Origin IGS: tgcaaatgtaaacgaaaagtattgaacgccaaaacaaattaggattttttagatgtgtttttaaaccctattcacataacatatccatattttcctatatttaaacattttattattctatactccatattttataataaaaatagaatagcagcaaaattcttgcataataggaaagattagacacagaaaaagaccaacaagtatttgttctgagaactacaacttgctggtcttaccctattgacaaataaatttcaagtctggttatacagccccgcaattgcgagccataaacctacaaacgttta .........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.........1.........2.........3.........4.........5.........6.........7.........8.........9 taaacgtttgtaggtttatggctcgcaattgcggggctgtataaccagacttgaaatttatttgtcaatagggtaagaccagcaagttgtagttctcagaacaaatacttgttggtctttttctgtgtctaatctttcctattatgcaagaattttgctgctattctatttttattataaaatatggagtatagaataataaaatgtttaaatataggaaaatatggatatgttatgtgaatagggtttaaaaacacatctaaaaaatcctaatttgttttggcgttcaatacttttcgtttacatttgca Mask Tandem Repeat Region ================================================ tgcaaatgtaaacgaaaagtattgaacgccaaaacaaattaggattttttagatgtgtttttaaaccctattcacataacatatccatattttcctatatttaaacattttattattctatactccatattttataataaaaatagaatagcagcaaaattcttgcataataggaaagattagacacagaaaaagaccaacaagtatttgttctgagaactacaacttgctggtcttaccctattgacaaataaatttcaagtctggttatacagccccgcaattgcgagccataaacctacaaacgttta Find is-nt database================================================ Query_seq: PI1562:PI1563|PI1562:PI1563:methyltransferase:thiol:disulfide interchange protein dsbD:->->:1480510..1480820 311 tgcaaatgtaaacgaaaagtattgaacgccaaaacaaattaggattttttagatgtgtttttaaaccctattcacataacatatccatattttcctatatttaaacattttattattctatactccatattttataataaaaatagaatagcagcaaaattcttgcataataggaaagattagacacagaaaaagaccaacaagtatttgttctgagaactacaacttgctggtcttaccctattgacaaataaatttcaagtctggttatacagccccgcaattgcgagccataaacctacaaacgttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI1562:PI1563|PI1562:PI1563:methyltransferase:thiol:disulfide interchange protein dsbD:->->:1480510..1480820 311 tgcaaatgtaaacgaaaagtattgaacgccaaaacaaattaggattttttagatgtgtttttaaaccctattcacataacatatccatattttcctatatttaaacattttattattctatactccatattttataataaaaatagaatagcagcaaaattcttgcataataggaaagattagacacagaaaaagaccaacaagtatttgttctgagaactacaacttgctggtcttaccctattgacaaataaatttcaagtctggttatacagccccgcaattgcgagccataaacctacaaacgttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI1562:PI1563|PI1562:PI1563:methyltransferase:thiol:disulfide interchange protein dsbD:->->:1480510..1480820 311 tgcaaatgtaaacgaaaagtattgaacgccaaaacaaattaggattttttagatgtgtttttaaaccctattcacataacatatccatattttcctatatttaaacattttattattctatactccatattttataataaaaatagaatagcagcaaaattcttgcataataggaaagattagacacagaaaaagaccaacaagtatttgttctgagaactacaacttgctggtcttaccctattgacaaataaatttcaagtctggttatacagccccgcaattgcgagccataaacctacaaacgttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tgcaaatgtaaacgaaaagtattgaacgccaaaacaaattaggattttttagatgtgtttttaaaccctattcacataacatatccatattttcctatatttaaacattttattattctatactccatattttataataaaaatagaatagcagcaaaattcttgcataataggaaagattagacacagaaaaagaccaacaagtatttgttctgagaactacaacttgctggtcttaccctattgacaaataaatttcaagtctggttatacagccccgcaattgcgagccataaacctacaaacgttta Predict ORF larger than 30AA ================================================ Protein_Len: 42 Strand: + Start: 55 End: 180 ...................................................... M F L N P I H I T Y P Y F P I F K H F I I L Y S I F Y N K N R I A A K F L H N R K D ................................................................................................................................... tgcaaatgtaaacgaaaagtattgaacgccaaaacaaattaggattttttagatgtgtttttaaaccctattcacataacatatccatattttcctatatttaaacattttattattctatactccatattttataataaaaatagaatagcagcaaaattcttgcataataggaaagattagacacagaaaaagaccaacaagtatttgttctgagaactacaacttgctggtcttaccctattgacaaataaatttcaagtctggttatacagccccgcaattgcgagccataaacctacaaacgttta 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: 82 Start: 129 End: 158 ................................................................................................................................TTTGCTGCTATTCTATTTTTATTATAAAAT......................................................................................................................................................... PromScan Matrix: RpoD-17 Strand: + Score: 81 Start: 109 End: 138 ............................................................................................................TTTATTATTCTATACTCCATATTTTATAAT............................................................................................................................................................................