Origin IGS: tagcgcgagttcgatctatcgtcacctcggaaatacgtcccaaaaaatctgtaattgcggtctgagtttcctgaaaaagtggaaccacagttttttcgtttcggcgcgtaaattttttatttctcgcgccgccgtaaaaaaaatctcgcgccacgttttggggagtgtcaaacggggaaattttggcgcgtggcctgtgctgaaaaagctatgagccaaggatgtgaagagaaccctaaaagttgtttgtctaagttttagggttcgcttcaattcacttcatttgacatagcctcttgttttatttatttttgtatcagaacaagaaaataagcatcaagttg .........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 caacttgatgcttattttcttgttctgatacaaaaataaataaaacaagaggctatgtcaaatgaagtgaattgaagcgaaccctaaaacttagacaaacaacttttagggttctcttcacatccttggctcatagctttttcagcacaggccacgcgccaaaatttccccgtttgacactccccaaaacgtggcgcgagattttttttacggcggcgcgagaaataaaaaatttacgcgccgaaacgaaaaaactgtggttccactttttcaggaaactcagaccgcaattacagattttttgggacgtatttccgaggtgacgatagatcgaactcgcgcta Mask Tandem Repeat Region ================================================ tagcgcgagttcgatctatcgtcacctcggaaatacgtcccaaaaaatctgtaattgcggtctgagtttcctgaaaaagtggaaccacagttttttcgtttcggcgcgtaaattttttatttctcgcgccgccgtaaaaaaaatctcgcgccacgttttggggagtgtcaaacggggaaattttggcgcgtggcctgtgctgaaaaagctatgagccaaggatgtgaagagaaccctaaaagttgtttgtctaagttttagggttcgcttcaattcacttcatttgacatagcctcttgttttatttatttttgtatcagaacaagaaaataagcatcaagttg Find is-nt database================================================ Query_seq: PG1024:PG1025|PG1024:PG1025:hypothetical protein:hypothetical protein:->->:1086937..1087280 344 tagcgcgagttcgatctatcgtcacctcggaaatacgtcccaaaaaatctgtaattgcggtctgagtttcctgaaaaagtggaaccacagttttttcgtttcggcgcgtaaattttttatttctcgcgccgccgtaaaaaaaatctcgcgccacgttttggggagtgtcaaacggggaaattttggcgcgtggcctgtgctgaaaaagctatgagccaaggatgtgaagagaaccctaaaagttgtttgtctaagttttagggttcgcttcaattcacttcatttgacatagcctcttgttttatttatttttgtatcagaacaagaaaataagcatcaagttg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG1024:PG1025|PG1024:PG1025:hypothetical protein:hypothetical protein:->->:1086937..1087280 344 tagcgcgagttcgatctatcgtcacctcggaaatacgtcccaaaaaatctgtaattgcggtctgagtttcctgaaaaagtggaaccacagttttttcgtttcggcgcgtaaattttttatttctcgcgccgccgtaaaaaaaatctcgcgccacgttttggggagtgtcaaacggggaaattttggcgcgtggcctgtgctgaaaaagctatgagccaaggatgtgaagagaaccctaaaagttgtttgtctaagttttagggttcgcttcaattcacttcatttgacatagcctcttgttttatttatttttgtatcagaacaagaaaataagcatcaagttg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG1024:PG1025|PG1024:PG1025:hypothetical protein:hypothetical protein:->->:1086937..1087280 344 tagcgcgagttcgatctatcgtcacctcggaaatacgtcccaaaaaatctgtaattgcggtctgagtttcctgaaaaagtggaaccacagttttttcgtttcggcgcgtaaattttttatttctcgcgccgccgtaaaaaaaatctcgcgccacgttttggggagtgtcaaacggggaaattttggcgcgtggcctgtgctgaaaaagctatgagccaaggatgtgaagagaaccctaaaagttgtttgtctaagttttagggttcgcttcaattcacttcatttgacatagcctcttgttttatttatttttgtatcagaacaagaaaataagcatcaagttg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 3 Min: 23 Max: 187 Len: 165 Subject: UniRef90_Q7MTB1 Cluster: Hypothetical protein; n=1; Porphyromonas gingivalis|Rep: Hypothetical protein - Porphyromonas gingivalis (Bacteroides gingivalis) HSP 1 e-value: 1.0E-9 bit: 64.3 Len: 135 Query Start:31 Query End:165 Subject Strand: null Subject Start: 2 Subject End: 46 .............................. L P K T W R E I F F T A A R E I K N L R A E T K K L W F H F F R K L R P Q L Q I F W D V F ................................................................................................................................................................................... .............................. L P K T W R E N F F V L V R E V K N L R A T A K K I S R H F F R K Y E P Q P G V F W F V F ................................................................................................................................................................................... Subject: UniRef90_Q7MU89 Cluster: Hypothetical protein; n=1; Porphyromonas gingivalis|Rep: Hypothetical protein - Porphyromonas gingivalis (Bacteroides gingivalis) HSP 1 e-value: 3.0E-8 bit: 59.7 Len: 165 Query Start:23 Query End:187 Subject Strand: null Subject Start: 9 Subject End: 63 ...................... H L G N T S Q K I C N C G L S F L K K W N H S F F V S A R K F F I S R A A V K K I S R H V L G S V K R G N F G ............................................................................................................................................................. ...................... H H G N T N Q K S S D C G S C F L K K W R E I F F V L A C K F F N C R A K T K K F S R H V F V G N K C E N S G ............................................................................................................................................................. Subject: UniRef90_Q7MUH1 Cluster: Hypothetical protein; n=1; Porphyromonas gingivalis|Rep: Hypothetical protein - Porphyromonas gingivalis (Bacteroides gingivalis) HSP 1 e-value: 2.0E-6 bit: 53.5 Len: 156 Query Start:32 Query End:187 Subject Strand: null Subject Start: 11 Subject End: 62 ............................... A K I S P F D T P Q N V A R D F F Y G G A R N K K F T R R N E K T V V P L F Q E T Q T A I T D F L G R I ............................................................................................................................................................. ............................... S K I F P F A T P Q N A V R K L F Y F G V G S K K F S R H N E K I L A P L F Q G I R A T I G A F P V R V ............................................................................................................................................................. tagcgcgagttcgatctatcgtnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnngcgtggcctgtgctgaaaaagctatgagccaaggatgtgaagagaaccctaaaagttgtttgtctaagttttagggttcgcttcaattcacttcatttgacatagcctcttgttttatttatttttgtatcagaacaagaaaataagcatcaagttg Predict ORF larger than 30AA ================================================ Protein_Len: 60 Strand: + Start: 14 End: 211 ............. M Y R H L G N T S Q K I C N C G L S F L K K W N H S F F V S A R K F F I S R A A V K K I S R H V L G S V K R G N F G A W ..................................................................................................................................... Protein_Len: 49 Strand: + Start: 112 End: 258 ............................................................................................................... M F Y F S R R R K K N L A P R F G E C Q T G K F W R V A C A E K A M S Q G C E E N P K S C L S K F ...................................................................................... Protein_Len: 60 Strand: - Start: 25 End: 273 ........................ K T E A R L N K I E R A A T F F I E R W T K P L T L R P F K P A H G T S F F S H A L S T F L V R F T T Q R L K L T R K M ....................................................................... Protein_Len: 37 Strand: - Start: 3 End: 113 .. R S N S R D D G R F Y T G F F R Y N R D S N G S F T S G C N K R K P A Y M ....................................................................................................................................................................................................................................... Protein_Len: 60 Strand: - Start: 2 End: 181 . A R T R D I T V E S I R G L F D T I A T Q T E Q F L P V V T K E N R R T F K K N R A G G Y F F D R A V N Q P T D F P S M ................................................................................................................................................................... tagcgcgagttcgatctatcgtnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnngcgtggcctgtgctgaaaaagctatgagccaaggatgtgaagagaaccctaaaagttgtttgtctaagttttagggttcgcttcaattcacttcatttgacatagcctcttgttttatttatttttgtatcagaacaagaaaataagcatcaagttg Predict Promoter with matrix: RpoD-15 score > 80================================================ Predict Promoter with matrix: RpoD-16 score > 80================================================ Predict Promoter with matrix: RpoD-17 score > 80================================================ PromScan Matrix: RpoD-17 Strand: + Score: 87 Start: 283 End: 312 ..........................................................................................................................................................................................................................................................................................TTTGACATAGCCTCTTGTTTTATTTATTTT................................ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tagcgcgagttcgatctatcgtnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnngcgtggcctgtgctgaaaaagctatgagccaaggatgtgaagagaaccctaaaagttgtttgtctaagttttagggttcgcttcaattcacttcatttgacatagcctcttgttttatttatttttgtatcagaacaagaaaataagcatcaagttg Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 55 HP_score: -4.8 Tail_Score: -3.53031 Start: 220 End: 278 Full_Region: AAAGCTATGAGCCAA GGATGTGAAGAGAACCCTAAAAGTTG TTTGTC TAAGTTTTAGGGTTCGCTTCAATTCAC TTCATTTGACATAGC ...........................................................................................................................................................................................................................GGATGTGAAGAGAACCCTAAAAGTTGTTTGTCTAAGTTTTAGGGTTCGCTTCAATTCAC.................................................................. TransTerm Strand: + Conf: 71 HP_score: -8.8 Tail_Score: -3.26596 Start: 224 End: 273 Full_Region: CTATGAGCCAAGGAT GTGAAGAGAACCCTAAAAGTTG TTTGTC TAAGTTTTAGGGTTCGCTTCAA TTCACTTCATTTGAC ...............................................................................................................................................................................................................................GTGAAGAGAACCCTAAAAGTTGTTTGTCTAAGTTTTAGGGTTCGCTTCAA....................................................................... TransTerm Strand: - Conf: 63 HP_score: -7.8 Tail_Score: -3.08015 Start: 231 End: 266 Full_Region: gaagtgaattgaagc gaaccctaaaactt agacaaac aacttttagggttc tcttcacatccttgg ......................................................................................................................................................................................................................................gaaccctaaaacttagacaaacaacttttagggttc.............................................................................. TransTerm Strand: - Conf: 53 HP_score: -3.7 Tail_Score: -3.67878 Start: 234 End: 263 Full_Region: gtgaattgaagcgaa ccctaaaactt agacaaac aacttttaggg ttctcttcacatcct .........................................................................................................................................................................................................................................ccctaaaacttagacaaacaacttttaggg................................................................................. Find igs database================================================ Query_seq: PG1024:PG1025|PG1024:PG1025:hypothetical protein:hypothetical protein:->->:1086937..1087280 344 tagcgcgagttcgatctatcgtnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnngcgtggcctgtgctgaaaaagctatgagccaaggatgtgaagagaaccctaaaagttgtttgtctaagttttagggttcgcttcaattcacttcatttgacatagcctcttgttttatttatttttgtatcagaacaagaaaataagcatcaagttg Intra-Species Hit: Count: 1 Min: 189 Max: 344 Len: 156 Subject: NC_002950_PG1024_PG1025|hypothetical protein:hypothetical protein|POSITIVE:POSITIVE|[1086937,1087280]|344 HSP 1 e-value: 3.0E-83 bit: 309.0 Len: 156 Query Start:189 Query End:344 Subject Strand: POSITIVE Subject Start: 189 Subject End: 344 ............................................................................................................................................................................................cgtggcctgtgctgaaaaagctatgagccaaggatgtgaagagaaccctaaaagttgtttgtctaagttttagggttcgcttcaattcacttcatttgacatagcctcttgttttatttatttttgtatcagaacaagaaaataagcatcaagttg ............................................................................................................................................................................................cgtggcctgtgctgaaaaagctatgagccaaggatgtgaagagaaccctaaaagttgtttgtctaagttttagggttcgcttcaattcacttcatttgacatagcctcttgttttatttatttttgtatcagaacaagaaaataagcatcaagttg Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CGUGGCCUGUGCUGAAAAAGCUAUGAGCCAAGGAUGUGAAGAGAACCCUAAAAGUUGUUUGUCUAAGUUUUAGGGUUCGCUUCAAUUCACUUCAUUUGACAUAGCCUCUUGUUUUAUUUAUUUUUGUAUCAGAACAAGAAAAUAAGCAUCAAGUUG ...(((.((((((......((((((....(((((..(((((.(((((((((((.(((......))).))))))))))).)))))..)).))).......)))))).(((((((((...(((....)))