Origin IGS: atcatatcccctgtatttcagacacaggtttccaaaacaggataaaaacagtaagcccgaaagcgacgtgtcgctttcgggcttacgttttacgtggtattgagaccgcataaatgagg .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 cctcatttatgcggtctcaataccacgtaaaacgtaagcccgaaagcgacacgtcgctttcgggcttactgtttttatcctgttttggaaacctgtgtctgaaatacaggggatatgat Mask Tandem Repeat Region ================================================ atcatatcccctgtatttcagacacaggtttccaaaacaggataaaaacagtaagcccgaaagcgacgtgtcgctttcgggcttacgttttacgtggtattgagaccgcataaatgagg Find is-nt database================================================ Query_seq: PG1788:PG1789|PG1788:PG1789:cysteine peptidase, putative:peptidyl-dipeptidase Dcp:-><-:1877388..1877506 119 atcatatcccctgtatttcagacacaggtttccaaaacaggataaaaacagtaagcccgaaagcgacgtgtcgctttcgggcttacgttttacgtggtattgagaccgcataaatgagg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG1788:PG1789|PG1788:PG1789:cysteine peptidase, putative:peptidyl-dipeptidase Dcp:-><-:1877388..1877506 119 atcatatcccctgtatttcagacacaggtttccaaaacaggataaaaacagtaagcccgaaagcgacgtgtcgctttcgggcttacgttttacgtggtattgagaccgcataaatgagg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG1788:PG1789|PG1788:PG1789:cysteine peptidase, putative:peptidyl-dipeptidase Dcp:-><-:1877388..1877506 119 atcatatcccctgtatttcagacacaggtttccaaaacaggataaaaacagtaagcccgaaagcgacgtgtcgctttcgggcttacgttttacgtggtattgagaccgcataaatgagg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 atcatatcccctgtatttcagacacaggtttccaaaacaggataaaaacagtaagcccgaaagcgacgtgtcgctttcgggcttacgttttacgtggtattgagaccgcataaatgagg Predict ORF larger than 30AA ================================================ Protein_Len: 30 Strand: + Start: 11 End: 100 .......... M Y F R H R F P K Q D K N S K P E S D V S L S G L R F T W Y ................... Protein_Len: 35 Strand: + Start: 6 End: 110 ..... M P C I S D T G F Q N R I K T V S P K A T C R F R A Y V L R G I E T A ......... Protein_Len: 37 Strand: - Start: 1 End: 111 D Y G R Y K L C L N G F C S L F L L G S L S T D S E P K R K V H Y Q S R M ........ atcatatcccctgtatttcagacacaggtttccaaaacaggataaaaacagtaagcccgaaagcgacgtgtcgctttcgggcttacgttttacgtggtattgagaccgcataaatgagg 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================================================ atcatatcccctgtatttcagacacaggtttccaaaacaggataaaaacagtaagcccgaaagcgacgtgtcgctttcgggcttacgttttacgtggtattgagaccgcataaatgagg Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 100 HP_score: -21.3 Tail_Score: -5.02201 Start: 49 End: 87 Full_Region: caataccacgtaaaa cgtaagcccgaaagcga cacg tcgctttcgggcttactg tttttatcctgtttt ................................................cgtaagcccgaaagcgacacgtcgctttcgggcttactg................................ TransTerm Strand: + Conf: 100 HP_score: -21.5 Tail_Score: -4.23723 Start: 50 End: 87 Full_Region: AAACAGGATAAAAAC AGTAAGCCCGAAAGCGA CGTG TCGCTTTCGGGCTTACG TTTTACGTGGTATTG .................................................AGTAAGCCCGAAAGCGACGTGTCGCTTTCGGGCTTACG................................ TransTerm Strand: - Conf: 100 HP_score: -25.0 Tail_Score: -4.10552 Start: 51 End: 86 Full_Region: aataccacgtaaaac gtaagcccgaaagcga cacg tcgctttcgggcttac tgtttttatcctgtt ..................................................gtaagcccgaaagcgacacgtcgctttcgggcttac................................. Find igs database================================================ Query_seq: PG1788:PG1789|PG1788:PG1789:cysteine peptidase, putative:peptidyl-dipeptidase Dcp:-><-:1877388..1877506 119 atcatatcccctgtatttcagacacaggtttccaaaacaggataaaaacagtaagcccgaaagcgacgtgtcgctttcgggcttacgttttacgtggtattgagaccgcataaatgagg Intra-Species Hit: Count: 1 Min: 1 Max: 119 Len: 119 Subject: NC_002950_PG1788_PG1789|cysteine peptidase, putative:peptidyl-dipeptidase Dcp|POSITIVE:NEGATIVE|[1877388,1877506]|119 HSP 1 e-value: 1.0E-61 bit: 236.0 Len: 119 Query Start:1 Query End:119 Subject Strand: POSITIVE Subject Start: 1 Subject End: 119 atcatatcccctgtatttcagacacaggtttccaaaacaggataaaaacagtaagcccgaaagcgacgtgtcgctttcgggcttacgttttacgtggtattgagaccgcataaatgagg atcatatcccctgtatttcagacacaggtttccaaaacaggataaaaacagtaagcccgaaagcgacgtgtcgctttcgggcttacgttttacgtggtattgagaccgcataaatgagg HSP 2 e-value: 3.0E-7 bit: 56.0 Len: 36 Query Start:51 Query End:86 Subject Strand: NEGATIVE Subject Start: 51 Subject End: 86 ..................................................gtaagcccgaaagcgacgtgtcgctttcgggcttac................................. ..................................................gtaagcccgaaagcgacacgtcgctttcgggcttac................................. Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUCAUAUCCCCUGUAUUUCAGACACAGGUUUCCAAAACAGGAUAAAAACAGUAAGCCCGAAAGCGACGUGUCGCUUUCGGGCUUACGUUUUACGUGGUAUUGAGACCGCAUAAAUGAGG .((((....(((((.((..((((....))))..)).)))))...(((((.((((((((((((((((....)))))))))))))))))))))..(((((......)))))....)))).. (-49.00) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CCUCAUUUAUGCGGUCUCAAUACCACGUAAAACGUAAGCCCGAAAGCGACACGUCGCUUUCGGGCUUACUGUUUUUAUCCUGUUUUGGAAACCUGUGUCUGAAAUACAGGGGAUAUGAU .....((((((.(((......))).))))))..((((((((((((((((....))))))))))))))))........(((......)))..(((((((.....)))))))......... (-49.20) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 427 98 55 171 122 NC_002950:PG1747|5end_ribose_5-phosphate_isomerase_B,_putative_1832815..1833045_NEGATIVE 379 109 62 228 174 NC_002950:PG1594|5end_ComEC/Rec2-related_protein_1673587..1673817_NEGATIVE 367 110 62 168 119 NC_002950:PG0374|5end_hypothetical_protein_405564..405794_NEGATIVE 361 84 45 59 9 NC_002950:PG1126|5end_uracil_permease_1202933..1203163_NEGATIVE 334 109 61 212 161 NC_002950:PG1559|5end_aminomethyltransferase_1638992..1639222_NEGATIVE 332 99 52 77 26 NC_002950:PG0343|5end_methionine_gamma-lyase_378362..378592_NEGATIVE 328 100 56 192 135 NC_002950:PG1945|5end_hypothetical_protein_2031697..2031927_POSITIVE 326 88 48 188 150 NC_002950:PG1818|5end_hypothetical_protein_1913744..1913974_NEGATIVE 322 98 57 57 15 NC_002950:PG0950|5end_glycine_cleavage_system_protein_H_1009861..1010091_POSITIVE 315 109 62 193 145 