Origin IGS: tattattgggtaaggttgtaccgagatgtcgtattcggatttcgtttccccaaaagtacaaaaaagagaccgtgtaacatgactaacttaaacttcctttttagtccggatcagttttgtcggaaatacgaaccgcaaatgatctgattgtggcgcgtgttttctgaacgaagtggtgcgagaactttttcgttgtggcgcgagaatttttcacttcccgaaccaaaacaaaaaagtttacgcaccacgttttatggcgtggcatgtaagaagattttggtgcgtaggccgatcctgcatgagatgcatctctacgctttaggggggccgggtgagtgggggcggaatctttttgccgatttgttggcctgttctctttatctttgcgctacaggcgagtaataatcatacaaagaatcatataaaa .........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 ttttatatgattctttgtatgattattactcgcctgtagcgcaaagataaagagaacaggccaacaaatcggcaaaaagattccgcccccactcacccggcccccctaaagcgtagagatgcatctcatgcaggatcggcctacgcaccaaaatcttcttacatgccacgccataaaacgtggtgcgtaaacttttttgttttggttcgggaagtgaaaaattctcgcgccacaacgaaaaagttctcgcaccacttcgttcagaaaacacgcgccacaatcagatcatttgcggttcgtatttccgacaaaactgatccggactaaaaaggaagtttaagttagtcatgttacacggtctcttttttgtacttttggggaaacgaaatccgaatacgacatctcggtacaaccttacccaataata Mask Tandem Repeat Region ================================================ tattattgggtaaggttgtaccgagatgtcgtattcggatttcgtttccccaaaagtacaaaaaagagaccgtgtaacatgactaacttaaacttcctttttagtccggatcagttttgtcggaaatacgaaccgcaaatgatctgattgtggcgcgtgttttctgaacgaagtggtgcgagaactttttcgttgtggcgcgagaatttttcacttcccgaaccaaaacaaaaaagtttacgcaccacgttttatggcgtggcatgtaagaagattttggtgcgtaggccgatcctgcatgagatgcatctctacgctttaggggggccgggtgagtgggggcggaatctttttgccgatttgttggcctgttctctttatctttgcgctacaggcgagtaataatcatacaaagaatcatataaaa Find is-nt database================================================ Query_seq: PG0676:PG0677|PG0676:PG0677:oxidoreductase, short chain dehydrogenase/reductase family:saccharopine dehydrogenase:<-->:727366..727792 427 tattattgggtaaggttgtaccgagatgtcgtattcggatttcgtttccccaaaagtacaaaaaagagaccgtgtaacatgactaacttaaacttcctttttagtccggatcagttttgtcggaaatacgaaccgcaaatgatctgattgtggcgcgtgttttctgaacgaagtggtgcgagaactttttcgttgtggcgcgagaatttttcacttcccgaaccaaaacaaaaaagtttacgcaccacgttttatggcgtggcatgtaagaagattttggtgcgtaggccgatcctgcatgagatgcatctctacgctttaggggggccgggtgagtgggggcggaatctttttgccgatttgttggcctgttctctttatctttgcgctacaggcgagtaataatcatacaaagaatcatataaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG0676:PG0677|PG0676:PG0677:oxidoreductase, short chain dehydrogenase/reductase family:saccharopine dehydrogenase:<-->:727366..727792 427 tattattgggtaaggttgtaccgagatgtcgtattcggatttcgtttccccaaaagtacaaaaaagagaccgtgtaacatgactaacttaaacttcctttttagtccggatcagttttgtcggaaatacgaaccgcaaatgatctgattgtggcgcgtgttttctgaacgaagtggtgcgagaactttttcgttgtggcgcgagaatttttcacttcccgaaccaaaacaaaaaagtttacgcaccacgttttatggcgtggcatgtaagaagattttggtgcgtaggccgatcctgcatgagatgcatctctacgctttaggggggccgggtgagtgggggcggaatctttttgccgatttgttggcctgttctctttatctttgcgctacaggcgagtaataatcatacaaagaatcatataaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG0676:PG0677|PG0676:PG0677:oxidoreductase, short chain dehydrogenase/reductase family:saccharopine dehydrogenase:<-->:727366..727792 427 tattattgggtaaggttgtaccgagatgtcgtattcggatttcgtttccccaaaagtacaaaaaagagaccgtgtaacatgactaacttaaacttcctttttagtccggatcagttttgtcggaaatacgaaccgcaaatgatctgattgtggcgcgtgttttctgaacgaagtggtgcgagaactttttcgttgtggcgcgagaatttttcacttcccgaaccaaaacaaaaaagtttacgcaccacgttttatggcgtggcatgtaagaagattttggtgcgtaggccgatcctgcatgagatgcatctctacgctttaggggggccgggtgagtgggggcggaatctttttgccgatttgttggcctgttctctttatctttgcgctacaggcgagtaataatcatacaaagaatcatataaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 1 Min: 171 Max: 296 Len: 126 Subject: UniRef90_Q7MUH1 Cluster: Hypothetical protein; n=1; Porphyromonas gingivalis|Rep: Hypothetical protein - Porphyromonas gingivalis (Bacteroides gingivalis) HSP 1 e-value: 9.0E-10 bit: 64.7 Len: 126 Query Start:171 Query End:296 Subject Strand: null Subject Start: 6 Subject End: 47 .......................................................................................................................................................................... R I G L R T K I F L H A T P * N V V R K L F C F G S G S E K F S R H N E K V L A P L ................................................................................................................................... .......................................................................................................................................................................... R I G L G 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 ................................................................................................................................... tattattgggtaaggttgtaccgagatgtcgtattcggatttcgtttccccaaaagtacaaaaaagagaccgtgtaacatgactaacttaaacttcctttttagtccggatcagttttgtcggaaatacgaaccgcaaatgatctgattgtggcgcgtgttttctgaacgnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnngcatgagatgcatctctacgctttaggggggccgggtgagtgggggcggaatctttttgccgatttgttggcctgttctctttatctttgcgctacaggcgagtaataatcatacaaagaatcatataaaa Predict ORF larger than 30AA ================================================ Protein_Len: 43 Strand: + Start: 16 End: 144 ............... M Y R D V V F G F R F P K S T K K R P C N M T N L N F L F S P D Q F C R K Y E P Q M I ........................................................................................................................................................................................................................................................................................... Protein_Len: 52 Strand: + Start: 164 End: 319 ................................................................................................................................................................... M N E V V R E L F R C G A R I F H F P N Q N K K V Y A P R F M A W H V R R F W C V G R S C M R C I S T L ............................................................................................................ Protein_Len: 60 Strand: + Start: 148 End: 399 ................................................................................................................................................... M W R V F S E R S G A R T F S L W R E N F S L P E P K Q K S L R T T F Y G V A C K K I L V R R P I L H E M H L Y A L G G ............................ Protein_Len: 30 Strand: + Start: 336 End: 422 ............................................................................................................................................................................................................................................................................................................................................... M G A E S F C R F V G L F S L S L R Y R R V I I I Q R I I * ..... Protein_Len: 32 Strand: + Start: 332 End: 427 ........................................................................................................................................................................................................................................................................................................................................... M S G G G I F L P I C W P V L F I F A L Q A S N N H T K N H I K Protein_Len: 45 Strand: - Start: 114 End: 248 ................................................................................................................. N Q R F Y S G C I I Q N H R T N E S R L P A L V K E N H R S F K E S G S G F C F L K R V M ................................................................................................................................................................................... Protein_Len: 54 Strand: - Start: 104 End: 265 ....................................................................................................... D