Origin IGS: ctatctttttcccaccgcttttagggtgggttcaattcctttctttcttaattttaatatttcatagaaagactagcccgagttcaattcaaactcagatgcccttcctttctgtgtttatttgaaagatagtttttcgctcgtgttcaaatctgaacacactctagctttctttagtttaatgattttatcggctagatagaaaggctgttccgggtttaattaccaacccagacactacgcctttcaacattttt .........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 aaaaatgttgaaaggcgtagtgtctgggttggtaattaaacccggaacagcctttctatctagccgataaaatcattaaactaaagaaagctagagtgtgttcagatttgaacacgagcgaaaaactatctttcaaataaacacagaaaggaagggcatctgagtttgaattgaactcgggctagtctttctatgaaatattaaaattaagaaagaaaggaattgaacccaccctaaaagcggtgggaaaaagatag Mask Tandem Repeat Region ================================================ ctatctttttcccaccgcttttagggtgggttcaattcctttctttcttaattttaatatttcatagaaagactagcccgagttcaattcaaactcagatgcccttcctttctgtgtttatttgaaagatagtttttcgctcgtgttcaaatctgaacacactctagctttctttagtttaatgattttatcggctagatagaaaggctgttccgggtttaattaccaacccagacactacgcctttcaacattttt Find is-nt database================================================ Query_seq: SSA_1258:SSA_1259|SSA_1258:SSA_1259:Purine nucleoside phosphorylase, family 1, putative:Purine nucleoside phosphorylase, putative:<-<-:1284743..1284999 257 ctatctttttcccaccgcttttagggtgggttcaattcctttctttcttaattttaatatttcatagaaagactagcccgagttcaattcaaactcagatgcccttcctttctgtgtttatttgaaagatagtttttcgctcgtgttcaaatctgaacacactctagctttctttagtttaatgattttatcggctagatagaaaggctgttccgggtttaattaccaacccagacactacgcctttcaacattttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1258:SSA_1259|SSA_1258:SSA_1259:Purine nucleoside phosphorylase, family 1, putative:Purine nucleoside phosphorylase, putative:<-<-:1284743..1284999 257 ctatctttttcccaccgcttttagggtgggttcaattcctttctttcttaattttaatatttcatagaaagactagcccgagttcaattcaaactcagatgcccttcctttctgtgtttatttgaaagatagtttttcgctcgtgttcaaatctgaacacactctagctttctttagtttaatgattttatcggctagatagaaaggctgttccgggtttaattaccaacccagacactacgcctttcaacattttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1258:SSA_1259|SSA_1258:SSA_1259:Purine nucleoside phosphorylase, family 1, putative:Purine nucleoside phosphorylase, putative:<-<-:1284743..1284999 257 ctatctttttcccaccgcttttagggtgggttcaattcctttctttcttaattttaatatttcatagaaagactagcccgagttcaattcaaactcagatgcccttcctttctgtgtttatttgaaagatagtttttcgctcgtgttcaaatctgaacacactctagctttctttagtttaatgattttatcggctagatagaaaggctgttccgggtttaattaccaacccagacactacgcctttcaacattttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ctatctttttcccaccgcttttagggtgggttcaattcctttctttcttaattttaatatttcatagaaagactagcccgagttcaattcaaactcagatgcccttcctttctgtgtttatttgaaagatagtttttcgctcgtgttcaaatctgaacacactctagctttctttagtttaatgattttatcggctagatagaaaggctgttccgggtttaattaccaacccagacactacgcctttcaacattttt Predict ORF larger than 30AA ================================================ Protein_Len: 40 Strand: + Start: 3 End: 122 .. M F F P P L L G W V Q F L S F L I L I F H R K T S P S S I Q T Q M P F L S V F I ....................................................................................................................................... ctatctttttcccaccgcttttagggtgggttcaattcctttctttcttaattttaatatttcatagaaagactagcccgagttcaattcaaactcagatgcccttcctttctgtgtttatttgaaagatagtttttcgctcgtgttcaaatctgaacacactctagctttctttagtttaatgattttatcggctagatagaaaggctgttccgggtttaattaccaacccagacactacgcctttcaacattttt 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================================================ ctatctttttcccaccgcttttagggtgggttcaattcctttctttcttaattttaatatttcatagaaagactagcccgagttcaattcaaactcagatgcccttcctttctgtgtttatttgaaagatagtttttcgctcgtgttcaaatctgaacacactctagctttctttagtttaatgattttatcggctagatagaaaggctgttccgggtttaattaccaacccagacactacgcctttcaacattttt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_1258:SSA_1259|SSA_1258:SSA_1259:Purine nucleoside phosphorylase, family 1, putative:Purine nucleoside phosphorylase, putative:<-<-:1284743..1284999 257 ctatctttttcccaccgcttttagggtgggttcaattcctttctttcttaattttaatatttcatagaaagactagcccgagttcaattcaaactcagatgcccttcctttctgtgtttatttgaaagatagtttttcgctcgtgttcaaatctgaacacactctagctttctttagtttaatgattttatcggctagatagaaaggctgttccgggtttaattaccaacccagacactacgcctttcaacattttt Intra-Species Hit: Count: 1 Min: 1 Max: 257 Len: 257 Subject: NC_009009_SSA_1258_SSA_1259|Purine nucleoside phosphorylase, family 1, putative:Purine nucleoside phosphorylase, putative|NEGATIVE:NEGATIVE|[1284743,1284999]|257 HSP 1 e-value: 1.0E-143 bit: 509.0 Len: 257 Query Start:1 Query End:257 Subject Strand: POSITIVE Subject Start: 1 Subject End: 257 ctatctttttcccaccgcttttagggtgggttcaattcctttctttcttaattttaatatttcatagaaagactagcccgagttcaattcaaactcagatgcccttcctttctgtgtttatttgaaagatagtttttcgctcgtgttcaaatctgaacacactctagctttctttagtttaatgattttatcggctagatagaaaggctgttccgggtttaattaccaacccagacactacgcctttcaacattttt ctatctttttcccaccgcttttagggtgggttcaattcctttctttcttaattttaatatttcatagaaagactagcccgagttcaattcaaactcagatgcccttcctttctgtgtttatttgaaagatagtttttcgctcgtgttcaaatctgaacacactctagctttctttagtttaatgattttatcggctagatagaaaggctgttccgggtttaattaccaacccagacactacgcctttcaacattttt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUAUCUUUUUCCCACCGCUUUUAGGGUGGGUUCAAUUCCUUUCUUUCUUAAUUUUAAUAUUUCAUAGAAAGACUAGCCCGAGUUCAAUUCAAACUCAGAUGCCCUUCCUUUCUGUGUUUAUUUGAAAGAUAGUUUUUCGCUCGUGUUCAAAUCUGAACACACUCUAGCUUUCUUUAGUUUAAUGAUUUUAUCGGCUAGAUAGAAAGGCUGUUCCGGGUUUAAUUACCAACCCAGACACUACGCCUUUCAACAUUUUU (((((((((.((((((........)))))).........................((((...(((((((((....((..(((((.......)))))....)).....)))))))))..)))).)))))))))..........(((((((....)))))))..(((((((......((((....)))).....)))))))..(((((((.((((.(((((........))))).)).))...)))))))......... (-67.90) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAAAUGUUGAAAGGCGUAGUGUCUGGGUUGGUAAUUAAACCCGGAACAGCCUUUCUAUCUAGCCGAUAAAAUCAUUAAACUAAAGAAAGCUAGAGUGUGUUCAGAUUUGAACACGAGCGAAAAACUAUCUUUCAAAUAAACACAGAAAGGAAGGGCAUCUGAGUUUGAAUUGAACUCGGGCUAGUCUUUCUAUGAAAUAUUAAAAUUAAGAAAGAAAGGAAUUGAACCCACCCUAAAAGCGGUGGGAAAAAGAUAG .........(((((((...((.((((((((........)))))))))).)))))))..((((((.........................))))))..((((((......))))))..........((((((((........((.(((((((...(((..((((((((.....)))))))))))..))))))).))................................(((((((.....).))))))..)))))))) (-75.21) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 915 120 71 211 162 NC_009009:SSA_1258|5end_Purine_nucleoside_phosphorylase,_family_1,_putative_1284652..1284882_NEGATIVE 400 43 2 207 166 NC_009009:SSA_1226|5end_ParC,_putative_1251233..1251463_NEGATIVE 348 46 1 211 167 NC_009009:SSA_0914|5end_Phenylalanyl-tRNA_synthetase_beta_chain,_putative_924952..925182_POSITIVE 329 34 2 197 165 NC_009009:SSA_0241|5end_Ribosomal_protein_L11_methyltransferase,_putative_234021..234251_POSITIVE 320 221 184 187 146 NC_009009:SSA_1140|5end_Dihydrolipoamide_acetyl_transferase,_E2_component,_putative_1167868..1168098_POSITIVE 317 46 4 209 166 NC_009009:SSA_2005|5end_Chaperone_protein_dnaJ,_putative_2006384..2006614_NEGATIVE 315 148 101 151 94 NC_009009:SSA_0467|5end_Cobalt-precorrin-6A_synthase_[deacetylating],_putative_470588..470818_POSITIVE 302 230 182 76 20 