Origin IGS: aaaaaaaaggccggaaagacaagaagcccgcgctgctcttcagggtggattctgcctgtacattttgtctgctgatgacacaggtgaaaagcattacatttgtaatcatcaaaggatgaaaagcaacttaattgcaaaaaatctttttagcgggcttattatcatggataaatcacaactaagcaaactcagaaaaaggttttccctgtatctgcttgtgggaatagccttataccttttcaaggtaatcaatttcgattcttattggggaatatcttttttcgttttatggtcgataggccttttagcggccgtgatcaatgccattaaatcccccaaaagctaattgcatcg .........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 cgatgcaattagcttttgggggatttaatggcattgatcacggccgctaaaaggcctatcgaccataaaacgaaaaaagatattccccaataagaatcgaaattgattaccttgaaaaggtataaggctattcccacaagcagatacagggaaaacctttttctgagtttgcttagttgtgatttatccatgataataagcccgctaaaaagattttttgcaattaagttgcttttcatcctttgatgattacaaatgtaatgcttttcacctgtgtcatcagcagacaaaatgtacaggcagaatccaccctgaagagcagcgcgggcttcttgtctttccggcctttttttt Mask Tandem Repeat Region ================================================ aaaaaaaaggccggaaagacaagaagcccgcgctgctcttcagggtggattctgcctgtacattttgtctgctgatgacacaggtgaaaagcattacatttgtaatcatcaaaggatgaaaagcaacttaattgcaaaaaatctttttagcgggcttattatcatggataaatcacaactaagcaaactcagaaaaaggttttccctgtatctgcttgtgggaatagccttataccttttcaaggtaatcaatttcgattcttattggggaatatcttttttcgttttatggtcgataggccttttagcggccgtgatcaatgccattaaatcccccaaaagctaattgcatcg Find is-nt database================================================ Query_seq: PG1967:PG1968|PG1967:PG1968:TPR domain protein:hypothetical protein:-><-:2058196..2058549 354 aaaaaaaaggccggaaagacaagaagcccgcgctgctcttcagggtggattctgcctgtacattttgtctgctgatgacacaggtgaaaagcattacatttgtaatcatcaaaggatgaaaagcaacttaattgcaaaaaatctttttagcgggcttattatcatggataaatcacaactaagcaaactcagaaaaaggttttccctgtatctgcttgtgggaatagccttataccttttcaaggtaatcaatttcgattcttattggggaatatcttttttcgttttatggtcgataggccttttagcggccgtgatcaatgccattaaatcccccaaaagctaattgcatcg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG1967:PG1968|PG1967:PG1968:TPR domain protein:hypothetical protein:-><-:2058196..2058549 354 aaaaaaaaggccggaaagacaagaagcccgcgctgctcttcagggtggattctgcctgtacattttgtctgctgatgacacaggtgaaaagcattacatttgtaatcatcaaaggatgaaaagcaacttaattgcaaaaaatctttttagcgggcttattatcatggataaatcacaactaagcaaactcagaaaaaggttttccctgtatctgcttgtgggaatagccttataccttttcaaggtaatcaatttcgattcttattggggaatatcttttttcgttttatggtcgataggccttttagcggccgtgatcaatgccattaaatcccccaaaagctaattgcatcg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG1967:PG1968|PG1967:PG1968:TPR domain protein:hypothetical protein:-><-:2058196..2058549 354 aaaaaaaaggccggaaagacaagaagcccgcgctgctcttcagggtggattctgcctgtacattttgtctgctgatgacacaggtgaaaagcattacatttgtaatcatcaaaggatgaaaagcaacttaattgcaaaaaatctttttagcgggcttattatcatggataaatcacaactaagcaaactcagaaaaaggttttccctgtatctgcttgtgggaatagccttataccttttcaaggtaatcaatttcgattcttattggggaatatcttttttcgttttatggtcgataggccttttagcggccgtgatcaatgccattaaatcccccaaaagctaattgcatcg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aaaaaaaaggccggaaagacaagaagcccgcgctgctcttcagggtggattctgcctgtacattttgtctgctgatgacacaggtgaaaagcattacatttgtaatcatcaaaggatgaaaagcaacttaattgcaaaaaatctttttagcgggcttattatcatggataaatcacaactaagcaaactcagaaaaaggttttccctgtatctgcttgtgggaatagccttataccttttcaaggtaatcaatttcgattcttattggggaatatcttttttcgttttatggtcgataggccttttagcggccgtgatcaatgccattaaatcccccaaaagctaattgcatcg Predict ORF larger than 30AA ================================================ Protein_Len: 