Origin IGS: tagttgtgtctttaatggcaatttgttgatgttcacatattatataatagcgaattaaaaaataagtaaaagcgatggcagatttaagtgtaaatataggcaacctacaactaaagaaccctgta .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tacagggttctttagttgtaggttgcctatatttacacttaaatctgccatcgcttttacttattttttaattcgctattatataatatgtgaacatcaacaaattgccattaaagacacaacta Mask Tandem Repeat Region ================================================ tagttgtgtctttaatggcaatttgttgatgttcacatattatataatagcgaattaaaaaataagtaaaagcgatggcagatttaagtgtaaatataggcaacctacaactaaagaaccctgta Find is-nt database================================================ Query_seq: PI0664:PI0665|PI0664:PI0665:dihydroorotate dehydrogenase, electron transfer subunit:dihydroorotate dehydrogenase:->->:607880..608004 125 tagttgtgtctttaatggcaatttgttgatgttcacatattatataatagcgaattaaaaaataagtaaaagcgatggcagatttaagtgtaaatataggcaacctacaactaaagaaccctgta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI0664:PI0665|PI0664:PI0665:dihydroorotate dehydrogenase, electron transfer subunit:dihydroorotate dehydrogenase:->->:607880..608004 125 tagttgtgtctttaatggcaatttgttgatgttcacatattatataatagcgaattaaaaaataagtaaaagcgatggcagatttaagtgtaaatataggcaacctacaactaaagaaccctgta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI0664:PI0665|PI0664:PI0665:dihydroorotate dehydrogenase, electron transfer subunit:dihydroorotate dehydrogenase:->->:607880..608004 125 tagttgtgtctttaatggcaatttgttgatgttcacatattatataatagcgaattaaaaaataagtaaaagcgatggcagatttaagtgtaaatataggcaacctacaactaaagaaccctgta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tagttgtgtctttaatggcaatttgttgatgttcacatattatataatagcgaattaaaaaataagtaaaagcgatggcagatttaagtgtaaatataggcaacctacaactaaagaaccctgta Predict ORF larger than 30AA ================================================ Protein_Len: 34 Strand: - Start: 2 End: 103 . T T D K I A I Q Q H E C I I Y Y R I L F Y T F A I A S K L T F I P M ...................... tagttgtgtctttaatggcaatttgttgatgttcacatattatataatagcgaattaaaaaataagtaaaagcgatggcagatttaagtgtaaatataggcaacctacaactaaagaaccctgta 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================================================ tagttgtgtctttaatggcaatttgttgatgttcacatattatataatagcgaattaaaaaataagtaaaagcgatggcagatttaagtgtaaatataggcaacctacaactaaagaaccctgta Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PI0664:PI0665|PI0664:PI0665:dihydroorotate dehydrogenase, electron transfer subunit:dihydroorotate dehydrogenase:->->:607880..608004 125 tagttgtgtctttaatggcaatttgttgatgttcacatattatataatagcgaattaaaaaataagtaaaagcgatggcagatttaagtgtaaatataggcaacctacaactaaagaaccctgta Intra-Species Hit: Count: 1 Min: 1 Max: 125 Len: 125 Subject: pint_PI0664_PI0665|dihydroorotate dehydrogenase, electron transfer subunit:dihydroorotate dehydrogenase|POSITIVE:POSITIVE|[607880,608004]|125 HSP 1 e-value: 4.0E-65 bit: 248.0 Len: 125 Query Start:1 Query End:125 Subject Strand: POSITIVE Subject Start: 1 Subject End: 125 tagttgtgtctttaatggcaatttgttgatgttcacatattatataatagcgaattaaaaaataagtaaaagcgatggcagatttaagtgtaaatataggcaacctacaactaaagaaccctgta tagttgtgtctttaatggcaatttgttgatgttcacatattatataatagcgaattaaaaaataagtaaaagcgatggcagatttaagtgtaaatataggcaacctacaactaaagaaccctgta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAGUUGUGUCUUUAAUGGCAAUUUGUUGAUGUUCACAUAUUAUAUAAUAGCGAAUUAAAAAAUAAGUAAAAGCGAUGGCAGAUUUAAGUGUAAAUAUAGGCAACCUACAACUAAAGAACCCUGUA ((((((((((......)))...((((..(((((.((((...........((..(((....)))..))....((....))........)))).)))))..))))...)))))))............ (-18.00) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UACAGGGUUCUUUAGUUGUAGGUUGCCUAUAUUUACACUUAAAUCUGCCAUCGCUUUUACUUAUUUUUUAAUUCGCUAUUAUAUAAUAUGUGAACAUCAACAAAUUGCCAUUAAAGACACAACUA ......((((((((((.((((.(((.....................((....)).(((((.((((...((((.....))))