..))))))))).....)))).)).))). (-45.90) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CAACUUGAUGCUUAUUUUCUUGUUCUGAUACAAAAAUAAAUAAAACAAGAGGCUAUGUCAAAUGAAGUGAAUUGAAGCGAACCCUAAAACUUAGACAAACAACUUUUAGGGUUCUCUUCACAUCCUUGGCUCAUAGCUUUUUCAGCACAGGCCACG ...((((.(((((((((..((((......))))....)))))....(((((((((((.....(.(((.((..(((((.(((((((((((.((........)).))))))))))).)))))..))))).)..))))))))))).))))))))..... (-41.70) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 491 80 35 105 55 NC_002950:PG0554|5end_hypothetical_protein_611465..611695_POSITIVE 310 60 12 55 1 NC_002950:PG0501|5end_hypothetical_protein_540344..540574_POSITIVE 307 47 1 110 65 NC_002950:PG1270|5end_hypothetical_protein_1350207..1350437_NEGATIVE 301 43 4 169 129 NC_002950:PG0935|5end_4-diphosphocytidyl-2C-methyl-D-erythritol_kinase_995121..995351_NEGATIVE 301 43 1 113 49 NC_002950:PG0422|5end_hypothetical_protein_462302..462532_NEGATIVE 293 48 1 206 148 NC_002950:PG1788|5end_cysteine_peptidase,_putative_1875976..1876206_POSITIVE 292 47 1 61 20 NC_002950:PG0217|5end_hypothetical_protein_252490..252720_POSITIVE 291 44 2 180 137 NC_002950:PG2064|5end_hypothetical_protein_2160550..2160780_POSITIVE 289 70 25 84 39 NC_002950:PG2155|5end_lipoprotein,_putative_2261862..2262092_NEGATIVE 289 37 2 57 15 NC_002950:PG1588|5end_hypothetical_protein_1666532..1666762_NEGATIVE 289 44 1 60 1 NC_002950:PG0285|5end_hypothetical_protein_318459..318689_POSITIVE 288 43 1 40 1 NC_002950:PG0328|5end_imidazolonepropionase_363426..363656_NEGATIVE 286 43 2 154 119 NC_002950:PG0496|5end_hypothetical_protein_537168..537398_POSITIVE 281 45 1 218 169 NC_002950:PG0683|5end_ABC_transporter,_permease_protein,_putative_735255..735485_POSITIVE 280 38 4 69 36 NC_002950:PG2187|5end_1,4-dihydroxy-2-naphthoate_octaprenyltransferase_2294643..2294873_NEGATIVE 280 117 72 222 175 NC_002950:PG1739|5end_hypothetical_protein_1825709..1825939_NEGATIVE 280 35 1 207 169 NC_002950:PG0963|5end_hypothetical_protein_1024332..1024562_NEGATIVE 279 48 2 51 4 NC_002950:PG2096|5end_hypothetical_protein_2205415..2205645_NEGATIVE 277 79 31 59 5 NC_002950:PG1370|5end_lysyl-tRNA_synthetase_1452229..1452459_NEGATIVE 275 60 13 155 108 NC_002950:PG1079|5end_enoyl-CoA_hydratase/isomerase_family_protein_1146549..1146779_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 510 90 43 49 1 NC_002950:PG1385|3end_TPR_domain_protein_1465133..1465283_NEGATIVE 373 84 43 52 11 NC_002950:PG2192|3end_peptidase,_M23/M37_family_2299334..2299484_POSITIVE 336 90 43 47 1 NC_002950:PG1080|3end_3-hydroxyacyl-CoA_dehydrogenase_family_protein_1148291..1148441_POSITIVE 307 47 1 103 58 NC_002950:PG1271|3end_acetylornithine_aminotransferase,_putative_1350214..1350364_NEGATIVE 301 43 4 140 100 NC_002950:PG0936|3end_xanthine/uracil_permease_family_protein_995150..995300_NEGATIVE 289 70 25 47 2 NC_002950:PG2156|3end_conserved_hypothetical_protein_TIGR00046_2261899..2262049_NEGATIVE 280 38 4 79 46 NC_002950:PG2188|3end_diaminopimelate_decarboxylase_2294633..2294783_NEGATIVE 280 117 72 75 28 NC_002950:PG1741|3end_aspartate_ammonia-lyase_1825856..1826006_NEGATIVE 278 49 2 79 38 NC_002950:PG0123|3end_hypothetical_protein_145585..145735_POSITIVE 275 60 13 51 4 NC_002950:PG1078|3end_electron_transfer_flavoprotein,_alpha_subunit_1146525..1146675_POSITIVE 274 38 2 75 42 NC_002950:PG0809|3end_hypothetical_protein_865064..865214_NEGATIVE 272 112 72 72 38 NC_002950:PG0899|3end_cytochrome_d_ubiquinol_oxidase,_subunit_II_963497..963647_NEGATIVE 268 112 72 61 27 NC_002950:PG0769|3end_fibronectin_type_III_domain_protein_822555..822705_NEGATIVE 267 106 67 38 7 NC_002950:PG1758|3end_ribosomal_protein_S15_1845534..1845684_POSITIVE 265 37 1 140 99 NC_002950:PG2171|3end_D-isomer_specific_2-hydroxyacid_dehydrogenase_family_protein_2278013..2278163_NEGATIVE 265 117 72 70 22 NC_002950:PG1414|3end_hypothetical_protein_1499704..1499854_POSITIVE 265 45 1 67 15 NC_002950:PG0645|3end_hypothetical_protein_696883..697033_NEGATIVE 261 39 1 143 98 NC_002950:PG0106|3end_glycosyl_transferase,_group_4_family_protein_129934..130084_POSITIVE 258 39 1 70 27 NC_002950:PG1621|3end_hypothetical_protein_1700484..1700634_NEGATIVE 255 128 95 82 41 NC_002950:PG2170|3end_sugar_transporter_2276685..2276835_NEGATIVE