Origin IGS: ttttcttaatttttaaaattattattgatattcatctgtggcaacgtatataccaagacgttacgcacaggcgcttttctgcgtcttctcttcaaagatacatcaagctttctta .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 taagaaagcttgatgtatctttgaagagaagacgcagaaaagcgcctgtgcgtaacgtcttggtatatacgttgccacagatgaatatcaataataattttaaaaattaagaaaa Mask Tandem Repeat Region ================================================ ttttcttaatttttaaaattattattgatattcatctgtggcaacgtatataccaagacgttacgcacaggcgcttttctgcgtcttctcttcaaagatacatcaagctttctta Find is-nt database================================================ Query_seq: PI1145:PI1146|PI1145:PI1146:50S ribosomal protein L35:translation initiation factor IF3:->->:1072855..1072969 115 ttttcttaatttttaaaattattattgatattcatctgtggcaacgtatataccaagacgttacgcacaggcgcttttctgcgtcttctcttcaaagatacatcaagctttctta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI1145:PI1146|PI1145:PI1146:50S ribosomal protein L35:translation initiation factor IF3:->->:1072855..1072969 115 ttttcttaatttttaaaattattattgatattcatctgtggcaacgtatataccaagacgttacgcacaggcgcttttctgcgtcttctcttcaaagatacatcaagctttctta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI1145:PI1146|PI1145:PI1146:50S ribosomal protein L35:translation initiation factor IF3:->->:1072855..1072969 115 ttttcttaatttttaaaattattattgatattcatctgtggcaacgtatataccaagacgttacgcacaggcgcttttctgcgtcttctcttcaaagatacatcaagctttctta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ttttcttaatttttaaaattattattgatattcatctgtggcaacgtatataccaagacgttacgcacaggcgcttttctgcgtcttctcttcaaagatacatcaagctttctta Predict ORF larger than 30AA ================================================ Protein_Len: 35 Strand: + Start: 9 End: 113 ........ M F K I I I D I H L W Q R I Y Q D V T H R R F S A S S L Q R Y I K L S .. Protein_Len: 30 Strand: + Start: 25 End: 114 ........................ M I F I C G N V Y T K T L R T G A F L R L L F K D T S S F L . ttttcttaatttttaaaattattattgatattcatctgtggcaacgtatataccaagacgttacgcacaggcgcttttctgcgtcttctcttcaaagatacatcaagctttctta 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================================================ ttttcttaatttttaaaattattattgatattcatctgtggcaacgtatataccaagacgttacgcacaggcgcttttctgcgtcttctcttcaaagatacatcaagctttctta Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PI1145:PI1146|PI1145:PI1146:50S ribosomal protein L35:translation initiation factor IF3:->->:1072855..1072969 115 ttttcttaatttttaaaattattattgatattcatctgtggcaacgtatataccaagacgttacgcacaggcgcttttctgcgtcttctcttcaaagatacatcaagctttctta Intra-Species Hit: Count: 1 Min: 1 Max: 115 Len: 115 Subject: pint_PI1145_PI1146|50S ribosomal protein L35:translation initiation factor IF3|POSITIVE:POSITIVE|[1072855,1072969]|115 HSP 1 e-value: 3.0E-59 bit: 228.0 Len: 115 Query Start:1 Query End:115 Subject Strand: POSITIVE Subject Start: 1 Subject End: 115 ttttcttaatttttaaaattattattgatattcatctgtggcaacgtatataccaagacgttacgcacaggcgcttttctgcgtcttctcttcaaagatacatcaagctttctta ttttcttaatttttaaaattattattgatattcatctgtggcaacgtatataccaagacgttacgcacaggcgcttttctgcgtcttctcttcaaagatacatcaagctttctta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUUCUUAAUUUUUAAAAUUAUUAUUGAUAUUCAUCUGUGGCAACGUAUAUACCAAGACGUUACGCACAGGCGCUUUUCUGCGUCUUCUCUUCAAAGAUACAUCAAGCUUUCUUA ........................(((((..((...((((..(((((..........))))).)))).((((((......))))))..........))...)))))......... (-18.40) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAGAAAGCUUGAUGUAUCUUUGAAGAGAAGACGCAGAAAAGCGCCUGUGCGUAACGUCUUGGUAUAUACGUUGCCACAGAUGAAUAUCAAUAAUAAUUUUAAAAAUUAAGAAAA (((((..((((..((..(((((.....)))))..))...))))..(((((.(((((((.(......).)))))))))))).................)))))