Origin IGS: cgacgcgcgagtactaacaaacagatcggggcagcatggcgagaggttttctctctctccgatgttgccccgattgctttattatcctgacttcatcatcgtggcatcccgaaatcctcgtcgaatagttttgtgattattgctctttaaccccggattggtcatacaacgatagaattaaggcaagattaaacggaaagagtccggtacaataccgactctttctataacacaaggatcggattaacctctccgacttccggccctttttcagcacacgtcgccctcgaacgattataaagagggctgtc .........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 gacagccctctttataatcgttcgagggcgacgtgtgctgaaaaagggccggaagtcggagaggttaatccgatccttgtgttatagaaagagtcggtattgtaccggactctttccgtttaatcttgccttaattctatcgttgtatgaccaatccggggttaaagagcaataatcacaaaactattcgacgaggatttcgggatgccacgatgatgaagtcaggataataaagcaatcggggcaacatcggagagagagaaaacctctcgccatgctgccccgatctgtttgttagtactcgcgcgtcg Mask Tandem Repeat Region ================================================ cgacgcgcgagtactaacaaacagatcggggcagcatggcgagaggttttctctctctccgatgttgccccgattgctttattatcctgacttcatcatcgtggcatcccgaaatcctcgtcgaatagttttgtgattattgctctttaaccccggattggtcatacaacgatagaattaaggcaagattaaacggaaagagtccggtacaataccgactctttctataacacaaggatcggattaacctctccgacttccggccctttttcagcacacgtcgccctcgaacgattataaagagggctgtc Find is-nt database================================================ Query_seq: PG0495:PG0496|PG0495:PG0496:hypothetical protein:hypothetical protein:->->:536997..537307 311 cgacgcgcgagtactaacaaacagatcggggcagcatggcgagaggttttctctctctccgatgttgccccgattgctttattatcctgacttcatcatcgtggcatcccgaaatcctcgtcgaatagttttgtgattattgctctttaaccccggattggtcatacaacgatagaattaaggcaagattaaacggaaagagtccggtacaataccgactctttctataacacaaggatcggattaacctctccgacttccggccctttttcagcacacgtcgccctcgaacgattataaagagggctgtc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG0495:PG0496|PG0495:PG0496:hypothetical protein:hypothetical protein:->->:536997..537307 311 cgacgcgcgagtactaacaaacagatcggggcagcatggcgagaggttttctctctctccgatgttgccccgattgctttattatcctgacttcatcatcgtggcatcccgaaatcctcgtcgaatagttttgtgattattgctctttaaccccggattggtcatacaacgatagaattaaggcaagattaaacggaaagagtccggtacaataccgactctttctataacacaaggatcggattaacctctccgacttccggccctttttcagcacacgtcgccctcgaacgattataaagagggctgtc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG0495:PG0496|PG0495:PG0496:hypothetical protein:hypothetical protein:->->:536997..537307 311 cgacgcgcgagtactaacaaacagatcggggcagcatggcgagaggttttctctctctccgatgttgccccgattgctttattatcctgacttcatcatcgtggcatcccgaaatcctcgtcgaatagttttgtgattattgctctttaaccccggattggtcatacaacgatagaattaaggcaagattaaacggaaagagtccggtacaataccgactctttctataacacaaggatcggattaacctctccgacttccggccctttttcagcacacgtcgccctcgaacgattataaagagggctgtc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 cgacgcgcgagtactaacaaacagatcggggcagcatggcgagaggttttctctctctccgatgttgccccgattgctttattatcctgacttcatcatcgtggcatcccgaaatcctcgtcgaatagttttgtgattattgctctttaaccccggattggtcatacaacgatagaattaaggcaagattaaacggaaagagtccggtacaataccgactctttctataacacaaggatcggattaacctctccgacttccggccctttttcagcacacgtcgccctcgaacgattataaagagggctgtc Predict ORF larger than 30AA ================================================ Protein_Len: 30 Strand: + Start: 36 End: 125 ................................... M A R G F L S L R C C P D C F I I L T S S S W H P E I L V E .......................................................................................................................................................................................... Protein_Len: 53 Strand: - Start: 140 End: 298 ........................................................................................................................................... Q E K V G S Q D Y L S L I L A L N F P F L G T C Y R S K R Y C L S R I L R E S K R G K K L V R R G R V I M ............. Protein_Len: 33 Strand: - Start: 17 End: 115 ................ C V S R P L M A L P K R E R R H Q G S Q K I I R V E D D H C G S M .................................................................................................................................................................................................... cgacgcgcgagtactaacaaacagatcggggcagcatggcgagaggttttctctctctccgatgttgccccgattgctttattatcctgacttcatcatcgtggcatcccgaaatcctcgtcgaatagttttgtgattattgctctttaaccccggattggtcatacaacgatagaattaaggcaagattaaacggaaagagtccggtacaataccgactctttctataacacaaggatcggattaacctctccgacttccggccctttttcagcacacgtcgccctcgaacgattataaagagggctgtc 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================================================ cgacgcgcgagtactaacaaacagatcggggcagcatggcgagaggttttctctctctccgatgttgccccgattgctttattatcctgacttcatcatcgtggcatcccgaaatcctcgtcgaatagttttgtgattattgctctttaaccccggattggtcatacaacgatagaattaaggcaagattaaacggaaagagtccggtacaataccgactctttctataacacaaggatcggattaacctctccgacttccggccctttttcagcacacgtcgccctcgaacgattataaagagggctgtc Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 95 HP_score: -12.5 Tail_Score: -4.35885 Start: 21 End: 77 Full_Region: CGCGAGTACTAACAA ACAGATCGGGGCAGCATGGCGAGAGG TTTTC TCTCTCTCCGATGTTGCCCCGATTGC TTTATTATCCTGACT ....................ACAGATCGGGGCAGCATGGCGAGAGGTTTTCTCTCTCTCCGATGTTGCCCCGATTGC.......................................................................................................................................................................................................................................... TransTerm Strand: - Conf: 100 HP_score: -13.1 Tail_Score: -4.2704 Start: 22 End: 76 Full_Region: gtcaggataataaag caatcggggcaacatcggagagag agaaaac ctctcgccatgctgccccgatctg tttgttagtactcgc .....................caatcggggcaacatcggagagagagaaaacctctcgccatgctgccccgatctg........................................................................................................................................................................................................................................... TransTerm Strand: + Conf: 100 HP_score: -17.9 Tail_Score: -3.73387 Start: 26 End: 73 Full_Region: GTACTAACAAACAGA TCGGGGCAGCATGGCGAGAGG TTTTC TCTCTCTCCGATGTTGCCCCGA TTGCTTTATTATCCT .........................TCGGGGCAGCATGGCGAGAGGTTTTCTCTCTCTCCGATGTTGCCCCGA.............................................................................................................................................................................................................................................. TransTerm Strand: - Conf: 93 HP_score: -15.0 Tail_Score: -3.43925 Start: 26 End: 73 Full_Region: aggataataaagcaa tcggggcaacatcggagagag agaaaac ctctcgccatgctgccccga tctgtttgttagtac .........................tcggggcaacatcggagagagagaaaacctctcgccatgctgccccga.............................................................................................................................................................................................................................................. TransTerm Strand: - Conf: 73 HP_score: -8.3 Tail_Score: -3.94853 Start: 194 End: 227 Full_Region: ccgatccttgtgtta tagaaagagtcggta ttg taccggactctttccg tttaatcttgcctta .................................................................................................................................................................................................tagaaagagtcggtattgtaccggactctttccg.................................................................................... TransTerm