Origin IGS: gagagaggtcgataggaaaaagttgcatcctgcatgagcgatttgtttgccgcaagtcgtttgtgcaggattcttttaatgattgtgccctcgtgttgcactgcagggtggaatctatagagatcttgataataatccgatatgattacctttgtacaaacgaaaaagtagc .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 gctactttttcgtttgtacaaaggtaatcatatcggattattatcaagatctctatagattccaccctgcagtgcaacacgagggcacaatcattaaaagaatcctgcacaaacgacttgcggcaaacaaatcgctcatgcaggatgcaactttttcctatcgacctctctc Mask Tandem Repeat Region ================================================ gagagaggtcgataggaaaaagttgcatcctgcatgagcgatttgtttgccgcaagtcgtttgtgcaggattcttttaatgattgtgccctcgtgttgcactgcagggtggaatctatagagatcttgataataatccgatatgattacctttgtacaaacgaaaaagtagc Find is-nt database================================================ Query_seq: PG2216:PG2217|PG2216:PG2217:hypothetical protein:1-deoxy-D-xylulose-5-phosphate synthase:->->:2329591..2329762 172 gagagaggtcgataggaaaaagttgcatcctgcatgagcgatttgtttgccgcaagtcgtttgtgcaggattcttttaatgattgtgccctcgtgttgcactgcagggtggaatctatagagatcttgataataatccgatatgattacctttgtacaaacgaaaaagtagc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG2216:PG2217|PG2216:PG2217:hypothetical protein:1-deoxy-D-xylulose-5-phosphate synthase:->->:2329591..2329762 172 gagagaggtcgataggaaaaagttgcatcctgcatgagcgatttgtttgccgcaagtcgtttgtgcaggattcttttaatgattgtgccctcgtgttgcactgcagggtggaatctatagagatcttgataataatccgatatgattacctttgtacaaacgaaaaagtagc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG2216:PG2217|PG2216:PG2217:hypothetical protein:1-deoxy-D-xylulose-5-phosphate synthase:->->:2329591..2329762 172 gagagaggtcgataggaaaaagttgcatcctgcatgagcgatttgtttgccgcaagtcgtttgtgcaggattcttttaatgattgtgccctcgtgttgcactgcagggtggaatctatagagatcttgataataatccgatatgattacctttgtacaaacgaaaaagtagc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gagagaggtcgataggaaaaagttgcatcctgcatgagcgatttgtttgccgcaagtcgtttgtgcaggattcttttaatgattgtgccctcgtgttgcactgcagggtggaatctatagagatcttgataataatccgatatgattacctttgtacaaacgaaaaagtagc Predict ORF larger than 30AA ================================================ Protein_Len: 53 Strand: + Start: 12 End: 170 ........... M G K S C I L H E R F V C R K S F V Q D S F N D C A L V L H C R V E S I E I L I I I R Y D Y L C T N E K V .. Protein_Len: 48 Strand: - Start: 3 End: 146 .. L P R Y S F T A D Q M L S K N A A L R K H L I R K I I T G E H Q V A P H F R Y L D Q Y Y D S I M .......................... Protein_Len: 45 Strand: - Start: 2 End: 136 . S L D I P F L Q M R C S R N T Q R L D N T C S E K L S Q A R T N C Q L T S D I S I K I I M .................................... gagagaggtcgataggaaaaagttgcatcctgcatgagcgatttgtttgccgcaagtcgtttgtgcaggattcttttaatgattgtgccctcgtgttgcactgcagggtggaatctatagagatcttgataataatccgatatgattacctttgtacaaacgaaaaagtagc 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================================================ gagagaggtcgataggaaaaagttgcatcctgcatgagcgatttgtttgccgcaagtcgtttgtgcaggattcttttaatgattgtgccctcgtgttgcactgcagggtggaatctatagagatcttgataataatccgatatgattacctttgtacaaacgaaaaagtagc Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 100 HP_score: -12.6 Tail_Score: -4.37527 Start: 25 End: 73 Full_Region: CGATAGGAAAAAGTT