Origin IGS: aatagtccatgattatggaacaaagataatgaaatacggccgcagtttatggctttttgagacctgtacggaagtgtgtagattccagctatcagggctcgcatttcagccactaacgtacatctaaagctcatgatgctacgctcggttatcaaacaagtacgaatccatatatcagagattcaattcatagaggaaagagactaaaaattttcaaacgcgatcgccctgacaggctgccaagggccgacgcatcaaa .........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 tttgatgcgtcggcccttggcagcctgtcagggcgatcgcgtttgaaaatttttagtctctttcctctatgaattgaatctctgatatatggattcgtacttgtttgataaccgagcgtagcatcatgagctttagatgtacgttagtggctgaaatgcgagccctgatagctggaatctacacacttccgtacaggtctcaaaaagccataaactgcggccgtatttcattatctttgttccataatcatggactatt Mask Tandem Repeat Region ================================================ aatagtccatgattatggaacaaagataatgaaatacggccgcagtttatggctttttgagacctgtacggaagtgtgtagattccagctatcagggctcgcatttcagccactaacgtacatctaaagctcatgatgctacgctcggttatcaaacaagtacgaatccatatatcagagattcaattcatagaggaaagagactaaaaattttcaaacgcgatcgccctgacaggctgccaagggccgacgcatcaaa Find is-nt database================================================ Query_seq: PG1362:PG1363|PG1362:PG1363:hypothetical protein:hypothetical protein:<-->:1443685..1443943 259 aatagtccatgattatggaacaaagataatgaaatacggccgcagtttatggctttttgagacctgtacggaagtgtgtagattccagctatcagggctcgcatttcagccactaacgtacatctaaagctcatgatgctacgctcggttatcaaacaagtacgaatccatatatcagagattcaattcatagaggaaagagactaaaaattttcaaacgcgatcgccctgacaggctgccaagggccgacgcatcaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG1362:PG1363|PG1362:PG1363:hypothetical protein:hypothetical protein:<-->:1443685..1443943 259 aatagtccatgattatggaacaaagataatgaaatacggccgcagtttatggctttttgagacctgtacggaagtgtgtagattccagctatcagggctcgcatttcagccactaacgtacatctaaagctcatgatgctacgctcggttatcaaacaagtacgaatccatatatcagagattcaattcatagaggaaagagactaaaaattttcaaacgcgatcgccctgacaggctgccaagggccgacgcatcaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG1362:PG1363|PG1362:PG1363:hypothetical protein:hypothetical protein:<-->:1443685..1443943 259 aatagtccatgattatggaacaaagataatgaaatacggccgcagtttatggctttttgagacctgtacggaagtgtgtagattccagctatcagggctcgcatttcagccactaacgtacatctaaagctcatgatgctacgctcggttatcaaacaagtacgaatccatatatcagagattcaattcatagaggaaagagactaaaaattttcaaacgcgatcgccctgacaggctgccaagggccgacgcatcaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 1 Min: 100 Max: 218 Len: 119 Subject: UniRef90_Q7MVZ0 Cluster: Hypothetical protein; n=1; Porphyromonas gingivalis|Rep: Hypothetical protein - Porphyromonas gingivalis (Bacteroides gingivalis) HSP 1 e-value: 1.0E-6 bit: 46.6 Len: 81 Query Start:138 Query End:218 Subject Strand: null Subject Start: 27 Subject End: 53 ......................................................................................................................................... A T L G Y Q T S T N P Y I R D S I H R G K R L K I F K ......................................... ......................................................................................................................................... A T L S Y Q T S T N S F V R D S N Y R G K R L K I F K ......................................... HSP 2 e-value: 1.0E-6 bit: 27.3 Len: 39 Query Start:100 Query End:138 Subject Strand: null Subject Start: 14 Subject End: 26 ................................................................................................... R I S A T N V H L K L M M ......................................................................................................................... ................................................................................................... R I S A T N V H L K L M I ......................................................................................................................... aatagtccatgattatggaacaaagataatgaaatacggccgcagtttatggctttttgagacctgtacggaagtgtgtagattccagctatcagggctnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnncgcgatcgccctgacaggctgccaagggccgacgcatcaaa Predict ORF larger than 30AA ================================================ Protein_Len: 41 Strand: + Start: 2 End: 124 . M V H D Y G T K I