NC_009009:SSA_1775|5end_Potassium_uptake_protein,_Trk_family,_putative_1761284..1761514_POSITIVE 299 140 94 150 92 NC_009009:SSA_0529|5end_Ethanolamine_utilization_protein,_putative_525945..526175_POSITIVE 291 108 71 49 7 NC_009009:SSA_2359|5end_Glucose_inhibited_division_protein_A,_putative_2362520..2362750_NEGATIVE 291 80 36 140 95 NC_009009:SSA_0258|5end_hypothetical_protein_251845..252075_POSITIVE 287 229 186 64 23 NC_009009:SSA_0204|5end_Nisin_biosynthesis_two-component_response_transcriptional_regulator_nisR,_putative_202057..202287_POSITIVE 285 219 171 132 85 NC_009009:SSA_2001|5end_Hydroxymethylpyrimidine/phosphomethylpyrimidine_kinase,_putative_1998220..1998450_NEGATIVE 285 218 171 140 98 NC_009009:SSA_0744|5end_S-adenosylmethio_nine:tRNA-ribosyltransferase-isomerase_(queuine_synthetase),_putative_726804..727034_NEGATIVE 284 78 37 209 174 NC_009009:SSA_1255|5end_hypothetical_protein_1282244..1282474_NEGATIVE 283 250 201 68 15 NC_009009:SSA_1390|5end_hypothetical_protein_1406118..1406348_NEGATIVE 281 237 191 80 25 NC_009009:SSA_0830|5end_Glycosyltransferase,_putative_812430..812660_POSITIVE 279 47 2 110 43 NC_009009:SSA_1447|5end_ATP_phosphoribosyltransferase,_putative_1449831..1450061_NEGATIVE 278 49 3 128 79 NC_009009:SSA_1103|5end_hypothetical_protein_1123833..1124063_POSITIVE 278 238 191 223 169 NC_009009:SSA_0708|5end_hypothetical_protein_694144..694374_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 329 34 2 56 24 NC_009009:SSA_0240|3end_Acetyltransferase,_GNAT_family,_putative_233960..234110_POSITIVE 325 137 93 146 101 NC_009009:SSA_1044|3end_Homoserine_kinase,_putative_1060799..1060949_POSITIVE 315 148 101 151 94 NC_009009:SSA_0466|3end_Precorrin-8X_methylmutase_/_precorrin_isomerase,_putative_470668..470818_POSITIVE 300 100 61 47 18 NC_009009:SSA_1621|3end_Amino_acid_transporter,_putative_1623172..1623322_NEGATIVE 299 140 94 135 77 NC_009009:SSA_0528|3end_Conserved_uncharacterized_protein_526010..526160_POSITIVE 291 80 36 55 10 NC_009009:SSA_0257|3end_N-acetylmuramidase/lysin,_putative_251840..251990_POSITIVE 287 229 186 51 10 NC_009009:SSA_0203|3end_hypothetical_protein_202124..202274_POSITIVE 286 119 74 61 11 NC_009009:SSA_1227|3end_Aminoglycoside_adenylyltransferase,_putative_1251479..1251629_NEGATIVE 285 219 171 142 95 NC_009009:SSA_2002|3end_tRNA_pseudouridine_synthase_A,_putative_1998210..1998360_NEGATIVE 285 218 171 130 88 NC_009009:SSA_0745|3end_hypothetical_protein_726814..726964_NEGATIVE 284 78 37 96 61 NC_009009:SSA_1256|3end_NAD-dependent_deacetylase,_putative_1282357..1282507_NEGATIVE 279 47 2 113 46 NC_009009:SSA_1448|3end_ATP_phosphoribosyltransferase_regulatory_subunit,_putative_1449828..1449978_NEGATIVE 277 143 101 68 24 NC_009009:SSA_1846|3end_Phosphoprotein_phosphatase,_putative_1840178..1840328_NEGATIVE 276 47 15 72 39 NC_009009:SSA_2122|3end_hypothetical_protein_2127200..2127350_NEGATIVE 272 38 4 57 20 NC_009009:SSA_1760|3end_hypothetical_protein_1747126..1747276_NEGATIVE 271 210 164 106 60 NC_009009:SSA_1797|3end_Aminodeoxychorismate_lyase,_putative_1778448..1778598_NEGATIVE 270 118 74 63 6 NC_009009:SSA_1938|3end_Enoyl-acyl_carrier_protein(ACP)_reductase,_putative_1924764..1924914_NEGATIVE 268 245 208 53 12 NC_009009:SSA_0812|3end_hypothetical_protein_794434..794584_POSITIVE 266 111 72 81 32 NC_009009:SSA_0834|3end_Accessory_secretory_protein_Asp2,_putative_821119..821269_POSITIVE 265 44 8 149 118 NC_009009:SSA_1664|3end_Phosphatidylethanolamine_N-methyltransferase,_putative_1664449..1664599_NEGATIVE