Origin IGS: ataaaaaaccgattataatttgctggattttaagccctgcaaatatatggcatttccctttatcccattgagttgcatgcttgttttgcaataattcgaacctatcgtttataagcagaacacgatgttccttgggattatacttaaaagtccacggactttatactataaaccctccatactttatacttaaaacccctatggctttatactataaagtctcctgcgtttatacttaaaacccttggggctttatagtataaagtctcaaggtaatcgaaaatagacccgacataagttttttcatacatttgtttcagtttttagccattatattat .........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.........1.........2.........3.........4.........5.........6.........7.........8.........9 ataatataatggctaaaaactgaaacaaatgtatgaaaaaacttatgtcgggtctattttcgattaccttgagactttatactataaagccccaagggttttaagtataaacgcaggagactttatagtataaagccataggggttttaagtataaagtatggagggtttatagtataaagtccgtggacttttaagtataatcccaaggaacatcgtgttctgcttataaacgataggttcgaattattgcaaaacaagcatgcaactcaatgggataaagggaaatgccatatatttgcagggcttaaaatccagcaaattataatcggttttttat Mask Tandem Repeat Region ================================================ ataaaaaaccgattataatttgctggattttaagccctgcaaatatatggcatttccctttatcccattgagttgcatgcttgttttgcaataattcgaacctatcgtttataagcagaacacgatgttccttgggattatacttaaaagtccacgnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnngtctcaaggtaatcgaaaatagacccgacataagttttttcatacatttgtttcagtttttagccattatattat Find is-nt database================================================ Query_seq: PG1126:PG1127|PG1126:PG1127:uracil permease:transcriptional regulator, AsnC Family:<-->:1203024..1203362 339 ataaaaaaccgattataatttgctggattttaagccctgcaaatatatggcatttccctttatcccattgagttgcatgcttgttttgcaataattcgaacctatcgtttataagcagaacacgatgttccttgggattatacttaaaagtccacggactttatactataaaccctccatactttatacttaaaacccctatggctttatactataaagtctcctgcgtttatacttaaaacccttggggctttatagtataaagtctcaaggtaatcgaaaatagacccgacataagttttttcatacatttgtttcagtttttagccattatattat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG1126:PG1127|PG1126:PG1127:uracil permease:transcriptional regulator, AsnC Family:<-->:1203024..1203362 339 ataaaaaaccgattataatttgctggattttaagccctgcaaatatatggcatttccctttatcccattgagttgcatgcttgttttgcaataattcgaacctatcgtttataagcagaacacgatgttccttgggattatacttaaaagtccacggactttatactataaaccctccatactttatacttaaaacccctatggctttatactataaagtctcctgcgtttatacttaaaacccttggggctttatagtataaagtctcaaggtaatcgaaaatagacccgacataagttttttcatacatttgtttcagtttttagccattatattat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG1126:PG1127|PG1126:PG1127:uracil permease:transcriptional regulator, AsnC Family:<-->:1203024..1203362 339 ataaaaaaccgattataatttgctggattttaagccctgcaaatatatggcatttccctttatcccattgagttgcatgcttgttttgcaataattcgaacctatcgtttataagcagaacacgatgttccttgggattatacttaaaagtccacggactttatactataaaccctccatactttatacttaaaacccctatggctttatactataaagtctcctgcgtttatacttaaaacccttggggctttatagtataaagtctcaaggtaatcgaaaatagacccgacataagttttttcatacatttgtttcagtttttagccattatattat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ataaaaaaccgattataatttgctggattttaagccctgcaaatatatggcatttccctttatcccattgagttgcatgcttgttttgcaataattcgaacctatcgtttataagcagaacacgatgttccttgggattatacttaaaagtccacggactttatactataaaccctccatactttatacttaaaacccctatggctttatactataaagtctcctgcgtttatacttaaaacccttggggctttatagtataaagtctcaaggtaatcgaaaatagacccgacataagttttttcatacatttgtttcagtttttagccattatattat Predict ORF larger than 30AA ================================================ Protein_Len: 52 Strand: + Start: 81 End: 236 ................................................................................ M F C N N S N L S F I S R T R C S L G L Y L K V H G L Y T I N P P Y F I L K T P M A L Y Y K V S C V Y T ....................................................................................................... Protein_Len: 37 Strand: - Start: 210 End: 320 ................................................................................................................................................................................................................. V I F D G A N I S L V R P A K Y Y L T E L Y D F I S G V Y T K E Y M Q K M ................... Protein_Len: 30 Strand: - Start: 16 End: 105 ............... L K S S K L G Q L Y I A N G K I G N L Q M S T K C Y N S G M .......................................................................................................................................................................................................................................... Protein_Len: 39 Strand: - Start: 2 End: 118 . L F G I I I Q Q I K L G A F I H C K G K D W Q T A H K N Q L L E F R D N I L M ............................................................................................................................................................................................................................. ataaaaaaccgattataatttgctggattttaagccctgcaaatatatggcatttccctttatcccattgagttgcatgcttgttttgcaataattcgaacctatcgtttataagcagaacacgatgttccttgggattatacttaaaagtccacggactttatactataaaccctccatactttatacttaaaacccctatggctttatactataaagtctcctgcgtttatacttaaaacccttggggctttatagtataaagtctcaaggtaatcgaaaatagacccgacataagttttttcatacatttgtttcagtttttagccattatattat 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================================================ ataaaaaaccgattataatttgctggattttaagccctgcaaatatatggcatttccctttatcccattgagttgcatgcttgttttgcaataattcgaacctatcgtttataagcagaacacgatgttccttgggattatacttaaaagtccacggactttatactataaaccctccatactttatacttaaaacccctatggctttatactataaagtctcctgcgtttatacttaaaacccttggggctttatagtataaagtctcaaggtaatcgaaaatagacccgacataagttttttcatacatttgtttcagtttttagccattatattat Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 71 HP_score: -6.3 Tail_Score: -4.2349 Start: 242 End: 274 Full_Region: ggtctattttcgatt accttgagactttat act ataaagccccaaggg ttttaagtataaacg .................................................................................................................................................................................................................................................accttgagactttatactataaagccccaaggg................................................................. TransTerm Strand: - Conf: 77 HP_score: -9.8 Tail_Score: -3.13773 Start: 243 End: 273 Full_Region: gtctattttcgatta ccttgagactttat act ataaagccccaagg gttttaagtataaac ..................................................................................................................................................................................................................................................ccttgagactttatactataaagccccaagg.................................................................. Find igs database================================================ Query_seq: PG1126:PG1127|PG1126:PG1127:uracil permease:transcriptional regulator, AsnC Family:<-->:1203024..1203362 339 ataaaaaaccgattataatttgctggattttaagccctgcaaatatatggcatttccctttatcccattgagttgcatgcttgttttgcaataattcgaacctatcgtttataagcagaacacgatgttccttgggattatacttaaaagtccacggactttatactataaaccctccatactttatacttaaaacccctatggctttatactataaagtctcctgcgtttatacttaaaacccttggggctttatagtataaagtctcaaggtaatcgaaaatagacccgacataagttttttcatacatttgtttcagtttttagccattatattat Intra-Species Hit: Count: 2 Min: 1 Max: 339 Len: 339 Subject: NC_002950_PG1126_PG1127|uracil permease:transcriptional regulator, AsnC Family|NEGATIVE:POSITIVE|[1203024,1203362]|339 HSP 1 e-value: 0.0 bit: 672.0 Len: 339 Query Start:1 Query