Origin IGS: taagcaaccgactgactgaaaaaggttttacaatacaaaacattatggacagtctctcactctcctatcagccttcttccccaaaaagtaaaaaggcaggataggaaagtaagagactttttatttaacctgccgacaagacgaagaagattgcattctataacaaacaatacaaactaatttaaaaagcagaaat .........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 atttctgctttttaaattagtttgtattgtttgttatagaatgcaatcttcttcgtcttgtcggcaggttaaataaaaagtctcttactttcctatcctgcctttttactttttggggaagaaggctgataggagagtgagagactgtccataatgttttgtattgtaaaacctttttcagtcagtcggttgctta Mask Tandem Repeat Region ================================================ taagcaaccgactgactgaaaaaggttttacaatacaaaacattatggacagtctctcactctcctatcagccttcttccccaaaaagtaaaaaggcaggataggaaagtaagagactttttatttaacctgccgacaagacgaagaagattgcattctataacaaacaatacaaactaatttaaaaagcagaaat Find is-nt database================================================ Query_seq: PI1369:PI1370|PI1369:PI1370:alkyl hydroperoxide reductase, subunit C:alkyl hydroperoxide reductase, subunit F:->->:1290484..1290679 196 taagcaaccgactgactgaaaaaggttttacaatacaaaacattatggacagtctctcactctcctatcagccttcttccccaaaaagtaaaaaggcaggataggaaagtaagagactttttatttaacctgccgacaagacgaagaagattgcattctataacaaacaatacaaactaatttaaaaagcagaaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI1369:PI1370|PI1369:PI1370:alkyl hydroperoxide reductase, subunit C:alkyl hydroperoxide reductase, subunit F:->->:1290484..1290679 196 taagcaaccgactgactgaaaaaggttttacaatacaaaacattatggacagtctctcactctcctatcagccttcttccccaaaaagtaaaaaggcaggataggaaagtaagagactttttatttaacctgccgacaagacgaagaagattgcattctataacaaacaatacaaactaatttaaaaagcagaaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI1369:PI1370|PI1369:PI1370:alkyl hydroperoxide reductase, subunit C:alkyl hydroperoxide reductase, subunit F:->->:1290484..1290679 196 taagcaaccgactgactgaaaaaggttttacaatacaaaacattatggacagtctctcactctcctatcagccttcttccccaaaaagtaaaaaggcaggataggaaagtaagagactttttatttaacctgccgacaagacgaagaagattgcattctataacaaacaatacaaactaatttaaaaagcagaaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taagcaaccgactgactgaaaaaggttttacaatacaaaacattatggacagtctctcactctcctatcagccttcttccccaaaaagtaaaaaggcaggataggaaagtaagagactttttatttaacctgccgacaagacgaagaagattgcattctataacaaacaatacaaactaatttaaaaagcagaaat Predict ORF larger than 30AA ================================================ Protein_Len: 30 Strand: + Start: 12 End: 101 ........... M T E K G F T I Q N I M D S L S L S Y Q P S S P K S K K A G ............................................................................................... Protein_Len: 54 Strand: + Start: 16 End: 177 ............... M K K V L Q Y K T L W T V S H S P I S L L P Q K V K R Q D R K V R D F L F N L P T R R R R L H S I T N N T N ................... Protein_Len: 37 Strand: - Start: 60 End: 170 ........................................................... E G I L R R G W F T F L C S L F T L S K K N L R G V L R L L N C E I V F M .......................... taagcaaccgactgactgaaaaaggttttacaatacaaaacattatggacagtctctcactctcctatcagccttcttccccaaaaagtaaaaaggcaggataggaaagtaagagactttttatttaacctgccgacaagacgaagaagattgcattctataacaaacaatacaaactaatttaaaaagcagaaat 