Origin IGS: cgccattttccacctgacataatcccgaatagtcccatggacagttgtataaaaacgaaaatcacagcgaattgaggttcgctgtgattttcgttggttatacccgacaagcctaatacctatcaggtatacaagattacgcagaa .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 ttctgcgtaatcttgtatacctgataggtattaggcttgtcgggtataaccaacgaaaatcacagcgaacctcaattcgctgtgattttcgtttttatacaactgtccatgggactattcgggattatgtcaggtggaaaatggcg Mask Tandem Repeat Region ================================================ cgccattttccacctgacataatcccgaatagtcccatggacagttgtataaaaacgaaaatcacagcgaattgaggttcgctgtgattttcgttggttatacccgacaagcctaatacctatcaggtatacaagattacgcagaa Find is-nt database================================================ Query_seq: PG1794:PG1795|PG1794:PG1795:DNA polymerase type I:hypothetical protein:-><-:1888899..1889044 146 cgccattttccacctgacataatcccgaatagtcccatggacagttgtataaaaacgaaaatcacagcgaattgaggttcgctgtgattttcgttggttatacccgacaagcctaatacctatcaggtatacaagattacgcagaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG1794:PG1795|PG1794:PG1795:DNA polymerase type I:hypothetical protein:-><-:1888899..1889044 146 cgccattttccacctgacataatcccgaatagtcccatggacagttgtataaaaacgaaaatcacagcgaattgaggttcgctgtgattttcgttggttatacccgacaagcctaatacctatcaggtatacaagattacgcagaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG1794:PG1795|PG1794:PG1795:DNA polymerase type I:hypothetical protein:-><-:1888899..1889044 146 cgccattttccacctgacataatcccgaatagtcccatggacagttgtataaaaacgaaaatcacagcgaattgaggttcgctgtgattttcgttggttatacccgacaagcctaatacctatcaggtatacaagattacgcagaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 cgccattttccacctgacataatcccgaatagtcccatggacagttgtataaaaacgaaaatcacagcgaattgaggttcgctgtgattttcgttggttatacccgacaagcctaatacctatcaggtatacaagattacgcagaa Predict ORF larger than 30AA ================================================ Protein_Len: 36 Strand: - Start: 3 End: 110 .. W K G G S M I G F L G M S L Q I F V F I V A F Q P E S H N E N T I G S M .................................... Protein_Len: 48 Strand: - Start: 1 End: 144 A M K W R V Y D R I T G H V T T Y F R F D C R I S T R Q S K R Q N Y G V L R I G I L Y V L N R M .. cgccattttccacctgacataatcccgaatagtcccatggacagttgtataaaaacgaaaatcacagcgaattgaggttcgctgtgattttcgttggttatacccgacaagcctaatacctatcaggtatacaagattacgcagaa 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================================================ cgccattttccacctgacataatcccgaatagtcccatggacagttgtataaaaacgaaaatcacagcgaattgaggttcgctgtgattttcgttggttatacccgacaagcctaatacctatcaggtatacaagattacgcagaa Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 100 HP_score: -20.9 Tail_Score: -3.44146 Start: 56 End: 93 Full_Region: ACAGTTGTATAAAAA CGAAAATCACAGCGAAT TGAG GTTCGCTGTGATTTTCG TTGGTTATACCCGAC .......................................................CGAAAATCACAGCGAATTGAGGTTCGCTGTGATTTTCG..................................................... TransTerm Strand: - Conf: 100 HP_score: -20.2 Tail_Score: -4.84761 Start: 56 End: 93 Full_Region: gtcgggtataaccaa cgaaaatcacagcgaa cctcaa ttcgctgtgattttcg tttttatacaactgt .......................................................cgaaaatcacagcgaacctcaattcgctgtgattttcg..................................................... Find igs database================================================ Query_seq: PG1794:PG1795|PG1794:PG1795:DNA polymerase type I:hypothetical protein:-><-:1888899..1889044 146 cgccattttccacctgacataatcccgaatagtcccatggacagttgtataaaaacgaaaatcacagcgaattgaggttcgctgtgattttcgttggttatacccgacaagcctaatacctatcaggtatacaagattacgcagaa Intra-Species Hit: Count: 1 Min: 1 Max: 146 Len: 146 Subject: NC_002950_PG1794_PG1795|DNA polymerase type I:hypothetical protein|POSITIVE:NEGATIVE|[1888899,1889044]|146 HSP 1 e-value: 1.0E-77 bit: 289.0 Len: 146 Query Start:1 Query End:146 Subject Strand: POSITIVE Subject Start: 1 Subject End: 146 cgccattttccacctgacataatcccgaatagtcccatggacagttgtataaaaacgaaaatcacagcgaattgaggttcgctgtgattttcgttggttatacccgacaagcctaatacctatcaggtatacaagattacgcagaa cgccattttccacctgacataatcccgaatagtcccatggacagttgtataaaaacgaaaatcacagcgaattgaggttcgctgtgattttcgttggttatacccgacaagcctaatacctatcaggtatacaagattacgcagaa Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CGCCAUUUUCCACCUGACAUAAUCCCGAAUAGUCCCAUGGACAGUUGUAUAAAAACGAAAAUCACAGCGAAUUGAGGUUCGCUGUGAUUUUCGUUGGUUAUACCCGACAAGCCUAAUACCUAUCAGGUAUACAAGAUUACGCAGAA .............(((.(.(((((.......