End:339 Subject Strand: POSITIVE Subject Start: 1 Subject End: 339 ataaaaaaccgattataatttgctggattttaagccctgcaaatatatggcatttccctttatcccattgagttgcatgcttgttttgcaataattcgaacctatcgtttataagcagaacacgatgttccttgggattatacttaaaagtccacggactttatactataaaccctccatactttatacttaaaacccctatggctttatactataaagtctcctgcgtttatacttaaaacccttggggctttatagtataaagtctcaaggtaatcgaaaatagacccgacataagttttttcatacatttgtttcagtttttagccattatattat ataaaaaaccgattataatttgctggattttaagccctgcaaatatatggcatttccctttatcccattgagttgcatgcttgttttgcaataattcgaacctatcgtttataagcagaacacgatgttccttgggattatacttaaaagtccacggactttatactataaaccctccatactttatacttaaaacccctatggctttatactataaagtctcctgcgtttatacttaaaacccttggggctttatagtataaagtctcaaggtaatcgaaaatagacccgacataagttttttcatacatttgtttcagtttttagccattatattat Subject: NC_002950_PG1363_PG1364|hypothetical protein:1-deoxy-D-xylulose 5-phosphate reductoisomerase|POSITIVE:NEGATIVE|[1444220,1444477]|258 HSP 1 e-value: 1.0E-54 bit: 214.0 Len: 108 Query Start:137 Query End:244 Subject Strand: NEGATIVE Subject Start: 36 Subject End: 143 ........................................................................................................................................attatacttaaaagtccacggactttatactataaaccctccatactttatacttaaaacccctatggctttatactataaagtctcctgcgtttatacttaaaaccc............................................................................................... ........................................................................................................................................attatacttaaaagtccacggactttatactataaaccctccatactttatacttaaaacccctatggctttatactataaagtctcctgcgtttatacttaaaaccc............................................................................................... Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUAAAAAACCGAUUAUAAUUUGCUGGAUUUUAAGCCCUGCAAAUAUAUGGCAUUUCCCUUUAUCCCAUUGAGUUGCAUGCUUGUUUUGCAAUAAUUCGAACCUAUCGUUUAUAAGCAGAACACGAUGUUCCUUGGGAUUAUACUUAAAAGUCCACGGACUUUAUACUAUAAACCCUCCAUACUUUAUACUUAAAACCCCUAUGGCUUUAUACUAUAAAGUCUCCUGCGUUUAUACUUAAAACCCUUGGGGCUUUAUAGUAUAAAGUCUCAAGGUAAUCGAAAAUAGACCCGACAUAAGUUUUUUCAUACAUUUGUUUCAGUUUUUAGCCAUUAUAUUAU ...((((((((((((..((((((.((.........)).)))))).(((((...................(((..((((.(.((((((((.((((..(((.....))).))))..)))))))).)))))..)))(((.(((((....((((((....))))))....))))).))).)))))................(((..(((((((((((((((((((((..(.((((.......)))).)..)))))))))))))))))))))...)))))))))...........((.((((((.(......).)))))).)).)))))).............. (-80.20) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUAAUAUAAUGGCUAAAAACUGAAACAAAUGUAUGAAAAAACUUAUGUCGGGUCUAUUUUCGAUUACCUUGAGACUUUAUACUAUAAAGCCCCAAGGGUUUUAAGUAUAAACGCAGGAGACUUUAUAGUAUAAAGCCAUAGGGGUUUUAAGUAUAAAGUAUGGAGGGUUUAUAGUAUAAAGUCCGUGGACUUUUAAGUAUAAUCCCAAGGAACAUCGUGUUCUGCUUAUAAACGAUAGGUUCGAAUUAUUGCAAAACAAGCAUGCAACUCAAUGGGAUAAAGGGAAAUGCCAUAUAUUUGCAGGGCUUAAAAUCCAGCAAAUUAUAAUCGGUUUUUUAU ..............(((((((((........................(((..((((((........((.....((((((((((.(((((((((...((((((((.(((((....((....))))))).).)))))))...)))))))))))))))))))..)).(((.(((((.(..((((((....))))))..).))))).)))..(((((.....)))))..........))))))..)))....((((.....((((.(((((....((((.((........)).))))....)))))..))))........)))).......)))))))))