Origin IGS: tcttttatcgtaatctgtgtaattttactttgtcgtaaaaatgttatagaaacacttttatgctactgcaaagttagcagaattagtagataacacaaaaaatattcattatttttaatgctttcgcagctattcgactatcattttcatacactttttacattgcattagaccatattctcacaaaaaagttataattttgcagccactttacaggttagtttgaaatttcaactaccattgaggaattaactgaagaga .........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 tctcttcagttaattcctcaatggtagttgaaatttcaaactaacctgtaaagtggctgcaaaattataacttttttgtgagaatatggtctaatgcaatgtaaaaagtgtatgaaaatgatagtcgaatagctgcgaaagcattaaaaataatgaatattttttgtgttatctactaattctgctaactttgcagtagcataaaagtgtttctataacatttttacgacaaagtaaaattacacagattacgataaaaga Mask Tandem Repeat Region ================================================ tcttttatcgtaatctgtgtaattttactttgtcgtaaaaatgttatagaaacacttttatgctactgcaaagttagcagaattagtagataacacaaaaaatattcattatttttaatgctttcgcagctattcgactatcattttcatacactttttacattgcattagaccatattctcacaaaaaagttataattttgcagccactttacaggttagtttgaaatttcaactaccattgaggaattaactgaagaga Find is-nt database================================================ Query_seq: PI2087:PI2088|PI2087:PI2088:dihydropicolinate reductase:conserved hypothetical protein; possible PAP2 superfamily protein:->->:2044316..2044576 261 tcttttatcgtaatctgtgtaattttactttgtcgtaaaaatgttatagaaacacttttatgctactgcaaagttagcagaattagtagataacacaaaaaatattcattatttttaatgctttcgcagctattcgactatcattttcatacactttttacattgcattagaccatattctcacaaaaaagttataattttgcagccactttacaggttagtttgaaatttcaactaccattgaggaattaactgaagaga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI2087:PI2088|PI2087:PI2088:dihydropicolinate reductase:conserved hypothetical protein; possible PAP2 superfamily protein:->->:2044316..2044576 261 tcttttatcgtaatctgtgtaattttactttgtcgtaaaaatgttatagaaacacttttatgctactgcaaagttagcagaattagtagataacacaaaaaatattcattatttttaatgctttcgcagctattcgactatcattttcatacactttttacattgcattagaccatattctcacaaaaaagttataattttgcagccactttacaggttagtttgaaatttcaactaccattgaggaattaactgaagaga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI2087:PI2088|PI2087:PI2088:dihydropicolinate reductase:conserved hypothetical protein; possible PAP2 superfamily protein:->->:2044316..2044576 261 tcttttatcgtaatctgtgtaattttactttgtcgtaaaaatgttatagaaacacttttatgctactgcaaagttagcagaattagtagataacacaaaaaatattcattatttttaatgctttcgcagctattcgactatcattttcatacactttttacattgcattagaccatattctcacaaaaaagttataattttgcagccactttacaggttagtttgaaatttcaactaccattgaggaattaactgaagaga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tcttttatcgtaatctgtgtaattttactttgtcgtaaaaatgttatagaaacacttttatgctactgcaaagttagcagaattagtagataacacaaaaaatattcattatttttaatgctttcgcagctattcgactatcattttcatacactttttacattgcattagaccatattctcacaaaaaagttataattttgcagccactttacaggttagtttgaaatttcaactaccattgaggaattaactgaagaga Predict ORF larger than 30AA ================================================ Protein_Len: 35 Strand: + Start: 90 End: 194 ......................................................................................... M T Q K I F I I F N A F A A I R L S F S Y T F Y I A L D H I L T K K L ................................................................... tcttttatcgtaatctgtgtaattttactttgtcgtaaaaatgttatagaaacacttttatgctactgcaaagttagcagaattagtagataacacaaaaaatattcattatttttaatgctttcgcagctattcgactatcattttcatacactttttacattgcattagaccatattctcacaaaaaagttataattttgcagccactttacaggttagtttgaaatttcaactaccattgaggaattaactgaagaga 