Origin IGS: ttcctcatagactttatcttcttgctgctgcacagttgctcctttgagaagcgcacgcgcatagcgaacagatattacacctatatccatagtttatttattta .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 taaataaataaactatggatataggtgtaatatctgttcgctatgcgcgtgcgcttctcaaaggagcaactgtgcagcagcaagaagataaagtctatgaggaa Mask Tandem Repeat Region ================================================ ttcctcatagactttatcttcttgctgctgcacagttgctcctttgagaagcgcacgcgcatagcgaacagatattacacctatatccatagtttatttattta Find is-nt database================================================ Query_seq: PI1284:PI1285|PI1284:PI1285:ATP synthase, delta subunit:ATP synthase, B subunit:->->:1200384..1200487 104 ttcctcatagactttatcttcttgctgctgcacagttgctcctttgagaagcgcacgcgcatagcgaacagatattacacctatatccatagtttatttattta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI1284:PI1285|PI1284:PI1285:ATP synthase, delta subunit:ATP synthase, B subunit:->->:1200384..1200487 104 ttcctcatagactttatcttcttgctgctgcacagttgctcctttgagaagcgcacgcgcatagcgaacagatattacacctatatccatagtttatttattta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI1284:PI1285|PI1284:PI1285:ATP synthase, delta subunit:ATP synthase, B subunit:->->:1200384..1200487 104 ttcctcatagactttatcttcttgctgctgcacagttgctcctttgagaagcgcacgcgcatagcgaacagatattacacctatatccatagtttatttattta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ttcctcatagactttatcttcttgctgctgcacagttgctcctttgagaagcgcacgcgcatagcgaacagatattacacctatatccatagtttatttattta Predict ORF larger than 30AA ================================================ Protein_Len: 32 Strand: + Start: 7 End: 102 ...... M D F I F L L L H S C S F E K R T R I A N R Y Y T Y I H S L F I .. Protein_Len: 30 Strand: - Start: 1 End: 90 E E Y V K D E Q Q Q V T A G K L L A R A Y R V S I V G I D M .............. ttcctcatagactttatcttcttgctgctgcacagttgctcctttgagaagcgcacgcgcatagcgaacagatattacacctatatccatagtttatttattta 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================================================ ttcctcatagactttatcttcttgctgctgcacagttgctcctttgagaagcgcacgcgcatagcgaacagatattacacctatatccatagtttatttattta Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PI1284:PI1285|PI1284:PI1285:ATP synthase, delta subunit:ATP synthase, B subunit:->->:1200384..1200487 104 ttcctcatagactttatcttcttgctgctgcacagttgctcctttgagaagcgcacgcgcatagcgaacagatattacacctatatccatagtttatttattta Intra-Species Hit: Count: 1 Min: 1 Max: 104 Len: 104 Subject: pint_PI1284_PI1285|ATP synthase, delta subunit:ATP synthase, B subunit|POSITIVE:POSITIVE|[1200384,1200487]|104 HSP 1 e-value: 1.0E-52 bit: 206.0 Len: 104 Query Start:1 Query End:104 Subject Strand: POSITIVE Subject Start: 1 Subject End: 104 ttcctcatagactttatcttcttgctgctgcacagttgctcctttgagaagcgcacgcgcatagcgaacagatattacacctatatccatagtttatttattta ttcctcatagactttatcttcttgctgctgcacagttgctcctttgagaagcgcacgcgcatagcgaacagatattacacctatatccatagtttatttattta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUCCUCAUAGACUUUAUCUUCUUGCUGCUGCACAGUUGCUCCUUUGAGAAGCGCACGCGCAUAGCGAACAGAUAUUACACCUAUAUCCAUAGUUUAUUUAUUUA ......(((((((.(((((..((((((.(((.(.((((((.(.....).)))).))).)))))))))..)))))................)))))))....... (-19.63) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAAUAAAUAAACUAUGGAUAUAGGUGUAAUAUCUGUUCGCUAUGCGCGUGCGCUUCUCAAAGGAGCAACUGUGCAGCAGCAAGAAGAUAAAGUCUAUGAGGAA .............((((((((((((((...)))))))..(((.(((((((..(((((.....))))).)).)))))..)))...........)))))))