Origin IGS: tagccctgctggtacaaccccattatcgggcatatcttagatagtggatgtattcatctttgcaggtaaatataccggcaaagaaatgaacagtgaattgtataacaataaaattaagtaagt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 acttacttaattttattgttatacaattcactgttcatttctttgccggtatatttacctgcaaagatgaatacatccactatctaagatatgcccgataatggggttgtaccagcagggcta Mask Tandem Repeat Region ================================================ tagccctgctggtacaaccccattatcgggcatatcttagatagtggatgtattcatctttgcaggtaaatataccggcaaagaaatgaacagtgaattgtataacaataaaattaagtaagt Find is-nt database================================================ Query_seq: PI0398:PI0399|PI0398:PI0399:hypothetical protein:conserved hypothetical protein:->->:363602..363724 123 tagccctgctggtacaaccccattatcgggcatatcttagatagtggatgtattcatctttgcaggtaaatataccggcaaagaaatgaacagtgaattgtataacaataaaattaagtaagt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI0398:PI0399|PI0398:PI0399:hypothetical protein:conserved hypothetical protein:->->:363602..363724 123 tagccctgctggtacaaccccattatcgggcatatcttagatagtggatgtattcatctttgcaggtaaatataccggcaaagaaatgaacagtgaattgtataacaataaaattaagtaagt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI0398:PI0399|PI0398:PI0399:hypothetical protein:conserved hypothetical protein:->->:363602..363724 123 tagccctgctggtacaaccccattatcgggcatatcttagatagtggatgtattcatctttgcaggtaaatataccggcaaagaaatgaacagtgaattgtataacaataaaattaagtaagt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tagccctgctggtacaaccccattatcgggcatatcttagatagtggatgtattcatctttgcaggtaaatataccggcaaagaaatgaacagtgaattgtataacaataaaattaagtaagt Predict ORF larger than 30AA ================================================ tagccctgctggtacaaccccattatcgggcatatcttagatagtggatgtattcatctttgcaggtaaatataccggcaaagaaatgaacagtgaattgtataacaataaaattaagtaagt 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: 83 Start: 69 End: 98 ....................................................................ATTCACTGTTCATTTCTTTGCCGGTATATT......................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tagccctgctggtacaaccccattatcgggcatatcttagatagtggatgtattcatctttgcaggtaaatataccggcaaagaaatgaacagtgaattgtataacaataaaattaagtaagt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PI0398:PI0399|PI0398:PI0399:hypothetical protein:conserved hypothetical protein:->->:363602..363724 123 tagccctgctggtacaaccccattatcgggcatatcttagatagtggatgtattcatctttgcaggtaaatataccggcaaagaaatgaacagtgaattgtataacaataaaattaagtaagt Intra-Species Hit: Count: 1 Min: 1 Max: 123 Len: 123 Subject: pint_PI0398_PI0399|hypothetical protein:conserved hypothetical protein|POSITIVE:POSITIVE|[363602,363724]|123 HSP 1 e-value: 6.0E-64 bit: 244.0 Len: 123 Query Start:1 Query End:123 Subject Strand: POSITIVE Subject Start: 1 Subject End: 123 tagccctgctggtacaaccccattatcgggcatatcttagatagtggatgtattcatctttgcaggtaaatataccggcaaagaaatgaacagtgaattgtataacaataaaattaagtaagt tagccctgctggtacaaccccattatcgggcatatcttagatagtggatgtattcatctttgcaggtaaatataccggcaaagaaatgaacagtgaattgtataacaataaaattaagtaagt Inter-species Hit: Count: 2 Min: 1 Max: 123 Len: 123 Subject: NC_002950_PG1442_PG1444|hypothetical protein:hypothetical protein|NEGATIVE:POSITIVE|[1528121,1528885]|765 HSP 1 e-value: 6.0E-64 bit: 244.0 Len: 123 Query Start:1 Query End:123 Subject Strand: NEGATIVE Subject Start: 1 Subject End: 123 tagccctgctggtacaaccccattatcgggcatatcttagatagtggatgtattcatctttgcaggtaaatataccggcaaagaaatgaacagtgaattgtataacaataaaattaagtaagt tagccctgctggtacaaccccattatcgggcatatcttagatagtggatgtattcatctttgcaggtaaatataccggcaaagaaatgaacagtgaattgtataacaataaaattaagtaagt Subject: NC_002950_PG0829_PG0831|hypothetical protein:hypothetical protein|NEGATIVE:POSITIVE|[886837,887542]|706 HSP 1 e-value: 3.0E-22 bit: 105.0 Len: 113 Query Start:1 Query End:113 Subject Strand: POSITIVE Subject Start: 583 Subject End: 695 tagccctgctggtacaaccccattatcgggcatatcttagatagtggatgtattcatctttgcaggtaaatataccggcaaagaaatgaacagtgaattgtataacaataaaa.......... tagccctactggtacaagccgattattgggcatatcttcgatagcggatgtattcatcttcatcggtaaatatactggcaacgaaatgaacaatgaattgtgtaataataaaa.......... Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAGCCCUGCUGGUACAACCCCAUUAUCGGGCAUAUCUUAGAUAGUGGAUGUAUUCAUCUUUGCAGGUAAAUAUACCGGCAAAGAAAUGAACAGUGAAUUGUAUAACAAUAAAAUUAAGUAAGU .......