Origin IGS: agtctttattatttattatttattttttttcttttttggaggattattgtctcttcctttaccactggggtttcctgtttttgaaggccaacctgcagtgttaacttgttctttgatttcttttgccatagtctttattatttatttttttcttttttggaggattattgtctcttcctttaccactggggtttcctgtttttgaaggccaacctgcagtgttaacttgttctgatttttttgttttgccca .........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 tgggcaaaacaaaaaaatcagaacaagttaacactgcaggttggccttcaaaaacaggaaaccccagtggtaaaggaagagacaataatcctccaaaaaagaaaaaaataaataataaagactatggcaaaagaaatcaaagaacaagttaacactgcaggttggccttcaaaaacaggaaaccccagtggtaaaggaagagacaataatcctccaaaaaagaaaaaaaataaataataaataataaagact Mask Tandem Repeat Region ================================================ agtctttattannnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnngatttttttgttttgccca Find is-nt database================================================ Query_seq: PG0520:PG0521|PG0520:PG0521:chaperonin GroEL:co-chaperonin GroES:<-<-:565346..565597 252 agtctttattatttattatttattttttttcttttttggaggattattgtctcttcctttaccactggggtttcctgtttttgaaggccaacctgcagtgttaacttgttctttgatttcttttgccatagtctttattatttatttttttcttttttggaggattattgtctcttcctttaccactggggtttcctgtttttgaaggccaacctgcagtgttaacttgttctgatttttttgttttgccca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG0520:PG0521|PG0520:PG0521:chaperonin GroEL:co-chaperonin GroES:<-<-:565346..565597 252 agtctttattatttattatttattttttttcttttttggaggattattgtctcttcctttaccactggggtttcctgtttttgaaggccaacctgcagtgttaacttgttctttgatttcttttgccatagtctttattatttatttttttcttttttggaggattattgtctcttcctttaccactggggtttcctgtttttgaaggccaacctgcagtgttaacttgttctgatttttttgttttgccca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG0520:PG0521|PG0520:PG0521:chaperonin GroEL:co-chaperonin GroES:<-<-:565346..565597 252 agtctttattatttattatttattttttttcttttttggaggattattgtctcttcctttaccactggggtttcctgtttttgaaggccaacctgcagtgttaacttgttctttgatttcttttgccatagtctttattatttatttttttcttttttggaggattattgtctcttcctttaccactggggtttcctgtttttgaaggccaacctgcagtgttaacttgttctgatttttttgttttgccca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 agtctttattatttattatttattttttttcttttttggaggattattgtctcttcctttaccactggggtttcctgtttttgaaggccaacctgcagtgttaacttgttctttgatttcttttgccatagtctttattatttatttttttcttttttggaggattattgtctcttcctttaccactggggtttcctgtttttgaaggccaacctgcagtgttaacttgttctgatttttttgttttgccca Predict ORF larger than 30AA ================================================ Protein_Len: 60 Strand: + Start: 8 End: 202 ....... M I Y Y L F F F F F G G L L S L P L P L G F P V F E G Q P A V L T C S L I S F A I V F I I Y F F L F W R I I V S S F T T .................................................. Protein_Len: 39 Strand: + Start: 106 End: 222 ......................................................................................................... M F F D F F C H S L Y Y L F F S F L E D Y C L F L Y H W G F L F L K A N L Q C .............................. Protein_Len: 36 Strand: + Start: 144 End: 251 ............................................................................................................................................... M F F F F G G L L S L P L P L G F P V F E G Q P A V L T C S D F F V L P . Protein_Len: 41 Strand: - Start: 19 End: 141 .................. K N K K K K P P N N D R G K G S P N G T K S P W G A T N V Q E K I E K A M T K I M ............................................................................................................... agtctttattatttattatttattttttttcttttttggaggattattgtctcttcctttaccactggggtttcctgtttttgaaggccaacctgcagtgttaacttgttctttgatttcttttgccatagtctttattatttatttttttcttttttggaggattattgtctcttcctttaccactggggtttcctgtttttgaaggccaacctgcagtgttaacttgttctgatttttttgttttgccca Predict Promoter with matrix: RpoD-15 score > 80================================================ Predict Promoter with matrix: RpoD-16 score > 80================================================ Predict Promoter with matrix: RpoD-17 score > 80================================================ PromScan Matrix: RpoD-17 Strand: + Score: 85 Start: 112 End: 141 ...............................................................................................................TTTGATTTCTTTTGCCATAGTCTTTATTAT............................