M K Y G R S L W L F E T C T E V C R F Q L S G L A F Q P L T Y I ....................................................................................................................................... Protein_Len: 41 Strand: + Start: 82 End: 204 ................................................................................. M P A I R A R I S A T N V H L K L M M L R S V I K Q V R I H I S E I Q F I E E R D ....................................................... Protein_Len: 60 Strand: - Start: 3 End: 182 .. L G H N H F L S L S I R G C N I A K Q S R Y P L T Y I G A I L A R M E A V L T C R F S M I S R E T I L C T R I W I D S M ............................................................................. aatagtccatgattatggaacaaagataatgaaatacggccgcagtttatggctttttgagacctgtacggaagtgtgtagattccagctatcagggctnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnncgcgatcgccctgacaggctgccaagggccgacgcatcaaa 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================================================ aatagtccatgattatggaacaaagataatgaaatacggccgcagtttatggctttttgagacctgtacggaagtgtgtagattccagctatcagggctnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnncgcgatcgccctgacaggctgccaagggccgacgcatcaaa Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PG1362:PG1363|PG1362:PG1363:hypothetical protein:hypothetical protein:<-->:1443685..1443943 259 aatagtccatgattatggaacaaagataatgaaatacggccgcagtttatggctttttgagacctgtacggaagtgtgtagattccagctatcagggctnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnncgcgatcgccctgacaggctgccaagggccgacgcatcaaa Intra-Species Hit: Count: 1 Min: 1 Max: 259 Len: 259 Subject: NC_002950_PG1362_PG1363|hypothetical protein:hypothetical protein|NEGATIVE:POSITIVE|[1443685,1443943]|259 HSP 1 e-value: 3.0E-49 bit: 196.0 Len: 99 Query Start:1 Query End:99 Subject Strand: POSITIVE Subject Start: 1 Subject End: 99 aatagtccatgattatggaacaaagataatgaaatacggccgcagtttatggctttttgagacctgtacggaagtgtgtagattccagctatcagggct................................................................................................................................................................ aatagtccatgattatggaacaaagataatgaaatacggccgcagtttatggctttttgagacctgtacggaagtgtgtagattccagctatcagggct................................................................................................................................................................ HSP 2 e-value: 1.0E-14 bit: 81.8 Len: 41 Query Start:219 Query End:259 Subject Strand: POSITIVE Subject Start: 219 Subject End: 259 ..........................................................................................................................................................................................................................cgcgatcgccctgacaggctgccaagggccgacgcatcaaa ..........................................................................................................................................................................................................................cgcgatcgccctgacaggctgccaagggccgacgcatcaaa Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUAGUCCAUGAUUAUGGAACAAAGAUAAUGAAAUACGGCCGCAGUUUAUGGCUUUUUGAGACCUGUACGGAAGUGUGUAGAUUCCAGCUAUCAGGGCUCGCAUUUCAGCCACUAACGUACAUCUAAAGCUCAUGAUGCUACGCUCGGUUAUCAAACAAGUACGAAUCCAUAUAUCAGAGAUUCAAUUCAUAGAGGAAAGAGACUAAAAAUUUUCAAACGCGAUCGCCCUGACAGGCUGCCAAGGGCCGACGCAUCAAA ..((((((.((((((((((.....((((((......((..((.(((((((((((((...(((..((((((..((((.((.((..(.((((.....)))).)....)).))))))..)))))))))))))).))))).))).))..))))))))...(......)..)))))).))))..((......))..........).))))).............(((.(((((((............)))).))))))...... (-63.10) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUGAUGCGUCGGCCCUUGGCAGCCUGUCAGGGCGAUCGCGUUUGAAAAUUUUUAGUCUCUUUCCUCUAUGAAUUGAAUCUCUGAUAUAUGGAUUCGUACUUGUUUGAUAACCGAGCGUAGCAUCAUGAGCUUUAGAUGUACGUUAGUGGCUGAAAUGCGAGCCCUGAUAGCUGGAAUCUACACACUUCCGUACAGGUCUCAAAAAGCCAUAAACUGCGGCCGUAUUUCAUUAUCUUUGUUCCAUAAUCAUGGACUAUU ..(((((...((((((.((((...((((((((((..(((((((.........((((((.((....