Origin IGS: ctttattgtttttatttctgcttgtaaaggtacaaaaaaaagcgtaagtctcaaaaagacttacgcttttttaattctatattaccatattaaagtcttgacaaaactttaacaaggtataatagttagctttaaatta .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 taatttaaagctaactattataccttgttaaagttttgtcaagactttaatatggtaatatagaattaaaaaagcgtaagtctttttgagacttacgcttttttttgtacctttacaagcagaaataaaaacaataaag Mask Tandem Repeat Region ================================================ ctttattgtttttatttctgcttgtaaaggtacaaaaaaaagcgtaagtctcaaaaagacttacgcttttttaattctatattaccatattaaagtcttgacaaaactttaacaaggtataatagttagctttaaatta Find is-nt database================================================ Query_seq: PI1238:PI1239|PI1238:PI1239:single-strand DNA-specific exonuclease:possible peptidase C1-like family (aminopeptidase C):->->:1163499..1163637 139 ctttattgtttttatttctgcttgtaaaggtacaaaaaaaagcgtaagtctcaaaaagacttacgcttttttaattctatattaccatattaaagtcttgacaaaactttaacaaggtataatagttagctttaaatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI1238:PI1239|PI1238:PI1239:single-strand DNA-specific exonuclease:possible peptidase C1-like family (aminopeptidase C):->->:1163499..1163637 139 ctttattgtttttatttctgcttgtaaaggtacaaaaaaaagcgtaagtctcaaaaagacttacgcttttttaattctatattaccatattaaagtcttgacaaaactttaacaaggtataatagttagctttaaatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI1238:PI1239|PI1238:PI1239:single-strand DNA-specific exonuclease:possible peptidase C1-like family (aminopeptidase C):->->:1163499..1163637 139 ctttattgtttttatttctgcttgtaaaggtacaaaaaaaagcgtaagtctcaaaaagacttacgcttttttaattctatattaccatattaaagtcttgacaaaactttaacaaggtataatagttagctttaaatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ctttattgtttttatttctgcttgtaaaggtacaaaaaaaagcgtaagtctcaaaaagacttacgcttttttaattctatattaccatattaaagtcttgacaaaactttaacaaggtataatagttagctttaaatta Predict ORF larger than 30AA ================================================ Protein_Len: 35 Strand: + Start: 5 End: 109 .... M V F I S A C K G T K K S V S L K K T Y A F L I L Y Y H I K V L T K L .............................. ctttattgtttttatttctgcttgtaaaggtacaaaaaaaagcgtaagtctcaaaaagacttacgcttttttaattctatattaccatattaaagtcttgacaaaactttaacaaggtataatagttagctttaaatta 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: 97 End: 126 ................................................................................................CTTGACAAAACTTTAACAAGGTATAATAGT............. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ ctttattgtttttatttctgcttgtaaaggtacaaaaaaaagcgtaagtctcaaaaagacttacgcttttttaattctatattaccatattaaagtcttgacaaaactttaacaaggtataatagttagctttaaatta Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 100 HP_score: -13.0 Tail_Score: -5.35354 Start: 42 End: 66 Full_Region: AAGGTACAAAAAAAA GCGTAAGTCT CAAAA AGACTTACGC TTTTTTAATTCTATA .........................................GCGTAAGTCTCAAAAAGACTTACGC......................................................................... TransTerm Strand: - Conf: 100 HP_score: -13.7 Tail_Score: -5.97575 Start: 42 End: 66 Full_Region: tatagaattaaaaaa gcgtaagtctt ttt gagacttacgc ttttttttgtacctt .........................................gcgtaagtctttttgagacttacgc......................................................................... Find igs database================================================ Query_seq: PI1238:PI1239|PI1238:PI1239:single-strand DNA-specific exonuclease:possible peptidase C1-like family (aminopeptidase C):->->:1163499..1163637 139 ctttattgtttttatttctgcttgtaaaggtacaaaaaaaagcgtaagtctcaaaaagacttacgcttttttaattctatattaccatattaaagtcttgacaaaactttaacaaggtataatagttagctttaaatta Intra-Species Hit: Count: 1 Min: 1 Max: 139 Len: 139 Subject: pint_PI1238_PI1239|single-strand DNA-specific exonuclease:possible peptidase C1-like family (aminopeptidase C)|POSITIVE:POSITIVE|[1163499,1163637]|139 HSP 1 e-value: 4.0E-59 bit: 228.0 Len: 139 Query Start:1 Query End:139 Subject Strand: POSITIVE Subject Start: 1 Subject End: 139 ctttattgtttttatttctgcttgtaaaggtacnnnnnnnngcgtaagtctcaaaaagacttacgcttttttaattctatattaccatattaaagtcttgacaaaactttaacaaggtataatagttagctttaaatta ctttattgtttttatttctgcttgtaaaggtacaaaaaaaagcgtaagtctcaaaaagacttacgcttttttaattctatattaccatattaaagtcttgacaaaactttaacaaggtataatagttagctttaaatta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUUUAUUGUUUUUAUUUCUGCUUGUAAAGGUACAAAAAAAAGCGUAAGUCUCAAAAAGACUUACGCUUUUUUAAUUCUAUAUUACCAUAUUAAAGUCUUGACAAAACUUUAACAAGGUAUAAUAGUUAGCUUUAAAUUA .