52 Strand: + Start: 172 End: 327 ........................................................................................................................................................................... M T T K Q T Q K K V F P V S A C G N S L I P F Q G N Q F R F L L G N I F F R F M V D R P F S G R D Q C H ........................... Protein_Len: 60 Strand: + Start: 56 End: 343 ....................................................... M Y I L S A D D T G E K H Y I C N H Q R M K S N L I A K N L F S G L I I M D K S Q L S K L R K R F S L Y L L V G I A L Y ........... Protein_Len: 47 Strand: - Start: 112 End: 252 ............................................................................................................... L I F L L K I A F F R K L P S I I M S L D C S L L S L F L N E R Y R S T P I A K Y R K L T I M ...................................................................................................... Protein_Len: 45 Strand: - Start: 3 End: 137 .. F F A P F V L L G R Q E E P H I R G T C K T Q Q H C L H F A N C K Y D D F S S F C S L Q M ......................................................................................................................................................................................................................... Protein_Len: 37 Strand: - Start: 2 End: 112 . F F P R F S L F G A S S K L T S E A Q V N Q R S I V C T F L M V N T I M M .................................................................................................................................................................................................................................................. aaaaaaaaggccggaaagacaagaagcccgcgctgctcttcagggtggattctgcctgtacattttgtctgctgatgacacaggtgaaaagcattacatttgtaatcatcaaaggatgaaaagcaacttaattgcaaaaaatctttttagcgggcttattatcatggataaatcacaactaagcaaactcagaaaaaggttttccctgtatctgcttgtgggaatagccttataccttttcaaggtaatcaatttcgattcttattggggaatatcttttttcgttttatggtcgataggccttttagcggccgtgatcaatgccattaaatcccccaaaagctaattgcatcg 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================================================ aaaaaaaaggccggaaagacaagaagcccgcgctgctcttcagggtggattctgcctgtacattttgtctgctgatgacacaggtgaaaagcattacatttgtaatcatcaaaggatgaaaagcaacttaattgcaaaaaatctttttagcgggcttattatcatggataaatcacaactaagcaaactcagaaaaaggttttccctgtatctgcttgtgggaatagccttataccttttcaaggtaatcaatttcgattcttattggggaatatcttttttcgttttatggtcgataggccttttagcggccgtgatcaatgccattaaatcccccaaaagctaattgcatcg Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 41 HP_score: -2.8 Tail_Score: -2.58544 Start: 190 End: 214 Full_Region: ACAACTAAGCAAACT CAGAAAAAGG TTTTC CCTGTATCTG CTTGTGGGAATAGCC .............................................................................................................................................................................................CAGAAAAAGGTTTTCCCTGTATCTG............................................................................................................................................ Find igs database================================================ Query_seq: PG1967:PG1968|PG1967:PG1968:TPR domain protein:hypothetical protein:-><-:2058196..2058549 354 