GCATCCTGCATGAGCGATTTGT TTGCC GCAAGTCGTTTGTGCAGGATTC TTTTAATGATTGTGC ........................GCATCCTGCATGAGCGATTTGTTTGCCGCAAGTCGTTTGTGCAGGATTC................................................................................................... TransTerm Strand: + Conf: 100 HP_score: -12.9 Tail_Score: -4.29049 Start: 28 End: 70 Full_Region: TAGGAAAAAGTTGCA TCCTGCATGAGCGATTTGT TTGCC GCAAGTCGTTTGTGCAGGA TTCTTTTAATGATTG ...........................TCCTGCATGAGCGATTTGTTTGCCGCAAGTCGTTTGTGCAGGA...................................................................................................... Find igs database================================================ Query_seq: PG2216:PG2217|PG2216:PG2217:hypothetical protein:1-deoxy-D-xylulose-5-phosphate synthase:->->:2329591..2329762 172 gagagaggtcgataggaaaaagttgcatcctgcatgagcgatttgtttgccgcaagtcgtttgtgcaggattcttttaatgattgtgccctcgtgttgcactgcagggtggaatctatagagatcttgataataatccgatatgattacctttgtacaaacgaaaaagtagc Intra-Species Hit: Count: 1 Min: 1 Max: 172 Len: 172 Subject: NC_002950_PG2216_PG2217|hypothetical protein:1-deoxy-D-xylulose-5-phosphate synthase|POSITIVE:POSITIVE|[2329591,2329762]|172 HSP 1 e-value: 5.0E-93 bit: 341.0 Len: 172 Query Start:1 Query End:172 Subject Strand: POSITIVE Subject Start: 1 Subject End: 172 gagagaggtcgataggaaaaagttgcatcctgcatgagcgatttgtttgccgcaagtcgtttgtgcaggattcttttaatgattgtgccctcgtgttgcactgcagggtggaatctatagagatcttgataataatccgatatgattacctttgtacaaacgaaaaagtagc gagagaggtcgataggaaaaagttgcatcctgcatgagcgatttgtttgccgcaagtcgtttgtgcaggattcttttaatgattgtgccctcgtgttgcactgcagggtggaatctatagagatcttgataataatccgatatgattacctttgtacaaacgaaaaagtagc Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAGAGAGGUCGAUAGGAAAAAGUUGCAUCCUGCAUGAGCGAUUUGUUUGCCGCAAGUCGUUUGUGCAGGAUUCUUUUAAUGAUUGUGCCCUCGUGUUGCACUGCAGGGUGGAAUCUAUAGAGAUCUUGAUAAUAAUCCGAUAUGAUUACCUUUGUACAAACGAAAAAGUAGC .(.((((((.(((.(((.........((((((((..((((((((((.....))))))))))..))))))))(((((....((((.((((((.((........)))))))).))))...)))))............)))......))))))))).)................. (-53.40) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GCUACUUUUUCGUUUGUACAAAGGUAAUCAUAUCGGAUUAUUAUCAAGAUCUCUAUAGAUUCCACCCUGCAGUGCAACACGAGGGCACAAUCAUUAAAAGAAUCCUGCACAAACGACUUGCGGCAAACAAAUCGCUCAUGCAGGAUGCAACUUUUUCCUAUCGACCUCUCUC ...........(((.((((..(((.(((((((..(((((........))))).))).))))....)))...)))))))..(((((..........(((((.((((((((....(((.(((.......))).)))....))))))))....)))))..........))))).. (-35.15) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 386 68 23 70 27 NC_002950:PG0088|5end_peptidase,_M16_family_103275..103505_POSITIVE 364 69 21 56 2 NC_002950:PG0744|5end_RNA_methyltransferase,_TrmH_family_791897..792127_NEGATIVE 358 70 21 66 20 NC_002950:PG1475|5end_conjugative_transposon_protein_TraN_1551835..1552065_NEGATIVE 355 69 22 225 179 NC_002950:PG0221|5end_hypothetical_protein_255834..256064_NEGATIVE 348 68 22 87 31 NC_002950:PG1902|5end_uridylate_kinase_2002147..2002377_NEGATIVE 343 100 52 59 10 NC_002950:PG1398|5end_hypothetical_protein_1480694..1480924_POSITIVE 343 70 22 227 172 NC_002950:PG0009|5end_ISPg5_transposase_Orf1_8466..8696_NEGATIVE 