Origin IGS: ccagtcggcattggcaggatcgcggcggactatctgctccgtggcagatttaggatcgggggaaagagatgcagcgtagtagaggctatcgaagcggacaaagcgaatggagtccttcgcctcttgtgccgaaagggcaaaggcaaagaaaaacggcaaaaatacaagcagtattttcttcactaaatacgtatttcgtttcatcgatattcggtattgttgttagttgtacactccacaaataagtgcaactctaaggcaaatttaggaagaagcattcgaacggcgttctgaatcgggctatcgccagggcaatcgcatttgaaactgttaacatacttataaacctaacgattgctacgttcggttattaaacaagtacgaa .........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 ttcgtacttgtttaataaccgaacgtagcaatcgttaggtttataagtatgttaacagtttcaaatgcgattgccctggcgatagcccgattcagaacgccgttcgaatgcttcttcctaaatttgccttagagttgcacttatttgtggagtgtacaactaacaacaataccgaatatcgatgaaacgaaatacgtatttagtgaagaaaatactgcttgtatttttgccgtttttctttgcctttgccctttcggcacaagaggcgaaggactccattcgctttgtccgcttcgatagcctctactacgctgcatctctttcccccgatcctaaatctgccacggagcagatagtccgccgcgatcctgccaatgccgactgg Mask Tandem Repeat Region ================================================ ccagtcggcattggcaggatcgcggcggactatctgctccgtggcagatttaggatcgggggaaagagatgcagcgtagtagaggctatcgaagcggacaaagcgaatggagtccttcgcctcttgtgccgaaagggcaaaggcaaagaaaaacggcaaaaatacaagcagtattttcttcactaaatacgtatttcgtttcatcgatattcggtattgttgttagttgtacactccacaaataagtgcaactctaaggcaaatttaggaagaagcattcgaacggcgttctgaatcgggctatcgccagggcaatcgcatttgaaactgttaacatacttataaacctaacgattgctacgttcggttattaaacaagtacgaa Find is-nt database================================================ Query_seq: PG0877:PG0879|PG0877:PG0879:hypothetical protein:hypothetical protein:<-<-:941636..942020 385 ccagtcggcattggcaggatcgcggcggactatctgctccgtggcagatttaggatcgggggaaagagatgcagcgtagtagaggctatcgaagcggacaaagcgaatggagtccttcgcctcttgtgccgaaagggcaaaggcaaagaaaaacggcaaaaatacaagcagtattttcttcactaaatacgtatttcgtttcatcgatattcggtattgttgttagttgtacactccacaaataagtgcaactctaaggcaaatttaggaagaagcattcgaacggcgttctgaatcgggctatcgccagggcaatcgcatttgaaactgttaacatacttataaacctaacgattgctacgttcggttattaaacaagtacgaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG0877:PG0879|PG0877:PG0879:hypothetical protein:hypothetical protein:<-<-:941636..942020 385 ccagtcggcattggcaggatcgcggcggactatctgctccgtggcagatttaggatcgggggaaagagatgcagcgtagtagaggctatcgaagcggacaaagcgaatggagtccttcgcctcttgtgccgaaagggcaaaggcaaagaaaaacggcaaaaatacaagcagtattttcttcactaaatacgtatttcgtttcatcgatattcggtattgttgttagttgtacactccacaaataagtgcaactctaaggcaaatttaggaagaagcattcgaacggcgttctgaatcgggctatcgccagggcaatcgcatttgaaactgttaacatacttataaacctaacgattgctacgttcggttattaaacaagtacgaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG0877:PG0879|PG0877:PG0879:hypothetical protein:hypothetical protein:<-<-:941636..942020 385 ccagtcggcattggcaggatcgcggcggactatctgctccgtggcagatttaggatcgggggaaagagatgcagcgtagtagaggctatcgaagcggacaaagcgaatggagtccttcgcctcttgtgccgaaagggcaaaggcaaagaaaaacggcaaaaatacaagcagtattttcttcactaaatacgtatttcgtttcatcgatattcggtattgttgttagttgtacactccacaaataagtgcaactctaaggcaaatttaggaagaagcattcgaacggcgttctgaatcgggctatcgccagggcaatcgcatttgaaactgttaacatacttataaacctaacgattgctacgttcggttattaaacaagtacgaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ccagtcggcattggcaggatcgcggcggactatctgctccgtggcagatttaggatcgggggaaagagatgcagcgtagtagaggctatcgaagcggacaaagcgaatggagtccttcgcctcttgtgccgaaagggcaaaggcaaagaaaaacggcaaaaatacaagcagtattttcttcactaaatacgtatttcgtttcatcgatattcggtattgttgttagttgtacactccacaaataagtgcaactctaaggcaaatttaggaagaagcattcgaacggcgttctgaatcgggctatcgccagggcaatcgcatttgaaactgttaacatacttataaacctaacgattgctacgttcggttattaaacaagtacgaa Predict ORF larger than 30AA ================================================ Protein_Len: 58 Strand: + Start: 10 End: 183 ......... M G R I A A D Y L L R G R F R I G G K R C S V V E A I E A D K A N G V L R L L C R K G K G K E K R Q K Y K Q Y F L H .......................................................................................................................................................................................................... Protein_Len: 39 Strand: + Start: 107 End: 223 .......................................................................................................... M E S F A S C A E R A K A K K N G K N T S S I F F T K Y V F R F I D I R Y C C .................................................................................................................................................................. Protein_Len: 58 Strand: + Start: 69 End: 242 .................................................................... M Q R S R G Y R S G Q S E W S P S P L V P K G Q R Q R K T A K I Q A V F S S L N T Y F V S S I F G I V V S C T L H K ............................................................................................................................................... Protein_Len: 35 Strand: + Start: 187 End: 291 .......................................................................................................................................................................................... M R I S F H R Y S V L L L V V H S T N K C N S K A N L G R S I R T A F .............................................................................................. Protein_Len: 33 Strand: - Start: 257 End: 355 ................................................................................................................................................................................................................................................................ P L N L F F C E F P T R F R A I A L A I A N S V T L M S I F R V M .............................. Protein_Len: 31 Strand: - Start: 204 End: 296 ........................................................................................................................................................................................................... R Y E T N N N T T C E V F L H L E L A F K P L L M R V A N Q M ......................................................................................... Protein_Len: 51 Strand: - Start: 89 End: 241 ........................................................................................ R L P C L S H L G E G R T G F P C L C L F V A F I C A T N E E S F V Y K T E D I N P I T T L Q V S W M ................................................................................................................................................ Protein_Len: 45 Strand: - Start: 33 End: 167 ................................ R S R P L N L I P P F L H L T T S A I S A S L A F P T R R R K H R F P L P L S F R C F Y M .......................................................................................................................................................................................................................... Protein_Len: 60 Strand: - Start: 1 End: 210 I Q E T A S K P D P S L S A A Y Y L S D F R V F R I S D K A E Q A S L A F A F F F P L F V L L I K K V L Y T N R K M S M ............................................................................................................................................................................... ccagtcggcattggcaggatcgcggcggactatctgctccgtggcagatttaggatcgggggaaagagatgcagcgtagtagaggctatcgaagcggacaaagcgaatggagtccttcgcctcttgtgccgaaagggcaaaggcaaagaaaaacggcaaaaatacaagcagtattttcttcactaaatacgtatttcgtttcatcgatattcggtattgttgttagttgtacactccacaaataagtgcaactctaaggcaaatttaggaagaagcattcgaacggcgttctgaatcgggctatcgccagggcaatcgcatttgaaactgttaacatacttataaacctaacgattgctacgttcggttattaaacaagtacgaa 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================================================ ccagtcggcattggcaggatcgcggcggactatctgctccgtggcagatttaggatcgggggaaagagatgcagcgtagtagaggctatcgaagcggacaaagcgaatggagtccttcgcctcttgtgccgaaagggcaaaggcaaagaaaaacggcaaaaatacaagcagtattttcttcactaaatacgtatttcgtttcatcgatattcggtattgttgttagttgtacactccacaaataagtgcaactctaaggcaaatttaggaagaagcattcgaacggcgttctgaatcgggctatcgccagggcaatcgcatttgaaactgttaacatacttataaacctaacgattgctacgttcggttattaaacaagtacgaa Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 