Origin IGS: gaatagtgctttttttatcgagtttttcttagggctgccgttggaggacagctctactatcgagtcaatatccatcaaccactatcccaccgatacgagccgaaaatcctctgattgcggcgcgtcttttctgaagaaggtggtgccggaattttttcgttttggttcgagatttttttacttctcgcgccaaagcgaaaaagtttacgcaccacgtttttccaaactgcaaacacaaaaattccggcacgtaaaccgatcggctgtgagatgatgcctgctacactttttcggcggattgatttttccgttg .........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 caacggaaaaatcaatccgccgaaaaagtgtagcaggcatcatctcacagccgatcggtttacgtgccggaatttttgtgtttgcagtttggaaaaacgtggtgcgtaaactttttcgctttggcgcgagaagtaaaaaaatctcgaaccaaaacgaaaaaattccggcaccaccttcttcagaaaagacgcgccgcaatcagaggattttcggctcgtatcggtgggatagtggttgatggatattgactcgatagtagagctgtcctccaacggcagccctaagaaaaactcgataaaaaaagcactattc Mask Tandem Repeat Region ================================================ gaatagtgctttttttatcgagtttttcttagggctgccgttggaggacagctctactatcgagtcaatatccatcaaccactatcccaccgatacgagccgaaaatcctctgattgcggcgcgtcttttctgaagaaggtggtgccggaattttttcgttttggttcgagatttttttacttctcgcgccaaagcgaaaaagtttacgcaccacgtttttccaaactgcaaacacaaaaattccggcacgtaaaccgatcggctgtgagatgatgcctgctacactttttcggcggattgatttttccgttg Find is-nt database================================================ Query_seq: PG0352:PG0354|PG0352:PG0354:sialidase, putative:hypothetical protein:-><-:388908..389220 313 gaatagtgctttttttatcgagtttttcttagggctgccgttggaggacagctctactatcgagtcaatatccatcaaccactatcccaccgatacgagccgaaaatcctctgattgcggcgcgtcttttctgaagaaggtggtgccggaattttttcgttttggttcgagatttttttacttctcgcgccaaagcgaaaaagtttacgcaccacgtttttccaaactgcaaacacaaaaattccggcacgtaaaccgatcggctgtgagatgatgcctgctacactttttcggcggattgatttttccgttg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG0352:PG0354|PG0352:PG0354:sialidase, putative:hypothetical protein:-><-:388908..389220 313 gaatagtgctttttttatcgagtttttcttagggctgccgttggaggacagctctactatcgagtcaatatccatcaaccactatcccaccgatacgagccgaaaatcctctgattgcggcgcgtcttttctgaagaaggtggtgccggaattttttcgttttggttcgagatttttttacttctcgcgccaaagcgaaaaagtttacgcaccacgtttttccaaactgcaaacacaaaaattccggcacgtaaaccgatcggctgtgagatgatgcctgctacactttttcggcggattgatttttccgttg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG0352:PG0354|PG0352:PG0354:sialidase, putative:hypothetical protein:-><-:388908..389220 313 gaatagtgctttttttatcgagtttttcttagggctgccgttggaggacagctctactatcgagtcaatatccatcaaccactatcccaccgatacgagccgaaaatcctctgattgcggcgcgtcttttctgaagaaggtggtgccggaattttttcgttttggttcgagatttttttacttctcgcgccaaagcgaaaaagtttacgcaccacgtttttccaaactgcaaacacaaaaattccggcacgtaaaccgatcggctgtgagatgatgcctgctacactttttcggcggattgatttttccgttg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 1 Min: 92 Max: 266 Len: 175 Subject: UniRef90_Q7MU89 Cluster: Hypothetical protein; n=1; Porphyromonas gingivalis|Rep: Hypothetical protein - Porphyromonas gingivalis (Bacteroides gingivalis) HSP 1 e-value: 4.0E-7 bit: 47.4 Len: 138 Query Start:129 Query End:266 Subject Strand: null Subject Start: 24 Subject End: 69 ................................................................................................................................ F * R R W C R N F F V L V R D F F T S R A K A K K F T H H V F P N C K H K N S G T * T D R L ............................................... ................................................................................................................................ 