Origin IGS: tctcccgaaagcgtttgcttacttctttgatgcctgagatgagctgcttcatttcaggcgtttctctgtttacaatctcgtgttccatagtttttcgtggaaaagattaggaatgaaaaaaatggtgggtaaatattctaaagtgagattatcccagatttgtcgttaggccttacttgaaaaatcaaaaaccgtgactcataaagtgcatcataaaagactgtatttcagctatttcgaagaccgatttgtctattttgacgggacagtagtgaattgtaataaaaagcctctaaagaggatttttaagtctgttttgcaaaacagactttgcaaaacagaaaaactatactacctttgttacctaaaca .........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.........1.........2.........3.........4.........5.........6.........7.........8.........9 tgtttaggtaacaaaggtagtatagtttttctgttttgcaaagtctgttttgcaaaacagacttaaaaatcctctttagaggctttttattacaattcactactgtcccgtcaaaatagacaaatcggtcttcgaaatagctgaaatacagtcttttatgatgcactttatgagtcacggtttttgatttttcaagtaaggcctaacgacaaatctgggataatctcactttagaatatttacccaccatttttttcattcctaatcttttccacgaaaaactatggaacacgagattgtaaacagagaaacgcctgaaatgaagcagctcatctcaggcatcaaagaagtaagcaaacgctttcgggaga Mask Tandem Repeat Region ================================================ tctcccgaaagcgtttgcttacttctttgatgcctgagatgagctgcttcatttcaggcgtttctctgtttacaatctcgtgttccatagtttttcgtggaaaagattaggaatgaaaaaaatggtgggtaaatattctaaagtgagattatcccagatttgtcgttaggccttacttgaaaaatcaaaaaccgtgactcataaagtgcatcataaaagactgtatttcagctatttcgaagaccgatttgtctattttgacgggacagtagtgaattgtaataaaaagcctctaaagaggatttttaagtctgtnnnnnnnnnnnnnnnnnnnnnnnnnnnaaaactatactacctttgttacctaaaca Find is-nt database================================================ Query_seq: PG0546:PG0547|PG0546:PG0547:hypothetical protein:hypothetical protein:<-->:600482..600852 371 tctcccgaaagcgtttgcttacttctttgatgcctgagatgagctgcttcatttcaggcgtttctctgtttacaatctcgtgttccatagtttttcgtggaaaagattaggaatgaaaaaaatggtgggtaaatattctaaagtgagattatcccagatttgtcgttaggccttacttgaaaaatcaaaaaccgtgactcataaagtgcatcataaaagactgtatttcagctatttcgaagaccgatttgtctattttgacgggacagtagtgaattgtaataaaaagcctctaaagaggatttttaagtctgttttgcaaaacagactttgcaaaacagaaaaactatactacctttgttacctaaaca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG0546:PG0547|PG0546:PG0547:hypothetical protein:hypothetical protein:<-->:600482..600852 371 tctcccgaaagcgtttgcttacttctttgatgcctgagatgagctgcttcatttcaggcgtttctctgtttacaatctcgtgttccatagtttttcgtggaaaagattaggaatgaaaaaaatggtgggtaaatattctaaagtgagattatcccagatttgtcgttaggccttacttgaaaaatcaaaaaccgtgactcataaagtgcatcataaaagactgtatttcagctatttcgaagaccgatttgtctattttgacgggacagtagtgaattgtaataaaaagcctctaaagaggatttttaagtctgttttgcaaaacagactttgcaaaacagaaaaactatactacctttgttacctaaaca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG0546:PG0547|PG0546:PG0547:hypothetical protein:hypothetical protein:<-->:600482..600852 371 tctcccgaaagcgtttgcttacttctttgatgcctgagatgagctgcttcatttcaggcgtttctctgtttacaatctcgtgttccatagtttttcgtggaaaagattaggaatgaaaaaaatggtgggtaaatattctaaagtgagattatcccagatttgtcgttaggccttacttgaaaaatcaaaaaccgtgactcataaagtgcatcataaaagactgtatttcagctatttcgaagaccgatttgtctattttgacgggacagtagtgaattgtaataaaaagcctctaaagaggatttttaagtctgttttgcaaaacagactttgcaaaacagaaaaactatactacctttgttacctaaaca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tctcccgaaagcgtttgcttacttctttgatgcctgagatgagctgcttcatttcaggcgtttctctgtttacaatctcgtgttccatagtttttcgtggaaaagattaggaatgaaaaaaatggtgggtaaatattctaaagtgagattatcccagatttgtcgttaggccttacttgaaaaatcaaaaaccgtgactcataaagtgcatcataaaagactgtatttcagctatttcgaagaccgatttgtctattttgacgggacagtagtgaattgtaataaaaagcctctaaagaggatttttaagtctgttttgcaaaacagactttgcaaaacagaaaaactatactacctttgttacctaaaca Predict ORF larger than 30AA ================================================ Protein_Len: 31 Strand: + Start: 15 End: 107 .............. M L T S L M P E M S C F I S G V S L F T I S C S I V F R G K D ........................................................................................................................................................................................................................................................................ Protein_Len: 41 Strand: + Start: 44 End: 166 ........................................... M L H F R R F S V Y N L V F H S F S W K R L G M K K M V G K Y S K V R L S Q I C R ............................................................................................................................................................................................................. Protein_Len: 59 Strand: + Start: 194 End: 370 ................................................................................................................................................................................................. M T H K V H H K R L Y F S Y F E D R F V Y F D G T V V N C N K K P L K R I F K S V L Q N R L C K T E K L Y Y L C Y L N . Protein_Len: 32 Strand: - Start: 188 End: 283 ........................................................................................................................................................................................... F G H S M F H M M F S Q I E A I E F V S K D I K V P C Y H I T M ........................................................................................ tctcccgaaagcgtttgcttacttctttgatgcctgagatgagctgcttcatttcaggcgtttctctgtttacaatctcgtgttccatagtttttcgtggaaaagattaggaatgaaaaaaatggtgggtaaatattctaaagtgagattatcccagatttgtcgttaggccttacttgaaaaatcaaaaaccgtgactcataaagtgcatcataaaagactgtatttcagctatttcgaagaccgatttgtctattttgacgggacagtagtgaattgtaataaaaagcctctaaagaggatttttaagtctgttttgcaaaacagactttgcaaaacagaaaaactatactacctttgttacctaaaca 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================================================ tctcccgaaagcgtttgcttacttctttgatgcctgagatgagctgcttcatttcaggcgtttctctgtttacaatctcgtgttccatagtttttcgtggaaaagattaggaatgaaaaaaatggtgggtaaatattctaaagtgagattatcccagatttgtcgttaggccttacttgaaaaatcaaaaaccgtgactcataaagtgcatcataaaagactgtatttcagctatttcgaagaccgatttgtctattttgacgggacagtagtgaattgtaataaaaagcctctaaagaggatttttaagtctgttttgcaaaacagactttgcaaaacagaaaaactatactacctttgttacctaaaca Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 86 HP_score: -10.1 Tail_Score: -4.27886 Start: 31 End: 60 Full_Region: TGCTTACTTCTTTGA TGCCTGAGATGAG CTGC TTCATTTCAGGCG TTTCTCTGTTTACAA ..............................TGCCTGAGATGAGCTGCTTCATTTCAGGCG....................................................................................................................................................................................................................................................................................................................... TransTerm Strand: + Conf: 78 HP_score: -9.4 Tail_Score: -3.53012 Start: 310 End: 329 Full_Region: AAAGAGGATTTTTAA GTCTGTTT TGCA AAACAGAC TTTGCAAAACAGAAA .....................................................................................................................................................................................................................................................................................................................GTCTGTTTTGCAAAACAGAC.......................................... Find