Origin IGS: agaaaatggtttttatattattattttatcttgaagtattcatacacttgcaaggtcttctttaaattaaaaggttcacctatactaagaactttaaatta .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 taatttaaagttcttagtataggtgaaccttttaatttaaagaagaccttgcaagtgtatgaatacttcaagataaaataataatataaaaaccattttct Mask Tandem Repeat Region ================================================ agaaaatggtttttatattattattttatcttgaagtattcatacacttgcaaggtcttctttaaattaaaaggttcacctatactaagaactttaaatta Find is-nt database================================================ Query_seq: PI1073:PI1074|PI1073:PI1074:hemogluttinin A-related protein (HagA):hypothetical protein:->->:993754..993854 101 agaaaatggtttttatattattattttatcttgaagtattcatacacttgcaaggtcttctttaaattaaaaggttcacctatactaagaactttaaatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI1073:PI1074|PI1073:PI1074:hemogluttinin A-related protein (HagA):hypothetical protein:->->:993754..993854 101 agaaaatggtttttatattattattttatcttgaagtattcatacacttgcaaggtcttctttaaattaaaaggttcacctatactaagaactttaaatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI1073:PI1074|PI1073:PI1074:hemogluttinin A-related protein (HagA):hypothetical protein:->->:993754..993854 101 agaaaatggtttttatattattattttatcttgaagtattcatacacttgcaaggtcttctttaaattaaaaggttcacctatactaagaactttaaatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 agaaaatggtttttatattattattttatcttgaagtattcatacacttgcaaggtcttctttaaattaaaaggttcacctatactaagaactttaaatta Predict ORF larger than 30AA ================================================ agaaaatggtttttatattattattttatcttgaagtattcatacacttgcaaggtcttctttaaattaaaaggttcacctatactaagaactttaaatta 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================================================ agaaaatggtttttatattattattttatcttgaagtattcatacacttgcaaggtcttctttaaattaaaaggttcacctatactaagaactttaaatta Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PI1073:PI1074|PI1073:PI1074:hemogluttinin A-related protein (HagA):hypothetical protein:->->:993754..993854 101 agaaaatggtttttatattattattttatcttgaagtattcatacacttgcaaggtcttctttaaattaaaaggttcacctatactaagaactttaaatta Intra-Species Hit: Count: 1 Min: 1 Max: 101 Len: 101 Subject: pint_PI1073_PI1074|hemogluttinin A-related protein (HagA):hypothetical protein|POSITIVE:POSITIVE|[993754,993854]|101 HSP 1 e-value: 6.0E-51 bit: 200.0 Len: 101 Query Start:1 Query End:101 Subject Strand: POSITIVE Subject Start: 1 Subject End: 101 agaaaatggtttttatattattattttatcttgaagtattcatacacttgcaaggtcttctttaaattaaaaggttcacctatactaagaactttaaatta agaaaatggtttttatattattattttatcttgaagtattcatacacttgcaaggtcttctttaaattaaaaggttcacctatactaagaactttaaatta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGAAAAUGGUUUUUAUAUUAUUAUUUUAUCUUGAAGUAUUCAUACACUUGCAAGGUCUUCUUUAAAUUAAAAGGUUCACCUAUACUAAGAACUUUAAAUUA .......((((((((............((((((((((........)))).))))))...............(((....)))....))))))))........ (-13.20) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAUUUAAAGUUCUUAGUAUAGGUGAACCUUUUAAUUUAAAGAAGACCUUGCAAGUGUAUGAAUACUUCAAGAUAAAAUAAUAAUAUAAAAACCAUUUUCU ..........(((((..((.(((....)))..)).....)))))...((((.((((((....))))))))))