...)))).)))))......))).)))).)))))))).))..... (-15.20) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 293 106 61 146 104 pint:PI0094|5end_protoporphyrinogen_oxidase_89571..89801_POSITIVE 293 106 61 72 30 pint:PI0091|5end_hypothetical_protein_89497..89727_POSITIVE 274 106 64 204 157 pint:PI0846|5end_transcription_regulator,_CRP_family_780435..780665_POSITIVE 256 102 64 101 66 pint:PI0168|5end_methionyl-tRNA_synthetase_(methionine--tRNA_ligase)_161181..161411_POSITIVE 252 110 66 218 167 pint:PI1969|5end_hypothetical_protein_1925496..1925726_POSITIVE 248 120 72 206 151 pint:PI0981|5end_outer_membrane_protein,_TonB_dependent_receptor_906968..907198_POSITIVE 247 81 42 139 104 pint:PI1774|5end_hypothetical_protein_1706184..1706414_POSITIVE 239 110 72 141 98 pint:PI0304|5end_hypothetical_protein_288582..288812_POSITIVE 233 120 78 43 1 pint:PI0228|5end_outer_membrane_cobalamin_receptor_protein_225752..225982_POSITIVE 229 102 65 90 53 pint:PI0910|5end_possible_sodium_hydrogen_antiporter_(Na+/H+_antiporter)_838085..838315_POSITIVE 224 102 62 170 120 pint:PI0920|5end_xanthan_lyase_849688..849918_POSITIVE 223 108 72 199 157 pint:PI1822|5end_ABC_transporter,_ATP-binding_/_permease_1761452..1761682_POSITIVE 222 82 44 54 24 pint:PI2028|5end_shikimate_kinase_1982162..1982392_POSITIVE 222 108 64 107 62 pint:PI0889|5end_pyruvate_kinase_818758..818988_POSITIVE 221 120 77 137 104 pint:PI0604|5end_O-succinylbenzoic_acid--CoA_ligase_550825..551055_POSITIVE 220 39 2 50 10 pint:PI0823|5end_glyceraldehyde_3-phosphate_dehydrogenase,_type_I_762042..762272_POSITIVE 219 101 61 134 93 pint:PI0321|5end_conserved_hypothetical_protein_302598..302828_POSITIVE 218 102 64 134 89 pint:PI1539|5end_3-phosphoshikimate_1-carboxyvinyltransferase_1459804..1460034_POSITIVE 218 53 15 135 96 pint:PI1428|5end_quinolinate_synthetase_A_1346626..1346856_POSITIVE 214 109 65 65 6 pint:PI1131|5end_folylpolyglutamate_synthase_1057124..1057354_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 293 106 61 146 104 pint:PI0092|3end_regulatory_protein_RecX_89651..89801_POSITIVE 274 106 64 128 81 pint:PI0845|3end_peptidyl-dipeptidase_780439..780589_POSITIVE 256 102 64 98 63 pint:PI0166|3end_hypothetical_protein_161258..161408_POSITIVE 243 36 3 97 68 pint:PI1191|3end_phosphoribosyl_pyrophosphate_synthetase_1110377..1110527_POSITIVE 224 102 62 121 71 pint:PI0919|3end_conserved_hypothetical_protein_849719..849869_POSITIVE 224 105 65 43 1 pint:PI0028|3end_aminopeptidase_32727..32877_POSITIVE 221 120 77 73 40 pint:PI0603|3end_3-dehydroquinate_synthase_550841..550991_POSITIVE 219 101 61 108 67 pint:PI0320|3end_probable_cobalamin_adenosyltransferase_302652..302802_POSITIVE 218 102 64 112 67 pint:PI1538|3end_conserved_hypothetical_protein_1459862..1460012_POSITIVE 218 53 15 89 50 pint:PI1427|3end_nicotinate-nucleotide_pyrophosphorylase_1346660..1346810_POSITIVE 213 112 71 137 101 pint:PI1749|3end_conserved_hypothetical_protein_1671637..1671787_POSITIVE 213 105 77 72 41 pint:PI1174|3end_hypothetical_protein_1097042..1097192_POSITIVE 210 90 50 60 29 pint:PI0925|3end_ribosomal_protein_L11_methyltransferase_856638..856788_POSITIVE 209 81 55 36 9 pint:PI1020|3end_hypothetical_protein_938779..938929_POSITIVE 207 83 48 84 41 pint:PI1885|3end_cell_division_protein_1827639..1827789_POSITIVE 205 51 12 99 63 pint:PI1614|3end_hypothetical_protein_1541408..1541558_POSITIVE 202 97 62 50 18 pint:PI0659|3end_hypothetical_protein_603396..603546_POSITIVE 200 116 71 86 40 pint:PI1990|3end_hypothetical_protein_1944766..1944916_POSITIVE 199 35 9 66 44 pint:PI0935|3end_collagenase,_protease_868320..868470_POSITIVE 198 119 71 149 84 pint:PI0184|3end_possible_fibronectin_type_III_domain_protein_176516..176666_POSITIVE