Strand: + Conf: 73 HP_score: -8.1 Tail_Score: -4.03234 Start: 200 End: 221 Full_Region: AAGATTAAACGGAAA GAGTCCGGTA CAA TACCGACTC TTTCTATAACACAAG .......................................................................................................................................................................................................GAGTCCGGTACAATACCGACTC.......................................................................................... Find igs database================================================ Query_seq: PG0495:PG0496|PG0495:PG0496:hypothetical protein:hypothetical protein:->->:536997..537307 311 cgacgcgcgagtactaacaaacagatcggggcagcatggcgagaggttttctctctctccgatgttgccccgattgctttattatcctgacttcatcatcgtggcatcccgaaatcctcgtcgaatagttttgtgattattgctctttaaccccggattggtcatacaacgatagaattaaggcaagattaaacggaaagagtccggtacaataccgactctttctataacacaaggatcggattaacctctccgacttccggccctttttcagcacacgtcgccctcgaacgattataaagagggctgtc Intra-Species Hit: Count: 1 Min: 1 Max: 311 Len: 311 Subject: NC_002950_PG0495_PG0496|hypothetical protein:hypothetical protein|POSITIVE:POSITIVE|[536997,537307]|311 HSP 1 e-value: 1.0E-175 bit: 617.0 Len: 311 Query Start:1 Query End:311 Subject Strand: POSITIVE Subject Start: 1 Subject End: 311 cgacgcgcgagtactaacaaacagatcggggcagcatggcgagaggttttctctctctccgatgttgccccgattgctttattatcctgacttcatcatcgtggcatcccgaaatcctcgtcgaatagttttgtgattattgctctttaaccccggattggtcatacaacgatagaattaaggcaagattaaacggaaagagtccggtacaataccgactctttctataacacaaggatcggattaacctctccgacttccggccctttttcagcacacgtcgccctcgaacgattataaagagggctgtc cgacgcgcgagtactaacaaacagatcggggcagcatggcgagaggttttctctctctccgatgttgccccgattgctttattatcctgacttcatcatcgtggcatcccgaaatcctcgtcgaatagttttgtgattattgctctttaaccccggattggtcatacaacgatagaattaaggcaagattaaacggaaagagtccggtacaataccgactctttctataacacaaggatcggattaacctctccgacttccggccctttttcagcacacgtcgccctcgaacgattataaagagggctgtc Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CGACGCGCGAGUACUAACAAACAGAUCGGGGCAGCAUGGCGAGAGGUUUUCUCUCUCUCCGAUGUUGCCCCGAUUGCUUUAUUAUCCUGACUUCAUCAUCGUGGCAUCCCGAAAUCCUCGUCGAAUAGUUUUGUGAUUAUUGCUCUUUAACCCCGGAUUGGUCAUACAACGAUAGAAUUAAGGCAAGAUUAAACGGAAAGAGUCCGGUACAAUACCGACUCUUUCUAUAACACAAGGAUCGGAUUAACCUCUCCGACUUCCGGCCCUUUUUCAGCACACGUCGCCCUCGAACGAUUAUAAAGAGGGCUGUC .((((((((((............((((((((((((((((.((((((.....)))))).)).)))))))))))))).......................(((.((...)))))....)))).))....(((.((((((((....(((........))).)))))))).)))....(((..(.(((..........((((((((((.((((...)))))))))))))).........((((((((........)))))..))).))).)..)))......))))((((((.............)))))).... (-100.32) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GACAGCCCUCUUUAUAAUCGUUCGAGGGCGACGUGUGCUGAAAAAGGGCCGGAAGUCGGAGAGGUUAAUCCGAUCCUUGUGUUAUAGAAAGAGUCGGUAUUGUACCGGACUCUUUCCGUUUAAUCUUGCCUUAAUUCUAUCGUUGUAUGACCAAUCCGGGGUUAAAGAGCAAUAAUCACAAAACUAUUCGACGAGGAUUUCGGGAUGCCACGAUGAUGAAGUCAGGAUAAUAAAGCAAUCGGGGCAACAUCGGAGAGAGAGAAAACCUCUCGCCAUGCUGCCCCGAUCUGUUUGUUAGUACUCGCGCGUCG (((.((((((.............))))))..((.(((((((.......((.((.((((..(.(((...((((((((((((......(((((((((((((...)))).))))))))).........(((((((((((((...((((......))))..)))))).))).))))..................)))))))..)))))..))).)..))))....)).))......((((((((((((((.(((.((.(((((.......))))).))))).))))))))).))))).))))))).))