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tgcaaatgtaaacgaaaagtattgaacgccaaaacaaattaggattttttagatgtgtttttaaaccctattcacataacatatccatattttcctatatttaaacattttattattctatactccatattttataataaaaatagaatagcagcaaaattcttgcataataggaaagattagacacagaaaaagaccaacaagtatttgttctgagaactacaacttgctggtcttaccctattgacaaataaatttcaagtctggttatacagccccgcaattgcgagccataaacctacaaacgttta Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 100 HP_score: -10.5 Tail_Score: -5.07275 Start: 195 End: 235 Full_Region: ttgtcaatagggtaa gaccagcaagttgtagttc tca gaacaaatacttgttggtc tttttctgtgtctaa ..................................................................................................................................................................................................gaccagcaagttgtagttctcagaacaaatacttgttggtc............................................................................ Find igs database================================================ Query_seq: PI1562:PI1563|PI1562:PI1563:methyltransferase:thiol:disulfide interchange protein dsbD:->->:1480510..1480820 311 tgcaaatgtaaacgaaaagtattgaacgccaaaacaaattaggattttttagatgtgtttttaaaccctattcacataacatatccatattttcctatatttaaacattttattattctatactccatattttataataaaaatagaatagcagcaaaattcttgcataataggaaagattagacacagaaaaagaccaacaagtatttgttctgagaactacaacttgctggtcttaccctattgacaaataaatttcaagtctggttatacagccccgcaattgcgagccataaacctacaaacgttta Intra-Species Hit: Count: 1 Min: 1 Max: 311 Len: 311 Subject: pint_PI1562_PI1563|methyltransferase:thiol:disulfide interchange protein dsbD|POSITIVE:POSITIVE|[1480510,1480820]|311 HSP 1 e-value: 9.0E-93 bit: 341.0 Len: 172 Query Start:140 Query End:311 Subject Strand: POSITIVE Subject Start: 140 Subject End: 311 ...........................................................................................................................................aaaatagaatagcagcaaaattcttgcataataggaaagattagacacagaaaaagaccaacaagtatttgttctgagaactacaacttgctggtcttaccctattgacaaataaatttcaagtctggttatacagccccgcaattgcgagccataaacctacaaacgttta ...........................................................................................................................................aaaatagaatagcagcaaaattcttgcataataggaaagattagacacagaaaaagaccaacaagtatttgttctgagaactacaacttgctggtcttaccctattgacaaataaatttcaagtctggttatacagccccgcaattgcgagccataaacctacaaacgttta HSP 2 e-value: 7.0E-35 bit: 149.0 Len: 75 Query Start:1 Query End:75 Subject Strand: POSITIVE Subject Start: 1 Subject End: 75 tgcaaatgtaaacgaaaagtattgaacgccaaaacaaattaggattttttagatgtgtttttaaaccctattcac............................................................................................................................................................................................................................................ tgcaaatgtaaacgaaaagtattgaacgccaaaacaaattaggattttttagatgtgtttttaaaccctattcac............................................................................................................................................................................................................................................ Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGCAAAUGUAAACGAAAAGUAUUGAACGCCAAAACAAAUUAGGAUUUUUUAGAUGUGUUUUUAAACCCUAUUCACAUAACAUAUCCAUAUUUUCCUAUAUUUAAACAUUUUAUUAUUCUAUACUCCAUAUUUUAUAAUAAAAAUAGAAUAGCAGCAAAAUUCUUGCAUAAUAGGAAAGAUUAGACACAGAAAAAGACCAACAAGUAUUUGUUCUGAGAACUACAACUUGCUGGUCUUACCCUAUUGACAAAUAAAUUUCAAGUCUGGUUAUACAGCCCCGCAAUUGCGAGCCAUAAACCUACAAACGUUUA ........((((((....((.(((.....))).))....((((........((((((((..................)))))))).....((((((((..............(((((((((.....................)))))))))..((((.....))))...))))))))((((((((.......(((((((.(((((....((((...))))....))))).)))))))....((((....))))........)))))))).....((..(((....))).))......))))....)))))) (-59.47) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAACGUUUGUAGGUUUAUGGCUCGCAAUUGCGGGGCUGUAUAACCAGACUUGAAAUUUAUUUGUCAAUAGGGUAAGACCAGCAAGUUGUAGUUCUCAGAACAAAUACUUGUUGGUCUUUUUCUGUGUCUAAUCUUUCCUAUUAUGCAAGAAUUUUGCUGCUAUUCUAUUUUUAUUAUAAAAUAUGGAGUAUAGAAUAAUAAAAUGUUUAAAUAUAGGAAAAUAUGGAUAUGUUAUGUGAAUAGGGUUUAAAAACACAUCUAAAAAAUCCUAAUUUGUUUUGGCGUUCAAUACUUUUCGUUUACAUUUGCA .....