Origin IGS: acaagcataaataatcccctgaagataggggcgactgaaaagcagagggcgcatcttaccgatgcgccctctttgtgtttttttcttttctgagacctttcggcaataagcaggcactttatccattcattttacagtgtgtcggccgattgttttgtgtgt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 acacacaaaacaatcggccgacacactgtaaaatgaatggataaagtgcctgcttattgccgaaaggtctcagaaaagaaaaaaacacaaagagggcgcatcggtaagatgcgccctctgcttttcagtcgcccctatcttcaggggattatttatgcttgt Mask Tandem Repeat Region ================================================ acaagcataaataatcccctgaagataggggcgactgaaaagcagagggcgcatcttaccgatgcgccctctttgtgtttttttcttttctgagacctttcggcaataagcaggcactttatccattcattttacagtgtgtcggccgattgttttgtgtgt Find is-nt database================================================ Query_seq: PG0196:PG0197|PG0196:PG0197:peptidase, M16 family:hypothetical protein:-><-:235869..236030 162 acaagcataaataatcccctgaagataggggcgactgaaaagcagagggcgcatcttaccgatgcgccctctttgtgtttttttcttttctgagacctttcggcaataagcaggcactttatccattcattttacagtgtgtcggccgattgttttgtgtgt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG0196:PG0197|PG0196:PG0197:peptidase, M16 family:hypothetical protein:-><-:235869..236030 162 acaagcataaataatcccctgaagataggggcgactgaaaagcagagggcgcatcttaccgatgcgccctctttgtgtttttttcttttctgagacctttcggcaataagcaggcactttatccattcattttacagtgtgtcggccgattgttttgtgtgt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG0196:PG0197|PG0196:PG0197:peptidase, M16 family:hypothetical protein:-><-:235869..236030 162 acaagcataaataatcccctgaagataggggcgactgaaaagcagagggcgcatcttaccgatgcgccctctttgtgtttttttcttttctgagacctttcggcaataagcaggcactttatccattcattttacagtgtgtcggccgattgttttgtgtgt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 acaagcataaataatcccctgaagataggggcgactgaaaagcagagggcgcatcttaccgatgcgccctctttgtgtttttttcttttctgagacctttcggcaataagcaggcactttatccattcattttacagtgtgtcggccgattgttttgtgtgt Predict ORF larger than 30AA ================================================ Protein_Len: 40 Strand: - Start: 3 End: 122 .. L M F L G R F I P A V S F C L A C R V S A G E K H K K R K Q S R E A I L L C K M ........................................ Protein_Len: 42 Strand: - Start: 1 End: 126 C A Y I I G Q L Y P R S F L L P R M K G I R G R Q T K K K E S V K R C Y A P V K D M .................................... acaagcataaataatcccctgaagataggggcgactgaaaagcagagggcgcatcttaccgatgcgccctctttgtgtttttttcttttctgagacctttcggcaataagcaggcactttatccattcattttacagtgtgtcggccgattgttttgtgtgt 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================================================ acaagcataaataatcccctgaagataggggcgactgaaaagcagagggcgcatcttaccgatgcgccctctttgtgtttttttcttttctgagacctttcggcaataagcaggcactttatccattcattttacagtgtgtcggccgattgttttgtgtgt Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 100 HP_score: -8.1 Tail_Score: -6.14618 Start: 39 End: 77 Full_Region: GATAGGGGCGACTGA AAAGCAGAGGGCGCATC TTACC GATGCGCCCTCTTTGTG TTTTTTTCTTTTCTG ......................................AAAGCAGAGGGCGCATCTTACCGATGCGCCCTCTTTGTG..................................................................................... TransTerm Strand: + Conf: 100 HP_score: -18.1 Tail_Score: -4.74406 Start: 45 End: 71 Full_Region: GGCGACTGAAAAGCA GAGGGCGCATC