P D T K D S I R V A F S R I T A R T K Q V F H H S F K K T T A R S N K V E R V L V F F N V C W T K H R P M .................................................................................................................................................................. Protein_Len: 39 Strand: - Start: 91 End: 207 .......................................................................................... V E K K T R I L K T P F V F R L H D S Q P A H K R F S T T R S S K R Q P A L M ............................................................................................................................................................................................................................ tattattgggtaaggttgtaccgagatgtcgtattcggatttcgtttccccaaaagtacaaaaaagagaccgtgtaacatgactaacttaaacttcctttttagtccggatcagttttgtcggaaatacgaaccgcaaatgatctgattgtggcgcgtgttttctgaacgnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnngcatgagatgcatctctacgctttaggggggccgggtgagtgggggcggaatctttttgccgatttgttggcctgttctctttatctttgcgctacaggcgagtaataatcatacaaagaatcatataaaa 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================================================ tattattgggtaaggttgtaccgagatgtcgtattcggatttcgtttccccaaaagtacaaaaaagagaccgtgtaacatgactaacttaaacttcctttttagtccggatcagttttgtcggaaatacgaaccgcaaatgatctgattgtggcgcgtgttttctgaacgnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnngcatgagatgcatctctacgctttaggggggccgggtgagtgggggcggaatctttttgccgatttgttggcctgttctctttatctttgcgctacaggcgagtaataatcatacaaagaatcatataaaa Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 71 HP_score: -9.6 Tail_Score: -3.29461 Start: 185 End: 236 Full_Region: aacgtggtgcgtaaa cttttttgttttggttcgggaagt gaaa aattctcgcgccacaacgaaaaag ttctcgcaccacttc ........................................................................................................................................................................................cttttttgttttggttcgggaagtgaaaaattctcgcgccacaacgaaaaag............................................................................................................................................................................................... TransTerm Strand: - Conf: 43 HP_score: -3.0 Tail_Score: -3.02051 Start: 238 End: 269 Full_Region: cgcaccaaaatcttc ttacatgccacg ccataaaa cgtggtgcgtaa acttttttgttttgg .............................................................................................................................................................................................................................................ttacatgccacgccataaaacgtggtgcgtaa.............................................................................................................................................................. Find igs database================================================ Query_seq: PG0676:PG0677|PG0676:PG0677:oxidoreductase, short chain dehydrogenase/reductase family:saccharopine dehydrogenase:<-->:727366..727792 427 tattattgggtaaggttgtaccgagatgtcgtattcggatttcgtttccccaaaagtacaaaaaagagaccgtgtaacatgactaacttaaacttcctttttagtccggatcagttttgtcggaaatacgaaccgcaaatgatctgattgtggcgcgtgttttctgaacgnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnngcatgagatgcatctctacgctttaggggggccgggtgagtgggggcggaatctttttgccgatttgttggcctgttctctttatctttgcgctacaggcgagtaataatcatacaaagaatcatataaaa Intra-Species Hit: Count: 1 Min: 1 Max: 427 Len: 427 Subject: NC_002950_PG0676_PG0677|oxidoreductase, short chain dehydrogenase/reductase family:saccharopine dehydrogenase|NEGATIVE:POSITIVE|[727366,727792]|427 HSP 1 e-value: 8.0E-91 bit: 335.0 Len: 169 Query Start:1 Query End:169 Subject Strand: POSITIVE Subject Start: 1 Subject End: 169 