((((...)))).(((((((((.(((((((((((((((((((....)))))))))))))))))))..))))))..))).......(((((.....)))))....))))).)))).. (-49.30) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUCUGCGUAAUCUUGUAUACCUGAUAGGUAUUAGGCUUGUCGGGUAUAACCAACGAAAAUCACAGCGAACCUCAAUUCGCUGUGAUUUUCGUUUUUAUACAACUGUCCAUGGGACUAUUCGGGAUUAUGUCAGGUGGAAAAUGGCG .((((((((((((((((((((((((((((.....))))))))))))))...((((((((((((((((((......))))))))))))))))))...........((((...))))....)))))))))).))))............ (-60.90) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 317 113 74 66 18 NC_002950:PG0672|5end_iron_compound_ABC_transporter,_ATP-binding_protein_723002..723232_POSITIVE 315 130 82 58 13 NC_002950:PG2174|5end_hypothetical_protein_2282578..2282808_NEGATIVE 309 110 62 152 96 NC_002950:PG1862|5end_hypothetical_protein_1960363..1960593_NEGATIVE 307 107 62 163 112 NC_002950:PG0703|5end_cobalamin_(5'-phosphate)_synthase,_putative_758144..758374_POSITIVE 303 126 81 79 29 NC_002950:PG2002|5end_dihydrodipicolinate_reductase_2091587..2091817_NEGATIVE 302 42 2 48 6 NC_002950:PG0661|5end_hypothetical_protein_709853..710083_NEGATIVE 302 42 2 206 164 NC_002950:PG0660|5end_nitroreductase_family_protein_709695..709925_NEGATIVE 298 115 71 51 4 NC_002950:PG1094|5end_phosphomannomutase_1158753..1158983_POSITIVE 295 109 67 158 118 NC_002950:PG1659|5end_hypothetical_protein_1743747..1743977_NEGATIVE 295 48 2 83 36 NC_002950:PG0888|5end_hypothetical_protein_949910..950140_POSITIVE 295 130 81 201 149 NC_002950:PG0791|5end_adenylate_kinase_843177..843407_NEGATIVE 292 112 79 204 165 NC_002950:PG0848|5end_hypothetical_protein_910487..910717_NEGATIVE 289 129 81 163 106 NC_002950:PG1817|5end_hypothetical_protein_1913035..1913265_NEGATIVE 285 70 26 54 7 NC_002950:PG0236|5end_hypothetical_protein_273224..273454_POSITIVE 283 40 2 229 191 NC_002950:PG1343|5end_lipoate-protein_ligase_B_1423628..1423858_POSITIVE 283 118 76 101 56 NC_002950:PG0278|5end_hypothetical_protein_310047..310277_POSITIVE 281 50 9 194 148 NC_002950:PG1057|5end_hypothetical_protein_1123419..1123649_POSITIVE 279 49 2 174 112 NC_002950:PG1312|5end_capA_protein,_putative_1390286..1390516_POSITIVE 279 108 67 222 183 NC_002950:PG0032|5end_beta-mannosidase,_putative_40212..40442_NEGATIVE 277 112 73 228 181 NC_002950:PG0433|5end_tetrapyrrole_methylase_family_protein_471396..471626_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 448 108 61 59 3 NC_002950:PG1794|3end_DNA_polymerase_type_I_1888838..1888988_POSITIVE 338 107 62 67 11 NC_002950:PG2079|3end_hypothetical_protein_2178890..2179040_NEGATIVE 309 110 62 151 95 NC_002950:PG1863|3end_hypothetical_protein_1960364..1960514_NEGATIVE 300 106 66 148 111 NC_002950:PG0401|3end_hypothetical_protein_437765..437915_NEGATIVE 291 107 67 145 109 NC_002950:PG0767|3end_4-alpha-glucanotransferase_818557..818707_NEGATIVE 285 114 76 138 101 NC_002950:PG0731|3end_hypothetical_protein_782020..782170_NEGATIVE 275 94 65 137 106 NC_002950:PG2167|3end_immunoreactive_53_kDa_antigen_PG123_2272104..2272254_NEGATIVE 275 114 74 130 94 NC_002950:PG0222|3end_DNA-binding_protein,_histone-like_family_255913..256063_NEGATIVE 274 107 65 145 92 NC_002950:PG1854|3end_5-formyltetrahydrofolate_cyclo-ligase_family_protein_1953325..1953475_NEGATIVE 271 106 61 136 93 NC_002950:PG1978|3end_hypothetical_protein_2066723..2066873_NEGATIVE 270 96 67 60 21 NC_002950:PG1410|3end_hypothetical_protein_1493436..1493586_POSITIVE 270 41 2 150 101 NC_002950:PG1311|3end_hypothetical_protein_1390355..1390505_POSITIVE 269 48 1 90 38 NC_002950:PG2032|3end_primosomal_protein_N'_2130868..2131018_NEGATIVE 268 93 67 55 17 NC_002950:PG1777|3end_hypothetical_protein_1867105..1867255_POSITIVE 266 136 92 86 40 NC_002950:PG1522|3end_mandelate_racemase/muconate_lactonizing_enzyme_family_protein_1599100..1599250_NEGATIVE 266 77 39 133 106 NC_002950:PG1378|3end_A/G-specific_adenine_glycosylase_1457715..1457865_NEGATIVE 266 108 62 150 105 NC_002950:PG0702|3end_nicotinate-nucleotide--dimethylbenzimidazole_phosphoribosyltransferase,_putative_758217..758367_POSITIVE 262 106 61 100 45 NC_002950:PG0603|3end_cytidylate_kinase_660345..660495_POSITIVE 261 113 74 36 1 NC_002950:PG1217|3end_hypothetical_protein_1295987..1296137_POSITIVE 260 44 1 123 68 NC_002950:PG1886|3end_GTP-binding_protein_HflX_1983316..1983466_NEGATIVE