aaaaaaaaggccggaaagacaagaagcccgcgctgctcttcagggtggattctgcctgtacattttgtctgctgatgacacaggtgaaaagcattacatttgtaatcatcaaaggatgaaaagcaacttaattgcaaaaaatctttttagcgggcttattatcatggataaatcacaactaagcaaactcagaaaaaggttttccctgtatctgcttgtgggaatagccttataccttttcaaggtaatcaatttcgattcttattggggaatatcttttttcgttttatggtcgataggccttttagcggccgtgatcaatgccattaaatcccccaaaagctaattgcatcg Intra-Species Hit: Count: 1 Min: 9 Max: 354 Len: 346 Subject: NC_002950_PG1967_PG1968|TPR domain protein:hypothetical protein|POSITIVE:NEGATIVE|[2058196,2058549]|354 HSP 1 e-value: 0.0 bit: 686.0 Len: 346 Query Start:9 Query End:354 Subject Strand: POSITIVE Subject Start: 9 Subject End: 354 ........ggccggaaagacaagaagcccgcgctgctcttcagggtggattctgcctgtacattttgtctgctgatgacacaggtgaaaagcattacatttgtaatcatcaaaggatgaaaagcaacttaattgcaaaaaatctttttagcgggcttattatcatggataaatcacaactaagcaaactcagaaaaaggttttccctgtatctgcttgtgggaatagccttataccttttcaaggtaatcaatttcgattcttattggggaatatcttttttcgttttatggtcgataggccttttagcggccgtgatcaatgccattaaatcccccaaaagctaattgcatcg ........ggccggaaagacaagaagcccgcgctgctcttcagggtggattctgcctgtacattttgtctgctgatgacacaggtgaaaagcattacatttgtaatcatcaaaggatgaaaagcaacttaattgcaaaaaatctttttagcgggcttattatcatggataaatcacaactaagcaaactcagaaaaaggttttccctgtatctgcttgtgggaatagccttataccttttcaaggtaatcaatttcgattcttattggggaatatcttttttcgttttatggtcgataggccttttagcggccgtgatcaatgccattaaatcccccaaaagctaattgcatcg Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GGCCGGAAAGACAAGAAGCCCGCGCUGCUCUUCAGGGUGGAUUCUGCCUGUACAUUUUGUCUGCUGAUGACACAGGUGAAAAGCAUUACAUUUGUAAUCAUCAAAGGAUGAAAAGCAACUUAAUUGCAAAAAAUCUUUUUAGCGGGCUUAUUAUCAUGGAUAAAUCACAACUAAGCAAACUCAGAAAAAGGUUUUCCCUGUAUCUGCUUGUGGGAAUAGCCUUAUACCUUUUCAAGGUAAUCAAUUUCGAUUCUUAUUGGGGAAUAUCUUUUUUCGUUUUAUGGUCGAUAGGCCUUUUAGCGGCCGUGAUCAAUGCCAUUAAAUCCCCCAAAAGCUAAUUGCAUCG ((((((.............))).)))........(((.(((((..((((((...(((..(((..((((((.(((((((..........)))))))..))))))..)))..))).((((.....))))..............))))))........((((....(((((...............(((((((((.(((((((.........((((((((.......(((((.....)))))..........))))))))))))))).)))))))))((((....((((....))))....))))...))))).....))))..))))))))....((.....)).... (-88.75) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CGAUGCAAUUAGCUUUUGGGGGAUUUAAUGGCAUUGAUCACGGCCGCUAAAAGGCCUAUCGACCAUAAAACGAAAAAAGAUAUUCCCCAAUAAGAAUCGAAAUUGAUUACCUUGAAAAGGUAUAAGGCUAUUCCCACAAGCAGAUACAGGGAAAACCUUUUUCUGAGUUUGCUUAGUUGUGAUUUAUCCAUGAUAAUAAGCCCGCUAAAAAGAUUUUUUGCAAUUAAGUUGCUUUUCAUCCUUUGAUGAUUACAAAUGUAAUGCUUUUCACCUGUGUCAUCAGCAGACAAAAUGUACAGGCAGAAUCCACCCUGAAGAGCAGCGCGGGCUUCUUGUCUUUCCGGCC ((((........((((((((((((...((((..(((((...((((.......)))).)))))))))....(.......)..))))))))).))).))))........(((((.....)))))...((((.....(((((((((((.(((..((.....))..))).)))))))....))))..........(((((.((((((((......((((......))))..(((((((((((..........(((((....)))))....(((.((((((.(((...........)))))))))..))).......))))))))))))))))))).))))).....)))) (-93.90) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 404 48 3 141 83 NC_002950:PG1980|5end_hypothetical_protein_2067930..2068160_NEGATIVE 402 44 4 218 174 NC_002950:PG0596|5end_ribosomal_protein_S18_653365..653595_POSITIVE 400 70 21 182 126 NC_002950:PG1617|5end_hypothetical_protein_1697755..1697985_NEGATIVE 394 69 21 190 145 NC_002950:PG1220|5end_erythronate-4-phosphate_dehydrogenase_1296986..1297216_POSITIVE 385 46 1 73 20 