Origin IGS: gtgcgaaccgccaggagcataggaatgattttttgagagaaaatagcataaacccgactgtagagagtcattttttcaatcctaatatcccactaaaatgatgatgacagactgtttttcgccggcttgcagtggctccaaagccttaccgtcactcactttctgtggaatgatgacttctcaatcggtttcaaattcgatgggggtaggttggatctaccctctattcgaagggtacacacaacttcttgtcgaagtaaaacatcttgcctccagttggatctaccctctattcgaagggtacacacaaccatagacgtaaggcatacccgtttcgatctgttggatctaccctctattcgaagggtacacacaacataagactatatcttatataaccaaattctgttggatctaccctctattcgaagggtacacacaactcaagggtcgggttc .........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.........1.........2.........3.........4.........5.........6.........7.........8.........9 gaacccgacccttgagttgtgtgtacccttcgaatagagggtagatccaacagaatttggttatataagatatagtcttatgttgtgtgtacccttcgaatagagggtagatccaacagatcgaaacgggtatgccttacgtctatggttgtgtgtacccttcgaatagagggtagatccaactggaggcaagatgttttacttcgacaagaagttgtgtgtacccttcgaatagagggtagatccaacctacccccatcgaatttgaaaccgattgagaagtcatcattccacagaaagtgagtgacggtaaggctttggagccactgcaagccggcgaaaaacagtctgtcatcatcattttagtgggatattaggattgaaaaaatgactctctacagtcgggtttatgctattttctctcaaaaaatcattcctatgctcctggcggttcgcac Mask Tandem Repeat Region ================================================ gtgcgaaccgccaggagcataggaatgattttttgagagaaaatagcataaacccgactgtagagagtcattttttcaatcctaatatcccactaaaatgatgatgacagactgtttttcgccggcttgcagtggctccaaagccttaccgtcactcactttctgtggaatgatgacttctcaatcggtttcaaattcgatgggggtaggttggatctaccctctattcgaagggtacacacaacttcttgtcgaagtaaaacatcttgcctccagttggatctaccctctattcgaagggtacacacaaccatagacgtaaggcatacccgtttcgatctgttggatctaccctctattcgaagggtacacacaacataagactatatcttatataaccaaattctgttggatctaccctctattcgaagggtacacacaactcaagggtcgggttc Find is-nt database================================================ Query_seq: PG0339:PG0340|PG0339:PG0340:hypothetical protein:hypothetical protein:->->:375748..376205 458 gtgcgaaccgccaggagcataggaatgattttttgagagaaaatagcataaacccgactgtagagagtcattttttcaatcctaatatcccactaaaatgatgatgacagactgtttttcgccggcttgcagtggctccaaagccttaccgtcactcactttctgtggaatgatgacttctcaatcggtttcaaattcgatgggggtaggttggatctaccctctattcgaagggtacacacaacttcttgtcgaagtaaaacatcttgcctccagttggatctaccctctattcgaagggtacacacaaccatagacgtaaggcatacccgtttcgatctgttggatctaccctctattcgaagggtacacacaacataagactatatcttatataaccaaattctgttggatctaccctctattcgaagggtacacacaactcaagggtcgggttc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG0339:PG0340|PG0339:PG0340:hypothetical protein:hypothetical protein:->->:375748..376205 458 gtgcgaaccgccaggagcataggaatgattttttgagagaaaatagcataaacccgactgtagagagtcattttttcaatcctaatatcccactaaaatgatgatgacagactgtttttcgccggcttgcagtggctccaaagccttaccgtcactcactttctgtggaatgatgacttctcaatcggtttcaaattcgatgggggtaggttggatctaccctctattcgaagggtacacacaacttcttgtcgaagtaaaacatcttgcctccagttggatctaccctctattcgaagggtacacacaaccatagacgtaaggcatacccgtttcgatctgttggatctaccctctattcgaagggtacacacaacataagactatatcttatataaccaaattctgttggatctaccctctattcgaagggtacacacaactcaagggtcgggttc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG0339:PG0340|PG0339:PG0340:hypothetical protein:hypothetical protein:->->:375748..376205 458 gtgcgaaccgccaggagcataggaatgattttttgagagaaaatagcataaacccgactgtagagagtcattttttcaatcctaatatcccactaaaatgatgatgacagactgtttttcgccggcttgcagtggctccaaagccttaccgtcactcactttctgtggaatgatgacttctcaatcggtttcaaattcgatgggggtaggttggatctaccctctattcgaagggtacacacaacttcttgtcgaagtaaaacatcttgcctccagttggatctaccctctattcgaagggtacacacaaccatagacgtaaggcatacccgtttcgatctgttggatctaccctctattcgaagggtacacacaacataagactatatcttatataaccaaattctgttggatctaccctctattcgaagggtacacacaactcaagggtcgggttc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 1 Min: 210 Max: 452 Len: 243 Subject: UniRef90_Q7MX72 Cluster: Hypothetical protein; n=1; Porphyromonas gingivalis|Rep: Hypothetical protein - Porphyromonas gingivalis (Bacteroides gingivalis) HSP 1 e-value: 1.0E-18 bit: 94.0 Len: 234 Query Start:210 Query End:443 Subject Strand: null Subject Start: 6 Subject End: 83 ................................................................................................................................................................................................................. V G S T L Y S K G T H N F L S K * N I L P P V G S T L Y S K G T H N H R R K A Y P F R S V G S T L Y S K G T H N I R L Y L I * P N S V G S T L Y S K G T H N ............... ................................................................................................................................................................................................................. V G S T L Y S K G T H N Y K G L F K E C A T V G S T L Y S K G T H N D A D N V P V L R L V G S T L Y S K G T H N S R L A R P P T R L V G S T L Y S K G T H N ............... HSP 2 e-value: 