Origin IGS: aggattgcctcgtactatacttcccactgaaaagagtacaagtaaaagcaatattttcttcataagattatacgtttagttctaaagtaattctaattctattatatttatagtctaaaattctcccaactctacaagttacaatagcaaacttctttaaagttaccttaacttcttttttgtttaaaggaaacccataacctaattgcagatatgagtttccttaagtattccgaacgaattctacatcgtactcaaacatttataaactactgttctttcgatgcaaattcgtttctcagcattgctta .........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.........1.........2.........3.........4.........5.........6.........7.........8.........9 taagcaatgctgagaaacgaatttgcatcgaaagaacagtagtttataaatgtttgagtacgatgtagaattcgttcggaatacttaaggaaactcatatctgcaattaggttatgggtttcctttaaacaaaaaagaagttaaggtaactttaaagaagtttgctattgtaacttgtagagttgggagaattttagactataaatataatagaattagaattactttagaactaaacgtataatcttatgaagaaaatattgcttttacttgtactcttttcagtgggaagtatagtacgaggcaatcct Mask Tandem Repeat Region ================================================ aggattgcctcgtactatacttcccactgaaaagagtacaagtaaaagcaatattttcttcataagattatacgtttagttctaaagtaattctaattctattatatttatagtctaaaattctcccaactctacaagttacaatagcaaacttctttaaagttaccttaacttcttttttgtttaaaggaaacccataacctaattgcagatatgagtttccttaagtattccgaacgaattctacatcgtactcaaacatttataaactactgttctttcgatgcaaattcgtttctcagcattgctta Find is-nt database================================================ Query_seq: PI1993:PI1995|PI1993:PI1995:thiol protease/hemagglutinin, PrtT precursor:hypothetical protein:->->:1949053..1949363 311 aggattgcctcgtactatacttcccactgaaaagagtacaagtaaaagcaatattttcttcataagattatacgtttagttctaaagtaattctaattctattatatttatagtctaaaattctcccaactctacaagttacaatagcaaacttctttaaagttaccttaacttcttttttgtttaaaggaaacccataacctaattgcagatatgagtttccttaagtattccgaacgaattctacatcgtactcaaacatttataaactactgttctttcgatgcaaattcgtttctcagcattgctta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI1993:PI1995|PI1993:PI1995:thiol protease/hemagglutinin, PrtT precursor:hypothetical protein:->->:1949053..1949363 311 aggattgcctcgtactatacttcccactgaaaagagtacaagtaaaagcaatattttcttcataagattatacgtttagttctaaagtaattctaattctattatatttatagtctaaaattctcccaactctacaagttacaatagcaaacttctttaaagttaccttaacttcttttttgtttaaaggaaacccataacctaattgcagatatgagtttccttaagtattccgaacgaattctacatcgtactcaaacatttataaactactgttctttcgatgcaaattcgtttctcagcattgctta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI1993:PI1995|PI1993:PI1995:thiol protease/hemagglutinin, PrtT precursor:hypothetical protein:->->:1949053..1949363 311 aggattgcctcgtactatacttcccactgaaaagagtacaagtaaaagcaatattttcttcataagattatacgtttagttctaaagtaattctaattctattatatttatagtctaaaattctcccaactctacaagttacaatagcaaacttctttaaagttaccttaacttcttttttgtttaaaggaaacccataacctaattgcagatatgagtttccttaagtattccgaacgaattctacatcgtactcaaacatttataaactactgttctttcgatgcaaattcgtttctcagcattgctta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aggattgcctcgtactatacttcccactgaaaagagtacaagtaaaagcaatattttcttcataagattatacgtttagttctaaagtaattctaattctattatatttatagtctaaaattctcccaactctacaagttacaatagcaaacttctttaaagttaccttaacttcttttttgtttaaaggaaacccataacctaattgcagatatgagtttccttaagtattccgaacgaattctacatcgtactcaaacatttataaactactgttctttcgatgcaaattcgtttctcagcattgctta Predict ORF larger than 30AA ================================================ Protein_Len: 35 Strand: + Start: 205 End: 