TTACC GATGCGCCCTC TTTGTGTTTTTTTCT ............................................GAGGGCGCATCTTACCGATGCGCCCTC........................................................................................... TransTerm Strand: - Conf: 100 HP_score: -18.1 Tail_Score: -3.11208 Start: 45 End: 71 Full_Region: agaaaaaaacacaaa gagggcgcatc ggtaa gatgcgccctc tgcttttcagtcgcc ............................................gagggcgcatcggtaagatgcgccctc........................................................................................... TransTerm Strand: - Conf: 89 HP_score: -14.9 Tail_Score: -3.11281 Start: 47 End: 69 Full_Region: aaaaaaacacaaaga gggcgcatc ggtaa gatgcgccc tctgcttttcagtcg ..............................................gggcgcatcggtaagatgcgccc............................................................................................. Find igs database================================================ Query_seq: PG0196:PG0197|PG0196:PG0197:peptidase, M16 family:hypothetical protein:-><-:235869..236030 162 acaagcataaataatcccctgaagataggggcgactgaaaagcagagggcgcatcttaccgatgcgccctctttgtgtttttttcttttctgagacctttcggcaataagcaggcactttatccattcattttacagtgtgtcggccgattgttttgtgtgt Intra-Species Hit: Count: 1 Min: 1 Max: 162 Len: 162 Subject: NC_002950_PG0196_PG0197|peptidase, M16 family:hypothetical protein|POSITIVE:NEGATIVE|[235869,236030]|162 HSP 1 e-value: 1.0E-74 bit: 280.0 Len: 162 Query Start:1 Query End:162 Subject Strand: POSITIVE Subject Start: 1 Subject End: 162 acaagcataaataatcccctgaagataggggcgactgaaaagcagagggcgcatcttaccgatgcgccctctttgtgnnnnnnncttttctgagacctttcggcaataagcaggcactttatccattcattttacagtgtgtcggccgattgttttgtgtgt acaagcataaataatcccctgaagataggggcgactgaaaagcagagggcgcatcttaccgatgcgccctctttgtgtttttttcttttctgagacctttcggcaataagcaggcactttatccattcattttacagtgtgtcggccgattgttttgtgtgt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACAAGCAUAAAUAAUCCCCUGAAGAUAGGGGCGACUGAAAAGCAGAGGGCGCAUCUUACCGAUGCGCCCUCUUUGUGUUUUUUUCUUUUCUGAGACCUUUCGGCAAUAAGCAGGCACUUUAUCCAUUCAUUUUACAGUGUGUCGGCCGAUUGUUUUGUGUGU ....(((((......((((((....)))))).....(((((((((((((((((((.....)))))))))))....))))))))........(((((...(((((.....(.(.(((((.((...........)).))))).)).)))))..))))).))))) (-51.60) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACACACAAAACAAUCGGCCGACACACUGUAAAAUGAAUGGAUAAAGUGCCUGCUUAUUGCCGAAAGGUCUCAGAAAAGAAAAAAACACAAAGAGGGCGCAUCGGUAAGAUGCGCCCUCUGCUUUUCAGUCGCCCCUAUCUUCAGGGGAUUAUUUAUGCUUGU .........((((.((..((((...........(((.......((((....))))...(((....))).)))((((((............((((((((((((.....)))))))))))).)))))).))))(((((......)))))........)).)))) (-49.22) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 907 150 101 200 150 NC_002950:PG0033|5end_RmuC_domain_protein_41540..41770_NEGATIVE 647 158 111 231 176 NC_002950:PG0267|5end_arginyl-tRNA_synthetase_299100..299330_POSITIVE 618 147 103 231 179 NC_002950:PG1714|5end_pyridoxamine-phosphate_oxidase_1802492..1802722_NEGATIVE 486 69 29 219 181 NC_002950:PG0032|5end_beta-mannosidase,_putative_40212..40442_NEGATIVE 446 57 17 201 156 NC_002950:PG1829|5end_long-chain-fatty-acid--CoA_ligase,_putative_1922980..1923210_NEGATIVE 400 90 41 221 166 