igs database================================================ Query_seq: PG0546:PG0547|PG0546:PG0547:hypothetical protein:hypothetical protein:<-->:600482..600852 371 tctcccgaaagcgtttgcttacttctttgatgcctgagatgagctgcttcatttcaggcgtttctctgtttacaatctcgtgttccatagtttttcgtggaaaagattaggaatgaaaaaaatggtgggtaaatattctaaagtgagattatcccagatttgtcgttaggccttacttgaaaaatcaaaaaccgtgactcataaagtgcatcataaaagactgtatttcagctatttcgaagaccgatttgtctattttgacgggacagtagtgaattgtaataaaaagcctctaaagaggatttttaagtctgttttgcaaaacagactttgcaaaacagaaaaactatactacctttgttacctaaaca Intra-Species Hit: Count: 1 Min: 1 Max: 371 Len: 371 Subject: NC_002950_PG0546_PG0547|hypothetical protein:hypothetical protein|NEGATIVE:POSITIVE|[600482,600852]|371 HSP 1 e-value: 0.0 bit: 694.0 Len: 371 Query Start:1 Query End:371 Subject Strand: POSITIVE Subject Start: 1 Subject End: 371 tctcccgaaagcgtttgcttacttctttgatgcctgagatgagctgcttcatttcaggcgtttctctgtttacaatctcgtgttccatagtttttcgtggaaaagattaggaatgnnnnnnntggtgggtaaatattctaaagtgagattatcccagatttgtcgttaggccttacttgaaaaatcaaaaaccgtgactcataaagtgcatcataaaagactgtatttcagctatttcgaagaccgatttgtctattttgacgggacagtagtgaattgtaataaaaagcctctaaagaggatttttaagtctgttttgcaaaacagactttgcaaaacagaaaaactatactacctttgttacctaaaca tctcccgaaagcgtttgcttacttctttgatgcctgagatgagctgcttcatttcaggcgtttctctgtttacaatctcgtgttccatagtttttcgtggaaaagattaggaatgaaaaaaatggtgggtaaatattctaaagtgagattatcccagatttgtcgttaggccttacttgaaaaatcaaaaaccgtgactcataaagtgcatcataaaagactgtatttcagctatttcgaagaccgatttgtctattttgacgggacagtagtgaattgtaataaaaagcctctaaagaggatttttaagtctgttttgcaaaacagactttgcaaaacagaaaaactatactacctttgttacctaaaca Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCUCCCGAAAGCGUUUGCUUACUUCUUUGAUGCCUGAGAUGAGCUGCUUCAUUUCAGGCGUUUCUCUGUUUACAAUCUCGUGUUCCAUAGUUUUUCGUGGAAAAGAUUAGGAAUGAAAAAAAUGGUGGGUAAAUAUUCUAAAGUGAGAUUAUCCCAGAUUUGUCGUUAGGCCUUACUUGAAAAAUCAAAAACCGUGACUCAUAAAGUGCAUCAUAAAAGACUGUAUUUCAGCUAUUUCGAAGACCGAUUUGUCUAUUUUGACGGGACAGUAGUGAAUUGUAAUAAAAAGCCUCUAAAGAGGAUUUUUAAGUCUGUUUUGCAAAACAGACUUUGCAAAACAGAAAAACUAUACUACCUUUGUUACCUAAACA ..(((((..(((.((((((((((.....(((((((((((((((....))))))))))))))).....((((..(((((....((((((........)))))).)))))..)))).........)))))))))).........(((((.((((....(((((....(((((.....))))).))))).......))))))))).(((((((((......)).)))))))..))).......((((......)))).......)))))..((((((........((((((.((((....)))).))))))..(((((((((((((......))))))))))))).......))))))................ (-96.00) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGUUUAGGUAACAAAGGUAGUAUAGUUUUUCUGUUUUGCAAAGUCUGUUUUGCAAAACAGACUUAAAAAUCCUCUUUAGAGGCUUUUUAUUACAAUUCACUACUGUCCCGUCAAAAUAGACAAAUCGGUCUUCGAAAUAGCUGAAAUACAGUCUUUUAUGAUGCACUUUAUGAGUCACGGUUUUUGAUUUUUCAAGUAAGGCCUAACGACAAAUCUGGGAUAAUCUCACUUUAGAAUAUUUACCCACCAUUUUUUUCAUUCCUAAUCUUUUCCACGAAAAACUAUGGAACACGAGAUUGUAAACAGAGAAACGCCUGAAAUGAAGCAGCUCAUCUCAGGCAUCAAAGAAGUAAGCAAACGCUUUCGGGAGA ((((.....))))..((((((........((((((((((((((....))))))))))))))..((((((.((((....)))).)))))).........)))))).(((((.......((((......))))...(((..((((.....))))..)))....((((((((....(((..(((((((((....)))...))))))....)))...((((..((((((((.(....)............((((.((((((..................))))))..)))).....))))))))...)))).....((((((.((((......)))).))))))......)))))..)))