((((((.(((........))).))))))..(((((..(((((.....)))))..(((.......)))......)))))..)).))))))))))))))))))))))).((..((((..((......))..))))..))....))))......).))))).....))))).......(((((....)))))..... (-68.90) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 1014 110 61 201 152 NC_002950:PG1362|5end_hypothetical_protein_1443594..1443824_NEGATIVE 821 140 91 182 130 NC_002950:PG1060|5end_carboxyl-terminal_protease_1126658..1126888_POSITIVE 820 146 101 230 184 NC_002950:PG0880|5end_bacterioferritin_comigratory_protein_942539..942769_POSITIVE 563 167 122 229 185 NC_002950:PG2221|5end_MiaB-like_tRNA_modifying_enzyme_2335426..2335656_POSITIVE 481 167 122 226 186 NC_002950:PG0500|5end_queuine_tRNA-ribosyltransferase_539197..539427_POSITIVE 421 150 101 228 174 NC_002950:PG0801|5end_polyA_polymerase_family_protein_857714..857944_NEGATIVE 395 250 218 177 143 NC_002950:PG1405|5end_hypothetical_protein_1490669..1490899_NEGATIVE 364 249 219 184 148 NC_002950:PG2170|5end_sugar_transporter_2277974..2278204_NEGATIVE 362 110 63 225 177 NC_002950:PG1683|5end_hypothetical_protein_1769644..1769874_POSITIVE 356 110 62 182 141 NC_002950:PG1920|5end_ribosomal_protein_L30_2016483..2016713_NEGATIVE 353 140 93 167 118 NC_002950:PG1788|5end_cysteine_peptidase,_putative_1875976..1876206_POSITIVE 350 250 211 139 99 NC_002950:PG2002|5end_dihydrodipicolinate_reductase_2091587..2091817_NEGATIVE 343 148 109 51 2 NC_002950:PG0223|5end_exonuclease_257610..257840_NEGATIVE 342 80 37 183 133 NC_002950:PG1959|5end_ribosomal_protein_L33_2048405..2048635_NEGATIVE 341 106 73 137 95 NC_002950:PG2220|5end_hypothetical_protein_2334935..2335165_POSITIVE 336 250 210 218 166 NC_002950:PG1947|5end_TPR_domain_protein_2032932..2033162_POSITIVE 334 109 63 50 5 NC_002950:PG0790|5end_GTP-binding_protein_Obg_842583..842813_NEGATIVE 334 249 219 97 65 NC_002950:PG0145|5end_hypothetical_protein_167831..168061_POSITIVE 333 80 36 204 149 NC_002950:PG0851|5end_hypothetical_protein_912732..912962_NEGATIVE 332 89 43 197 148 NC_002950:PG1108|5end_hypothetical_protein_1181108..1181338_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 563 167 122 91 47 NC_002950:PG2220|3end_hypothetical_protein_2335368..2335518_POSITIVE 563 167 122 91 47 NC_002950:PG1251|3end_hypothetical_protein_1328212..1328362_POSITIVE 481 167 122 91 51 NC_002950:PG0499|3end_hypothetical_protein_539142..539292_POSITIVE 409 167 122 91 51 NC_002950:PG0879|3end_hypothetical_protein_941931..942081_NEGATIVE 364 249 219 145 109 NC_002950:PG2171|3end_D-isomer_specific_2-hydroxyacid_dehydrogenase_family_protein_2278013..2278163_NEGATIVE 350 250 211 78 38 NC_002950:PG2003|3end_deoxyguanosinetriphosphate_triphosphohydrolase_2091648..2091798_NEGATIVE 349 71 37 55 17 NC_002950:PG0261|3end_ISPg3,_transposase_293862..294012_NEGATIVE 333 250 211 74 29 NC_002950:PG1391|3end_hypothetical_protein_1472961..1473111_POSITIVE 329 130 83 116 68 NC_002950:PG0361|3end_hypothetical_protein_395481..395631_POSITIVE 327 246 219 86 53 NC_002950:PG0606|3end_hypothetical_protein_662451..662601_NEGATIVE 316 64 37 144 114 NC_002950:PG1960|3end_ribosomal_protein_L28_2048424..2048574_NEGATIVE 311 130 88 132 99 NC_002950:PG1181|3end_transcriptional_regulator,_tetR_family_1263656..1263806_NEGATIVE 311 240 192 57 5 NC_002950:PG0861|3end_helicase,_SNF2/RAD54_family_922809..922959_POSITIVE 310 90 41 59 6 NC_002950:PG0156|3end_modification_methylase,_HemK_family_179789..179939_POSITIVE 309 246 202 103 57 NC_002950:PG0508|3end_HAD-superfamily_subfamily_IB_hydrolase,_TIGR01490_548136..548286_NEGATIVE 307 247 220 123 94 NC_002950:PG1232|3end_glutamate_dehydrogenase_1308274..1308424_NEGATIVE 305 78 37 41 2 NC_002950:PG1256|3end_ribonuclease,_Rne/Rng_family_1332748..1332898_NEGATIVE 302 80 37 52 11 NC_002950:PG1125|3end_hypothetical_protein_1201071..1201221_NEGATIVE 301 110 61 130 67 NC_002950:PG0141|3end_spoOJ_protein_163878..164028_NEGATIVE 298 107 65 108 63 NC_002950:PG1353|3end_orotate_phosphoribosyltransferase_1433201..1433351_NEGATIVE