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 T Q T Y R I ............................................... HSP 2 e-value: 4.0E-7 bit: 28.5 Len: 48 Query Start:92 Query End:139 Subject Strand: null Subject Start: 12 Subject End: 27 ........................................................................................... D T S R K S S D C G A S F L K K .............................................................................................................................................................................. ........................................................................................... N T N Q K S S D C G S C F L K K .............................................................................................................................................................................. gaatagtgctttttttatcgagtttttcttagggctgccgttggaggacagctctactatcgagtcaatatccatcaaccactatcccaccnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnntgagatgatgcctgctacactttttcggcggattgatttttccgttg Predict ORF larger than 30AA ================================================ Protein_Len: 30 Strand: + Start: 162 End: 251 ................................................................................................................................................................. M V R D F F T S R A K A K K F T H H V F P N C K H K N S G T .............................................................. Protein_Len: 60 Strand: + Start: 17 End: 271 ................ M E F F L G L P L E D S S T I E S I S I N H Y P T D T S R K S S D C G A S F L K K V V P E F F R F G S R F F Y F S R Q S .......................................... Protein_Len: 60 Strand: + Start: 115 End: 312 .................................................................................................................. M R R V F S E E G G A G I F S F W F E I F L L L A P K R K S L R T T F F Q T A N T K I P A R K P I G C E M M P A T L F R . Protein_Len: 32 Strand: - Start: 208 End: 303 ............................................................................................................................................................................................................... A G R K E L S C V C F N R C T F R D A T L H H R S C K K P P N M .......... Protein_Len: 60 Strand: - Start: 78 End: 299 ............................................................................. R T K E S S P P A P I K E N Q N S I K K S R A G F R F L K R V V N K W V A F V F I G A R L G I P Q S I I G A V S K R R M .............. Protein_Len: 60 Strand: - Start: 68 End: 250 ................................................................... G D V V I G G I R A S F G R I A A R R K Q L L H H R F K K T K T R S K K V E R A L A F F N V C W T K G F Q L C L F E P M ............................................................... gaatagtgctttttttatcgagtttttcttagggctgccgttggaggacagctctactatcgagtcaatatccatcaaccactatcccaccnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnntgagatgatgcctgctacactttttcggcggattgatttttccgttg 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================================================ gaatagtgctttttttatcgagtttttcttagggctgccgttggaggacagctctactatcgagtcaatatccatcaaccactatcccaccnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnntgagatgatgcctgctacactttttcggcggattgatttttccgttg Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 75 HP_score: -9.7 Tail_Score: -3.53343 Start: 152 End: 203 Full_Region: AAGGTGGTGCCGGAA TTTTTTCGTTTTGGTTCGAGA TTTTTTTACT TCTCGCGCCAAAGCGAAAAAG TTTACGCACCACGTT .......................................................................................................................................................TTTTTTCGTTTTGGTTCGAGATTTTTTTACTTCTCGCGCCAAAGCGAAAAAG.............................................................................................................. TransTerm Strand: + Conf: 73 HP_score: -11.0 Tail_Score: -2.71791 Start: 153 End: 202 Full_Region: AGGTGGTGCCGGAAT TTTTTCGTTTTGGTTCGAGA TTTTTTTACT TCTCGCGCCAAAGCGAAAAA GTTTACGCACCACGT ........................................................................................................................................................TTTTTCGTTTTGGTTCGAGATTTTTTTACTTCTCGCGCCAAAGCGAAAAA............................................................................................................... Find igs database================================================ Query_seq: PG0352:PG0354|PG0352:PG0354:sialidase, putative:hypothetical protein:-><-:388908..389220 313 gaatagtgctttttttatcgagtttttcttagggctgccgttggaggacagctctactatcgagtcaatatccatcaaccactatcccaccnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnntgagatgatgcctgctacactttttcggcggattgatttttccgttg Intra-Species Hit: Count: 1 Min: 17 Max: 313 Len: 297 Subject: NC_002950_PG0352_PG0354|sialidase, putative:hypothetical protein|POSITIVE:NEGATIVE|[388908,389220]|313 HSP 1 e-value: 7.0E-35 bit: 149.0 Len: 75 Query Start:17 Query End:91 Subject Strand: POSITIVE Subject Start: 17 Subject End: 91 ................atcgagtttttcttagggctgccgttggaggacagctctactatcgagtcaatatccatcaaccactatcccacc.............................................................................................................................................................................................................................. ................atcgagtttttcttagggctgccgttggaggacagctctactatcgagtcaatatccatcaaccactatcccacc.............................................................................................................................................................................................................................. HSP 2 e-value: 3.0E-18 bit: 93.7 Len: 47 Query Start:267 Query End:313 Subject Strand: POSITIVE Subject Start: 267 Subject End: 313 ..........................................................................................................................................................................................................................................................................tgagatgatgcctgctacactttttcggcggattgatttttccgttg ..........................................................................................................................................................................................................................................................................tgagatgatgcctgctacactttttcggcggattgatttttccgttg Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUCGAGUUUUUCUUAGGGCUGCCGUUGGAGGACAGCUCUACUAUCGAGUCAAUAUCCAUCAACCACUAUCCCACCGAUACGAGCCGAAAAUCCUCUGAUUGCGGCGCGUCUUUUCUGAAGAAGGUGGUGCCGGAAUUUUUUCGUUUUGGUUCGAGAUUUUUUUACUUCUCGCGCCAAAGCGAAAAAGUUUACGCACCACGUUUUUCCAAACUGCAAACACAAAAAUUCCGGCACGUAAACCGAUCGGCUGUGAGAUGAUGCCUGCUACACUUUUUCGGCGGAUUGAUUUUUCCGUUG .............((((((((((......)).)))))))).....((((((..((((.........((((.....))))...((((((((.....((...((((.(((((.((((.((((((.(((((((..((((((((((((((((((.(((((..........))))).))))))))))))))))))..))))))).))))))......................((((.((.........)))))).)))).)))))))))..))..))))))))))))))))))........ (-101.80) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CAACGGAAAAAUCAAUCCGCCGAAAAAGUGUAGCAGGCAUCAUCUCACAGCCGAUCGGUUUACGUGCCGGAAUUUUUGUGUUUGCAGUUUGGAAAAACGUGGUGCGUAAACUUUUUCGCUUUGGCGCGAGAAGUAAAAAAAUCUCGAACCAAAACGAAAAAAUUCCGGCACCACCUUCUUCAGAAAAGACGCGCCGCAAUCAGAGGAUUUUCGGCUCGUAUCGGUGGGAUAGUGGUUGAUGGAUAUUGACUCGAUAGUAGAGCUGUCCUCCAACGGCAGCCCUAAGAAAAACUCGAU ...((((........)))).(((.......(((..(((...(((((((.(((....))).((((.(((((((.((((.((.((((.((((.(((.((.(((((((......(((((((.(((((..(((((..........)))))..))))).)))))))......))))))).)).))).....)))).....)))).)).)))).))))))).))))...))))))).((.((((..(((((..(.(((.......)))))))))..)))).)).))))))