47 HP_score: -2.5 Tail_Score: -3.62046 Start: 347 End: 367 Full_Region: TAACATACTTATAAA CCTAACG ATTGCTA CGTTCGG TTATTAAACAAGTAC ..........................................................................................................................................................................................................................................................................................................................................................CCTAACGATTGCTACGTTCGG.................. Find igs database================================================ Query_seq: PG0877:PG0879|PG0877:PG0879:hypothetical protein:hypothetical protein:<-<-:941636..942020 385 ccagtcggcattggcaggatcgcggcggactatctgctccgtggcagatttaggatcgggggaaagagatgcagcgtagtagaggctatcgaagcggacaaagcgaatggagtccttcgcctcttgtgccgaaagggcaaaggcaaagaaaaacggcaaaaatacaagcagtattttcttcactaaatacgtatttcgtttcatcgatattcggtattgttgttagttgtacactccacaaataagtgcaactctaaggcaaatttaggaagaagcattcgaacggcgttctgaatcgggctatcgccagggcaatcgcatttgaaactgttaacatacttataaacctaacgattgctacgttcggttattaaacaagtacgaa Intra-Species Hit: Count: 1 Min: 1 Max: 385 Len: 385 Subject: NC_002950_PG0877_PG0879|hypothetical protein:hypothetical protein|NEGATIVE:NEGATIVE|[941636,942020]|385 HSP 1 e-value: 0.0 bit: 763.0 Len: 385 Query Start:1 Query End:385 Subject Strand: POSITIVE Subject Start: 1 Subject End: 385 ccagtcggcattggcaggatcgcggcggactatctgctccgtggcagatttaggatcgggggaaagagatgcagcgtagtagaggctatcgaagcggacaaagcgaatggagtccttcgcctcttgtgccgaaagggcaaaggcaaagaaaaacggcaaaaatacaagcagtattttcttcactaaatacgtatttcgtttcatcgatattcggtattgttgttagttgtacactccacaaataagtgcaactctaaggcaaatttaggaagaagcattcgaacggcgttctgaatcgggctatcgccagggcaatcgcatttgaaactgttaacatacttataaacctaacgattgctacgttcggttattaaacaagtacgaa ccagtcggcattggcaggatcgcggcggactatctgctccgtggcagatttaggatcgggggaaagagatgcagcgtagtagaggctatcgaagcggacaaagcgaatggagtccttcgcctcttgtgccgaaagggcaaaggcaaagaaaaacggcaaaaatacaagcagtattttcttcactaaatacgtatttcgtttcatcgatattcggtattgttgttagttgtacactccacaaataagtgcaactctaaggcaaatttaggaagaagcattcgaacggcgttctgaatcgggctatcgccagggcaatcgcatttgaaactgttaacatacttataaacctaacgattgctacgttcggttattaaacaagtacgaa Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CCAGUCGGCAUUGGCAGGAUCGCGGCGGACUAUCUGCUCCGUGGCAGAUUUAGGAUCGGGGGAAAGAGAUGCAGCGUAGUAGAGGCUAUCGAAGCGGACAAAGCGAAUGGAGUCCUUCGCCUCUUGUGCCGAAAGGGCAAAGGCAAAGAAAAACGGCAAAAAUACAAGCAGUAUUUUCUUCACUAAAUACGUAUUUCGUUUCAUCGAUAUUCGGUAUUGUUGUUAGUUGUACACUCCACAAAUAAGUGCAACUCUAAGGCAAAUUUAGGAAGAAGCAUUCGAACGGCGUUCUGAAUCGGGCUAUCGCCAGGGCAAUCGCAUUUGAAACUGUUAACAUACUUAUAAACCUAACGAUUGCUACGUUCGGUUAUUAAACAAGUACGAA ...((((((..((((......((.((((((.....).))))).)).(((((((((((.(..........(((..((((((....)))).))..))).......((((((..((((((.((((.((((.((....)))))))))).)))......)))..((((((.....))))))(((((.(((((..((.((.(((......))).)).))...(((((...((((((((.............))))))))....))))).))))))))))..))))))..).).))))))))))..))))..)))..)))..(((.(((((.....((......)).....((((.((((.......)))).))))......))))).))). (-100.62) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUCGUACUUGUUUAAUAACCGAACGUAGCAAUCGUUAGGUUUAUAAGUAUGUUAACAGUUUCAAAUGCGAUUGCCCUGGCGAUAGCCCGAUUCAGAACGCCGUUCGAAUGCUUCUUCCUAAAUUUGCCUUAGAGUUGCACUUAUUUGUGGAGUGUACAACUAACAACAAUACCGAAUAUCGAUGAAACGAAAUACGUAUUUAGUGAAGAAAAUACUGCUUGUAUUUUUGCCGUUUUUCUUUGCCUUUGCCCUUUCGGCACAAGAGGCGAAGGACUCCAUUCGCUUUGUCCGCUUCGAUAGCCUCUACUACGCUGCAUCUCUUUCCCCCGAUCCUAAAUCUGCCACGGAGCAGAUAGUCCGCCGCGAUCCUGCCAAUGCCGACUGG ..(((((((((.....((((.((((.......)))).)))).)))))))))....(((((.((...((((((((...((((..(((...((((.((((...)))))))))))..................((((.((((.......((((((.((.................((.....))......((((...((.((..((((((((((((((.....)))))))).......(((((((((((((((.....))))...))))))))))).....))))))..)).)).))))...)))))))).....)))).))))...............((((((......))))))