Origin IGS: gaattcgttgaatcccatttatctattgtattttttgtagctgttatgatatgtgcggagtacccgcgtaagagcgaaagactcctttctcttcttcccgaatagtatgt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 acatactattcgggaagaagagaaaggagtctttcgctcttacgcgggtactccgcacatatcataacagctacaaaaaatacaatagataaatgggattcaacgaattc Mask Tandem Repeat Region ================================================ gaattcgttgaatcccatttatctattgtattttttgtagctgttatgatatgtgcggagtacccgcgtaagagcgaaagactcctttctcttcttcccgaatagtatgt Find is-nt database================================================ Query_seq: PG0514:PG0515|PG0514:PG0515:translocase:hypothetical protein:<-<-:556343..556452 110 gaattcgttgaatcccatttatctattgtattttttgtagctgttatgatatgtgcggagtacccgcgtaagagcgaaagactcctttctcttcttcccgaatagtatgt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG0514:PG0515|PG0514:PG0515:translocase:hypothetical protein:<-<-:556343..556452 110 gaattcgttgaatcccatttatctattgtattttttgtagctgttatgatatgtgcggagtacccgcgtaagagcgaaagactcctttctcttcttcccgaatagtatgt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG0514:PG0515|PG0514:PG0515:translocase:hypothetical protein:<-<-:556343..556452 110 gaattcgttgaatcccatttatctattgtattttttgtagctgttatgatatgtgcggagtacccgcgtaagagcgaaagactcctttctcttcttcccgaatagtatgt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gaattcgttgaatcccatttatctattgtattttttgtagctgttatgatatgtgcggagtacccgcgtaagagcgaaagactcctttctcttcttcccgaatagtatgt Predict ORF larger than 30AA ================================================ gaattcgttgaatcccatttatctattgtattttttgtagctgttatgatatgtgcggagtacccgcgtaagagcgaaagactcctttctcttcttcccgaatagtatgt 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================================================ gaattcgttgaatcccatttatctattgtattttttgtagctgttatgatatgtgcggagtacccgcgtaagagcgaaagactcctttctcttcttcccgaatagtatgt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PG0514:PG0515|PG0514:PG0515:translocase:hypothetical protein:<-<-:556343..556452 110 gaattcgttgaatcccatttatctattgtattttttgtagctgttatgatatgtgcggagtacccgcgtaagagcgaaagactcctttctcttcttcccgaatagtatgt Intra-Species Hit: Count: 1 Min: 1 Max: 110 Len: 110 Subject: NC_002950_PG0514_PG0515|translocase:hypothetical protein|NEGATIVE:NEGATIVE|[556343,556452]|110 HSP 1 e-value: 3.0E-56 bit: 218.0 Len: 110 Query Start:1 Query End:110 Subject Strand: POSITIVE Subject Start: 1 Subject End: 110 gaattcgttgaatcccatttatctattgtattttttgtagctgttatgatatgtgcggagtacccgcgtaagagcgaaagactcctttctcttcttcccgaatagtatgt gaattcgttgaatcccatttatctattgtattttttgtagctgttatgatatgtgcggagtacccgcgtaagagcgaaagactcctttctcttcttcccgaatagtatgt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAAUUCGUUGAAUCCCAUUUAUCUAUUGUAUUUUUUGUAGCUGUUAUGAUAUGUGCGGAGUACCCGCGUAAGAGCGAAAGACUCCUUUCUCUUCUUCCCGAAUAGUAUGU ..(((((..(((...(((.((((.((.((..........)).))...)))).))).(((((...(((......)))....))))).........))).)))))....... (-17.60) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACAUACUAUUCGGGAAGAAGAGAAAGGAGUCUUUCGCUCUUACGCGGGUACUCCGCACAUAUCAUAACAGCUACAAAAAAUACAAUAGAUAAAUGGGAUUCAACGAAUUC .....(((((.(..((((.(.(((((....))))).)))))..((((.....))))..........................)))))).......