........))).. (-94.36) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 589 205 166 85 46 NC_002950:PG0313|5end_hypothetical_protein_347366..347596_POSITIVE 556 200 152 114 66 NC_002950:PG1980|5end_hypothetical_protein_2067930..2068160_NEGATIVE 521 189 141 101 53 NC_002950:PG1617|5end_hypothetical_protein_1697755..1697985_NEGATIVE 486 130 86 44 1 NC_002950:PG0174|5end_pyridine_nucleotide-disulphide_oxidoreductase_family_protein_197628..197858_NEGATIVE 483 205 161 83 39 NC_002950:PG2064|5end_hypothetical_protein_2160550..2160780_POSITIVE 478 143 102 54 15 NC_002950:PG0472|5end_iron-sulfur_cluster_binding_protein,_putative_513339..513569_POSITIVE 460 170 121 62 13 NC_002950:PG1799|5end_hypothetical_protein_1894499..1894729_POSITIVE 454 150 102 122 75 NC_002950:PG0132|5end_hypothetical_protein_152879..153109_POSITIVE 415 109 67 83 34 NC_002950:PG1703|5end_MazG_family_protein_1790753..1790983_NEGATIVE 413 156 111 225 182 NC_002950:PG0470|5end_hypothetical_protein_511883..512113_NEGATIVE 403 187 141 172 126 NC_002950:PG2063|5end_hypothetical_protein_2160596..2160826_NEGATIVE 403 180 131 55 6 NC_002950:PG0080|5end_hypothetical_protein_93832..94062_NEGATIVE 400 180 131 116 66 NC_002950:PG0007|5end_hypothetical_protein_6913..7143_NEGATIVE 399 133 92 218 161 NC_002950:PG0881|5end_recombinase_A_943063..943293_POSITIVE 385 40 3 169 121 NC_002950:PG1009|5end_hypothetical_protein_1068495..1068725_NEGATIVE 384 265 228 49 9 NC_002950:PG1946|5end_ABC_3_transporter_family_protein_2032133..2032363_POSITIVE 376 194 152 203 159 NC_002950:PG0081|5end_hypothetical_protein_93805..94035_POSITIVE 375 134 92 56 10 NC_002950:PG1242|5end_replicative_DNA_helicase_1317435..1317665_POSITIVE 373 279 231 111 47 NC_002950:PG2019|5end_hypothetical_protein_2111662..2111892_NEGATIVE 373 107 66 184 148 NC_002950:PG0525|5end_CTP_synthetase_568999..569229_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 601 186 141 146 101 NC_002950:PG1718|3end_hypothetical_protein_1806532..1806682_NEGATIVE 478 143 102 67 28 NC_002950:PG0471|3end_hypothetical_protein_513432..513582_POSITIVE 463 206 166 58 18 NC_002950:PG0542|3end_hypothetical_protein_595377..595527_NEGATIVE 425 58 15 69 25 NC_002950:PG0435|3end_capsular_polysaccharide_biosythesis_protein,_putative_472708..472858_NEGATIVE 415 109 67 65 16 NC_002950:PG1704|3end_thiol:disulfide_interchange_protein_dsbD,_putative_1790771..1790921_NEGATIVE 411 204 165 46 7 NC_002950:PG1546|3end_hypothetical_protein_1624355..1624505_POSITIVE 384 265 228 56 16 NC_002950:PG1945|3end_hypothetical_protein_2032220..2032370_POSITIVE 373 105 62 132 87 NC_002950:PG1750|3end_alpha-1,3/4-fucosidase,_putative_1837223..1837373_POSITIVE 373 107 66 68 32 NC_002950:PG0524|3end_hypothetical_protein_568963..569113_POSITIVE 369 130 81 89 33 NC_002950:PG0881|3end_recombinase_A_944165..944315_POSITIVE 361 113 80 61 20 NC_002950:PG1855|3end_carboxyl-terminal_protease_1953842..1953992_NEGATIVE 352 105 62 139 84 NC_002950:PG0210|3end_precorrin-6x_reductase/cobalamin_biosynthetic_protein_CbiD_244161..244311_NEGATIVE 347 48 1 121 70 NC_002950:PG1391|3end_hypothetical_protein_1472961..1473111_POSITIVE 346 110 66 144 88 NC_002950:PG0384|3end_MutS2_family_protein_418697..418847_POSITIVE 344 149 103 62 13 NC_002950:PG1346|3end_glycosyl_transferase,_group_1_family_protein_1428059..1428209_POSITIVE 344 130 83 149 96 NC_002950:PG0678|3end_pyrazinamidase/nicotinamidase,_putative_729471..729621_POSITIVE 343 287 242 120 76 NC_002950:PG1595|3end_ribulose-phosphate_3-epimerase_1673594..1673744_NEGATIVE 339 148 102 55 1 NC_002950:PG0787|3end_hypothetical_protein_837997..838147_POSITIVE 338 134 94 130 86 NC_002950:PG1715|3end_hypothetical_protein_1803393..1803543_NEGATIVE 338 134 91 147 97 NC_002950:PG0060|3end_hypothetical_protein_72178..72328_POSITIVE