tattattgggtaaggttgtaccgagatgtcgtattcggatttcgtttccccaaaagtacaaaaaagagaccgtgtaacatgactaacttaaacttcctttttagtccggatcagttttgtcggaaatacgaaccgcaaatgatctgattgtggcgcgtgttttctgaac.................................................................................................................................................................................................................................................................. tattattgggtaaggttgtaccgagatgtcgtattcggatttcgtttccccaaaagtacaaaaaagagaccgtgtaacatgactaacttaaacttcctttttagtccggatcagttttgtcggaaatacgaaccgcaaatgatctgattgtggcgcgtgttttctgaac.................................................................................................................................................................................................................................................................. HSP 2 e-value: 1.0E-67 bit: 258.0 Len: 130 Query Start:298 Query End:427 Subject Strand: POSITIVE Subject Start: 298 Subject End: 427 .........................................................................................................................................................................................................................................................................................................catgagatgcatctctacgctttaggggggccgggtgagtgggggcggaatctttttgccgatttgttggcctgttctctttatctttgcgctacaggcgagtaataatcatacaaagaatcatataaaa .........................................................................................................................................................................................................................................................................................................catgagatgcatctctacgctttaggggggccgggtgagtgggggcggaatctttttgccgatttgttggcctgttctctttatctttgcgctacaggcgagtaataatcatacaaagaatcatataaaa Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAUUAUUGGGUAAGGUUGUACCGAGAUGUCGUAUUCGGAUUUCGUUUCCCCAAAAGUACAAAAAAGAGACCGUGUAACAUGACUAACUUAAACUUCCUUUUUAGUCCGGAUCAGUUUUGUCGGAAAUACGAACCGCAAAUGAUCUGAUUGUGGCGCGUGUUUUCUGAACGAAGUGGUGCGAGAACUUUUUCGUUGUGGCGCGAGAAUUUUUCACUUCCCGAACCAAAACAAAAAAGUUUACGCACCACGUUUUAUGGCGUGGCAUGUAAGAAGAUUUUGGUGCGUAGGCCGAUCCUGCAUGAGAUGCAUCUCUACGCUUUAGGGGGGCCGGGUGAGUGGGGGCGGAAUCUUUUUGCCGAUUUGUUGGCCUGUUCUCUUUAUCUUUGCGCUACAGGCGAGUAAUAAUCAUACAAAGAAUCAUAUAAAA .........(((.((((((...(((.(.(((((((...(((((((((..........((((((..((..(((........((((((..............))))))))).))..)))))).(((((((((..((((((.........))))))..))))))))).)))))))))))))))).).))).(((((((((((((((..........((((((..(((((((........((((((..(((((((....)))))))..))))))....)))))))(((((((..((...(((((...))))))))))))))....))))))..(((((((.((((((((.........(((((....)))))))))))))))))))))))))))))).)))))..)))))).)))................ (-124.54) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUUAUAUGAUUCUUUGUAUGAUUAUUACUCGCCUGUAGCGCAAAGAUAAAGAGAACAGGCCAACAAAUCGGCAAAAAGAUUCCGCCCCCACUCACCCGGCCCCCCUAAAGCGUAGAGAUGCAUCUCAUGCAGGAUCGGCCUACGCACCAAAAUCUUCUUACAUGCCACGCCAUAAAACGUGGUGCGUAAACUUUUUUGUUUUGGUUCGGGAAGUGAAAAAUUCUCGCGCCACAACGAAAAAGUUCUCGCACCACUUCGUUCAGAAAACACGCGCCACAAUCAGAUCAUUUGCGGUUCGUAUUUCCGACAAAACUGAUCCGGACUAAAAAGGAAGUUUAAGUUAGUCAUGUUACACGGUCUCUUUUUUGUACUUUUGGGGAAACGAAAUCCGAAUACGACAUCUCGGUACAACCUUACCCAAUAAUA ..(((((..(....)..))))).........((((((..(...........)...))))))..........(((((((((..(((.............((((..(((...((((.((((....)))))))))))...))))((((.(((.((((..(((....((...(((........((((((((..((((((((((((.((((.((((((.(....).)))))).)))).))))))))))))..))))))))...(((.....)))..)))...))...)))..))))..))).)))).....((((..((((((..(((((........)))))..))))))..))))...)))..)).)))))))....(((((..........((((..........))))..........)))))