..... (-25.00) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 372 56 14 207 162 pint:PI1344|5end_hypothetical_protein_1258551..1258781_POSITIVE 354 67 23 68 18 pint:PI1890|5end_cell_division_protein_FtsW_1832886..1833116_POSITIVE 347 68 23 61 14 pint:PI1011|5end_cytochrome_c_biogenesis_protein_CycY_932115..932345_POSITIVE 342 70 26 99 57 pint:PI1808|5end_LacI_family_transcriptional_regulator_1742167..1742397_POSITIVE 342 70 26 85 43 pint:PI1807|5end_hypothetical_protein_1742153..1742383_POSITIVE 341 70 21 90 43 pint:PI0703|5end_hypothetical_protein_639655..639885_POSITIVE 341 43 1 65 11 pint:PI0593|5end_NAD-specific_glutamate_dehydrogenase_542967..543197_POSITIVE 338 66 22 204 161 pint:PI1796|5end_2-hydroxyhepta-2,4-diene-1,7-dioate_isomerase,_fumarylacetoacetate_hydrolase_family_protein_1730452..1730682_POSITIVE 334 65 21 78 16 pint:PI1985|5end_hypothetical_protein_1940291..1940521_POSITIVE 332 65 22 207 151 pint:PI1736|5end_topoisomerase_IV,_subunit_A_1654254..1654484_POSITIVE 330 60 20 211 164 pint:PI1413|5end_hypothetical_protein_1333727..1333957_POSITIVE 329 67 26 87 42 pint:PI1501|5end_GTP-binding_elongation_factor_family_protein_TypA/BipA_1421424..1421654_POSITIVE 326 60 18 147 80 pint:PI0108|5end_L-lactate_permease_104892..105122_POSITIVE 323 68 26 180 134 pint:PI0854|5end_MiaB-like_tRNA_modifying_enzyme_786513..786743_POSITIVE 320 67 23 231 197 pint:PI1873|5end_hypothetical_protein_1817878..1818108_POSITIVE 313 57 11 65 6 pint:PI0976|5end_dihydrolipoamide_dehydrogenase_(dihydrolipoyl_dehydrogenanse)_902297..902527_POSITIVE 312 80 35 109 49 pint:PI0670|5end_hypothetical_protein_611000..611230_POSITIVE 309 70 26 195 143 pint:PI2006|5end_potassium_uptake_system_protein_1964480..1964710_POSITIVE 307 72 31 53 5 pint:PI1484|5end_conserved_hypothetical_protein_1404619..1404849_POSITIVE 306 62 26 57 17 pint:PI0045|5end_thiamine_biosynthesis_protein_43768..43998_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 372 56 14 115 70 pint:PI1343|3end_conserved_hypothetical_protein_1258539..1258689_POSITIVE 358 69 21 86 22 pint:PI0091|3end_hypothetical_protein_89774..89924_POSITIVE 347 68 23 61 14 pint:PI1010|3end_conserved_hypothetical_protein_932195..932345_POSITIVE 342 70 26 43 1 pint:PI1806|3end_integral_membrane_transport_protein;_possible_sugar_transport_proteins_1742191..1742341_POSITIVE 329 68 22 109 65 pint:PI1722|3end_possible_peptidyl-prolyl_cis-trans_isomerase_1640995..1641145_POSITIVE 328 53 11 150 98 pint:PI1638|3end_conserved_hypothetical_protein_1556613..1556763_POSITIVE 324 60 17 141 95 pint:PI0378|3end_conserved_hypothetical_protein;_possible_helicase_349539..349689_POSITIVE 318 66 21 74 28 pint:PI1466|3end_GTP-binding_protein,_possible_GTP1/OBG_family_1393133..1393283_POSITIVE 315 70 21 101 41 pint:PI0683|3end_hypothetical_protein_619797..619947_POSITIVE 309 45 1 72 13 pint:PI1654|3end_hypothetical_protein_1567958..1568108_POSITIVE 306 66 24 34 1 pint:PI2044|3end_hypothetical_protein_1997351..1997501_POSITIVE 306 61 22 149 115 pint:PI1795|3end_conserved_hypothetical_protein_1730486..1730636_POSITIVE 306 62 26 66 26 pint:PI0044|3end_thiamine_biosynthetic_enzyme_43857..44007_POSITIVE 304 67 24 62 21 pint:PI1002|3end_metal_dependent_hydrolase_924674..924824_POSITIVE 298 59 17 109 59 pint:PI0728|3end_integrase_661508..661658_POSITIVE 297 61 23 53 23 pint:PI1253|3end_hypothetical_protein_1175691..1175841_POSITIVE 292 70 21 123 76 pint:PI2132|3end_hypothetical_protein_2081139..2081289_POSITIVE 290 77 34 59 11 pint:PI0764|3end_permease_699145..699295_POSITIVE 289 57 11 150 90 pint:PI0258|3end_conjugative_transposon_protein,_TraG_252285..252435_POSITIVE 288 65 24 124 84 pint:PI1227|3end_conserved_hypothetical_protein;_possible_DNA-binding_protein,_histone-like_family_1148974..1149124_POSITIVE