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================================================ tcttttatcgtaatctgtgtaattttactttgtcgtaaaaatgttatagaaacacttttatgctactgcaaagttagcagaattagtagataacacaaaaaatattcattatttttaatgctttcgcagctattcgactatcattttcatacactttttacattgcattagaccatattctcacaaaaaagttataattttgcagccactttacaggttagtttgaaatttcaactaccattgaggaattaactgaagaga Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PI2087:PI2088|PI2087:PI2088:dihydropicolinate reductase:conserved hypothetical protein; possible PAP2 superfamily protein:->->:2044316..2044576 261 tcttttatcgtaatctgtgtaattttactttgtcgtaaaaatgttatagaaacacttttatgctactgcaaagttagcagaattagtagataacacaaaaaatattcattatttttaatgctttcgcagctattcgactatcattttcatacactttttacattgcattagaccatattctcacaaaaaagttataattttgcagccactttacaggttagtttgaaatttcaactaccattgaggaattaactgaagaga Intra-Species Hit: Count: 1 Min: 1 Max: 261 Len: 261 Subject: pint_PI2087_PI2088|dihydropicolinate reductase:conserved hypothetical protein; possible PAP2 superfamily protein|POSITIVE:POSITIVE|[2044316,2044576]|261 HSP 1 e-value: 1.0E-146 bit: 517.0 Len: 261 Query Start:1 Query End:261 Subject Strand: POSITIVE Subject Start: 1 Subject End: 261 tcttttatcgtaatctgtgtaattttactttgtcgtaaaaatgttatagaaacacttttatgctactgcaaagttagcagaattagtagataacacaaaaaatattcattatttttaatgctttcgcagctattcgactatcattttcatacactttttacattgcattagaccatattctcacaaaaaagttataattttgcagccactttacaggttagtttgaaatttcaactaccattgaggaattaactgaagaga tcttttatcgtaatctgtgtaattttactttgtcgtaaaaatgttatagaaacacttttatgctactgcaaagttagcagaattagtagataacacaaaaaatattcattatttttaatgctttcgcagctattcgactatcattttcatacactttttacattgcattagaccatattctcacaaaaaagttataattttgcagccactttacaggttagtttgaaatttcaactaccattgaggaattaactgaagaga Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCUUUUAUCGUAAUCUGUGUAAUUUUACUUUGUCGUAAAAAUGUUAUAGAAACACUUUUAUGCUACUGCAAAGUUAGCAGAAUUAGUAGAUAACACAAAAAAUAUUCAUUAUUUUUAAUGCUUUCGCAGCUAUUCGACUAUCAUUUUCAUACACUUUUUACAUUGCAUUAGACCAUAUUCUCACAAAAAAGUUAUAAUUUUGCAGCCACUUUACAGGUUAGUUUGAAAUUUCAACUACCAUUGAGGAAUUAACUGAAGAGA ((((((...((((...(((((.....((((((((((((((.((((.....)))).))))))).....)))))))(((..((((.(((.((...((..(((((((.....)))))))..))...))...)))))))..))).........)))))...))))................((((((......((((..((((((((((((........)))).))..))))))..)))).....))))))........)))))) (-45.60) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCUCUUCAGUUAAUUCCUCAAUGGUAGUUGAAAUUUCAAACUAACCUGUAAAGUGGCUGCAAAAUUAUAACUUUUUUGUGAGAAUAUGGUCUAAUGCAAUGUAAAAAGUGUAUGAAAAUGAUAGUCGAAUAGCUGCGAAAGCAUUAAAAAUAAUGAAUAUUUUUUGUGUUAUCUACUAAUUCUGCUAACUUUGCAGUAGCAUAAAAGUGUUUCUAUAACAUUUUUACGACAAAGUAAAAUUACACAGAUUACGAUAAAAGA ..((((..(((...........(((((((((....)).)))).))).((((.((.((((((((.(((((((((((((((.(((......)))...)))....))))))).)))))......((((.((((((.((.((.(((((.(((((((.....))))))).))))).)))))).)))).))))..)))))))).)).((((((((((.....)))))))))).............)))).........)))