..... (-113.85) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 890 60 11 151 102 NC_002950:PG0676|5end_oxidoreductase,_short_chain_dehydrogenase/reductase_family_727275..727505_NEGATIVE 865 220 171 85 36 NC_002950:PG1980|5end_hypothetical_protein_2067930..2068160_NEGATIVE 675 220 171 63 14 NC_002950:PG1799|5end_hypothetical_protein_1894499..1894729_POSITIVE 645 229 181 58 10 NC_002950:PG2064|5end_hypothetical_protein_2160550..2160780_POSITIVE 516 190 143 53 9 NC_002950:PG0174|5end_pyridine_nucleotide-disulphide_oxidoreductase_family_protein_197628..197858_NEGATIVE 512 220 173 178 131 NC_002950:PG0081|5end_hypothetical_protein_93805..94035_POSITIVE 476 334 295 224 175 NC_002950:PG0512|5end_guanylate_kinase_551914..552144_NEGATIVE 469 210 161 230 183 NC_002950:PG0470|5end_hypothetical_protein_511883..512113_NEGATIVE 457 370 321 166 112 NC_002950:PG1079|5end_enoyl-CoA_hydratase/isomerase_family_protein_1146549..1146779_POSITIVE 456 368 321 72 1 NC_002950:PG1338|5end_umuC_protein_1418246..1418476_POSITIVE 447 368 321 113 65 NC_002950:PG1880|5end_glycosyl_transferase,_group_2_family_protein_1975481..1975711_POSITIVE 447 220 173 107 60 NC_002950:PG0007|5end_hypothetical_protein_6913..7143_NEGATIVE 446 250 201 81 32 NC_002950:PG0313|5end_hypothetical_protein_347366..347596_POSITIVE 421 369 323 176 122 NC_002950:PG0229|5end_hypothetical_protein_264872..265102_POSITIVE 417 370 323 163 108 NC_002950:PG0268|5end_tRNA_(5-methylaminomethyl-2-thiouridylate)-methyltransferase_300898..301128_POSITIVE 415 369 321 159 104 NC_002950:PG0348|5end_ATP-dependent_DNA_helicase_RecG_382345..382575_POSITIVE 412 289 242 200 138 NC_002950:PG0374|5end_hypothetical_protein_405564..405794_NEGATIVE 411 340 291 73 26 NC_002950:PG1223|5end_hypothetical_protein_1299461..1299691_POSITIVE 407 367 321 231 178 NC_002950:PG0413|5end_hypothetical_protein_451781..452011_NEGATIVE 405 369 326 61 7 NC_002950:PG1214|5end_hypothetical_protein_1293032..1293262_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 494 320 271 66 15 NC_002950:PG0354|3end_hypothetical_protein_389131..389281_NEGATIVE 472 370 321 122 68 NC_002950:PG0130|3end_phosphoglyceromutase_151922..152072_NEGATIVE 457 370 321 62 8 NC_002950:PG1078|3end_electron_transfer_flavoprotein,_alpha_subunit_1146525..1146675_POSITIVE 447 368 321 102 54 NC_002950:PG1879|3end_hypothetical_protein_1975550..1975700_POSITIVE 423 360 314 88 12 NC_002950:PG0143|3end_hydrolase,_carbon-nitrogen_family_165747..165897_NEGATIVE 417 228 188 36 1 NC_002950:PG1626|3end_hypothetical_protein_1710486..1710636_POSITIVE 415 369 321 116 61 NC_002950:PG0347|3end_UDP-glucose_4-epimerase_382382..382532_POSITIVE 412 330 283 148 96 NC_002950:PG1285|3end_glucosamine-6-phosphate_deaminase_1364941..1365091_POSITIVE 405 369 326 112 58 NC_002950:PG1213|3end_ribonuclease_H_1293163..1293313_POSITIVE 404 370 322 115 61 NC_002950:PG1975|3end_hemagglutinin_protein_HagC_2064350..2064500_POSITIVE 401 368 326 64 3 NC_002950:PG1337|3end_umuD_protein_1418318..1418468_POSITIVE 393 370 321 139 93 NC_002950:PG0164|3end_hypothetical_protein_187081..187231_NEGATIVE 386 369 321 123 57 NC_002950:PG0222|3end_DNA-binding_protein,_histone-like_family_255913..256063_NEGATIVE 383 280 231 73 24 NC_002950:PG1546|3end_hypothetical_protein_1624355..1624505_POSITIVE 383 358 317 143 98 NC_002950:PG0267|3end_arginyl-tRNA_synthetase_300973..301123_POSITIVE 380 368 323 47 9 NC_002950:PG0477|3end_pantoate--beta-alanine_ligase_518752..518902_NEGATIVE 377 339 297 80 36 NC_002950:PG1219|3end_hypothetical_protein_1297062..1297212_POSITIVE 373 366 324 79 36 NC_002950:PG0926|3end_hypothetical_protein_984407..984557_NEGATIVE 371 370 321 116 53 NC_002950:PG1898|3end_transporter,_putative_1996727..1996877_NEGATIVE 370 368 321 83 32 NC_002950:PG1226|3end_peptidyl-prolyl_cis-trans_isomerase,_cyclophilin-type_1304048..1304198_POSITIVE