342 70 25 177 137 NC_002950:PG2109|5end_thiamine-phosphate_pyrophosphorylase_2219452..2219682_NEGATIVE 340 70 23 187 125 NC_002950:PG1970|5end_hypothetical_protein_2059783..2060013_NEGATIVE 339 68 29 44 4 NC_002950:PG1992|5end_glucose-inhibited_division_protein_A_2081410..2081640_POSITIVE 335 63 25 216 165 NC_002950:PG1579|5end_ATPase,_MoxR_family_1656493..1656723_POSITIVE 325 108 63 125 71 NC_002950:PG1640|5end_DNA-damage-inducible_protein_F_1721245..1721475_NEGATIVE 323 110 61 188 126 NC_002950:PG1727|5end_yitL_protein_1816709..1816939_POSITIVE 321 70 21 187 145 NC_002950:PG2080|5end_adenosylmethionine--8-amino-7-oxononanoate_transaminase_2180679..2180909_NEGATIVE 321 69 24 61 16 NC_002950:PG0380|5end_excinuclease_ABC_subunit_B_409102..409332_POSITIVE 320 69 21 70 26 NC_002950:PG1715|5end_hypothetical_protein_1806056..1806286_NEGATIVE 318 110 63 128 79 NC_002950:PG0499|5end_hypothetical_protein_538709..538939_POSITIVE 317 126 81 99 37 NC_002950:PG1256|5end_ribonuclease,_Rne/Rng_family_1334262..1334492_NEGATIVE 315 99 56 112 65 NC_002950:PG2212|5end_hypothetical_protein_2324767..2324997_NEGATIVE 313 69 23 150 103 NC_002950:PG0125|5end_hypothetical_protein_146786..147016_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 489 70 27 63 20 NC_002950:PG2216|3end_hypothetical_protein_2329530..2329680_POSITIVE 355 69 22 146 100 NC_002950:PG0222|3end_DNA-binding_protein,_histone-like_family_255913..256063_NEGATIVE 337 108 61 118 54 NC_002950:PG1027|3end_hypothetical_protein_1089197..1089347_NEGATIVE 335 63 25 115 64 NC_002950:PG1578|3end_quinolinate_synthetase_1656472..1656622_POSITIVE 335 69 22 138 87 NC_002950:PG0555|3end_DNA-binding_protein,_histone-like_family_611716..611866_NEGATIVE 328 39 1 56 17 NC_002950:PG2147|3end_xanthine_phosphoribosyltransferase_2254819..2254969_NEGATIVE 325 108 63 110 56 NC_002950:PG1641|3end_phosphotyrosine_protein_phosphatase_1721260..1721410_NEGATIVE 313 60 14 51 2 NC_002950:PG0843|3end_hypothetical_protein_904871..905021_NEGATIVE 309 69 23 151 95 NC_002950:PG1078|3end_electron_transfer_flavoprotein,_alpha_subunit_1146525..1146675_POSITIVE 309 140 91 146 95 NC_002950:PG0442|3end_hypothetical_protein_481514..481664_NEGATIVE 308 140 93 83 35 NC_002950:PG1039|3end_integral_membrane_protein_1105325..1105475_NEGATIVE 304 50 3 113 74 NC_002950:PG1494|3end_hypothetical_protein_1571234..1571384_POSITIVE 303 70 27 43 3 NC_002950:PG1476|3end_conjugative_transposon_protein_TraM_1551858..1552008_NEGATIVE 302 70 21 81 38 NC_002950:PG1834|3end_glycogen_synthase-related_protein_1927050..1927200_POSITIVE 301 130 85 88 37 NC_002950:PG1773|3end_PAP2_superfamily_protein_1861232..1861382_POSITIVE 301 124 81 66 27 NC_002950:PG1367|3end_hypothetical_protein_1447411..1447561_NEGATIVE 300 49 1 56 1 NC_002950:PG0360|3end_lemA_protein_394152..394302_POSITIVE 298 63 24 135 94 NC_002950:PG0022|3end_sulfate_permease_family_protein_25120..25270_NEGATIVE 297 49 2 79 32 NC_002950:PG1953|3end_YitT_family_protein_2044589..2044739_POSITIVE 297 77 31 61 15 NC_002950:PG1829|3end_long-chain-fatty-acid--CoA_ligase,_putative_1921307..1921457_NEGATIVE