Origin IGS: attttattttatgtttactaatctattatttgcaaagatagctaaaaactgatttatatcaaaacttgcaaggtgcttttttataattgttatactttttctatgttttgctaaataaaagtagt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 actacttttatttagcaaaacatagaaaaagtataacaattataaaaaagcaccttgcaagttttgatataaatcagtttttagctatctttgcaaataatagattagtaaacataaaataaaat Mask Tandem Repeat Region ================================================ attttattttatgtttactaatctattatttgcaaagatagctaaaaactgatttatatcaaaacttgcaaggtgcttttttataattgttatactttttctatgttttgctaaataaaagtagt Find is-nt database================================================ Query_seq: PI0656:PI0657|PI0656:PI0657:peptidase T (tripeptide aminopeptidase):conserved hypothetical protein:->->:601194..601318 125 attttattttatgtttactaatctattatttgcaaagatagctaaaaactgatttatatcaaaacttgcaaggtgcttttttataattgttatactttttctatgttttgctaaataaaagtagt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI0656:PI0657|PI0656:PI0657:peptidase T (tripeptide aminopeptidase):conserved hypothetical protein:->->:601194..601318 125 attttattttatgtttactaatctattatttgcaaagatagctaaaaactgatttatatcaaaacttgcaaggtgcttttttataattgttatactttttctatgttttgctaaataaaagtagt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI0656:PI0657|PI0656:PI0657:peptidase T (tripeptide aminopeptidase):conserved hypothetical protein:->->:601194..601318 125 attttattttatgtttactaatctattatttgcaaagatagctaaaaactgatttatatcaaaacttgcaaggtgcttttttataattgttatactttttctatgttttgctaaataaaagtagt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 attttattttatgtttactaatctattatttgcaaagatagctaaaaactgatttatatcaaaacttgcaaggtgcttttttataattgttatactttttctatgttttgctaaataaaagtagt Predict ORF larger than 30AA ================================================ attttattttatgtttactaatctattatttgcaaagatagctaaaaactgatttatatcaaaacttgcaaggtgcttttttataattgttatactttttctatgttttgctaaataaaagtagt 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================================================ attttattttatgtttactaatctattatttgcaaagatagctaaaaactgatttatatcaaaacttgcaaggtgcttttttataattgttatactttttctatgttttgctaaataaaagtagt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PI0656:PI0657|PI0656:PI0657:peptidase T (tripeptide aminopeptidase):conserved hypothetical protein:->->:601194..601318 125 attttattttatgtttactaatctattatttgcaaagatagctaaaaactgatttatatcaaaacttgcaaggtgcttttttataattgttatactttttctatgttttgctaaataaaagtagt Intra-Species Hit: Count: 1 Min: 1 Max: 125 Len: 125 Subject: pint_PI0656_PI0657|peptidase T (tripeptide aminopeptidase):conserved hypothetical protein|POSITIVE:POSITIVE|[601194,601318]|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 attttattttatgtttactaatctattatttgcaaagatagctaaaaactgatttatatcaaaacttgcaaggtgcttttttataattgttatactttttctatgttttgctaaataaaagtagt attttattttatgtttactaatctattatttgcaaagatagctaaaaactgatttatatcaaaacttgcaaggtgcttttttataattgttatactttttctatgttttgctaaataaaagtagt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUUUUAUUUUAUGUUUACUAAUCUAUUAUUUGCAAAGAUAGCUAAAAACUGAUUUAUAUCAAAACUUGCAAGGUGCUUUUUUAUAAUUGUUAUACUUUUUCUAUGUUUUGCUAAAUAAAAGUAGU ................((((..((.((((((((((((((((..(((...((((...(((.((((...((.....)).)))).)))...))))...)))..)))).)))))).)))))).)))))) (-14.30) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACUACUUUUAUUUAGCAAAACAUAGAAAAAGUAUAACAAUUAUAAAAAAGCACCUUGCAAGUUUUGAUAUAAAUCAGUUUUUAGCUAUCUUUGCAAAUAAUAGAUUAGUAAACAUAAAAUAAAAU ((((((.((((((.(((((..((((..((((..................((.....)).....(((((....))))).))))..)))).))))))))))).))..))))................ (-14.70) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 227 113 75 144 108 pint:PI0420|5end_hypothetical_protein_386551..386781_POSITIVE 227 113 75 130 94 pint:PI0417|5end_hypothetical_protein_386537..386767_POSITIVE 222 41 2 172 135 pint:PI0518|5end_5'-nucleotidase_precursor_477076..477306_POSITIVE 220 102 63 62 21 pint:PI1504|5end_non-specific_DNA-binding_protein_1424318..1424548_POSITIVE 220 60 28 208 176 pint:PI1361|5end_CTP_synthase_(UTP-ammonia_lyase)_1278245..1278475_POSITIVE 213 110 64 174 119 pint:PI0666|5end_chorismate_synthase_609006..609236_POSITIVE 208 67 29 163 122 pint:PI0234|5end_integrase_234473..234703_POSITIVE 206 92 56 100 67 pint:PI0554|5end_hypothetical_protein_504415..504645_POSITIVE 201 89 46 231 188 pint:PI1368|5end_enolase_(phosphopyruvate_hydratase)_1288123..1288353_POSITIVE 198 109 65 171 123 pint:PI0290|5end_conserved_hypothetical_protein_273245..273475_POSITIVE 196 74 41 204 171 pint:PI1933|5end_hypothetical_protein_1879925..1880155_POSITIVE 193 89 48 45 10 pint:PI2177|5end_phosphoribosylaminoimidazole_carboxylase_2117127..2117357_POSITIVE 191 94 53 195 149 pint:PI2149|5end_3-oxoacyl-acyl-carrier-protein_synthase_2095454..2095684_POSITIVE 191 109 68 134 86 pint:PI0698|5end_conserved_hypothetical_protein_635372..635602_POSITIVE 188 108 66 161 117 pint:PI0019|5end_conserved_hypothetical_protein_23742..23972_POSITIVE 186 76 37 156 116 pint:PI1766|5end_sugar_transporter,_possible_glucose/galactose_transporter_1693119..1693349_POSITIVE 185 76 40 123 93 pint:PI1439|5end_hypothetical_protein_1360009..1360239_POSITIVE 185 77 32 63 29 pint:PI0177|5end_2-oxoglutarate_synthase,_subunit_korB_168499..168729_POSITIVE 184 57 13 122 73 pint:PI1776|5end_probable_peptidase_of_the_M22_family_(inactive?_chaperone?))_1708623..1708853_POSITIVE 184 76 31 121 87 pint:PI0802|5end_hypothetical_protein_739544..739774_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 222 41 2 100 63 pint:PI0517|3end_apparent_PorT_homolog_477084..477234_POSITIVE 200 78 31 84 26 pint:PI1379|3end_hypothetical_protein_1302292..1302442_POSITIVE 198 109 65 96 48 pint:PI0289|3end_hypothetical_protein_273250..273400_POSITIVE 192 120 72 100 54 pint:PI0622|3end_hypothetical_protein_572087..572237_POSITIVE 186 76 37 135 95 pint:PI1765|3end_fructanase,_glycoside_hydrolase_family_1693178..1693328_POSITIVE 182 78 32 133 85 pint:PI0720|3end_conserved_hypothetical_protein_654460..654610_POSITIVE 177 80 31 131 92 pint:PI1512|3end_hypothetical_protein_1429893..1430043_POSITIVE 173 72 31 82 39 pint:PI1882|3end_hypothetical_protein_1826487..1826637_POSITIVE 172 78 31 52 5 pint:PI0447|3end_DNA-directed_RNA_polymerase,_beta'_subunit_421755..421905_POSITIVE 169 78 32 148 107 pint:PI0908|3end_conserved_hypothetical_protein_837612..837762_POSITIVE 169 107 65 144 94 pint:PI0758|3end_hypothetical_protein_690506..690656_POSITIVE 168 44 25 37 15 pint:PI1782|3end_possible_LPS_biosynthesis_protein_1715395..1715545_POSITIVE 167 74 43 119 75 pint:PI1443|3end_conserved_hypotehtical_protein;_possible_tonB-dependent_outer_membrane_receptor_1365344..1365494_POSITIVE 166 79 32 55 1 pint:PI1510|3end_cell_division_protein_1429274..1429424_POSITIVE 165 109 66 110 71 pint:PI1356|3end_hypothetical_protein_1273340..1273490_POSITIVE 163 80 32 41 1 pint:PI0065|3end_conserved_hypothetical_protein_65312..65462_POSITIVE 162 96 66 61 25 pint:PI0965|3end_hypothetical_protein_894392..894542_POSITIVE 160 77 31 110 62 pint:PI0734|3end_ABC_transporter,_ATP-binding_/_permease_668760..668910_POSITIVE 157 107 64 69 24 pint:PI2061|3end_type_I_restriction_enzyme_restriction_subunit_2021647..2021797_POSITIVE 157 44 24 124 104 pint:PI1786|3end_hypothetical_protein_1718380..1718530_POSITIVE