............................. (-12.20) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 279 80 36 84 25 pint:PI0820|5end_hypothetical_protein_759694..759924_POSITIVE 247 75 39 51 15 pint:PI2177|5end_phosphoribosylaminoimidazole_carboxylase_2117127..2117357_POSITIVE 231 85 45 176 133 pint:PI1448|5end_hypothetical_protein_1371579..1371809_POSITIVE 216 49 7 206 158 pint:PI1935|5end_possible__internalin-related_protein_1883324..1883554_POSITIVE 207 77 45 131 100 pint:PI1876|5end_possible_flagellar_motor_protein,_OmpA_family_1819082..1819312_POSITIVE 207 67 30 66 29 pint:PI1703|5end_conserved_hypothetical_protein_1620876..1621106_POSITIVE 197 58 26 175 142 pint:PI0647|5end_potassium_uptake_protein_587505..587735_POSITIVE 196 62 24 173 123 pint:PI1650|5end_N-acetylmuramoyl-L-alanine_amidase_1563195..1563425_POSITIVE 196 62 24 58 8 pint:PI1649|5end_hypothetical_protein_1563080..1563310_POSITIVE 196 62 24 58 8 pint:PI0354|5end_hypothetical_protein_325886..326116_POSITIVE 193 56 24 101 71 pint:PI0237|5end_predicted_two-component_system_sensor_histidine_kinase_235979..236209_POSITIVE 190 56 23 55 19 pint:PI1820|5end_hypothetical_protein_1759962..1760192_POSITIVE 186 59 17 178 129 pint:PI1000|5end_conserved_hypothetical_protein_923332..923562_POSITIVE 185 58 11 106 59 pint:PI1258|5end_elongation_factor_Tu_1178909..1179139_POSITIVE 185 63 23 148 101 pint:PI0428|5end_hypothetical_protein_393080..393310_POSITIVE 185 60 11 140 86 pint:PI0265|5end_conjugative_transposon_protein,_TraO_257296..257526_POSITIVE 185 55 33 222 194 pint:PI0079|5end_hypothetical_protein_78565..78795_POSITIVE 184 56 23 224 196 pint:PI1880|5end_phosphoenolpyruvate_carboxykinase_(ATP)_1821667..1821897_POSITIVE 181 79 38 182 141 pint:PI0114|5end_hypothetical_protein_108139..108369_POSITIVE 181 79 38 105 64 pint:PI0115|5end_hypothetical_protein_108062..108292_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 258 90 42 69 28 pint:PI0645|3end_hypothetical_protein_586807..586957_POSITIVE 215 59 25 123 87 pint:PI0708|3end_conserved_hypothetical_protein_646234..646384_POSITIVE 207 77 45 75 44 pint:PI1875|3end_hypothetical_protein_1819106..1819256_POSITIVE 186 59 17 102 53 pint:PI0998|3end_possible_flavin_reductase_domain_protein_923336..923486_POSITIVE 185 58 11 133 86 pint:PI1257|3end_dTDP-4-dehydrorhamnose_reductase_1179016..1179166_POSITIVE 185 63 23 76 29 pint:PI0427|3end_conserved_hypothetical_protein_393088..393238_POSITIVE 185 60 11 135 81 pint:PI0264|3end_transfer_region-related_protein,_TraN_257371..257521_POSITIVE 176 63 27 97 58 pint:PI1013|3end_probable_transcriptional_regulator_934368..934518_POSITIVE 176 58 11 113 64 pint:PI0094|3end_protoporphyrinogen_oxidase_90511..90661_POSITIVE 174 63 44 151 124 pint:PI0282|3end_hypothetical_protein_266826..266976_POSITIVE 173 61 30 120 87 pint:PI1790|3end_hypothetical_protein_1722762..1722912_POSITIVE 170 59 25 150 119 pint:PI0798|3end_malonyl_CoA-acyl_carrier_protein_transacylase_736975..737125_POSITIVE 170 56 21 88 60 pint:PI0571|3end_conserved_hypothetical_protein;_possible_permease_516449..516599_POSITIVE 169 59 22 88 40 pint:PI0974|3end_hypothetical_protein_899591..899741_POSITIVE 168 58 31 62 21 pint:PI2159|3end_immunoreactive_84_kDa_antigen_PG93_2107371..2107521_POSITIVE 168 62 21 122 88 pint:PI2102|3end_DNA_topoisomerase_IV,_subunit_B_2057729..2057879_POSITIVE 168 63 23 108 67 pint:PI1942|3end_hypothetical_protein_1901269..1901419_POSITIVE 168 90 48 127 91 pint:PI0520|3end_hypothetical_protein_478951..479101_POSITIVE 167 55 17 81 48 pint:PI0545|3end_sugar_kinase_497867..498017_POSITIVE 166 64 24 121 81 pint:PI0678|3end_hypothetical_protein_616979..617129_POSITIVE