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ agtctttattatttattatttattttttttcttttttggaggattattgtctcttcctttaccactggggtttcctgtttttgaaggccaacctgcagtgttaacttgttctttgatttcttttgccatagtctttattatttatttttttcttttttggaggattattgtctcttcctttaccactggggtttcctgtttttgaaggccaacctgcagtgttaacttgttctgatttttttgttttgccca Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PG0520:PG0521|PG0520:PG0521:chaperonin GroEL:co-chaperonin GroES:<-<-:565346..565597 252 agtctttattatttattatttattttttttcttttttggaggattattgtctcttcctttaccactggggtttcctgtttttgaaggccaacctgcagtgttaacttgttctttgatttcttttgccatagtctttattatttatttttttcttttttggaggattattgtctcttcctttaccactggggtttcctgtttttgaaggccaacctgcagtgttaacttgttctgatttttttgttttgccca Intra-Species Hit: Count: 1 Min: 38 Max: 235 Len: 198 Subject: NC_002950_PG0520_PG0521|chaperonin GroEL:co-chaperonin GroES|NEGATIVE:NEGATIVE|[565346,565597]|252 HSP 1 e-value: 4.0E-54 bit: 212.0 Len: 107 Query Start:38 Query End:144 Subject Strand: POSITIVE Subject Start: 38 Subject End: 144 .....................................ggaggattattgtctcttcctttaccactggggtttcctgtttttgaaggccaacctgcagtgttaacttgttctttgatttcttttgccatagtctttattattta............................................................................................................ .....................................ggaggattattgtctcttcctttaccactggggtttcctgtttttgaaggccaacctgcagtgttaacttgttctttgatttcttttgccatagtctttattattta............................................................................................................ HSP 2 e-value: 3.0E-36 bit: 153.0 Len: 77 Query Start:159 Query End:235 Subject Strand: POSITIVE Subject Start: 159 Subject End: 235 ..............................................................................................................................................................ggaggattattgtctcttcctttaccactggggtttcctgtttttgaaggccaacctgcagtgttaacttgttctga................. ..............................................................................................................................................................ggaggattattgtctcttcctttaccactggggtttcctgtttttgaaggccaacctgcagtgttaacttgttctga................. HSP 3 e-value: 5.0E-35 bit: 149.0 Len: 75 Query Start:159 Query End:233 Subject Strand: POSITIVE Subject Start: 38 Subject End: 112 ..............................................................................................................................................................ggaggattattgtctcttcctttaccactggggtttcctgtttttgaaggccaacctgcagtgttaacttgttct................... ..............................................................................................................................................................ggaggattattgtctcttcctttaccactggggtttcctgtttttgaaggccaacctgcagtgttaacttgttct................... HSP 4 e-value: 5.0E-35 bit: 149.0 Len: 75 Query Start:38 Query End:112 Subject Strand: POSITIVE Subject Start: 159 Subject End: 233 .....................................ggaggattattgtctcttcctttaccactggggtttcctgtttttgaaggccaacctgcagtgttaacttgttct............................................................................................................................................ .....................................ggaggattattgtctcttcctttaccactggggtttcctgtttttgaaggccaacctgcagtgttaacttgttct............................................................................................................................................ Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GGAGGAUUAUUGUCUCUUCCUUUACCACUGGGGUUUCCUGUUUUUGAAGGCCAACCUGCAGUGUUAACUUGUUCUUUGAUUUCUUUUGCCAUAGUCUUUAUUAUUUAUUUUUUUCUUUUUUGGAGGAUUAUUGUCUCUUCCUUUACCACUGGGGUUUCCUGUUUUUGAAGGCCAACCUGCAGUGUUAACUUGUUCUGA ((((((........)))))).(((.((((((((((....(((((..(((((.(((((.(((((.(((..........((((...........)))).........................((((((........)))))).))).))))))))))....)))))..))))).))))).))))).))).......... (-44.10) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCAGAACAAGUUAACACUGCAGGUUGGCCUUCAAAAACAGGAAACCCCAGUGGUAAAGGAAGAGACAAUAAUCCUCCAAAAAAGAAAAAAAUAAAUAAUAAAGACUAUGGCAAAAGAAAUCAAAGAACAAGUUAACACUGCAGGUUGGCCUUCAAAAACAGGAAACCCCAGUGGUAAAGGAAGAGACAAUAAUCCUCC ..............