........))))).. (-88.97) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 971 50 1 141 92 NC_002950:PG0546|5end_hypothetical_protein_600391..600621_NEGATIVE 375 68 24 88 37 NC_002950:PG2071|5end_hypothetical_protein_2166437..2166667_POSITIVE 342 49 2 153 101 NC_002950:PG1735|5end_MutT/nudix_family_protein_1823082..1823312_NEGATIVE 330 59 11 64 15 NC_002950:PG0083|5end_hypothetical_protein_96952..97182_POSITIVE 329 70 21 56 8 NC_002950:PG0578|5end_UDP-N-acetylmuramoylalanine--D-glutamate_ligase_634480..634710_POSITIVE 329 50 1 184 125 NC_002950:PG0398|5end_recF_protein_435710..435940_NEGATIVE 323 48 1 159 107 NC_002950:PG2087|5end_hypothetical_protein_2186990..2187220_POSITIVE 321 49 2 127 69 NC_002950:PG0605|5end_hypothetical_protein_662406..662636_NEGATIVE 320 73 31 83 37 NC_002950:PG1389|5end_DNA-binding_protein,_histone-like_family_1471328..1471558_NEGATIVE 319 45 2 216 168 NC_002950:PG2205|5end_2-dehydropantoate_2-reductase_2316121..2316351_POSITIVE 317 44 1 48 1 NC_002950:PG0790|5end_GTP-binding_protein_Obg_842583..842813_NEGATIVE 314 68 25 53 1 NC_002950:PG2131|5end_60_kDa_protein_2236174..2236404_POSITIVE 314 68 22 87 35 NC_002950:PG1831|5end_ATP-dependent_DNA_helicase_RecQ_1925422..1925652_NEGATIVE 314 68 21 192 130 NC_002950:PG1009|5end_hypothetical_protein_1068495..1068725_NEGATIVE 306 59 17 61 16 NC_002950:PG1053|5end_transcriptional_regulator,_putative_1120065..1120295_POSITIVE 305 44 1 193 149 NC_002950:PG0776|5end_electron_transfer_flavoprotein,_alpha_subunit_830184..830414_NEGATIVE 303 59 11 223 180 NC_002950:PG2214|5end_hypothetical_protein_2326575..2326805_NEGATIVE 303 50 1 166 109 NC_002950:PG0259|5end_hypothetical_protein_292278..292508_POSITIVE 303 49 5 58 17 NC_002950:PG0195|5end_rubrerythrin_232046..232276_POSITIVE 302 59 12 144 89 NC_002950:PG0268|5end_tRNA_(5-methylaminomethyl-2-thiouridylate)-methyltransferase_300898..301128_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 375 68 24 118 67 NC_002950:PG2070|3end_hypothetical_protein_2166547..2166697_POSITIVE 370 50 2 151 87 NC_002950:PG0412|3end_DNA_mismatch_repair_protein_MutL_449584..449734_NEGATIVE 330 59 11 58 9 NC_002950:PG0082|3end_hypothetical_protein_97026..97176_POSITIVE 323 69 22 147 99 NC_002950:PG0377|3end_30S_ribosomal_protein_S2_407845..407995_POSITIVE 321 49 2 82 24 NC_002950:PG0606|3end_hypothetical_protein_662451..662601_NEGATIVE 314 60 12 137 79 NC_002950:PG1174|3end_thioesterase_family_protein_1253210..1253360_NEGATIVE 309 49 1 82 46 NC_002950:PG1942|3end_30S_ribosomal_protein_S12_2027946..2028096_NEGATIVE 305 279 231 151 87 NC_002950:PG1118|3end_clpB_protein_1192083..1192233_NEGATIVE 302 59 12 139 84 NC_002950:PG0267|3end_arginyl-tRNA_synthetase_300973..301123_POSITIVE 302 50 1 69 21 NC_002950:PG0195|3end_rubrerythrin_232704..232854_POSITIVE 300 47 4 97 41 NC_002950:PG1638|3end_thioredoxin_family_protein_1718664..1718814_NEGATIVE 298 100 54 110 57 NC_002950:PG1778|3end_hypothetical_protein_1867922..1868072_POSITIVE 296 47 1 122 58 NC_002950:PG1969|3end_hypothetical_protein_2058613..2058763_NEGATIVE 294 77 31 84 26 NC_002950:PG2094|3end_hypothetical_protein_2193321..2193471_NEGATIVE 294 50 1 89 37 NC_002950:PG0334|3end_glycosyl_transferase,_group_2_family_protein_368792..368942_NEGATIVE 293 270 223 138 94 NC_002950:PG0769|3end_fibronectin_type_III_domain_protein_822555..822705_NEGATIVE 292 48 5 109 79 NC_002950:PG0344|3end_purple_acid_phosphatase_378543..378693_NEGATIVE 290 41 3 51 14 NC_002950:PG0810|3end_hypothetical_protein_871977..872127_NEGATIVE 285 79 34 138 87 NC_002950:PG1225|3end_ABC_transporter,_ATP-binding_protein_1303336..1303486_POSITIVE 285 80 33 134 98 NC_002950:PG0198|3end_hypothetical_protein_237501..237651_POSITIVE