Origin IGS: cttactaaactcctttttggtagttgccacctcaacttctgctgattgtgctttttcgtttgcaatcagtagtgttagatagtcagagagaagttctcctttctttatcttatatgtaagatgcaatattcgcatta .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 taatgcgaatattgcatcttacatataagataaagaaaggagaacttctctctgactatctaacactactgattgcaaacgaaaaagcacaatcagcagaagttgaggtggcaactaccaaaaaggagtttagtaag Mask Tandem Repeat Region ================================================ cttactaaactcctttttggtagttgccacctcaacttctgctgattgtgctttttcgtttgcaatcagtagtgttagatagtcagagagaagttctcctttctttatcttatatgtaagatgcaatattcgcatta Find is-nt database================================================ Query_seq: PI1053:PI1054|PI1053:PI1054:conserved hypothetical protein:conserved hypothetical protein:->->:973699..973835 137 cttactaaactcctttttggtagttgccacctcaacttctgctgattgtgctttttcgtttgcaatcagtagtgttagatagtcagagagaagttctcctttctttatcttatatgtaagatgcaatattcgcatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI1053:PI1054|PI1053:PI1054:conserved hypothetical protein:conserved hypothetical protein:->->:973699..973835 137 cttactaaactcctttttggtagttgccacctcaacttctgctgattgtgctttttcgtttgcaatcagtagtgttagatagtcagagagaagttctcctttctttatcttatatgtaagatgcaatattcgcatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI1053:PI1054|PI1053:PI1054:conserved hypothetical protein:conserved hypothetical protein:->->:973699..973835 137 cttactaaactcctttttggtagttgccacctcaacttctgctgattgtgctttttcgtttgcaatcagtagtgttagatagtcagagagaagttctcctttctttatcttatatgtaagatgcaatattcgcatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 cttactaaactcctttttggtagttgccacctcaacttctgctgattgtgctttttcgtttgcaatcagtagtgttagatagtcagagagaagttctcctttctttatcttatatgtaagatgcaatattcgcatta Predict ORF larger than 30AA ================================================ Protein_Len: 31 Strand: + Start: 24 End: 116 ....................... M P P Q L L L I V L F R L Q S V V L D S Q R E V L L S L S Y M ..................... Protein_Len: 45 Strand: - Start: 1 End: 135 K S F E K K T T A V E V E A S Q A K E N A I L L T L Y D S L L E G K K I K Y T L H L I R M .. cttactaaactcctttttggtagttgccacctcaacttctgctgattgtgctttttcgtttgcaatcagtagtgttagatagtcagagagaagttctcctttctttatcttatatgtaagatgcaatattcgcatta 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================================================ cttactaaactcctttttggtagttgccacctcaacttctgctgattgtgctttttcgtttgcaatcagtagtgttagatagtcagagagaagttctcctttctttatcttatatgtaagatgcaatattcgcatta Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PI1053:PI1054|PI1053:PI1054:conserved hypothetical protein:conserved hypothetical protein:->->:973699..973835 137 cttactaaactcctttttggtagttgccacctcaacttctgctgattgtgctttttcgtttgcaatcagtagtgttagatagtcagagagaagttctcctttctttatcttatatgtaagatgcaatattcgcatta Intra-Species Hit: Count: 1 Min: 1 Max: 137 Len: 137 Subject: pint_PI1053_PI1054|conserved hypothetical protein:conserved hypothetical protein|POSITIVE:POSITIVE|[973699,973835]|137 HSP 1 e-value: 3.0E-72 bit: 272.0 Len: 137 Query Start:1 Query End:137 Subject Strand: POSITIVE Subject Start: 1 Subject End: 137 cttactaaactcctttttggtagttgccacctcaacttctgctgattgtgctttttcgtttgcaatcagtagtgttagatagtcagagagaagttctcctttctttatcttatatgtaagatgcaatattcgcatta cttactaaactcctttttggtagttgccacctcaacttctgctgattgtgctttttcgtttgcaatcagtagtgttagatagtcagagagaagttctcctttctttatcttatatgtaagatgcaatattcgcatta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUUACUAAACUCCUUUUUGGUAGUUGCCACCUCAACUUCUGCUGAUUGUGCUUUUUCGUUUGCAAUCAGUAGUGUUAGAUAGUCAGAGAGAAGUUCUCCUUUCUUUAUCUUAUAUGUAAGAUGCAAUAUUCGCAUUA (((((..((((((.....)).))))........(((..(((((((((((((......))..))))))))))).))).(((((..((((((........)))))))))))......))))).(((.......)))... (-32.10) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAUGCGAAUAUUGCAUCUUACAUAUAAGAUAAAGAAAGGAGAACUUCUCUCUGACUAUCUAACACUACUGAUUGCAAACGAAAAAGCACAAUCAGCAGAAGUUGAGGUGGCAACUACCAAAAAGGAGUUUAGUAAG ..