............. (-26.80) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 364 110 62 138 80 pint:PI0635|5end_dephospho-CoA_kinase_580954..581184_POSITIVE 345 76 37 52 9 pint:PI1366|5end_conserved_hypothetical_protein;_possible_hydrolase,_HAD_superfamily_1286046..1286276_POSITIVE 337 97 53 148 104 pint:PI1985|5end_hypothetical_protein_1940291..1940521_POSITIVE 319 108 63 56 20 pint:PI0265|5end_conjugative_transposon_protein,_TraO_257296..257526_POSITIVE 312 99 54 36 2 pint:PI1862|5end_hypothetical_protein_1806189..1806419_POSITIVE 306 97 56 41 1 pint:PI1984|5end_MutT/nudix_family_protein_1940184..1940414_POSITIVE 304 79 40 173 133 pint:PI0790|5end_hypothetical_protein_728953..729183_POSITIVE 303 91 56 61 25 pint:PI1653|5end_hypothetical_protein_1565158..1565388_POSITIVE 297 83 41 207 163 pint:PI1974|5end_hypothetical_protein_1931193..1931423_POSITIVE 296 74 37 136 95 pint:PI0108|5end_L-lactate_permease_104892..105122_POSITIVE 295 98 59 187 145 pint:PI1831|5end_conserved_hypothetical_protein_1770298..1770528_POSITIVE 295 79 36 47 1 pint:PI0128|5end_dipeptidase,_pathogenicity_island-encoded_protein_D_120532..120762_POSITIVE 293 93 59 59 21 pint:PI0262|5end_conserved_hypothetical_protein_254685..254915_POSITIVE 291 83 41 193 149 pint:PI0055|5end_hypothetical_protein_54815..55045_POSITIVE 291 83 41 105 61 pint:PI0053|5end_hypothetical_protein_54727..54957_POSITIVE 288 84 45 152 116 pint:PI0869|5end_possible_exodeoxyribonuclease_VII_(small_subunit)_805518..805748_POSITIVE 284 109 65 79 40 pint:PI0263|5end_conjugative_transposon_protein,_TraM_255256..255486_POSITIVE 282 74 33 157 120 pint:PI1754|5end_conserved_hypothetical_protein_1681202..1681432_POSITIVE 280 85 59 81 49 pint:PI1633|5end_hypothetical_protein_1552504..1552734_POSITIVE 279 88 43 63 8 pint:PI0011|5end_conserved_hypothetical_protein_12142..12372_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 319 108 63 51 15 pint:PI0264|3end_transfer_region-related_protein,_TraN_257371..257521_POSITIVE 303 91 56 58 22 pint:PI1652|3end_hypothetical_protein_1565235..1565385_POSITIVE 297 83 41 105 61 pint:PI1973|3end_conserved_hypothetical_protein_1931171..1931321_POSITIVE 293 93 59 59 21 pint:PI0261|3end_conjugative_transposon_protein,_TraK_254765..254915_POSITIVE 291 83 41 127 83 pint:PI0054|3end_hypothetical_protein_54829..54979_POSITIVE 288 84 45 130 94 pint:PI0868|3end_exodeoxyribonuclease_VII,_large_subunit_805576..805726_POSITIVE 286 99 62 26 1 pint:PI1860|3end_hypothetical_protein_1806259..1806409_POSITIVE 282 74 33 145 108 pint:PI1752|3end_conserved_hypothetical_protein_1681270..1681420_POSITIVE 274 83 56 150 122 pint:PI1862|3end_hypothetical_protein_1806391..1806541_POSITIVE 267 90 57 62 35 pint:PI1572|3end_hypothetical_protein_1498215..1498365_POSITIVE 265 91 51 125 81 pint:PI2122|3end_conserved_hypothetical_protein_2070480..2070630_POSITIVE 264 84 41 70 29 pint:PI1634|3end_conserved_hypothetical_protein_1553819..1553969_POSITIVE 263 85 45 124 92 pint:PI1708|3end_hypothetical_protein_1625562..1625712_POSITIVE 263 89 41 71 4 pint:PI1595|3end_conserved_hypothetical_protein_1525129..1525279_POSITIVE 261 89 41 144 97 pint:PI1686|3end_hypothetical_protein_1601898..1602048_POSITIVE 258 73 38 145 113 pint:PI0965|3end_hypothetical_protein_894392..894542_POSITIVE 258 93 60 105 66 pint:PI0340|3end_conserved_hypothetical_protein_316735..316885_POSITIVE 251 74 36 83 44 pint:PI0675|3end_hypothetical_protein_613957..614107_POSITIVE 249 93 53 142 105 pint:PI1227|3end_conserved_hypothetical_protein;_possible_DNA-binding_protein,_histone-like_family_1148974..1149124_POSITIVE 248 74 33 73 26 pint:PI1136|3end_conserved_hypothetical_protein_1062541..1062691_POSITIVE