NC_002950:PG1495|5end_DNA_topoisomerase_III_1571243..1571473_POSITIVE 356 148 101 231 178 NC_002950:PG1945|5end_hypothetical_protein_2031697..2031927_POSITIVE 355 149 101 58 18 NC_002950:PG1684|5end_hypothetical_protein_1770927..1771157_POSITIVE 352 66 21 148 104 NC_002950:PG1173|5end_YkgG_family_protein_1252435..1252665_POSITIVE 348 70 25 220 171 NC_002950:PG1523|5end_naphthoate_synthase_1600988..1601218_NEGATIVE 348 80 32 72 25 NC_002950:PG1496|5end_hypothetical_protein_1573342..1573572_POSITIVE 340 68 23 55 13 NC_002950:PG0343|5end_methionine_gamma-lyase_378362..378592_NEGATIVE 338 70 24 210 166 NC_002950:PG1709|5end_ISPg5,_transposase_Orf1_1794914..1795144_POSITIVE 338 67 27 81 36 NC_002950:PG0740|5end_NLP/P60_family_protein_787836..788066_POSITIVE 337 69 29 210 158 NC_002950:PG1757|5end_hypothetical_protein_1844962..1845192_NEGATIVE 334 77 31 195 148 NC_002950:PG1837|5end_hemagglutinin_protein_HagA_1930337..1930567_POSITIVE 332 77 35 68 30 NC_002950:PG1270|5end_hypothetical_protein_1350207..1350437_NEGATIVE 332 75 31 210 169 NC_002950:PG0322|5end_serine/threonine_transporter_355708..355938_POSITIVE 330 66 24 216 167 NC_002950:PG0317|5end_peptidase,_M49_family_352431..352661_NEGATIVE 325 74 32 210 160 NC_002950:PG2143|5end_GTP-binding_protein_EngA_2248547..2248777_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 479 82 44 53 19 NC_002950:PG0196|3end_peptidase,_M16_family_235808..235958_POSITIVE 414 90 41 125 72 NC_002950:PG2076|3end_hypothetical_protein_2177073..2177223_POSITIVE 413 145 103 150 105 NC_002950:PG1251|3end_hypothetical_protein_1328212..1328362_POSITIVE 400 90 41 132 77 NC_002950:PG1494|3end_hypothetical_protein_1571234..1571384_POSITIVE 390 51 14 89 40 NC_002950:PG0173|3end_transcriptional_regulator,_putative_194388..194538_NEGATIVE 378 145 103 150 105 NC_002950:PG2220|3end_hypothetical_protein_2335368..2335518_POSITIVE 378 145 103 150 105 NC_002950:PG0499|3end_hypothetical_protein_539142..539292_POSITIVE 357 68 28 146 104 NC_002950:PG1859|3end_glycerate_kinase_family_protein_1957174..1957324_NEGATIVE 355 149 101 61 21 NC_002950:PG1683|3end_hypothetical_protein_1771010..1771160_POSITIVE 350 60 11 105 35 NC_002950:PG0685|3end_ABC_transporter,_ATP-binding_protein_740855..741005_POSITIVE 348 80 32 66 19 NC_002950:PG1495|3end_DNA_topoisomerase_III_1573416..1573566_POSITIVE 347 69 23 127 74 NC_002950:PG1715|3end_hypothetical_protein_1803393..1803543_NEGATIVE 346 70 23 63 14 NC_002950:PG0593|3end_htrA_protein_651938..652088_POSITIVE 342 66 21 75 27 NC_002950:PG1837|3end_hemagglutinin_protein_HagA_1936734..1936884_POSITIVE 339 74 42 61 18 NC_002950:PG1156|3end_S4_domain_protein_1237267..1237417_POSITIVE 338 67 27 106 61 NC_002950:PG0739|3end_ribonuclease_Z_787941..788091_POSITIVE 333 68 23 145 98 NC_002950:PG0800|3end_hypothetical_protein_854719..854869_NEGATIVE 332 77 35 61 23 NC_002950:PG1271|3end_acetylornithine_aminotransferase,_putative_1350214..1350364_NEGATIVE 328 108 65 55 2 NC_002950:PG1743|3end_2-dehydro-3-deoxyphosphooctonate_aldolase_1827530..1827680_NEGATIVE 325 74 32 147 97 NC_002950:PG2142|3end_GTP-binding_protein_Era_2248564..2248714_POSITIVE