... (-90.72) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 908 80 31 171 122 NC_002950:PG1126|5end_uracil_permease_1202933..1203163_NEGATIVE 289 269 225 183 139 NC_002950:PG1697|5end_type_II_restriction_endonuclease,_putative_1781020..1781250_POSITIVE 287 109 63 74 27 NC_002950:PG1514|5end_glycerol_dehydrogenase-related_protein_1589800..1590030_POSITIVE 287 79 33 83 30 NC_002950:PG1237|5end_transcriptional_regulator,_LuxR_family_1312229..1312459_POSITIVE 283 260 211 229 178 NC_002950:PG0576|5end_UDP-N-acetylmuramoylalanyl-D-glutamate--2,_6-diaminopimelate_ligase_631719..631949_POSITIVE 282 67 21 57 2 NC_002950:PG0932|5end_DNA_polymerase_III,_delta_prime_subunit,_putative_988503..988733_POSITIVE 273 78 33 187 146 NC_002950:PG0987|5end_hypothetical_protein_1048002..1048232_POSITIVE 271 80 48 55 13 NC_002950:PG1354|5end_hydrolase,_carbon-nitrogen_family_1434765..1434995_NEGATIVE 269 230 197 220 187 NC_002950:PG0164|5end_hypothetical_protein_187395..187625_NEGATIVE 268 227 195 152 118 NC_002950:PG0614|5end_hypothetical_protein_665847..666077_POSITIVE 266 88 47 66 19 NC_002950:PG0210|5end_precorrin-6x_reductase/cobalamin_biosynthetic_protein_CbiD_245969..246199_NEGATIVE 264 90 48 64 28 NC_002950:PG1985|5end_CRISPR-associated_TM1792_family_protein_2074580..2074810_NEGATIVE 263 140 95 198 157 NC_002950:PG1540|5end_S-adenosylmethionine:tRNA_ribosyltransferase-isomerase_1619277..1619507_POSITIVE 261 157 114 155 119 NC_002950:PG0374|5end_hypothetical_protein_405564..405794_NEGATIVE 258 80 34 89 44 NC_002950:PG1273|5end_hypothetical_protein_1351837..1352067_NEGATIVE 258 88 46 126 84 NC_002950:PG0850|5end_DNA_binding_protein,_excisionase_family,_putative_911578..911808_NEGATIVE 257 107 63 53 6 NC_002950:PG0855|5end_hypothetical_protein_916055..916285_NEGATIVE 255 57 23 185 152 NC_002950:PG1881|5end_hypothetical_protein_1976524..1976754_POSITIVE 255 98 53 215 174 NC_002950:PG0767|5end_4-alpha-glucanotransferase_820533..820763_NEGATIVE 255 90 48 90 52 NC_002950:PG0758|5end_peptidyl-dipeptidase_Dcp_808554..808784_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 793 240 191 51 2 NC_002950:PG1363|3end_hypothetical_protein_1444159..1444309_POSITIVE 287 109 63 59 12 NC_002950:PG1513|3end_phosphoribosyltransferase,_putative/phosphoglycerate_mutase_family_protein_1589865..1590015_POSITIVE 287 79 33 86 33 NC_002950:PG1236|3end_hypothetical_protein_1312312..1312462_POSITIVE 271 80 48 58 16 NC_002950:PG1355|3end_acyltransferase,_putative_1434762..1434912_NEGATIVE 267 88 47 136 99 NC_002950:PG2021|3end_hypothetical_protein_2112921..2113071_NEGATIVE 266 88 47 69 22 NC_002950:PG0211|3end_cobalamin_biosynthesis_protein_CbiG/precorrin-4_C11-methyltransferase_245966..246116_NEGATIVE 264 90 48 50 14 NC_002950:PG1986|3end_CRISPR-associated_TM1793_family_protein_2074594..2074744_NEGATIVE 264 158 114 146 113 NC_002950:PG1789|3end_peptidyl-dipeptidase_Dcp_1877417..1877567_NEGATIVE 258 88 46 138 96 NC_002950:PG0851|3end_hypothetical_protein_911566..911716_NEGATIVE 257 107 63 148 101 NC_002950:PG0855|3end_hypothetical_protein_915960..916110_NEGATIVE 253 268 222 60 18 NC_002950:PG1985|3end_CRISPR-associated_TM1792_family_protein_2073879..2074029_NEGATIVE 249 80 32 151 108 NC_002950:PG1759|3end_adhesion_protein,_putative_1846597..1846747_POSITIVE 249 66 21 59 7 NC_002950:PG0605|3end_hypothetical_protein_661165..661315_NEGATIVE 248 67 25 84 31 NC_002950:PG1483|3end_conjugative_transposon_protein_TraE_1558783..1558933_NEGATIVE 246 83 46 137 97 NC_002950:PG2020|3end_CRISPR-associated_TM1814_family_protein_2111608..2111758_NEGATIVE 245 89 43 57 4 NC_002950:PG1953|3end_YitT_family_protein_2044589..2044739_POSITIVE 244 80 35 149 105 NC_002950:PG0678|3end_pyrazinamidase/nicotinamidase,_putative_729471..729621_POSITIVE 242 90 49 67 17 NC_002950:PG1866|3end_hypothetical_protein_1964736..1964886_POSITIVE 240 138 97 50 3 NC_002950:PG2082|3end_POT_family_protein_2181843..2181993_NEGATIVE 240 280 242 83 45 NC_002950:PG1039|3end_integral_membrane_protein_1105325..1105475_NEGATIVE