Origin IGS: atcaaattgctgtgtaacaccgccacgcaacttgtcgaataattcttctttcttcattatagttcgtttttatgaagacgcaagacttccaacttgcgccttttataacta .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tagttataaaaggcgcaagttggaagtcttgcgtcttcataaaaacgaactataatgaagaaagaagaattattcgacaagttgcgtggcggtgttacacagcaatttgat Mask Tandem Repeat Region ================================================ atcaaattgctgtgtaacaccgccacgcaacttgtcgaataattcttctttcttcattatagttcgtttttatgaagacgcaagacttccaacttgcgccttttataacta Find is-nt database================================================ Query_seq: PI1333:PI1334|PI1333:PI1334:conserved hypothetical protein:ferrodoxin:->->:1251433..1251543 111 atcaaattgctgtgtaacaccgccacgcaacttgtcgaataattcttctttcttcattatagttcgtttttatgaagacgcaagacttccaacttgcgccttttataacta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI1333:PI1334|PI1333:PI1334:conserved hypothetical protein:ferrodoxin:->->:1251433..1251543 111 atcaaattgctgtgtaacaccgccacgcaacttgtcgaataattcttctttcttcattatagttcgtttttatgaagacgcaagacttccaacttgcgccttttataacta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI1333:PI1334|PI1333:PI1334:conserved hypothetical protein:ferrodoxin:->->:1251433..1251543 111 atcaaattgctgtgtaacaccgccacgcaacttgtcgaataattcttctttcttcattatagttcgtttttatgaagacgcaagacttccaacttgcgccttttataacta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 atcaaattgctgtgtaacaccgccacgcaacttgtcgaataattcttctttcttcattatagttcgtttttatgaagacgcaagacttccaacttgcgccttttataacta Predict ORF larger than 30AA ================================================ Protein_Len: 35 Strand: - Start: 5 End: 106 .... * I A T Y C R W A V Q R I I R R E E N Y N T K I F V C S K W S A G K M ..... atcaaattgctgtgtaacaccgccacgcaacttgtcgaataattcttctttcttcattatagttcgtttttatgaagacgcaagacttccaacttgcgccttttataacta Predict Promoter with matrix: RpoD-15 score > 80================================================ Predict Promoter with matrix: RpoD-16 score > 80================================================ Predict Promoter with matrix: RpoD-17 score > 80================================================ PromScan Matrix: RpoD-17 Strand: + Score: 81 Start: 31 End: 60 ..............................CTTGTCGAATAATTCTTCTTTCTTCATTAT................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ atcaaattgctgtgtaacaccgccacgcaacttgtcgaataattcttctttcttcattatagttcgtttttatgaagacgcaagacttccaacttgcgccttttataacta Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PI1333:PI1334|PI1333:PI1334:conserved hypothetical protein:ferrodoxin:->->:1251433..1251543 111 atcaaattgctgtgtaacaccgccacgcaacttgtcgaataattcttctttcttcattatagttcgtttttatgaagacgcaagacttccaacttgcgccttttataacta Intra-Species Hit: Count: 1 Min: 1 Max: 111 Len: 111 Subject: pint_PI1333_PI1334|conserved hypothetical protein:ferrodoxin|POSITIVE:POSITIVE|[1251433, 1251543]|111 HSP 1 e-value: 7.0E-57 bit: 220.0 Len: 111 Query Start:1 Query End:111 Subject Strand: POSITIVE Subject Start: 1 Subject End: 111 atcaaattgctgtgtaacaccgccacgcaacttgtcgaataattcttctttcttcattatagttcgtttttatgaagacgcaagacttccaacttgcgccttttataacta atcaaattgctgtgtaacaccgccacgcaacttgtcgaataattcttctttcttcattatagttcgtttttatgaagacgcaagacttccaacttgcgccttttataacta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUCAAAUUGCUGUGUAACACCGCCACGCAACUUGUCGAAUAAUUCUUCUUUCUUCAUUAUAGUUCGUUUUUAUGAAGACGCAAGACUUCCAACUUGCGCCUUUUAUAACUA ..(((.((((.(((.........))))))).))).(((((.((...............)).)))))...((((((((.((((((........))))))..))))))))... (-18.06) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAGUUAUAAAAGGCGCAAGUUGGAAGUCUUGCGUCUUCAUAAAAACGAACUAUAAUGAAGAAAGAAGAAUUAUUCGACAAGUUGCGUGGCGGUGUUACACAGCAAUUUGAU (((((....((((((((((........))))))))))..........)))))...........(((......)))..