309 ............................................................................................................................................................................................................ M A D M S F L K Y S E R I L H R T Q T F I N Y C S F D A N S F L S I A .. Protein_Len: 47 Strand: - Start: 71 End: 211 ...................................................................... V N L E L T I R I R N Y K Y D L I R G V R C T V I A F K K L T V K V E K K N L P F G Y G L Q M .................................................................................................... aggattgcctcgtactatacttcccactgaaaagagtacaagtaaaagcaatattttcttcataagattatacgtttagttctaaagtaattctaattctattatatttatagtctaaaattctcccaactctacaagttacaatagcaaacttctttaaagttaccttaacttcttttttgtttaaaggaaacccataacctaattgcagatatgagtttccttaagtattccgaacgaattctacatcgtactcaaacatttataaactactgttctttcgatgcaaattcgtttctcagcattgctta 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: 85 Start: 241 End: 270 ................................................................................................................................................................................................................................................GTTTATAAATGTTTGAGTACGATGTAGAAT......................................... PromScan Matrix: RpoD-17 Strand: - Score: 82 Start: 101 End: 130 ....................................................................................................GTTGGGAGAATTTTAGACTATAAATATAAT..................................................................................................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aggattgcctcgtactatacttcccactgaaaagagtacaagtaaaagcaatattttcttcataagattatacgtttagttctaaagtaattctaattctattatatttatagtctaaaattctcccaactctacaagttacaatagcaaacttctttaaagttaccttaacttcttttttgtttaaaggaaacccataacctaattgcagatatgagtttccttaagtattccgaacgaattctacatcgtactcaaacatttataaactactgttctttcgatgcaaattcgtttctcagcattgctta Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 74 HP_score: -2.3 Tail_Score: -5.63517 Start: 159 End: 175 Full_Region: ATAGCAAACTTCTTT AAAGTTA CCT TAACTTC TTTTTTGTTTAAAGG ..............................................................................................................................................................AAAGTTACCTTAACTTC........................................................................................................................................ TransTerm Strand: + Conf: 70 HP_score: -4.0 Tail_Score: -4.88687 Start: 162 End: 172 Full_Region: GCAAACTTCTTTAAA GTTA CCT TAAC TTCTTTTTTGTTTAA .................................................................................................................................................................GTTACCTTAAC........................................................................................................................................... Find igs database================================================ Query_seq: PI1993:PI1995|PI1993:PI1995:thiol protease/hemagglutinin, PrtT precursor:hypothetical protein:->->:1949053..1949363 311 