Origin IGS: tcggcttttaattatttatatatgcagaagcgtggaactgactatgtccacactttcagcctgaggtcctgagaaaacctaaacgaacgaatgtacagatagcagcccacgcctatgcgtgagaaccactatgcagcccctcgttcgttattgaaatttctcaggtttcaggccgaacagatgcaagcataacgcttcttctttttctacaatgtcttggagagagtttcctcaaaccacttgcaaagataatgataattgatggaaaattccacatttcttgcagaaatttacacctatggtaactttttgataa .........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 ttatcaaaaagttaccataggtgtaaatttctgcaagaaatgtggaattttccatcaattatcattatctttgcaagtggtttgaggaaactctctccaagacattgtagaaaaagaagaagcgttatgcttgcatctgttcggcctgaaacctgagaaatttcaataacgaacgaggggctgcatagtggttctcacgcataggcgtgggctgctatctgtacattcgttcgtttaggttttctcaggacctcaggctgaaagtgtggacatagtcagttccacgcttctgcatatataaataattaaaagccga Mask Tandem Repeat Region ================================================ tcggcttttaattatttatatatgcagaagcgtggaactgactatgtccacactttcagcctgaggtcctgagaaaacctaaacgaacgaatgtacagatagcagcccacgcctatgcgtgagaaccactatgcagcccctcgttcgttattgaaatttctcaggtttcaggccgaacagatgcaagcataacgcttcttctttttctacaatgtcttggagagagtttcctcaaaccacttgcaaagataatgataattgatggaaaattccacatttcttgcagaaatttacacctatggtaactttttgataa Find is-nt database================================================ Query_seq: PG1108:PG1109|PG1108:PG1109:hypothetical protein:mobilization protein:<-<-:1181199..1181514 316 tcggcttttaattatttatatatgcagaagcgtggaactgactatgtccacactttcagcctgaggtcctgagaaaacctaaacgaacgaatgtacagatagcagcccacgcctatgcgtgagaaccactatgcagcccctcgttcgttattgaaatttctcaggtttcaggccgaacagatgcaagcataacgcttcttctttttctacaatgtcttggagagagtttcctcaaaccacttgcaaagataatgataattgatggaaaattccacatttcttgcagaaatttacacctatggtaactttttgataa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG1108:PG1109|PG1108:PG1109:hypothetical protein:mobilization protein:<-<-:1181199..1181514 316 tcggcttttaattatttatatatgcagaagcgtggaactgactatgtccacactttcagcctgaggtcctgagaaaacctaaacgaacgaatgtacagatagcagcccacgcctatgcgtgagaaccactatgcagcccctcgttcgttattgaaatttctcaggtttcaggccgaacagatgcaagcataacgcttcttctttttctacaatgtcttggagagagtttcctcaaaccacttgcaaagataatgataattgatggaaaattccacatttcttgcagaaatttacacctatggtaactttttgataa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG1108:PG1109|PG1108:PG1109:hypothetical protein:mobilization protein:<-<-:1181199..1181514 316 tcggcttttaattatttatatatgcagaagcgtggaactgactatgtccacactttcagcctgaggtcctgagaaaacctaaacgaacgaatgtacagatagcagcccacgcctatgcgtgagaaccactatgcagcccctcgttcgttattgaaatttctcaggtttcaggccgaacagatgcaagcataacgcttcttctttttctacaatgtcttggagagagtttcctcaaaccacttgcaaagataatgataattgatggaaaattccacatttcttgcagaaatttacacctatggtaactttttgataa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tcggcttttaattatttatatatgcagaagcgtggaactgactatgtccacactttcagcctgaggtcctgagaaaacctaaacgaacgaatgtacagatagcagcccacgcctatgcgtgagaaccactatgcagcccctcgttcgttattgaaatttctcaggtttcaggccgaacagatgcaagcataacgcttcttctttttctacaatgtcttggagagagtttcctcaaaccacttgcaaagataatgataattgatggaaaattccacatttcttgcagaaatttacacctatggtaactttttgataa Predict ORF larger than 30AA ================================================ Protein_Len: 51 Strand: + Start: 150 End: 302 ..................................................................................................................................................... M E I S Q V S G R T D A S I T L L L F L Q C L G E S F L K P L A K I M I I D G K F H I S C R N L H L W .............. Protein_Len: 41 Strand: - Start: 164 End: 286 ................................................................................................................................................................... T E P R V S A L M V S R R K R C H R P S L K R L G S A F I I I I S P F N W M E Q M .............................. tcggcttttaattatttatatatgcagaagcgtggaactgactatgtccacactttcagcctgaggtcctgagaaaacctaaacgaacgaatgtacagatagcagcccacgcctatgcgtgagaaccactatgcagcccctcgttcgttattgaaatttctcaggtttcaggccgaacagatgcaagcataacgcttcttctttttctacaatgtcttggagagagtttcctcaaaccacttgcaaagataatgataattgatggaaaattccacatttcttgcagaaatttacacctatggtaactttttgataa 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================================================ tcggcttttaattatttatatatgcagaagcgtggaactgactatgtccacactttcagcctgaggtcctgagaaaacctaaacgaacgaatgtacagatagcagcccacgcctatgcgtgagaaccactatgcagcccctcgttcgttattgaaatttctcaggtttcaggccgaacagatgcaagcataacgcttcttctttttctacaatgtcttggagagagtttcctcaaaccacttgcaaagataatgataattgatggaaaattccacatttcttgcagaaatttacacctatggtaactttttgataa Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PG1108:PG1109|PG1108:PG1109:hypothetical protein:mobilization protein:<-<-:1181199..1181514 316 tcggcttttaattatttatatatgcagaagcgtggaactgactatgtccacactttcagcctgaggtcctgagaaaacctaaacgaacgaatgtacagatagcagcccacgcctatgcgtgagaaccactatgcagcccctcgttcgttattgaaatttctcaggtttcaggccgaacagatgcaagcataacgcttcttctttttctacaatgtcttggagagagtttcctcaaaccacttgcaaagataatgataattgatggaaaattccacatttcttgcagaaatttacacctatggtaactttttgataa Intra-Species Hit: Count: 1 Min: 1 Max: 316 Len: 316 Subject: NC_002950_PG1108_PG1109|hypothetical protein:mobilization protein|NEGATIVE:NEGATIVE|[1181199,1181514]|316 HSP 1 e-value: 1.0E-178 bit: 626.0 Len: 316 Query Start:1 Query End:316 Subject Strand: POSITIVE Subject Start: 1 Subject End: 316 tcggcttttaattatttatatatgcagaagcgtggaactgactatgtccacactttcagcctgaggtcctgagaaaacctaaacgaacgaatgtacagatagcagcccacgcctatgcgtgagaaccactatgcagcccctcgttcgttattgaaatttctcaggtttcaggccgaacagatgcaagcataacgcttcttctttttctacaatgtcttggagagagtttcctcaaaccacttgcaaagataatgataattgatggaaaattccacatttcttgcagaaatttacacctatggtaactttttgataa tcggcttttaattatttatatatgcagaagcgtggaactgactatgtccacactttcagcctgaggtcctgagaaaacctaaacgaacgaatgtacagatagcagcccacgcctatgcgtgagaaccactatgcagcccctcgttcgttattgaaatttctcaggtttcaggccgaacagatgcaagcataacgcttcttctttttctacaatgtcttggagagagtttcctcaaaccacttgcaaagataatgataattgatggaaaattccacatttcttgcagaaatttacacctatggtaactttttgataa Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCGGCUUUUAAUUAUUUAUAUAUGCAGAAGCGUGGAACUGACUAUGUCCACACUUUCAGCCUGAGGUCCUGAGAAAACCUAAACGAACGAAUGUACAGAUAGCAGCCCACGCCUAUGCGUGAGAACCACUAUGCAGCCCCUCGUUCGUUAUUGAAAUUUCUCAGGUUUCAGGCCGAACAGAUGCAAGCAUAACGCUUCUUCUUUUUCUACAAUGUCUUGGAGAGAGUUUCCUCAAACCACUUGCAAAGAUAAUGAUAAUUGAUGGAAAAUUCCACAUUUCUUGCAGAAAUUUACACCUAUGGUAACUUUUUGAUAA .......(((((((((..(((.(((((((((((.........(((((...(((((((.((((((((.(((((((((.....(((((((((.((((.((.......(.(((((....))))).).....)).)))).....))))))))).......))))))))))))))))).))).)).))...))))))))))))..(((((((((........)))))))))...............))))...)))..))))))))).(((....)))..........((((((.((((.......)))).)))))).... (-82.30) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUAUCAAAAAGUUACCAUAGGUGUAAAUUUCUGCAAGAAAUGUGGAAUUUUCCAUCAAUUAUCAUUAUCUUUGCAAGUGGUUUGAGGAAACUCUCUCCAAGACAUUGUAGAAAAAGAAGAAGCGUUAUGCUUGCAUCUGUUCGGCCUGAAACCUGAGAAAUUUCAAUAACGAACGAGGGGCUGCAUAGUGGUUCUCACGCAUAGGCGUGGGCUGCUAUCUGUACAUUCGUUCGUUUAGGUUUUCUCAGGACCUCAGGCUGAAAGUGUGGACAUAGUCAGUUCCACGCUUCUGCAUAUAUAAAUAAUUAAAAGCCGA ...................(((.(((.(((((((((.....(((((....)))))......................(((...(((....)))...))).....)))))))))..(.((((((((((((.(..(((...((((((((((..(((((((((...(...((((((((((..((.(.((((..(..(((((((....))))))))..))))).))...))))))))))...).)))))))))...)))))))))).)))..).)))).........)))))))).)............)))