((((((...)))))) (-17.00) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 1035 100 51 191 142 NC_002950:PG0514|5end_translocase_556252..556482_NEGATIVE 434 110 63 55 4 NC_002950:PG0790|5end_GTP-binding_protein_Obg_842583..842813_NEGATIVE 366 100 63 59 14 NC_002950:PG1212|5end_TPR_domain_protein_1291392..1291622_POSITIVE 332 100 55 189 132 NC_002950:PG1479|5end_conjugative_transposon_protein_TraJ_1555234..1555464_NEGATIVE 327 100 53 216 169 NC_002950:PG1475|5end_conjugative_transposon_protein_TraN_1551835..1552065_NEGATIVE 320 78 35 69 21 NC_002950:PG0159|5end_endopeptidase_PepO_183164..183394_NEGATIVE 319 87 41 223 171 NC_002950:PG0788|5end_hypothetical_protein_840676..840906_NEGATIVE 312 99 55 227 167 NC_002950:PG0227|5end_DNA_repair_protein_RadA_263978..264208_NEGATIVE 311 97 54 119 68 NC_002950:PG2075|5end_hypothetical_protein_2176466..2176696_NEGATIVE 311 97 54 119 68 NC_002950:PG1266|5end_hypothetical_protein_1346987..1347217_NEGATIVE 309 107 64 191 151 NC_002950:PG2003|5end_deoxyguanosinetriphosphate_triphosphohydrolase_2092991..2093221_NEGATIVE 308 100 53 184 131 NC_002950:PG2154|5end_hypothetical_protein_2260945..2261175_NEGATIVE 308 88 55 201 167 NC_002950:PG0241|5end_lipoprotein,_putative_278214..278444_NEGATIVE 308 100 57 205 162 NC_002950:PG0080|5end_hypothetical_protein_93832..94062_NEGATIVE 307 95 51 62 18 NC_002950:PG0636|5end_MATE_efflux_family_protein_689071..689301_NEGATIVE 307 100 53 218 159 NC_002950:PG0489|5end_polysaccharide_biosynthesis-related_protein_529247..529477_POSITIVE 304 100 52 93 32 NC_002950:PG1946|5end_ABC_3_transporter_family_protein_2032133..2032363_POSITIVE 304 97 55 119 77 NC_002950:PG1671|5end_hypothetical_protein_1757658..1757888_NEGATIVE 304 97 55 119 77 NC_002950:PG0101|5end_hypothetical_protein_119198..119428_POSITIVE 303 77 35 218 176 NC_002950:PG0431|5end_hypothetical_protein_468978..469208_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 366 100 63 46 1 NC_002950:PG1211|3end_hexapeptide_transferase_family_protein_1291459..1291609_POSITIVE 332 100 57 112 61 NC_002950:PG0173|3end_transcriptional_regulator,_putative_194388..194538_NEGATIVE 329 110 70 45 2 NC_002950:PG0791|3end_adenylate_kinase_842593..842743_NEGATIVE 323 90 41 43 3 NC_002950:PG1304|3end_hypothetical_protein_1382134..1382284_NEGATIVE 320 78 35 50 2 NC_002950:PG0160|3end_hypothetical_protein_183183..183333_NEGATIVE 309 107 64 47 7 NC_002950:PG2004|3end_hypothetical_protein_2093135..2093285_NEGATIVE 307 95 51 69 25 NC_002950:PG0637|3end_thiamine_monophosphate_kinase_689064..689214_NEGATIVE 304 100 52 100 39 NC_002950:PG1945|3end_hypothetical_protein_2032220..2032370_POSITIVE 303 98 51 83 42 NC_002950:PG0166|3end_peptidyl-tRNA_hydrolase_187813..187963_NEGATIVE 302 87 46 114 69 NC_002950:PG0356|3end_hypothetical_protein_391473..391623_POSITIVE 300 96 55 149 100 NC_002950:PG1480|3end_conjugative_transposon_protein_TraI_1555266..1555416_NEGATIVE 299 99 54 70 23 NC_002950:PG0580|3end_N-acetylglucosaminyl_transferase_638316..638466_POSITIVE 295 99 57 99 53 NC_002950:PG0151|3end_signal_recognition_particle-docking_protein_FtsY_173541..173691_NEGATIVE 290 87 41 69 4 NC_002950:PG1889|3end_hypothetical_protein_1987090..1987240_POSITIVE 286 106 64 110 67 NC_002950:PG0968|3end_Mrr_restriction_system_protein_1027825..1027975_POSITIVE 286 98 51 145 66 NC_002950:PG0883|3end_hypothetical_protein_946562..946712_POSITIVE 285 100 52 151 100 NC_002950:PG1474|3end_conjugative_transposon_protein_TraO_1550238..1550388_NEGATIVE 284 100 55 90 29 NC_002950:PG0793|3end_fructose-1,6-bisphosphatase_846335..846485_POSITIVE 282 79 31 45 1 NC_002950:PG0410|3end_hypothetical_protein_446581..446731_POSITIVE 280 72 34 149 103 NC_002950:PG0083|3end_hypothetical_protein_97817..97967_POSITIVE