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================================================ taagcaaccgactgactgaaaaaggttttacaatacaaaacattatggacagtctctcactctcctatcagccttcttccccaaaaagtaaaaaggcaggataggaaagtaagagactttttatttaacctgccgacaagacgaagaagattgcattctataacaaacaatacaaactaatttaaaaagcagaaat Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PI1369:PI1370|PI1369:PI1370:alkyl hydroperoxide reductase, subunit C:alkyl hydroperoxide reductase, subunit F:->->:1290484..1290679 196 taagcaaccgactgactgaaaaaggttttacaatacaaaacattatggacagtctctcactctcctatcagccttcttccccaaaaagtaaaaaggcaggataggaaagtaagagactttttatttaacctgccgacaagacgaagaagattgcattctataacaaacaatacaaactaatttaaaaagcagaaat Intra-Species Hit: Count: 1 Min: 1 Max: 196 Len: 196 Subject: pint_PI1369_PI1370|alkyl hydroperoxide reductase, subunit C:alkyl hydroperoxide reductase, subunit F|POSITIVE:POSITIVE|[1290484,1290679]|196 HSP 1 e-value: 1.0E-107 bit: 389.0 Len: 196 Query Start:1 Query End:196 Subject Strand: POSITIVE Subject Start: 1 Subject End: 196 taagcaaccgactgactgaaaaaggttttacaatacaaaacattatggacagtctctcactctcctatcagccttcttccccaaaaagtaaaaaggcaggataggaaagtaagagactttttatttaacctgccgacaagacgaagaagattgcattctataacaaacaatacaaactaatttaaaaagcagaaat taagcaaccgactgactgaaaaaggttttacaatacaaaacattatggacagtctctcactctcctatcagccttcttccccaaaaagtaaaaaggcaggataggaaagtaagagactttttatttaacctgccgacaagacgaagaagattgcattctataacaaacaatacaaactaatttaaaaagcagaaat Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAGCAACCGACUGACUGAAAAAGGUUUUACAAUACAAAACAUUAUGGACAGUCUCUCACUCUCCUAUCAGCCUUCUUCCCCAAAAAGUAAAAAGGCAGGAUAGGAAAGUAAGAGACUUUUUAUUUAACCUGCCGACAAGACGAAGAAGAUUGCAUUCUAUAACAAACAAUACAAACUAAUUUAAAAAGCAGAAAU ...((((.(..((..((.....(((((.................(((((.(((((((.(((.(((((((.((((((((.......)))....)))))..))))))).))).))))))).)))))..))))).......))....))..).)))).......................................... (-38.71) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUUUCUGCUUUUUAAAUUAGUUUGUAUUGUUUGUUAUAGAAUGCAAUCUUCUUCGUCUUGUCGGCAGGUUAAAUAAAAAGUCUCUUACUUUCCUAUCCUGCCUUUUUACUUUUUGGGGAAGAAGGCUGAUAGGAGAGUGAGAGACUGUCCAUAAUGUUUUGUAUUGUAAAACCUUUUUCAGUCAGUCGGUUGCUUA ....................((((((........))))))..((((((..((..(((.....))).((((........(((((((((((((((((((..((((((((.(((....))))))))))).)))))))))))))))))))....((((((.....))))))..))))..........))..))))))... (-57.40) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 371 116 71 57 11 pint:PI0268|5end_lysozyme-related_protein_259198..259428_POSITIVE 288 154 129 34 11 pint:PI0918|5end_Fe-S_oxidoreductase,_family_2_847078..847308_POSITIVE 279 117 74 82 36 pint:PI0786|5end_conserved_hypothetical_protein;_possible_glycosyltransferase_723240..723470_POSITIVE 278 137 93 76 42 pint:PI1476|5end_acyl-CoA_synthase/O-succinylbenzoic_acid-CoA_ligase_1397699..1397929_POSITIVE 267 164 127 113 65 pint:PI1271|5end_transcriptional_regulator,__AraC/XylS_family_1190755..1190985_POSITIVE 261 159 111 175 125 pint:PI0815|5end_hypothetical_protein_754475..754705_POSITIVE 261 105 70 69 34 pint:PI0128|5end_dipeptidase,_pathogenicity_island-encoded_protein_D_120532..120762_POSITIVE 260 82 41 186 152 