...))).. (-106.30) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 1076 140 91 231 182 NC_002950:PG1108|5end_hypothetical_protein_1181108..1181338_NEGATIVE 387 138 91 62 21 NC_002950:PG0441|5end_hypothetical_protein_478734..478964_POSITIVE 384 147 101 206 148 NC_002950:PG0538|5end_outer_membrane_efflux_protein_589142..589372_POSITIVE 382 149 101 72 6 NC_002950:PG0295|5end_DNA_processing_protein_DprA,_putative_331300..331530_NEGATIVE 353 148 105 221 171 NC_002950:PG0399|5end_lipoprotein,_putative_436237..436467_NEGATIVE 351 149 102 225 161 NC_002950:PG1342|5end_UDP-N-acetylenolpyruvoylglucosamine_reductase_1422585..1422815_POSITIVE 349 147 102 77 27 NC_002950:PG0246|5end_hypothetical_protein_281241..281471_NEGATIVE 341 148 106 197 151 NC_002950:PG0158|5end_competence_protein_F-related_protein_180175..180405_POSITIVE 339 148 101 61 3 NC_002950:PG1482|5end_conjugative_transposon_protein_TraF_1558779..1559009_NEGATIVE 334 69 22 150 101 NC_002950:PG1351|5end_hypothetical_protein_1432744..1432974_NEGATIVE 333 148 102 200 137 NC_002950:PG0576|5end_UDP-N-acetylmuramoylalanyl-D-glutamate--2,_6-diaminopimelate_ligase_631719..631949_POSITIVE 332 142 101 80 42 NC_002950:PG2168|5end_hypothetical_protein_2274157..2274387_NEGATIVE 330 120 77 214 151 NC_002950:PG0603|5end_cytidylate_kinase_659570..659800_POSITIVE 322 138 91 228 184 NC_002950:PG1913|5end_30S_ribosomal_protein_S11_2012926..2013156_NEGATIVE 319 85 45 58 7 NC_002950:PG1069|5end_alcohol_dehydrogenase,_zinc-containing,_putative_1135499..1135729_POSITIVE 317 63 23 88 44 NC_002950:PG0681|5end_hypothetical_protein_732719..732949_NEGATIVE 317 143 101 208 170 NC_002950:PG0635|5end_ribosomal_protein_L11_methyltransferase_687773..688003_NEGATIVE 315 147 103 201 155 NC_002950:PG1952|5end_DedA_family_protein_2042870..2043100_POSITIVE 314 180 134 125 68 NC_002950:PG0235|5end_carboxyl-terminal_protease_271629..271859_POSITIVE 312 146 101 216 164 NC_002950:PG0326|5end_hypothetical_protein_360974..361204_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 387 138 91 58 17 NC_002950:PG0439|3end_hypothetical_protein_478810..478960_POSITIVE 382 149 101 79 13 NC_002950:PG0296|3end_phosphoribosylformylglycinamidine_synthase_331293..331443_NEGATIVE 316 66 22 150 108 NC_002950:PG1352|3end_hypothetical_protein_1432737..1432887_NEGATIVE 313 148 101 141 81 NC_002950:PG1859|3end_glycerate_kinase_family_protein_1957174..1957324_NEGATIVE 309 154 111 63 13 NC_002950:PG1734|3end_transporter,_putative_1821620..1821770_NEGATIVE 309 148 101 73 20 NC_002950:PG0737|3end_hypothetical_protein_786546..786696_POSITIVE 307 147 107 65 6 NC_002950:PG1112|3end_hypothetical_protein_1185571..1185721_POSITIVE 304 180 132 84 27 NC_002950:PG0224|3end_hypothetical_protein_257614..257764_NEGATIVE 302 176 131 48 2 NC_002950:PG2110|3end_thiamine_biosynthesis_protein_ThiC_2219449..2219599_NEGATIVE 300 138 93 140 94 NC_002950:PG0259|3end_hypothetical_protein_293701..293851_POSITIVE 297 148 103 79 23 NC_002950:PG1429|3end_hypothetical_protein_1515003..1515153_NEGATIVE 297 149 101 61 3 NC_002950:PG1247|3end_3-dehydroquinate_synthase_1325585..1325735_POSITIVE 296 145 108 67 25 NC_002950:PG0798|3end_ISPg3,_transposase_853827..853977_POSITIVE 296 189 143 134 86 NC_002950:PG0729|3end_D-alanylalanine_synthetase_779826..779976_NEGATIVE 295 148 116 132 96 NC_002950:PG1625|3end_hypothetical_protein_1708718..1708868_POSITIVE 294 230 181 129 77 NC_002950:PG1014|3end_TPR_domain_protein_1075855..1076005_POSITIVE 294 68 22 92 36 NC_002950:PG0498|3end_S-ribosylhomocysteinase_538527..538677_POSITIVE 294 160 116 80 37 NC_002950:PG0373|3end_hypothetical_protein_405453..405603_POSITIVE 293 143 101 150 99 NC_002950:PG0902|3end_alpha-1,2-mannosidase_family_protein_966746..966896_NEGATIVE 292 180 132 47 3 NC_002950:PG1752|3end_hypothetical_protein_1838698..1838848_POSITIVE