....))))))))))..))...))..))))). (-96.00) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 1140 50 1 141 92 NC_002950:PG0877|5end_hypothetical_protein_941545..941775_NEGATIVE 728 358 311 231 185 NC_002950:PG1397|5end_bifunctional_phosphoribosylaminoimidazolecarboxamide_formyltransferase/IMP_cyclohydrolase_1480355..1480585_NEGATIVE 705 360 311 203 151 NC_002950:PG2221|5end_MiaB-like_tRNA_modifying_enzyme_2335426..2335656_POSITIVE 688 380 331 220 171 NC_002950:PG0500|5end_queuine_tRNA-ribosyltransferase_539197..539427_POSITIVE 644 370 321 229 177 NC_002950:PG0801|5end_polyA_polymerase_family_protein_857714..857944_NEGATIVE 578 366 321 231 187 NC_002950:PG2176|5end_ISPg2,_transposase_2284345..2284575_NEGATIVE 565 290 241 226 177 NC_002950:PG1707|5end_hypothetical_protein_1794597..1794827_NEGATIVE 455 321 284 175 130 NC_002950:PG0188|5end_lipoprotein,_putative_223934..224164_POSITIVE 453 339 295 148 105 NC_002950:PG1788|5end_cysteine_peptidase,_putative_1875976..1876206_POSITIVE 448 41 2 176 138 NC_002950:PG0423|5end_hypothetical_protein_462251..462481_POSITIVE 437 276 231 231 184 NC_002950:PG2165|5end_glycyl-tRNA_synthetase_2271669..2271899_NEGATIVE 434 137 93 148 99 NC_002950:PG2101|5end_hypothetical_protein_2211273..2211503_NEGATIVE 434 60 15 64 22 NC_002950:PG1872|5end_urocanate_hydratase_1968911..1969141_NEGATIVE 433 99 51 164 110 NC_002950:PG1418|5end_DNA_polymerase_III,_gamma_and_tau_subunits_1503064..1503294_POSITIVE 429 44 1 56 7 NC_002950:PG0653|5end_phosphoserine_phosphatase_705454..705684_NEGATIVE 426 49 1 193 148 NC_002950:PG0227|5end_DNA_repair_protein_RadA_263978..264208_NEGATIVE 423 60 13 211 159 NC_002950:PG1058|5end_OmpA_family_protein_1124034..1124264_POSITIVE 420 50 1 199 140 NC_002950:PG1691|5end_hypothetical_protein_1776484..1776714_NEGATIVE 419 46 4 165 114 NC_002950:PG0229|5end_hypothetical_protein_264872..265102_POSITIVE 418 60 13 216 167 NC_002950:PG1102|5end_hypothetical_protein_1173637..1173867_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 705 360 311 65 13 NC_002950:PG2220|3end_hypothetical_protein_2335368..2335518_POSITIVE 705 360 311 65 13 NC_002950:PG1251|3end_hypothetical_protein_1328212..1328362_POSITIVE 688 380 331 85 36 NC_002950:PG0499|3end_hypothetical_protein_539142..539292_POSITIVE 528 49 1 70 21 NC_002950:PG0605|3end_hypothetical_protein_661165..661315_NEGATIVE 444 128 82 108 51 NC_002950:PG0333|3end_hypothetical_protein_368811..368961_POSITIVE 437 49 6 55 11 NC_002950:PG0752|3end_uracil_phosphoribosyltransferase_798397..798547_POSITIVE 426 49 1 147 102 NC_002950:PG0228|3end_DdaH_family_protein_264024..264174_NEGATIVE 418 120 76 60 14 NC_002950:PG1417|3end_fumarate_hydratase_class_I,_anaerobic_1503021..1503171_POSITIVE 417 309 267 74 23 NC_002950:PG1835|3end_lipoprotein,_putative_1928520..1928670_POSITIVE 410 59 12 77 23 NC_002950:PG0522|3end_tRNA_delta(2)-isopentenylpyrophosphate_transferase_565993..566143_NEGATIVE 403 86 41 86 35 NC_002950:PG1585|3end_batD_protein_1664137..1664287_POSITIVE 403 48 1 130 71 NC_002950:PG0226|3end_transglutaminase-related_protein_259838..259988_NEGATIVE 395 47 6 111 60 NC_002950:PG0745|3end_lactoylglutathione_lyase,_putative_791982..792132_NEGATIVE 393 97 54 128 72 NC_002950:PG0164|3end_hypothetical_protein_187081..187231_NEGATIVE 392 49 4 147 97 NC_002950:PG0684|3end_ABC_transporter,_permease_protein,_putative_740103..740253_POSITIVE 391 46 1 138 98 NC_002950:PG2156|3end_conserved_hypothetical_protein_TIGR00046_2261899..2262049_NEGATIVE 391 130 81 64 12 NC_002950:PG0503|3end_dipeptidyl_aminopeptidase_IV_544211..544361_POSITIVE 389 49 1 150 115 NC_002950:PG1949|3end_malate_dehydrogenase_2038184..2038334_NEGATIVE 382 318 274 122 68 NC_002950:PG1389|3end_DNA-binding_protein,_histone-like_family_1470870..1471020_NEGATIVE 380 60 14 110 58 NC_002950:PG1641|3end_phosphotyrosine_protein_phosphatase_1721260..1721410_NEGATIVE