NC_002950:PG0231|5end_hypothetical_protein_266031..266261_POSITIVE 376 70 21 63 7 NC_002950:PG1173|5end_YkgG_family_protein_1252435..1252665_POSITIVE 368 47 1 71 5 NC_002950:PG1664|5end_ABC_transporter,_permease_protein,_putative_1745813..1746043_POSITIVE 368 45 1 145 78 NC_002950:PG1029|5end_hypothetical_protein_1091080..1091310_POSITIVE 364 64 22 53 8 NC_002950:PG1457|5end_hypothetical_protein_1538650..1538880_POSITIVE 362 67 23 49 8 NC_002950:PG0782|5end_MotA/TolQ/ExbB_proton_channel_family_protein_834530..834760_NEGATIVE 362 58 19 176 131 NC_002950:PG0032|5end_beta-mannosidase,_putative_40212..40442_NEGATIVE 357 36 3 100 61 NC_002950:PG1799|5end_hypothetical_protein_1894499..1894729_POSITIVE 356 48 4 230 176 NC_002950:PG1305|5end_glycine_dehydrogenase_1386538..1386768_NEGATIVE 351 48 1 66 9 NC_002950:PG2214|5end_hypothetical_protein_2326575..2326805_NEGATIVE 350 50 1 168 122 NC_002950:PG0327|5end_hypothetical_protein_362061..362291_NEGATIVE 349 70 24 195 133 NC_002950:PG0757|5end_hypothetical_protein_806370..806600_NEGATIVE 342 48 2 195 149 NC_002950:PG1997|5end_hypothetical_protein_2086831..2087061_POSITIVE 341 50 3 78 20 NC_002950:PG0309|5end_thiamine_biosynthesis_lipoprotein_ApbE_345023..345253_NEGATIVE 340 328 281 192 131 NC_002950:PG1964|5end_bacterial_sugar_transferase_2052910..2053140_POSITIVE 340 69 21 193 131 NC_002950:PG0242|5end_conserved_hypothetical_protein_TIGR00096_278960..279190_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 385 46 1 76 23 NC_002950:PG0230|3end_transaldolase_266114..266264_POSITIVE 376 70 21 87 31 NC_002950:PG1172|3end_iron-sulfur_cluster_binding_protein,_putative_1252539..1252689_POSITIVE 372 48 4 138 96 NC_002950:PG0278|3end_hypothetical_protein_310477..310627_POSITIVE 368 45 1 81 14 NC_002950:PG1028|3end_TPR_domain_protein_1091096..1091246_POSITIVE 362 50 1 150 96 NC_002950:PG2149|3end_hypothetical_protein_2256936..2257086_NEGATIVE 362 58 19 146 101 NC_002950:PG0033|3end_RmuC_domain_protein_40242..40392_NEGATIVE 360 53 11 115 59 NC_002950:PG2037|3end_hypothetical_protein_2137591..2137741_NEGATIVE 350 50 1 61 3 NC_002950:PG2040|3end_DNA-binding_protein,_histone-like_family_2138398..2138548_NEGATIVE 350 50 1 74 28 NC_002950:PG0328|3end_imidazolonepropionase_362155..362305_NEGATIVE 349 70 24 98 36 NC_002950:PG0758|3end_peptidyl-dipeptidase_Dcp_806467..806617_NEGATIVE 341 50 3 81 23 NC_002950:PG0310|3end_nitroreductase_family_protein_345020..345170_NEGATIVE 339 70 21 60 5 NC_002950:PG0144|3end_hypothetical_protein_166643..166793_NEGATIVE 336 59 17 55 3 NC_002950:PG1247|3end_3-dehydroquinate_synthase_1325585..1325735_POSITIVE 328 48 3 141 96 NC_002950:PG1692|3end_ABC_transporter,_ATP-binding_protein_1776514..1776664_NEGATIVE 327 47 1 57 18 NC_002950:PG1220|3end_erythronate-4-phosphate_dehydrogenase_1298199..1298349_POSITIVE 326 108 62 101 53 NC_002950:PG1475|3end_conjugative_transposon_protein_TraN_1550810..1550960_NEGATIVE 323 325 281 50 10 NC_002950:PG0488|3end_Holliday_junction_DNA_helicase_RuvB_529280..529430_POSITIVE 323 50 1 49 7 NC_002950:PG0360|3end_lemA_protein_394152..394302_POSITIVE 322 46 4 148 98 NC_002950:PG0723|3end_hypothetical_protein_775355..775505_POSITIVE 322 70 22 65 8 NC_002950:PG0346|3end_GTP-binding_protein_381344..381494_POSITIVE