 ......................................................................................................................................ccagcctcctaaaggctggcggataactctctctgaataagagga ......................................................................................................................................ccagcctcctaaaggctggcggataactctctctgaataagagga Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUCUGCCUCCUAGAUUGGUUGCUAAAUGUCACUUUAUUUCAAGACAAAUCUUUUGGACAUCUGUUCUAUAUUUUACCAUAAAGCGAUUGCAAUAGCUAUCCUUGAAGAGACUAAAUCUCAGAAAAAUUAAAAAACCAGCCUCCUAAAGGCUGGCGGAUAACUCUCUCUGAAUAAGAGGA .....((((.((((...(((((.....(((.((((((...((((....))))..((((....))))...........)))))).))).)))))...(((((.....((((.....))))...............(((((((.....))))))).)))))......)))).....)))). (-38.80) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCCUCUUAUUCAGAGAGAGUUAUCCGCCAGCCUUUAGGAGGCUGGUUUUUUAAUUUUUCUGAGAUUUAGUCUCUUCAAGGAUAGCUAUUGCAAUCGCUUUAUGGUAAAAUAUAGAACAGAUGUCCAAAAGAUUUGUCUUGAAAUAAAGUGACAUUUAGCAACCAAUCUAGGAGGCAGAU ........((((((((((.......(((((((((...))))))))).......)))))))))).....(((((((...((...((((......(((((((((..((......(((.(((((.(.....).))))))))))..)))))))))....))))..)).....))))))).... (-48.14) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 830 50 1 141 92 NC_009009:SSA_1378|5end_hypothetical_protein_1397998..1398228_NEGATIVE 319 170 125 227 177 NC_009009:SSA_1655|5end_hypothetical_protein_1651816..1652046_NEGATIVE 313 100 58 111 73 NC_009009:SSA_1266|5end_crcB-like_protein_1,_putative_1291000..1291230_NEGATIVE 278 109 71 154 119 NC_009009:SSA_0131|5end_30S_ribosomal_protein_S11,_putative_120717..120947_POSITIVE 275 156 135 60 42 NC_009009:SSA_0210|5end_hypothetical_protein_207757..207987_POSITIVE 271 169 138 87 45 NC_009009:SSA_0941|5end_ABC-type_phosphate_transport_system,_periplasmic_component,_putative_949157..949387_POSITIVE 270 155 115 58 20 NC_009009:SSA_1746|5end_hypothetical_protein_1732945..1733175_NEGATIVE 261 170 132 195 149 NC_009009:SSA_0548|5end_Alanine_racemase,_putative_542340..542570_POSITIVE 259 50 3 194 153 NC_009009:SSA_1681|5end_ABC-type_bacitracin_resistance_protein_A,_ATPase_component,_putative_1675960..1676190_NEGATIVE 259 156 112 46 3 NC_009009:SSA_1015|5end_4-hydroxybenzoate_octaprenyltransferase,_putative_1018703..1018933_POSITIVE 259 168 134 225 190 NC_009009:SSA_0625|5end_Phosphopantetheine_adenylyltransferase_615608..615838_POSITIVE 257 155 125 218 188 NC_009009:SSA_2182|5end_hypothetical_protein_2181020..2181250_NEGATIVE 257 170 135 147 116 NC_009009:SSA_0464|5end_Cobalamin_biosynthesis_protein_cobD,_putative_468225..468455_POSITIVE 255 169 133 143 100 NC_009009:SSA_1843|5end_Histidine_kinase,_putative_1837491..1837721_NEGATIVE 253 167 132 69 28 NC_009009:SSA_2219|5end_UDP-glucose_4-epimerase,_putative_2220827..2221057_NEGATIVE 251 103 61 153 115 NC_009009:SSA_2270|5end_Aspartyl-tRNA_synthetase,_putative_2272068..2272298_NEGATIVE 250 169 138 57 26 NC_009009:SSA_0907|5end_Fibronectin-binding_protein_A,_putative_919217..919447_NEGATIVE 250 46 2 132 96 NC_009009:SSA_0441|5end_hypothetical_protein_441481..441711_POSITIVE 249 170 137 190 158 NC_009009:SSA_1972|5end_Two-component_system_transcriptional_regulator_(CheY_domain_and_HTH-like_DNA-binding_domain),_putative_1968410..1968640_NEGATIVE 248 90 43 221 171 NC_009009:SSA_1698|5end_Galactose-6-phosphate_isomerase,_LacB_subunit,_putative_1690648..1690878_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 346 170 138 102 66 NC_009009:SSA_0070|3end_Acetylxylan_esterase,_putative_74914..75064_POSITIVE 313 100 58 138 100 NC_009009:SSA_1267|3end_crcB-like_protein_2,_putative_1290973..1291123_NEGATIVE 280 169 135 139 97 NC_009009:SSA_0865|3end_hypothetical_protein_856850..857000_POSITIVE 278 109 71 134 99 NC_009009:SSA_0130|3end_30S_ribosomal_protein_S13,_putative_120777..120927_POSITIVE 270 155 115 65 27 NC_009009:SSA_1747|3end_hypothetical_protein_1732938..1733088_NEGATIVE 268 168 135 86 54 NC_009009:SSA_0599|3end_hypothetical_protein_589007..589157_POSITIVE 265 158 111 70 22 NC_009009:SSA_1703|3end_Methionyl-tRNA_synthetase,_putative_1693640..1693790_NEGATIVE 261 153 125 142 113 NC_009009:SSA_1656|3end_Nisin_resistance_protein,_putative_1651880..1652030_NEGATIVE 260 140 95 151 102 NC_009009:SSA_2023|3end_Fructan_beta-fructosidase_precursor,_putative_2024609..2024759_NEGATIVE 259 156 112 61 18 NC_009009:SSA_1014|3end_Phosphatidylserine_decarboxylase_proenzyme_2,_putative_1018798..1018948_POSITIVE 259 153 115 76 41 NC_009009:SSA_0571|3end_Aspartyl/glutamyl-tRNA(Asn/Gln)_amidotransferase_subunit_B,_putative_566894..567044_POSITIVE 258 169 133 131 95 NC_009009:SSA_1972|3end_Two-component_system_transcriptional_regulator_(CheY_domain_and_HTH-like_DNA-binding_domain),_putative_1967811..1967961_NEGATIVE 257 155 125 83 53 NC_009009:SSA_2183|3end_Glucose-6-phosphate_isomerase,_putative_2181155..2181305_NEGATIVE 257 170 135 145 114 NC_009009:SSA_0463|3end_Cobyrinic_acid_A,C-diamide_synthase,_putative_468303..468453_POSITIVE 255 169 133 146 103 NC_009009:SSA_1844|3end_hypothetical_protein_1837488..1837638_NEGATIVE 253 167 132 62 21 NC_009009:SSA_2220|3end_Galactosyltransferase,_putative_2220834..2220984_NEGATIVE 248 150 101 67 12 NC_009009:SSA_1245|3end_Transcriptional_regulator,_LysR_family,_putative_1269710..1269860_POSITIVE 247 110 62 142 78 NC_009009:SSA_1412|3end_hypothetical_protein_1423994..1424144_NEGATIVE 247 170 135 84 41 NC_009009:SSA_0539|3end_PduO_protein,_putative_534867..535017_POSITIVE 245 169 133 135 100 NC_009009:SSA_0200|3end_Bifunctional_folate_synthesis_protein,_putative_199810..199960_POSITIVE