(((((..((((..(((........))).)))).))))).....(((.((........((.(((.........................((((.((..................))))))..(((((..((((..(((........))).)))).))))).....))).))........)).))) (-36.26) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 958 60 11 188 139 NC_002950:PG0520|5end_chaperonin_GroEL_565255..565485_NEGATIVE 311 169 121 173 127 NC_002950:PG0945|5end_ABC_transporter,_permease_protein,_putative_1006432..1006662_NEGATIVE 310 59 19 63 9 NC_002950:PG1017|5end_pyruvate_phosphate_dikinase_1076138..1076368_POSITIVE 310 59 16 154 100 NC_002950:PG0229|5end_hypothetical_protein_264872..265102_POSITIVE 305 60 12 193 142 NC_002950:PG1057|5end_hypothetical_protein_1123419..1123649_POSITIVE 305 89 45 207 161 NC_002950:PG0999|5end_hypothetical_protein_1057026..1057256_POSITIVE 305 89 45 110 64 NC_002950:PG0998|5end_hypothetical_protein_1056929..1057159_POSITIVE 304 50 2 202 157 NC_002950:PG2119|5end_oxidoreductase,_Gfo/Idh/MocA_family_2226547..2226777_POSITIVE 297 167 121 158 115 NC_002950:PG0398|5end_recF_protein_435710..435940_NEGATIVE 293 70 26 66 19 NC_002950:PG0530|5end_carbamoyl-phosphate_synthase,_large_subunit_575729..575959_POSITIVE 291 77 38 59 27 NC_002950:PG1481|5end_conjugative_transposon_protein_TraG_1558447..1558677_NEGATIVE 290 60 12 81 35 NC_002950:PG2225|5end_hypothetical_protein_2339440..2339670_POSITIVE 289 63 22 189 146 NC_002950:PG1641|5end_phosphotyrosine_protein_phosphatase_1721763..1721993_NEGATIVE 288 65 26 87 40 NC_002950:PG0309|5end_thiamine_biosynthesis_lipoprotein_ApbE_345023..345253_NEGATIVE 287 90 41 89 40 NC_002950:PG0417|5end_ATP-dependent_protease_ATP-binding_subunit_458624..458854_NEGATIVE 286 180 131 126 78 NC_002950:PG0806|5end_oxidoreductase,_Gfo/Idh/MocA_family_863592..863822_NEGATIVE 286 80 38 80 31 NC_002950:PG0361|5end_hypothetical_protein_394094..394324_POSITIVE 285 60 18 80 30 NC_002950:PG0787|5end_hypothetical_protein_837675..837905_POSITIVE 283 38 10 47 21 NC_002950:PG1476|5end_conjugative_transposon_protein_TraM_1553219..1553449_NEGATIVE 282 90 48 139 102 NC_002950:PG2101|5end_hypothetical_protein_2211273..2211503_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 332 180 131 144 94 NC_002950:PG0377|3end_30S_ribosomal_protein_S2_407845..407995_POSITIVE 326 59 12 151 94 NC_002950:PG0432|3end_NOL1/NOP2/sun_family_protein_469273..469423_NEGATIVE 314 64 30 37 7 NC_002950:PG1223|3end_hypothetical_protein_1299744..1299894_POSITIVE 305 89 45 113 67 NC_002950:PG0997|3end_transcriptional_regulator,_putative_1057012..1057162_POSITIVE 291 77 38 62 30 NC_002950:PG1482|3end_conjugative_transposon_protein_TraF_1558444..1558594_NEGATIVE 290 60 12 61 15 NC_002950:PG2224|3end_hypothetical_protein_2339500..2339650_POSITIVE 288 65 26 90 43 NC_002950:PG0310|3end_nitroreductase_family_protein_345020..345170_NEGATIVE 287 90 41 52 3 NC_002950:PG0418|3end_ATP-dependent_Clp_protease,_proteolytic_subunit_458661..458811_NEGATIVE 286 180 131 88 40 NC_002950:PG0807|3end_NusB_family_protein_863630..863780_NEGATIVE 286 80 38 58 9 NC_002950:PG0360|3end_lemA_protein_394152..394302_POSITIVE 283 38 10 57 31 NC_002950:PG1477|3end_hypothetical_protein_1553209..1553359_NEGATIVE 282 99 52 78 37 NC_002950:PG0880|3end_bacterioferritin_comigratory_protein_943122..943272_POSITIVE 282 130 87 93 53 NC_002950:PG0677|3end_saccharopine_dehydrogenase_728926..729076_POSITIVE 278 59 15 147 95 NC_002950:PG1556|3end_hypothetical_protein_1637001..1637151_POSITIVE 270 55 17 71 17 NC_002950:PG0119|3end_glycosyl_transferase,_WecB/TagA/CpsF_family_143078..143228_POSITIVE 268 120 72 111 51 NC_002950:PG1914|3end_30S_ribosomal_protein_S13_2012938..2013088_NEGATIVE 268 95 56 131 96 NC_002950:PG0535|3end_hypothetical_protein_585956..586106_NEGATIVE 267 50 17 136 102 NC_002950:PG0806|3end_oxidoreductase,_Gfo/Idh/MocA_family_862687..862837_NEGATIVE 266 70 27 47 1 NC_002950:PG0529|3end_carbamoyl-phosphate_synthase_small_subunit_575790..575940_POSITIVE 265 51 13 148 95 NC_002950:PG0227|3end_DNA_repair_protein_RadA_262593..262743_NEGATIVE