aggattgcctcgtactatacttcccactgaaaagagtacaagtaaaagcaatattttcttcataagattatacgtttagttctaaagtaattctaattctattatatttatagtctaaaattctcccaactctacaagttacaatagcaaacttctttaaagttaccttaacttcttttttgtttaaaggaaacccataacctaattgcagatatgagtttccttaagtattccgaacgaattctacatcgtactcaaacatttataaactactgttctttcgatgcaaattcgtttctcagcattgctta Intra-Species Hit: Count: 1 Min: 1 Max: 311 Len: 311 Subject: pint_PI1993_PI1995|thiol protease/hemagglutinin, PrtT precursor:hypothetical protein|POSITIVE:POSITIVE|[1949053,1949363]|311 HSP 1 e-value: 1.0E-175 bit: 617.0 Len: 311 Query Start:1 Query End:311 Subject Strand: POSITIVE Subject Start: 1 Subject End: 311 aggattgcctcgtactatacttcccactgaaaagagtacaagtaaaagcaatattttcttcataagattatacgtttagttctaaagtaattctaattctattatatttatagtctaaaattctcccaactctacaagttacaatagcaaacttctttaaagttaccttaacttcttttttgtttaaaggaaacccataacctaattgcagatatgagtttccttaagtattccgaacgaattctacatcgtactcaaacatttataaactactgttctttcgatgcaaattcgtttctcagcattgctta aggattgcctcgtactatacttcccactgaaaagagtacaagtaaaagcaatattttcttcataagattatacgtttagttctaaagtaattctaattctattatatttatagtctaaaattctcccaactctacaagttacaatagcaaacttctttaaagttaccttaacttcttttttgtttaaaggaaacccataacctaattgcagatatgagtttccttaagtattccgaacgaattctacatcgtactcaaacatttataaactactgttctttcgatgcaaattcgtttctcagcattgctta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGGAUUGCCUCGUACUAUACUUCCCACUGAAAAGAGUACAAGUAAAAGCAAUAUUUUCUUCAUAAGAUUAUACGUUUAGUUCUAAAGUAAUUCUAAUUCUAUUAUAUUUAUAGUCUAAAAUUCUCCCAACUCUACAAGUUACAAUAGCAAACUUCUUUAAAGUUACCUUAACUUCUUUUUUGUUUAAAGGAAACCCAUAACCUAAUUGCAGAUAUGAGUUUCCUUAAGUAUUCCGAACGAAUUCUACAUCGUACUCAAACAUUUAUAAACUACUGUUCUUUCGAUGCAAAUUCGUUUCUCAGCAUUGCUUA (((....))).(((((....(((.....)))...)))))......(((((((............((((((((.((.((((.....((.....))......)))).)).)))))))).......................(((......((((.......((((((...)))))).......)))).((((((((.((((..((......)).)))).))))))))..)))....(((((((((...(((((......((((............))))....)))))..)))))))))......))))))). (-46.14) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAGCAAUGCUGAGAAACGAAUUUGCAUCGAAAGAACAGUAGUUUAUAAAUGUUUGAGUACGAUGUAGAAUUCGUUCGGAAUACUUAAGGAAACUCAUAUCUGCAAUUAGGUUAUGGGUUUCCUUUAAACAAAAAAGAAGUUAAGGUAACUUUAAAGAAGUUUGCUAUUGUAACUUGUAGAGUUGGGAGAAUUUUAGACUAUAAAUAUAAUAGAAUUAGAAUUACUUUAGAACUAAACGUAUAAUCUUAUGAAGAAAAUAUUGCUUUUACUUGUACUCUUUUCAGUGGGAAGUAUAGUACGAGGCAAUCCU .((((((((((((...(((((((((((((((..(((((............)))))...).)))))))).)))))))))).((((..(((((((((((((((((....)))).)))))))))))))..........(.((((((.(((((((((...)))).)))))....)))))).)..((((.((((((((((((.((((.......))))..)))))))).))))..))))....))))................))))))))...(((((((((((((.....)))))...))))))))........ (-72.50) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 289 308 265 52 12 pint:PI0705|5end_conserved_hypothetical_protein;_possible_lipoprotein_641274..641504_POSITIVE 273 152 113 119 83 pint:PI1115|5end_conserved_hypothetical_protein_1039244..1039474_POSITIVE 264 308 270 171 131 pint:PI0088|5end_S-adenosylmethionine_synthetase_86663..86893_POSITIVE 261 169 125 98 47 pint:PI1120|5end_conserved_hypothetical_protein_1044870..1045100_POSITIVE 258 300 251 197 152 pint:PI2040|5end_conserved_hypothetical_protein;_possible_transporter_1993068..1993298_POSITIVE 