(((((((((((.........))).)))))))).. (-27.04) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 288 100 51 103 51 pint:PI1880|5end_phosphoenolpyruvate_carboxykinase_(ATP)_1821667..1821897_POSITIVE 278 107 62 103 62 pint:PI2137|5end_RNA_methylase_SpoU_family_2083173..2083403_POSITIVE 278 54 16 143 95 pint:PI0707|5end_conserved_hypothetical_protein;_possible_integral_membrane_protein_643358..643588_POSITIVE 273 39 7 67 38 pint:PI0168|5end_methionyl-tRNA_synthetase_(methionine--tRNA_ligase)_161181..161411_POSITIVE 272 39 7 73 39 pint:PI0089|5end_hypothetical_protein_88162..88392_POSITIVE 270 37 7 61 28 pint:PI1327|5end_conserved_hypothetical_protein_1245563..1245793_POSITIVE 265 39 7 132 98 pint:PI0867|5end_hypothetical_protein_803859..804089_POSITIVE 265 39 7 49 15 pint:PI0866|5end_hypothetical_protein_803776..804006_POSITIVE 265 39 7 132 98 pint:PI0119|5end_hypothetical_protein_111506..111736_POSITIVE 264 100 55 67 20 pint:PI0824|5end_large_conductance_mechanosensitive_channel_protein_763337..763567_POSITIVE 262 31 9 77 59 pint:PI1720|5end_conserved_hypothetical_protein_1636146..1636376_POSITIVE 253 53 11 137 99 pint:PI1332|5end_aminotransferase,_possible_pyridoxal-phosphate-dependent_aminotransferase_1249374..1249604_POSITIVE 253 48 7 211 170 pint:PI0080|5end_hypothetical_protein_79047..79277_POSITIVE 250 57 18 91 50 pint:PI0035|5end_NAD-dependent_protein_deacetylase,_SIR2_family_37873..38103_POSITIVE 249 101 78 116 90 pint:PI0762|5end_mannose-6-phosphate_isomerase,_class_I_696420..696650_POSITIVE 246 46 8 225 198 pint:PI1647|5end_hypothetical_protein_1561564..1561794_POSITIVE 242 25 2 231 208 pint:PI1229|5end_conserved_hypothetical_protein_1151260..1151490_POSITIVE 241 45 2 227 174 pint:PI0039|5end_conserved_hypothetical_protein;_possible_integral_membrane_protein_40503..40733_POSITIVE 241 42 3 42 1 pint:PI0013|5end_auxin-regulated_protein_15506..15736_POSITIVE 240 100 64 157 110 pint:PI0924|5end_possible_glycosyl_hydrolase_855004..855234_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 323 104 62 151 106 pint:PI2155|3end_hypothetical_protein_2101052..2101202_POSITIVE 278 107 62 103 62 pint:PI2135|3end_conserved_hypothetical_protein_2083253..2083403_POSITIVE 278 54 16 99 51 pint:PI0706|3end_pyridoxal_phosphate_biosynthetic_protein_(4-hydroxythreonine-4-phosphate_dehydrogenase)_643394..643544_POSITIVE 274 38 2 141 99 pint:PI0160|3end_conserved_hypothetical_protein_153268..153418_POSITIVE 273 39 7 64 35 pint:PI0166|3end_hypothetical_protein_161258..161408_POSITIVE 262 58 11 92 42 pint:PI1884|3end_conserved_hypothetical_protein_1827457..1827607_POSITIVE 262 31 9 58 40 pint:PI1719|3end_conserved_hypothetical_protein_1636207..1636357_POSITIVE 253 53 11 146 108 pint:PI1331|3end_conserved_hypothetical_protein_1249463..1249613_POSITIVE 250 40 7 126 91 pint:PI0819|3end_hypothetical_protein_759919..760069_POSITIVE 244 110 62 46 2 pint:PI0240|3end_conserved_hypothetical_protein_239342..239492_POSITIVE 242 88 45 146 95 pint:PI1572|3end_hypothetical_protein_1498215..1498365_POSITIVE 241 58 11 117 62 pint:PI1558|3end_conserved_hypothetical_protein_1476106..1476256_POSITIVE 240 50 7 144 110 pint:PI1227|3end_conserved_hypothetical_protein;_possible_DNA-binding_protein,_histone-like_family_1148974..1149124_POSITIVE 240 60 11 91 40 pint:PI1212|3end_shikimate_5-dehydrogenase_1131515..1131665_POSITIVE 240 100 64 124 77 pint:PI0923|3end_6-phosphofructokinase_855051..855201_POSITIVE 238 110 80 47 19 pint:PI2061|3end_type_I_restriction_enzyme_restriction_subunit_2021647..2021797_POSITIVE 236 67 23 119 78 pint:PI0802|3end_hypothetical_protein_739827..739977_POSITIVE 235 55 14 72 27 pint:PI0683|3end_hypothetical_protein_619797..619947_POSITIVE 235 47 9 74 40 pint:PI0302|3end_hypothetical_protein_287019..287169_POSITIVE 233 104 68 71 30 pint:PI1941|3end_outer_membrane_receptor;_ragA_protein_1900619..1900769_POSITIVE