..)))) (-46.70) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 294 168 125 101 56 pint:PI0361|5end_hypothetical_protein_333062..333292_POSITIVE 277 147 118 108 74 pint:PI0926|5end_hypothetical_protein_856824..857054_POSITIVE 267 208 167 135 94 pint:PI0284|5end_flavoprotein_A_268848..269078_POSITIVE 261 170 124 115 61 pint:PI0539|5end_hypothetical_protein_493406..493636_POSITIVE 260 79 34 117 59 pint:PI0652|5end_conserved_hypothetical_protein_592878..593108_POSITIVE 258 210 162 50 10 pint:PI0796|5end_competence_protein_733324..733554_POSITIVE 239 240 200 191 143 pint:PI0550|5end_possible_glycosyl_hydrolase_500650..500880_POSITIVE 230 147 118 222 188 pint:PI1890|5end_cell_division_protein_FtsW_1832886..1833116_POSITIVE 229 239 198 138 98 pint:PI1495|5end_conserved_hypothetical_protein_1414432..1414662_POSITIVE 229 78 42 150 106 pint:PI0471|5end_50S_ribosomal_protein_L24_437736..437966_POSITIVE 227 69 21 73 29 pint:PI0508|5end_possible_cell_filamentation_protein_466463..466693_POSITIVE 225 236 199 152 121 pint:PI0064|5end_hypothetical_protein_63622..63852_POSITIVE 224 152 111 167 123 pint:PI0559|5end_conserved_hypothetical_protein_507668..507898_POSITIVE 222 248 201 222 164 pint:PI1748|5end_guanosine-3',5'-bis(diphosphate)_3'-pyrophosphohydrolase/possible_(p)ppgpp_synthetase_II_1668536..1668766_POSITIVE 222 89 43 75 21 pint:PI1112|5end_glycosyltransferase_1036443..1036673_POSITIVE 221 149 115 81 45 pint:PI0773|5end_D-3-phosphoglycerate_dehydrogenase_708498..708728_POSITIVE 221 99 51 140 93 pint:PI0123|5end_outer_membrane_protein,_ompH_family_113906..114136_POSITIVE 219 131 102 132 107 pint:PI0902|5end_hypothetical_protein_832291..832521_POSITIVE 218 148 115 231 198 pint:PI1655|5end_hypothetical_protein_1569679..1569909_POSITIVE 217 139 104 74 40 pint:PI1912|5end_possible_DNA_repair_protein_1856364..1856594_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 267 208 167 88 47 pint:PI0283|3end_Zn-dependent_peptidase_268881..269031_POSITIVE 263 90 53 89 51 pint:PI0684|3end_coproporphyrinogen_III_oxidase_620507..620657_POSITIVE 233 239 203 103 69 pint:PI0444|3end_50S_ribosomal_protein_L7/L12_413390..413540_POSITIVE 233 239 203 72 38 pint:PI0445|3end_conserved_hypothetical_protein_413359..413509_POSITIVE 229 78 42 147 103 pint:PI0470|3end_50S_ribosomal_protein_L14_437813..437963_POSITIVE 227 250 205 148 112 pint:PI1009|3end_cytochrome_c_nitrite_reductase,_large_subunit_930840..930990_POSITIVE 227 51 16 129 92 pint:PI0893|3end_outer_membrane_protein_41_precursor_825662..825812_POSITIVE 227 78 48 149 123 pint:PI0822|3end_tRNA_delta(2)-isopentenylpyrophosphate_transferase_762025..762175_POSITIVE 227 69 21 77 33 pint:PI0507|3end_transcriptional_regulator_466547..466697_POSITIVE 225 236 199 70 39 pint:PI0063|3end_transcriptional_regulator,_GntR_family_63620..63770_POSITIVE 224 152 111 134 90 pint:PI0558|3end_probable_transcriptional_regulator,_TetR_family_507715..507865_POSITIVE 222 239 200 151 104 pint:PI0549|3end_hypothetical_protein_500691..500841_POSITIVE 221 99 51 53 6 pint:PI0122|3end_outer_membrane_protein,_ompH_family_113899..114049_POSITIVE 217 107 61 125 80 pint:PI0183|3end_hypothetical_protein_174810..174960_POSITIVE 216 167 124 51 10 pint:PI0053|3end_hypothetical_protein_55124..55274_POSITIVE 214 139 119 114 93 pint:PI1504|3end_non-specific_DNA-binding_protein_1424904..1425054_POSITIVE 211 136 110 151 125 pint:PI2090|3end_thioesterase_family_protein_2048066..2048216_POSITIVE 211 167 126 85 53 pint:PI0805|3end_conserved_hypothetical_protein_743807..743957_POSITIVE 211 89 61 56 24 pint:PI0422|3end_conserved_hypothetical_protein_388025..388175_POSITIVE 210 210 192 65 47 pint:PI1215|3end_orotidine_5'-phosphate_decarboxylase_1134871..1135021_POSITIVE