256 240 196 64 13 pint:PI0159|5end_hypothetical_protein_151273..151503_POSITIVE 248 309 273 131 95 pint:PI1475|5end_possible_short_chain_dehydrogenase_1397142..1397372_POSITIVE 247 39 1 215 175 pint:PI0334|5end_hypothetical_protein_313234..313464_POSITIVE 241 39 1 217 179 pint:PI0697|5end_5'-nucleotidase_family_protein_633560..633790_POSITIVE 238 216 171 227 173 pint:PI2126|5end_conserved_hypothetical_protein_2074907..2075137_POSITIVE 238 36 5 57 29 pint:PI0424|5end_methylated-DNA--[protein]-cysteine_S-methyltransferase_388429..388659_POSITIVE 234 173 134 141 101 pint:PI0791|5end_conserved_hypothetical_protein_728361..728591_POSITIVE 234 52 23 106 73 pint:PI0171|5end_hypothetical_protein_163850..164080_POSITIVE 232 308 270 58 17 pint:PI0335|5end_hypothetical_protein_313708..313938_POSITIVE 228 152 113 58 17 pint:PI1379|5end_hypothetical_protein_1301817..1302047_POSITIVE 228 236 194 137 88 pint:PI0560|5end_hypothetical_protein_508600..508830_POSITIVE 226 257 216 198 166 pint:PI1266|5end_hypothetical_protein_1185351..1185581_POSITIVE 224 310 273 186 147 pint:PI1413|5end_hypothetical_protein_1333727..1333957_POSITIVE 224 218 180 223 182 pint:PI1198|5end_acetyltransferase_1114582..1114812_POSITIVE 223 29 8 51 30 pint:PI2121|5end_glucose_inhibited_division_protein_A_2069889..2070119_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 289 308 265 62 22 pint:PI0704|3end_conserved_hypothetical_protein_641364..641514_POSITIVE 261 169 125 88 37 pint:PI1119|3end_glycosyl_transferases,_group_1_1044940..1045090_POSITIVE 260 212 172 120 80 pint:PI1865|3end_chromate_transport_protein_1811587..1811737_POSITIVE 256 240 196 98 47 pint:PI0157|3end_hypothetical_protein_151387..151537_POSITIVE 234 308 278 94 56 pint:PI1143|3end_hypothetical_protein_1070504..1070654_POSITIVE 234 173 134 85 45 pint:PI0789|3end_NAD-utilizing_dehydrogenase_728385..728535_POSITIVE 234 52 23 67 34 pint:PI0170|3end_hypothetical_protein_163891..164041_POSITIVE 233 310 262 148 104 pint:PI0664|3end_dihydroorotate_dehydrogenase,_electron_transfer_subunit_607819..607969_POSITIVE 232 308 270 58 17 pint:PI0333|3end_hypothetical_protein_313788..313938_POSITIVE 224 215 171 74 23 pint:PI1610|3end_Na+/H+_anti-porter_1538002..1538152_POSITIVE 224 218 180 50 9 pint:PI1197|3end_pseudouridylate_synthetase_1114489..1114639_POSITIVE 221 309 261 130 76 pint:PI2130|3end_DNA_polymerase_I_2080711..2080861_POSITIVE 220 310 273 76 32 pint:PI1940|3end_conserved_hypothetical_protein;_possible_outer_membrane_protein_1897267..1897417_POSITIVE 218 49 2 105 51 pint:PI0931|3end_hypothetical_protein_863073..863223_POSITIVE 217 310 262 105 58 pint:PI2085|3end_conserved_hypothetical_protein_2041803..2041953_POSITIVE 216 303 275 143 100 pint:PI2020|3end_glycosyl_transferase,_group_2_family_protein_1977926..1978076_POSITIVE 215 286 242 77 32 pint:PI0091|3end_hypothetical_protein_89774..89924_POSITIVE 213 209 166 113 73 pint:PI1444|3end_protease_ClpB_1368137..1368287_POSITIVE 213 236 193 116 62 pint:PI0154|3end_possible_UDP-2,3-diacylglucosamine_hydrolase_148311..148461_POSITIVE 211 308 282 56 33 pint:PI0809|3end_hypothetical_protein_747108..747258_POSITIVE