6.0E-14 bit: 78.6 Len: 186 Query Start:267 Query End:452 Subject Strand: null Subject Start: 3 Subject End: 64 .......................................................................................................................................................................................................................................................................... L P P V G S T L Y S K G T H N H R R K A Y P F R S V G S T L Y S K G T H N I R L Y L I * P N S V G S T L Y S K G T H N S R V ...... .......................................................................................................................................................................................................................................................................... L P P V G S T L Y S K G T H N Y K G L F K E C A T V G S T L Y S K G T H N D A D N V P V L R L V G S T L Y S K G T H N S R L ...... HSP 3 e-value: 8.0E-14 bit: 78.2 Len: 177 Query Start:210 Query End:386 Subject Strand: null Subject Start: 28 Subject End: 86 ................................................................................................................................................................................................................. V G S T L Y S K G T H N F L S K * N I L P P V G S T L Y S K G T H N H R R K A Y P F R S V G S T L Y S K G T H N I R L ........................................................................ ................................................................................................................................................................................................................. V G S T L Y S K G T H N D A D N V P V L R L V G S T L Y S K G T H N S R L A R P P T R L V G S T L Y S K G T H N M I L ........................................................................ gtgcgaaccgccaggagcataggaatgattttttgagagaaaatagcataaacccgactgtagagagtcattttttcaatcctaatatcccactaaaatgatgatgacagactgtttttcgccggcttgcagtggctccaaagccttaccgtcactcactttctgtggaatgatgacttctcaatcggtttcaaattcgatgggggtagnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnngggttc Predict ORF larger than 30AA ================================================ Protein_Len: 60 Strand: + Start: 98 End: 313 ................................................................................................. M M M T D C F S P A C S G S K A L P S L T F C G M M T S Q S V S N S M G V G W I Y P L F E G Y T Q L L V E V K H L A S S ................................................................................................................................................. Protein_Len: 60 Strand: + Start: 112 End: 378 ............................................................................................................... M F F A G L Q W L Q S L T V T H F L W N D D F S I G F K F D G G R L D L P S I R R V H T T S C R S K T S C L Q L D L P S ................................................................................ Protein_Len: 44 Strand: + Start: 264 End: 395 ....................................................................................................................................................................................................................................................................... M L P P V G S T L Y S K G T H N H R R K A Y P F R S V G S T L Y S K G T H N I R L Y L I ............................................................... Protein_Len: 44 Strand: + Start: 326 End: 457 ..................................................................................................................................................................................................................................................................................................................................... M P V S I C W I Y P L F E G Y T Q H K T I S Y I T K F C W I Y P L F E G Y T Q L K G R V . Protein_Len: 60 Strand: - Start: 159 End: 374 .............................................................................................................................................................. N S P P L N S R G E I R L T C V V E Q R L L V D Q R W N S R G E I R L T C V V M S T L C V R K S R N S R G E I R L T C M .................................................................................... Protein_Len: 30 Strand: - Start: 85 End: 174 .................................................................................... Y G V L I I I V S Q K E G A Q L P E L A K G D S V K Q P I M ............................................................................................................................................................................................................................................................................................ gtgcgaaccgccaggagcataggaatgattttttgagagaaaatagcataaacccgactgtagagagtcattttttcaatcctaatatcccactaaaatgatgatgacagactgtttttcgccggcttgcagtggctccaaagccttaccgtcactcactttctgtggaatgatgacttctcaatcggtttcaaattcgatgggggtagnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnngggttc 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================================================ gtgcgaaccgccaggagcataggaatgattttttgagagaaaatagcataaacccgactgtagagagtcattttttcaatcctaatatcccactaaaatgatgatgacagactgtttttcgccggcttgcagtggctccaaagccttaccgtcactcactttctgtggaatgatgacttctcaatcggtttcaaattcgatgggggtagnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnngggttc Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 76 HP_score: -10.6 Tail_Score: -3.02511 Start: 202 End: 224 Full_Region: GGTTTCAAATTCGAT GGGGGTAGGT TGG ATCTACCCTC TATTCGAAGGGTACA .........................................................................................................................................................................................................GGGGGTAGGTTGGATCTACCCTC.......................................................................................................................................................................................................................................... TransTerm Strand: + Conf: 71 HP_score: -9.6 Tail_Score: -3.07013 Start: 204 End: 222 Full_Region: TTTCAAATTCGATGG GGGTAGGT TGG ATCTACCC TCTATTCGAAGGGTA ...........................................................................................................................................................................................................GGGTAGGTTGGATCTACCC............................................................................................................................................................................................................................................ TransTerm Strand: - Conf: 47 HP_score: -2.4 Tail_Score: -3.51365 Start: 399 End: 412 Full_Region: gaatagagggtagat ccaa cagaat ttgg ttatataagatatag ..............................................................................................................................................................................................................................................................................................................................................................................................................ccaacagaatttgg.............................................. Find igs database================================================ Query_seq: PG0339:PG0340|PG0339:PG0340:hypothetical protein:hypothetical protein:->->:375748..376205 458 gtgcgaaccgccaggagcataggaatgattttttgagagaaaatagcataaacccgactgtagagagtcattttttcaatcctaatatcccactaaaatgatgatgacagactgtttttcgccggcttgcagtggctccaaagccttaccgtcactcactttctgtggaatgatgacttctcaatcggtttcaaattcgatgggggtagnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnngggttc Intra-Species Hit: Count: 1 Min: 1 Max: 208 Len: 208 Subject: NC_002950_PG0339_PG0340|hypothetical protein:hypothetical protein|POSITIVE:POSITIVE|[375748,376205]|458 HSP 1 e-value: 1.0E-114 bit: 412.0 Len: 208 Query Start:1 Query End:208 Subject Strand: POSITIVE Subject Start: 1 Subject End: 208 gtgcgaaccgccaggagcataggaatgattttttgagagaaaatagcataaacccgactgtagagagtcattttttcaatcctaatatcccactaaaatgatgatgacagactgtttttcgccggcttgcagtggctccaaagccttaccgtcactcactttctgtggaatgatgacttctcaatcggtttcaaattcgatgggggta.......................................................................................................................................................................................................................................................... gtgcgaaccgccaggagcataggaatgattttttgagagaaaatagcataaacccgactgtagagagtcattttttcaatcctaatatcccactaaaatgatgatgacagactgtttttcgccggcttgcagtggctccaaagccttaccgtcactcactttctgtggaatgatgacttctcaatcggtttcaaattcgatgggggta.......................................................................................................................................................................................................................................................... Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GUGCGAACCGCCAGGAGCAUAGGAAUGAUUUUUUGAGAGAAAAUAGCAUAAACCCGACUGUAGAGAGUCAUUUUUUCAAUCCUAAUAUCCCACUAAAAUGAUGAUGACAGACUGUUUUUCGCCGGCUUGCAGUGGCUCCAAAGCCUUACCGUCACUCACUUUCUGUGGAAUGAUGACUUCUCAAUCGGUUUCAAAUUCGAUGGGGGUA ((((...((....)).))))....