...))). (-108.62) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 420 279 231 207 151 NC_002950:PG1945|5end_hypothetical_protein_2031697..2031927_POSITIVE 416 79 31 193 149 NC_002950:PG0509|5end_hypothetical_protein_549588..549818_NEGATIVE 408 238 191 101 47 NC_002950:PG1525|5end_isochorismate_synthase,_putative_1603865..1604095_NEGATIVE 402 120 80 156 106 NC_002950:PG1282|5end_hypothetical_protein_1360035..1360265_POSITIVE 399 73 36 75 32 NC_002950:PG0166|5end_peptidyl-tRNA_hydrolase_188370..188600_NEGATIVE 390 78 31 77 26 NC_002950:PG1391|5end_hypothetical_protein_1471670..1471900_POSITIVE 388 289 249 119 77 NC_002950:PG0942|5end_ISPg5,_transposase_Orf1_1002063..1002293_POSITIVE 388 69 26 217 167 NC_002950:PG0226|5end_transglutaminase-related_protein_262531..262761_NEGATIVE 385 68 23 127 77 NC_002950:PG1825|5end_hypothetical_protein_1919671..1919901_NEGATIVE 382 47 1 158 118 NC_002950:PG0744|5end_RNA_methyltransferase,_TrmH_family_791897..792127_NEGATIVE 379 290 248 185 129 NC_002950:PG2055|5end_dihydroorotate_dehydrogenase_2153060..2153290_NEGATIVE 377 40 1 220 181 NC_002950:PG1058|5end_OmpA_family_protein_1124034..1124264_POSITIVE 367 78 32 75 18 NC_002950:PG0930|5end_hypothetical_protein_987542..987772_NEGATIVE 366 67 22 214 172 NC_002950:PG0635|5end_ribosomal_protein_L11_methyltransferase_687773..688003_NEGATIVE 366 275 234 97 56 NC_002950:PG0281|5end_ABC_transporter,_permease_protein,_putative_316023..316253_NEGATIVE 362 68 22 218 157 NC_002950:PG1481|5end_conjugative_transposon_protein_TraG_1558447..1558677_NEGATIVE 362 95 59 125 88 NC_002950:PG0049|5end_hypothetical_protein_60740..60970_NEGATIVE 359 289 241 105 54 NC_002950:PG0897|5end_alpha-amylase_family_protein_962472..962702_NEGATIVE 347 289 241 93 32 NC_002950:PG1762|5end_protein-export_membrane_protein_SecD/protein-export_membrane_protein_SecF_1847988..1848218_POSITIVE 344 68 22 226 156 NC_002950:PG0322|5end_serine/threonine_transporter_355708..355938_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 541 83 41 69 29 NC_002950:PG0652|3end_hypothetical_protein_703899..704049_NEGATIVE 504 70 23 62 13 NC_002950:PG0495|3end_hypothetical_protein_536936..537086_POSITIVE 433 289 241 133 88 NC_002950:PG2040|3end_DNA-binding_protein,_histone-like_family_2138398..2138548_NEGATIVE 402 120 80 132 82 NC_002950:PG1281|3end_hypothetical_protein_1360091..1360241_POSITIVE 400 77 31 61 7 NC_002950:PG0507|3end_hypothetical_protein_548190..548340_POSITIVE 396 70 22 127 59 NC_002950:PG0297|3end_hypothetical_protein_335297..335447_NEGATIVE 382 47 1 73 33 NC_002950:PG0745|3end_lactoylglutathione_lyase,_putative_791982..792132_NEGATIVE 382 294 253 141 101 NC_002950:PG0443|3end_hemagglutinin-related_protein_483147..483297_POSITIVE 372 46 1 130 78 NC_002950:PG0085|3end_alpha-galactosidase_100556..100706_POSITIVE 365 69 23 142 102 NC_002950:PG1826|3end_hypothetical_protein_1919646..1919796_NEGATIVE 365 70 26 112 47 NC_002950:PG0535|3end_hypothetical_protein_585956..586106_NEGATIVE 356 47 8 128 84 NC_002950:PG0237|3end_uracil-DNA_glycosylase_275526..275676_POSITIVE 347 68 23 147 95 NC_002950:PG1391|3end_hypothetical_protein_1472961..1473111_POSITIVE 346 79 31 134 98 NC_002950:PG1687|3end_HIT_family_protein_1773812..1773962_NEGATIVE 344 64 26 151 105 NC_002950:PG0227|3end_DNA_repair_protein_RadA_262593..262743_NEGATIVE 341 69 23 98 40 NC_002950:PG2099|3end_ATP-dependent_RNA_helicase,_DEAD/DEAH_box_family_2206649..2206799_NEGATIVE 341 70 26 147 101 NC_002950:PG1174|3end_thioesterase_family_protein_1253210..1253360_NEGATIVE 340 46 1 73 31 NC_002950:PG1808|3end_guanosine-3',5'-bis(diphosphate)_3'-pyrophosphohydrolase_1902955..1903105_NEGATIVE 334 70 22 67 19 NC_002950:PG1741|3end_aspartate_ammonia-lyase_1825856..1826006_NEGATIVE 334 297 252 93 27 NC_002950:PG1704|3end_thiol:disulfide_interchange_protein_dsbD,_putative_1790771..1790921_NEGATIVE