((((((...))))))(((((................(((((.....)))))..(((((((((.((.(((((((..............))))))).))..))).)))))).((((.((.....))))))..))))) (-26.54) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 372 59 12 173 120 pint:PI1668|5end_conserved_hypothetical_protein_1580692..1580922_POSITIVE 316 107 61 72 20 pint:PI0023|5end_internalin-related_protein_25924..26154_POSITIVE 299 86 41 221 181 pint:PI0496|5end_heat_shock_protein_hsp70_(chaperone_protein_dnaK)_456632..456862_POSITIVE 291 64 23 144 111 pint:PI0480|5end_preprotein_translocase,_SecY_subunit_441576..441806_POSITIVE 288 90 43 230 182 pint:PI1949|5end_aminotransferase,_class_V_1903218..1903448_POSITIVE 288 90 43 96 48 pint:PI1948|5end_hypothetical_protein_1903084..1903314_POSITIVE 288 63 24 88 36 pint:PI1658|5end_conserved_hypothetical_protein_1573607..1573837_POSITIVE 288 63 24 88 36 pint:PI0366|5end_conserved_hypothetical_protein_336765..336995_POSITIVE 283 58 13 121 73 pint:PI0113|5end_arginyl-tRNA_synthetase_108371..108601_POSITIVE 278 90 41 67 15 pint:PI1269|5end_conserved_hypothetical_protein;_possible_peptidase_1188147..1188377_POSITIVE 278 74 31 59 11 pint:PI0428|5end_hypothetical_protein_393080..393310_POSITIVE 278 51 11 209 163 pint:PI0355|5end_probable__N-acetylmuramoyl-L-alanine_amidase_326157..326387_POSITIVE 273 58 17 153 111 pint:PI0309|5end_hypothetical_protein_291503..291733_POSITIVE 271 42 10 203 168 pint:PI0352|5end_hypothetical_protein_324760..324990_POSITIVE 271 42 10 53 18 pint:PI0353|5end_hypothetical_protein_324610..324840_POSITIVE 269 60 12 162 107 pint:PI2160|5end_hypothetical_protein_2107270..2107500_POSITIVE 269 68 21 71 27 pint:PI1609|5end_Na+/H+_anti-porter_1536058..1536288_POSITIVE 269 72 35 184 153 pint:PI1136|5end_conserved_hypothetical_protein_1062195..1062425_POSITIVE 268 68 21 191 143 pint:PI2155|5end_hypothetical_protein_2100664..2100894_POSITIVE 267 50 9 142 99 pint:PI1443|5end_conserved_hypotehtical_protein;_possible_tonB-dependent_outer_membrane_receptor_1364560..1364790_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 291 64 23 136 103 pint:PI0479|3end_50S_ribosomal_protein_L15_441648..441798_POSITIVE 288 63 24 72 20 pint:PI1657|3end_hypothetical_protein_1573671..1573821_POSITIVE 288 63 24 72 20 pint:PI0364|3end_hypothetical_protein_336829..336979_POSITIVE 287 51 11 136 85 pint:PI1706|3end_GTP-binding_protein_1623668..1623818_POSITIVE 279 74 31 86 45 pint:PI0683|3end_hypothetical_protein_619797..619947_POSITIVE 274 62 23 91 55 pint:PI1734|3end_possible_carboxyl-terminal_protease-related_protein_1653829..1653979_POSITIVE 271 42 10 131 96 pint:PI0351|3end_hypothetical_protein_324768..324918_POSITIVE 270 51 18 54 13 pint:PI1000|3end_conserved_hypothetical_protein_923672..923822_POSITIVE 269 72 35 112 81 pint:PI1135|3end_hypothetical_protein_1062203..1062353_POSITIVE 267 50 9 151 108 pint:PI1442|3end_radical-activating_enzyme_(pyruvate-formate_lyase-activating_enzyme)_1364649..1364799_POSITIVE 265 62 22 82 41 pint:PI1633|3end_hypothetical_protein_1552955..1553105_POSITIVE 263 60 12 116 69 pint:PI1711|3end_ABC_transporter,_ATP-binding_protein_1628429..1628579_POSITIVE 263 67 24 87 38 pint:PI0528|3end_hypothetical_protein_483122..483272_POSITIVE 260 88 41 135 87 pint:PI1666|3end_conserved_hypothetical_protein_1579418..1579568_POSITIVE 256 58 18 127 92 pint:PI0242|3end_hypothetical_protein_240227..240377_POSITIVE 253 90 45 147 98 pint:PI1223|3end_conserved_hypothetical_protein_1144459..1144609_POSITIVE 249 90 41 126 68 pint:PI0150|3end_hypothetical_protein_143833..143983_POSITIVE 248 89 41 77 25 pint:PI0422|3end_conserved_hypothetical_protein_388025..388175_POSITIVE 246 42 12 144 120 pint:PI1667|3end_conserved_hypothetical_protein_1580772..1580922_POSITIVE 246 58 11 61 7 pint:PI0616|3end_electron_transfer_flavoprotein,_beta-subunit_566440..566590_POSITIVE