pint:PI0328|5end_conserved_hypothetical_protein_309476..309706_POSITIVE 259 154 115 122 81 pint:PI1818|5end_hypothetical_protein_1756891..1757121_POSITIVE 257 104 63 52 6 pint:PI1598|5end_phosphate_ABC_transporter,_phosphate-binding_component_1526646..1526876_POSITIVE 257 149 103 178 124 pint:PI1054|5end_conserved_hypothetical_protein_973696..973926_POSITIVE 255 99 51 83 25 pint:PI1495|5end_conserved_hypothetical_protein_1414432..1414662_POSITIVE 254 154 111 45 4 pint:PI0696|5end_NADH_pyrophosphatase,_MutT_family_hydrolase_(NAD+_diphosphatase)_632741..632971_POSITIVE 252 134 94 117 69 pint:PI1501|5end_GTP-binding_elongation_factor_family_protein_TypA/BipA_1421424..1421654_POSITIVE 252 46 2 92 42 pint:PI0347|5end_hypothetical_protein_321267..321497_POSITIVE 249 116 72 56 5 pint:PI0020|5end_conserved_hypothetical_protein_24525..24755_POSITIVE 247 76 40 64 29 pint:PI0097|5end_aspartate_aminotransferase_93235..93465_POSITIVE 245 100 51 127 75 pint:PI0705|5end_conserved_hypothetical_protein;_possible_lipoprotein_641274..641504_POSITIVE 244 149 102 175 114 pint:PI1137|5end_hypothetical_protein_1062970..1063200_POSITIVE 244 144 103 128 87 pint:PI0807|5end_hydrolase,_haloacid_dehalogenase-like_hydrolase_744407..744637_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 371 116 71 70 24 pint:PI0267|3end_conjugative_transposon_protein,_TraQ_259291..259441_POSITIVE 279 117 74 65 19 pint:PI0784|3end_possible_amidase_enhancer_precursor_723303..723453_POSITIVE 267 164 127 107 59 pint:PI1270|3end_probable_dipeptidyl_peptidase_1190829..1190979_POSITIVE 263 154 131 128 102 pint:PI1414|3end_conserved_hypothetical_protein_1334436..1334586_POSITIVE 263 135 95 90 42 pint:PI0410|3end_glutamyl-tRNA_synthetase_(glutamate--tRNA_ligase)_377490..377640_POSITIVE 262 136 91 91 34 pint:PI0107|3end_2-methylthioadenine_synthetase_104652..104802_POSITIVE 252 46 2 75 25 pint:PI0346|3end_hypothetical_protein_321330..321480_POSITIVE 250 159 120 46 4 pint:PI0814|3end_conserved_hypothetical_protein_754426..754576_POSITIVE 247 76 40 54 19 pint:PI0096|3end_glycerol-3-phosphate_cytidylyltransferase_93305..93455_POSITIVE 245 100 51 137 85 pint:PI0704|3end_conserved_hypothetical_protein_641364..641514_POSITIVE 243 155 111 71 16 pint:PI0007|3end_hypothetical_protein_7300..7450_POSITIVE 242 82 46 38 2 pint:PI1824|3end_ThiJ/PfpI_family_protein_1765005..1765155_POSITIVE 240 105 63 143 100 pint:PI1650|3end_N-acetylmuramoyl-L-alanine_amidase_1563901..1564051_POSITIVE 239 124 93 46 16 pint:PI1369|3end_alkyl_hydroperoxide_reductase,_subunit__C_1290423..1290573_POSITIVE 239 100 52 84 28 pint:PI1230|3end_probable_metallo-beta-lactamase_family_protein_1152729..1152879_POSITIVE 238 109 66 60 25 pint:PI2077|3end_hypothetical_protein_2036070..2036220_POSITIVE 238 139 95 138 93 pint:PI0682|3end_hypothetical_protein_619372..619522_POSITIVE 236 177 131 86 37 pint:PI0279|3end_hypothetical_protein_266081..266231_POSITIVE 234 154 127 67 37 pint:PI0671|3end_hypothetical_protein_611807..611957_POSITIVE 228 168 134 74 35 pint:PI0953|3end_hypothetical_protein_885390..885540_POSITIVE