((((..(((.(((((....(((((.(((((....((((((((((((((((.....))))))))))))))))......................((....))...))))).)))))....)))))..)))..))))... (-32.90) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAUUUAAAGCUAACUAUUAUACCUUGUUAAAGUUUUGUCAAGACUUUAAUAUGGUAAUAUAGAAUUAAAAAAGCGUAAGUCUUUUUGAGACUUACGCUUUUUUUUGUACCUUUACAAGCAGAAAUAAAAACAAUAAAG .........(((..((((..((((.(((((((((((.....))))))))))).))))..))))....(((((((((((((((((...))))))))))))))))).............)))................... (-40.00) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 244 35 2 231 204 pint:PI0985|5end_aspartyl-tRNA_synthetase_910174..910404_POSITIVE 242 110 64 221 180 pint:PI0480|5end_preprotein_translocase,_SecY_subunit_441576..441806_POSITIVE 240 69 22 80 36 pint:PI0926|5end_hypothetical_protein_856824..857054_POSITIVE 233 86 41 75 42 pint:PI0660|5end_conserved_hypothetical_protein_603438..603668_POSITIVE 227 80 32 179 124 pint:PI1775|5end_hypothetical_protein_1707255..1707485_POSITIVE 220 84 41 182 137 pint:PI1938|5end_hypothetical_protein_1891854..1892084_POSITIVE 218 70 22 109 64 pint:PI1760|5end_hypothetical_protein_1684413..1684643_POSITIVE 218 70 22 81 36 pint:PI1702|5end_hypothetical_protein_1620587..1620817_POSITIVE 215 69 21 158 100 pint:PI1769|5end_hypothetical_protein_1696507..1696737_POSITIVE 204 60 16 206 163 pint:PI0395|5end_Na+-driven_multidrug_efflux_pump_360388..360618_POSITIVE 203 70 21 200 145 pint:PI1324|5end_conserved_hypothetical_protein_1242520..1242750_POSITIVE 197 32 1 164 135 pint:PI1549|5end_conserved_hypothetical_protein_1467021..1467251_POSITIVE 196 43 6 133 101 pint:PI1326|5end_Na+-driven_multidrug_efflux_pump_1244182..1244412_POSITIVE 196 130 91 99 57 pint:PI1193|5end_conserved_hypothetical_protein_1110436..1110666_POSITIVE 194 69 21 230 175 pint:PI0770|5end_hypothetical_protein_706170..706400_POSITIVE 194 60 24 166 132 pint:PI0101|5end_lauroyl/myristoyl_acyltransferase_96729..96959_POSITIVE 194 47 9 158 128 pint:PI0056|5end_conserved_hypothetical_protein;_possible_DNA_uptake_protein_54967..55197_POSITIVE 193 88 41 202 159 pint:PI0786|5end_conserved_hypothetical_protein;_possible_glycosyltransferase_723240..723470_POSITIVE 193 88 41 106 63 pint:PI0783|5end_hypothetical_protein_723144..723374_POSITIVE 193 70 39 186 151 pint:PI0771|5end_conserved_hypothetical_protein_706524..706754_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 395 72 36 55 19 pint:PI1238|3end_single-strand_DNA-specific_exonuclease_1163438..1163588_POSITIVE 265 44 2 131 94 pint:PI0984|3end_hypothetical_protein_910144..910294_POSITIVE 223 69 22 135 91 pint:PI0905|3end_hypothetical_protein_834697..834847_POSITIVE 210 70 21 78 16 pint:PI1222|3end_hypothetical_protein_1143378..1143528_POSITIVE 209 69 22 113 69 pint:PI0560|3end_hypothetical_protein_508910..509060_POSITIVE 204 60 16 67 24 pint:PI0394|3end_transcriptional_regulator,_AraC_family_360329..360479_POSITIVE 203 70 21 83 28 pint:PI1323|3end_conserved_hypothetical_protein_1242483..1242633_POSITIVE 200 70 29 137 93 pint:PI1814|3end_hypothetical_protein_1753233..1753383_POSITIVE 194 48 5 151 99 pint:PI1325|3end_conserved_hypothetical_protein_1244094..1244244_POSITIVE 194 60 24 83 49 pint:PI0100|3end_LPS_biosynthesis_protein_(lipopolysaccharide_biosynthesis_protein)_96726..96876_POSITIVE 193 70 39 111 76 pint:PI1356|3end_hypothetical_protein_1273340..1273490_POSITIVE 193 70 39 137 102 pint:PI0689|3end_hypothetical_protein_625877..626027_POSITIVE 191 47 4 34 1 pint:PI0870|3end_branched-chain_amino_acid_aminotransferase_806894..807044_POSITIVE 190 51 16 39 4 pint:PI2115|3end_hypothetical_protein_2065165..2065315_POSITIVE 190 32 1 42 15 pint:PI1584|3end_A/G-specific_adenine_glycosylase_1512958..1513108_POSITIVE 185 68 21 151 97 pint:PI0769|3end_phosphomannomutase_706172..706322_POSITIVE 183 32 5 117 94 pint:PI1733|3end_hypothetical_protein_1652437..1652587_POSITIVE 182 68 21 90 46 pint:PI0890|3end_ribose_5-phosphate_isomerase_B_820931..821081_POSITIVE 181 49 6 140 99 pint:PI1813|3end_hypothetical_protein_1753086..1753236_POSITIVE 181 70 23 151 101 pint:PI1528|3end_hypothetical_protein_1449878..1450028_POSITIVE