((.((((((((((((((((((....)).)))))))).))))......((((..((((((((((.((((.(((((((((((((....((((...))))....))))))))))))).))))(((((((...((((((((...(((((...)))))...((((((((((((((........)))))).))))))))...............))))))))...)))))))..........((((((((...............)))))))).......))))))...))))..))))...))))...)). (-76.16) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 319 289 253 171 116 pint:PI0188|5end_phosphomethylpyrimidine_kinase_178433..178663_POSITIVE 296 308 274 202 159 pint:PI1891|5end_hypothetical_protein_1835196..1835426_POSITIVE 281 260 212 228 183 pint:PI1000|5end_conserved_hypothetical_protein_923332..923562_POSITIVE 274 308 264 174 139 pint:PI1639|5end_conserved_hypothetical_protein_1556725..1556955_POSITIVE 262 307 263 204 160 pint:PI0876|5end_hypothetical_protein_810767..810997_POSITIVE 262 307 263 45 1 pint:PI0875|5end_conserved_hypothetical_protein_810608..810838_POSITIVE 260 246 210 205 172 pint:PI1931|5end_alpha_glycan_phosphorylase,_maltodextrin_phosphorylase_1875456..1875686_POSITIVE 259 253 213 78 23 pint:PI1547|5end_hypothetical_protein_1465808..1466038_POSITIVE 259 293 259 191 143 pint:PI1543|5end_hypothetical_protein_1462773..1463003_POSITIVE 259 290 241 119 71 pint:PI0198|5end_hypothetical_protein_190719..190949_POSITIVE 257 310 262 93 38 pint:PI1971|5end_possible_IS1249-related_transposase_1928027..1928257_POSITIVE 257 310 262 93 38 pint:PI1533|5end_conserved_hypothetical_protein;_possible_transposase_1452667..1452897_POSITIVE 257 310 262 93 38 pint:PI0534|5end_conserved_hypothetical_protein;_possible_transposase_488568..488798_POSITIVE 255 293 264 80 48 pint:PI1067|5end_thymidylate_synthase_983940..984170_POSITIVE 254 219 177 75 27 pint:PI1263|5end_probable_integrase_1184502..1184732_POSITIVE 254 242 201 211 179 pint:PI0209|5end_hypothetical_protein_202723..202953_POSITIVE 251 309 272 88 43 pint:PI0705|5end_conserved_hypothetical_protein;_possible_lipoprotein_641274..641504_POSITIVE 250 309 267 68 33 pint:PI1827|5end_peptidase,_M23/M37_family,_N-terminal_1768013..1768243_POSITIVE 250 291 258 218 181 pint:PI0582|5end_hypothetical_protein_524853..525083_POSITIVE 250 266 226 208 157 pint:PI0475|5end_50S_ribosomal_protein_L6_439453..439683_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 276 303 273 45 13 pint:PI1706|3end_GTP-binding_protein_1623668..1623818_POSITIVE 264 259 212 151 107 pint:PI0998|3end_possible_flavin_reductase_domain_protein_923336..923486_POSITIVE 251 309 272 98 53 pint:PI0704|3end_conserved_hypothetical_protein_641364..641514_POSITIVE 243 292 255 130 95 pint:PI0205|3end_deoxyuridine_5'-triphosphate_nucleotidohydrolase_198095..198245_POSITIVE 243 299 255 85 22 pint:PI0057|3end_conserved_hypothetical_protein_56512..56662_POSITIVE 239 299 261 79 39 pint:PI2016|3end_ribosomal_large_subunit_pseudouridine_synthase_D_1974933..1975083_POSITIVE 239 293 254 66 24 pint:PI0706|3end_pyridoxal_phosphate_biosynthetic_protein_(4-hydroxythreonine-4-phosphate_dehydrogenase)_643394..643544_POSITIVE 238 310 263 58 14 pint:PI0666|3end_chorismate_synthase_610171..610321_POSITIVE 235 310 273 57 24 pint:PI1630|3end_hypothetical_protein_1552494..1552644_POSITIVE 233 297 261 109 66 pint:PI1983|3end_possible_xylanase_1940004..1940154_POSITIVE 233 283 241 142 101 pint:PI1794|3end_conserved_hypothetical_protein_1726696..1726846_POSITIVE 232 290 261 50 12 pint:PI0947|3end_conserved_hypothetical_protein_880709..880859_POSITIVE 230 299 263 138 96 pint:PI0633|3end_possible_preprotein_translocase,_YajC_subunit_580080..580230_POSITIVE 229 240 192 99 52 pint:PI1730|3end_hypothetical_protein_1650367..1650517_POSITIVE 229 177 145 39 9 pint:PI0319|3end_conserved_hypothetical_protein_302048..302198_POSITIVE 227 310 273 49 16 pint:PI0337|3end_hypothetical_protein_315402..315552_POSITIVE 226 290 241 133 93 pint:PI1789|3end_hypothetical_protein_1719037..1719187_POSITIVE 225 292 266 63 38 pint:PI0694|3end_Na+/dicarboxylate_or_sulfate_symporter_631177..631327_POSITIVE 224 299 251 145 87 pint:PI2073|3end_mobilization_protein_2033487..2033637_POSITIVE 222 291 262 139 109 pint:PI1716|3end_hypothetical_protein_1632006..1632156_POSITIVE