NC_002950:PG2080|5end_adenosylmethionine--8-amino-7-oxononanoate_transaminase_2180679..2180909_NEGATIVE 315 96 53 84 31 NC_002950:PG1483|5end_conjugative_transposon_protein_TraE_1559085..1559315_NEGATIVE 312 83 47 53 10 NC_002950:PG0231|5end_hypothetical_protein_266031..266261_POSITIVE 309 109 61 213 152 NC_002950:PG1348|5end_conserved_hypothetical_protein_TIGR00147_1428608..1428838_POSITIVE 308 99 55 134 83 NC_002950:PG1617|5end_hypothetical_protein_1697755..1697985_NEGATIVE 307 109 62 183 136 NC_002950:PG0657|5end_Maf-like_protein_707782..708012_NEGATIVE 306 108 65 119 68 NC_002950:PG0767|5end_4-alpha-glucanotransferase_820533..820763_NEGATIVE 305 109 63 208 160 NC_002950:PG1226|5end_peptidyl-prolyl_cis-trans_isomerase,_cyclophilin-type_1303264..1303494_POSITIVE 305 109 62 151 96 NC_002950:PG1172|5end_iron-sulfur_cluster_binding_protein,_putative_1251173..1251403_POSITIVE 305 80 40 79 29 NC_002950:PG0723|5end_hypothetical_protein_774949..775179_POSITIVE 305 108 62 227 189 NC_002950:PG0474|5end_low-specificity_L-threonine_aldolase_516048..516278_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 751 90 46 45 1 NC_002950:PG1788|3end_cysteine_peptidase,_putative_1877327..1877477_POSITIVE 427 98 55 84 35 NC_002950:PG1748|3end_transketolase_1832902..1833052_NEGATIVE 341 89 44 78 30 NC_002950:PG1145|3end_long-chain-fatty-acid--CoA_ligase,_putative_1228482..1228632_NEGATIVE 339 96 56 57 6 NC_002950:PG1677|3end_phosphoglycerate_kinase_1763678..1763828_POSITIVE 336 90 50 73 35 NC_002950:PG1678|3end_hypothetical_protein_1763755..1763905_NEGATIVE 335 107 62 118 65 NC_002950:PG1942|3end_30S_ribosomal_protein_S12_2027946..2028096_NEGATIVE 334 109 61 137 86 NC_002950:PG1560|3end_dTDP-glucose_4,6-dehydratase_1639067..1639217_NEGATIVE 333 93 55 99 42 NC_002950:PG2092|3end_hypothetical_protein_2191651..2191801_NEGATIVE 330 91 56 33 2 NC_002950:PG0046|3end_phosphatidate_cytidylyltransferase_56346..56496_NEGATIVE 329 109 63 105 58 NC_002950:PG1175|3end_ABC_transporter,_ATP-binding_protein,_putative_1254170..1254320_NEGATIVE 321 109 62 139 95 NC_002950:PG0569|3end_hypothetical_protein_624697..624847_NEGATIVE 316 82 56 33 7 NC_002950:PG1943|3end_hypothetical_protein_2028974..2029124_NEGATIVE 312 83 47 56 13 NC_002950:PG0230|3end_transaldolase_266114..266264_POSITIVE 307 95 54 50 3 NC_002950:PG1478|3end_conjugative_transposon_protein_TraK_1553493..1553643_NEGATIVE 305 109 62 73 18 NC_002950:PG1171|3end_oxidoreductase,_putative_1251175..1251325_POSITIVE 305 108 62 80 42 NC_002950:PG0211|3end_cobalamin_biosynthesis_protein_CbiG/precorrin-4_C11-methyltransferase_245966..246116_NEGATIVE 304 110 61 136 79 NC_002950:PG2202|3end_Holliday_junction_resolvase-like_protein_2309517..2309667_NEGATIVE 304 83 48 92 55 NC_002950:PG1411|3end_potassium_uptake_protein_TrkA,_putative_1493481..1493631_NEGATIVE 301 102 62 75 37 NC_002950:PG0095|3end_DNA_mismatch_repair_protein_112088..112238_NEGATIVE 300 97 55 62 10 NC_002950:PG1988|3end_hypothetical_protein_2077425..2077575_NEGATIVE