(((..(((((....)))))...)))..((((.......((((((((((.................((((..(((((((((((....(((((.............)))))((((....))))....))))).))).)))..))))...)))))).)))).(((((........)))))..)))). (-48.37) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UACCCCCAUCGAAUUUGAAACCGAUUGAGAAGUCAUCAUUCCACAGAAAGUGAGUGACGGUAAGGCUUUGGAGCCACUGCAAGCCGGCGAAAAACAGUCUGUCAUCAUCAUUUUAGUGGGAUAUUAGGAUUGAAAAAAUGACUCUCUACAGUCGGGUUUAUGCUAUUUUCUCUCAAAAAAUCAUUCCUAUGCUCCUGGCGGUUCGCAC .(((.(((.......((((.(((((((((((((((..(((((((..((((((((((((((...((((....))))..(((......))).........)))))))..))))))).))))))).......((....)).))))).))).))))))).)))).((...........................))...))).)))...... (-51.33) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 412 170 121 217 168 NC_002950:PG1847|5end_endoribonuclease_L-PSP,_putative_1946607..1946837_NEGATIVE 401 168 121 185 134 NC_002950:PG0307|5end_NADH-ubiquinone_oxidoreductase_342560..342790_POSITIVE 377 159 112 225 163 NC_002950:PG2032|5end_primosomal_protein_N'_2133381..2133611_NEGATIVE 375 166 121 212 171 NC_002950:PG1481|5end_conjugative_transposon_protein_TraG_1558447..1558677_NEGATIVE 374 145 110 188 159 NC_002950:PG2223|5end_glycosyl_transferase,_group_2_family_protein_2337713..2337943_POSITIVE 366 154 113 222 186 NC_002950:PG1269|5end_delta-1-pyrroline-5-carboxylate_dehydrogenase_1349201..1349431_NEGATIVE 363 155 111 70 15 NC_002950:PG0593|5end_htrA_protein_650362..650592_POSITIVE 356 169 121 64 21 NC_002950:PG1753|5end_selenide,_water_dikinase_1838615..1838845_POSITIVE 356 153 111 222 164 NC_002950:PG0986|5end_hypothetical_protein_1047426..1047656_POSITIVE 351 151 111 60 11 NC_002950:PG1486|5end_conjugative_transposon_protein_TraA_1561166..1561396_NEGATIVE 351 150 108 213 166 NC_002950:PG0201|5end_ribonuclease_P_238770..239000_NEGATIVE 350 149 102 101 40 NC_002950:PG0483|5end_kinase,_putative_523844..524074_NEGATIVE 346 157 115 222 169 NC_002950:PG1498|5end_hypothetical_protein_1574656..1574886_POSITIVE 345 159 113 49 4 NC_002950:PG1900|5end_ribosome-associated_GTPase_2000746..2000976_NEGATIVE 344 152 111 223 185 NC_002950:PG1034|5end_ABC_transporter,_ATP-binding_protein_1096163..1096393_POSITIVE 343 158 114 66 22 NC_002950:PG0332|5end_transcription_termination_factor_Rho_365619..365849_POSITIVE 342 160 111 56 2 NC_002950:PG2050|5end_hypothetical_protein_2149434..2149664_NEGATIVE 337 160 113 173 121 NC_002950:PG1116|5end_methylenetetrahydrofolate_dehydrogenase/methenyltetrahydrofolate_cyclohydrolase_1188931..1189161_POSITIVE 336 154 114 62 13 NC_002950:PG0949|5end_hypothetical_protein_1008686..1008916_POSITIVE 335 165 121 128 99 NC_002950:PG2023|5end_methionyl-tRNA_formyltransferase_2118536..2118766_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 374 145 110 149 120 NC_002950:PG2222|3end_acyltransferase,_HtrB/MsbB_family_2337754..2337904_POSITIVE 366 154 113 145 109 NC_002950:PG1270|3end_hypothetical_protein_1349278..1349428_NEGATIVE 356 169 121 67 24 NC_002950:PG1752|3end_hypothetical_protein_1838698..1838848_POSITIVE 350 149 102 94 33 NC_002950:PG0484|3end_hypothetical_protein_523851..524001_NEGATIVE 348 149 101 81 21 NC_002950:PG1482|3end_conjugative_transposon_protein_TraF_1558444..1558594_NEGATIVE 347 153 112 132 91 NC_002950:PG0198|3end_hypothetical_protein_237501..237651_POSITIVE 346 157 115 121 68 NC_002950:PG1497|3end_DNA-binding_protein,_histone-like_family_1574635..1574785_POSITIVE 336 130 85 122 66 NC_002950:PG1675|3end_hypothetical_protein_1760360..1760510_POSITIVE 332 168 123 112 68 NC_002950:PG1162|3end_ATP:cob(I)alamin_adenosyltransferase,_putative_1241473..1241623_NEGATIVE 329 160 114 68 15 NC_002950:PG2164|3end_peptidyl-prolyl_cis-trans_isomerase,_FKBP-type_2269568..2269718_NEGATIVE 328 150 107 135 93 NC_002950:PG0443|3end_hemagglutinin-related_protein_483147..483297_POSITIVE 327 138 102 146 108 NC_002950:PG0164|3end_hypothetical_protein_187081..187231_NEGATIVE 325 150 101 133 76 NC_002950:PG1594|3end_ComEC/Rec2-related_protein_1672052..1672202_NEGATIVE 320 170 121 105 62 NC_002950:PG1863|3end_hypothetical_protein_1960364..1960514_NEGATIVE 319 146 101 47 2 NC_002950:PG1342|3end_UDP-N-acetylenolpyruvoylglucosamine_reductase_1423681..1423831_POSITIVE 319 159 119 43 3 NC_002950:PG0439|3end_hypothetical_protein_478810..478960_POSITIVE 316 155 115 33 1 NC_002950:PG0362|3end_hypothetical_protein_397549..397699_POSITIVE 312 154 120 143 101 NC_002950:PG0045|3end_heat_shock_protein_90_56193..56343_POSITIVE 309 84 42 79 29 NC_002950:PG1978|3end_hypothetical_protein_2066723..2066873_NEGATIVE 309 169 124 63 12 NC_002950:PG1690|3end_Sua5/YciO/YrdC/YwlC_family_protein_1775171..1775321_NEGATIVE