((((.((((...((((((((............)))))))).))))....(((((((.((((....)))).)))))))......))))..((((.....)))).............. (-28.70) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACUUACUUAAUUUUAUUGUUAUACAAUUCACUGUUCAUUUCUUUGCCGGUAUAUUUACCUGCAAAGAUGAAUACAUCCACUAUCUAAGAUAUGCCCGAUAAUGGGGUUGUACCAGCAGGGCUA .....((((.....((((.....))))....((((((..(((((((.((((....)))).)))))))))))))...........))))....((((.....(((.......)))...)))).. (-31.00) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 316 60 18 102 50 pint:PI0895|5end_2-oxoglutarate_oxidoreductase,_beta_subunit,_possible_ketoisovalerate_oxidoreductase,__vorA_826347..826577_POSITIVE 287 38 2 168 135 pint:PI1630|5end_hypothetical_protein_1552127..1552357_POSITIVE 281 59 11 212 144 pint:PI1226|5end_hypothetical_protein_1147884..1148114_POSITIVE 281 59 11 86 18 pint:PI1225|5end_hypothetical_protein_1147758..1147988_POSITIVE 280 48 3 177 130 pint:PI1639|5end_conserved_hypothetical_protein_1556725..1556955_POSITIVE 279 38 3 42 4 pint:PI1859|5end_conserved_hypothetical_protein_1805394..1805624_POSITIVE 270 50 1 219 161 pint:PI1038|5end_hypothetical_protein_958685..958915_POSITIVE 268 37 7 104 73 pint:PI1876|5end_possible_flagellar_motor_protein,_OmpA_family_1819082..1819312_POSITIVE 261 46 3 177 139 pint:PI0337|5end_hypothetical_protein_314732..314962_POSITIVE 260 90 45 144 100 pint:PI1560|5end_integrase_1476962..1477192_POSITIVE 260 43 2 183 140 pint:PI0493|5end_surface_antigen_BspA_452844..453074_POSITIVE 258 46 7 52 5 pint:PI0547|5end_fructose-bisphosphate_aldolase_498376..498606_POSITIVE 256 38 3 144 99 pint:PI2162|5end_conserved_hypothetical_protein_2108796..2109026_POSITIVE 255 66 25 63 8 pint:PI0739|5end_conserved_hypothetical_protein_671794..672024_POSITIVE 255 56 19 198 156 pint:PI0235|5end_hypothetical_protein_234938..235168_POSITIVE 254 39 6 229 183 pint:PI0697|5end_5'-nucleotidase_family_protein_633560..633790_POSITIVE 253 58 17 197 147 pint:PI1227|5end_conserved_hypothetical_protein;_possible_DNA-binding_protein,_histone-like_family_1148448..1148678_POSITIVE 249 50 3 39 1 pint:PI1912|5end_possible_DNA_repair_protein_1856364..1856594_POSITIVE 248 50 2 227 180 pint:PI0334|5end_hypothetical_protein_313234..313464_POSITIVE 247 50 8 138 84 pint:PI1525|5end_CDP-diacylglycerol--serine_O-phosphatidyltransferase_1446758..1446988_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 271 31 3 70 41 pint:PI0042|3end_hypothetical_protein_43444..43594_POSITIVE 268 37 7 48 17 pint:PI1875|3end_hypothetical_protein_1819106..1819256_POSITIVE 260 90 45 74 30 pint:PI1559|3end_hypothetical_protein_1476972..1477122_POSITIVE 257 89 56 52 10 pint:PI1843|3end_hypothetical_protein_1788611..1788761_POSITIVE 255 66 25 60 5 pint:PI0738|3end_conserved_hypothetical_protein_671871..672021_POSITIVE 253 79 37 131 88 pint:PI1882|3end_hypothetical_protein_1826487..1826637_POSITIVE 251 50 2 107 50 pint:PI1818|3end_hypothetical_protein_1757270..1757420_POSITIVE 243 48 3 51 10 pint:PI1734|3end_possible_carboxyl-terminal_protease-related_protein_1653829..1653979_POSITIVE 242 90 53 38 1 pint:PI0398|3end_hypothetical_protein_363541..363691_POSITIVE 239 96 56 78 33 pint:PI0739|3end_conserved_hypothetical_protein_672161..672311_POSITIVE 239 40 2 69 29 pint:PI0478|3end_50S_ribosomal_protein_L30_441176..441326_POSITIVE 237 47 10 133 92 pint:PI0671|3end_hypothetical_protein_611807..611957_POSITIVE 235 69 26 42 3 pint:PI0257|3end_conjugative_transposon_protein,_TraF_249802..249952_POSITIVE 232 63 26 50 19 pint:PI0951|3end_hypothetical_protein_885448..885598_POSITIVE 231 90 44 51 5 pint:PI0076|3end_conserved_hypothetical_protein_76192..76342_POSITIVE 228 84 46 124 79 pint:PI1815|3end_polyphosphate-selective_porin_O_1754510..1754660_POSITIVE 227 49 4 53 2 pint:PI0941|3end_hypothetical_protein_874675..874825_POSITIVE 227 50 2 60 19 pint:PI0007|3end_hypothetical_protein_7300..7450_POSITIVE 226 31 3 130 93 pint:PI0843|3end_carboxyl-terminal_protease_777862..778012_POSITIVE 225 45 3 80 33 pint:PI0341|3end_conserved_hypothetical_protein_317615..317765_POSITIVE