Origin IGS: tgctgctatccatttaacaaacttaattactttctttaccataccgaagtacaaaggtagtaattttttgattaaatcgacttacaagatttgatatttatttgcgtggttcacgtttttatattaactttgcagcagtattaaaataggtgaaagaaa .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tttctttcacctattttaatactgctgcaaagttaatataaaaacgtgaaccacgcaaataaatatcaaatcttgtaagtcgatttaatcaaaaaattactacctttgtacttcggtatggtaaagaaagtaattaagtttgttaaatggatagcagca Mask Tandem Repeat Region ================================================ tgctgctatccatttaacaaacttaattactttctttaccataccgaagtacaaaggtagtaattttttgattaaatcgacttacaagatttgatatttatttgcgtggttcacgtttttatattaactttgcagcagtattaaaataggtgaaagaaa Find is-nt database================================================ Query_seq: PI1208:PI1209|PI1208:PI1209:monofunctional biosynthetic peptidoglycan transglycosylase:phosphate starvation-inducible protein, phoH family:->->:1127940..1128098 159 tgctgctatccatttaacaaacttaattactttctttaccataccgaagtacaaaggtagtaattttttgattaaatcgacttacaagatttgatatttatttgcgtggttcacgtttttatattaactttgcagcagtattaaaataggtgaaagaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI1208:PI1209|PI1208:PI1209:monofunctional biosynthetic peptidoglycan transglycosylase:phosphate starvation-inducible protein, phoH family:->->:1127940..1128098 159 tgctgctatccatttaacaaacttaattactttctttaccataccgaagtacaaaggtagtaattttttgattaaatcgacttacaagatttgatatttatttgcgtggttcacgtttttatattaactttgcagcagtattaaaataggtgaaagaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI1208:PI1209|PI1208:PI1209:monofunctional biosynthetic peptidoglycan transglycosylase:phosphate starvation-inducible protein, phoH family:->->:1127940..1128098 159 tgctgctatccatttaacaaacttaattactttctttaccataccgaagtacaaaggtagtaattttttgattaaatcgacttacaagatttgatatttatttgcgtggttcacgtttttatattaactttgcagcagtattaaaataggtgaaagaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tgctgctatccatttaacaaacttaattactttctttaccataccgaagtacaaaggtagtaattttttgattaaatcgacttacaagatttgatatttatttgcgtggttcacgtttttatattaactttgcagcagtattaaaataggtgaaagaaa Predict ORF larger than 30AA ================================================ tgctgctatccatttaacaaacttaattactttctttaccataccgaagtacaaaggtagtaattttttgattaaatcgacttacaagatttgatatttatttgcgtggttcacgtttttatattaactttgcagcagtattaaaataggtgaaagaaa 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: 82 Start: 13 End: 42 ............TTTAACAAACTTAATTACTTTCTTTACCAT..................................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tgctgctatccatttaacaaacttaattactttctttaccataccgaagtacaaaggtagtaattttttgattaaatcgacttacaagatttgatatttatttgcgtggttcacgtttttatattaactttgcagcagtattaaaataggtgaaagaaa Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 84 HP_score: -6.8 Tail_Score: -5.1167 Start: 105 End: 115 Full_Region: TTTGATATTTATTTG CGTG GTT CACG TTTTTATATTAACTT ........................................................................................................CGTGGTTCACG............................................ Find igs database================================================ Query_seq: PI1208:PI1209|PI1208:PI1209:monofunctional biosynthetic peptidoglycan transglycosylase:phosphate starvation-inducible protein, phoH family:->->:1127940..1128098 159 tgctgctatccatttaacaaacttaattactttctttaccataccgaagtacaaaggtagtaattttttgattaaatcgacttacaagatttgatatttatttgcgtggttcacgtttttatattaactttgcagcagtattaaaataggtgaaagaaa Intra-Species Hit: Count: 1 Min: 1 Max: 159 Len: 159 Subject: pint_PI1208_PI1209|monofunctional biosynthetic peptidoglycan transglycosylase:phosphate starvation-inducible protein, phoH family|POSITIVE:POSITIVE|[1127940,1128098]|159 HSP 1 e-value: 2.0E-85 bit: 315.0 Len: 159 Query Start:1 Query End:159 Subject Strand: POSITIVE Subject Start: 1 Subject End: 159 tgctgctatccatttaacaaacttaattactttctttaccataccgaagtacaaaggtagtaattttttgattaaatcgacttacaagatttgatatttatttgcgtggttcacgtttttatattaactttgcagcagtattaaaataggtgaaagaaa tgctgctatccatttaacaaacttaattactttctttaccataccgaagtacaaaggtagtaattttttgattaaatcgacttacaagatttgatatttatttgcgtggttcacgtttttatattaactttgcagcagtattaaaataggtgaaagaaa Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGCUGCUAUCCAUUUAACAAACUUAAUUACUUUCUUUACCAUACCGAAGUACAAAGGUAGUAAUUUUUUGAUUAAAUCGACUUACAAGAUUUGAUAUUUAUUUGCGUGGUUCACGUUUUUAUAUUAACUUUGCAGCAGUAUUAAAAUAGGUGAAAGAAA ((((((..((.((((((((((...(((((((.(((((....(((....))).))))).))))))).)))).)))))).))..........(((((((......(((((...)))))....)))))))....))))))...................... (-28.90) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUCUUUCACCUAUUUUAAUACUGCUGCAAAGUUAAUAUAAAAACGUGAACCACGCAAAUAAAUAUCAAAUCUUGUAAGUCGAUUUAAUCAAAAAAUUACUACCUUUGUACUUCGGUAUGGUAAAGAAAGUAAUUAAGUUUGUUAAAUGGAUAGCAGCA .......................(((((................((((...)))).......................(((.((((((.((((.(((((((..((((((((....))))...))))..)))))))...)))))))))).))).))))). (-31.90) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 273 138 105 133 104 pint:PI1817|5end_ISPg3-related_transposase_1755520..1755750_POSITIVE 260 127 83 149 101 pint:PI0020|5end_conserved_hypothetical_protein_24525..24755_POSITIVE 243 140 92 173 119 pint:PI1285|5end_ATP_synthase,_B_subunit_1200348..1200578_POSITIVE 243 136 103 131 91 pint:PI0902|5end_hypothetical_protein_832291..832521_POSITIVE 240 139 91 108 47 pint:PI1196|5end_hypothetical_protein_1113401..1113631_POSITIVE 227 115 75 45 1 pint:PI1127|5end_chloride_channel_protein_1052612..1052842_POSITIVE 226 136 104 167 133 pint:PI0367|5end_hypothetical_protein_337884..338114_POSITIVE 225 135 97 145 106 pint:PI1122|5end_pyridoxal-phosphate-dependent_aminotransferase_1046636..1046866_POSITIVE 220 137 103 71 33 pint:PI0149|5end_conserved_hypothetical_protein_142735..142965_POSITIVE 218 138 101 69 27 pint:PI1848|5end_hypothetical_protein_1793799..1794029_POSITIVE 216 136 101 228 194 pint:PI1591|5end_ISPg3-related_transposase_1518747..1518977_POSITIVE 216 120 78 64 22 pint:PI0460|5end_50S_ribosomal_protein_L3_432471..432701_POSITIVE 215 140 95 163 102 pint:PI1453|5end_probable_thiamine_pyrophosphokinase_1375982..1376212_POSITIVE 211 143 104 46 4 pint:PI0822|5end_tRNA_delta(2)-isopentenylpyrophosphate_transferase_761028..761258_POSITIVE 210 137 91 191 123 pint:PI1872|5end_glycosyl_transferase,_group_2_family_protein_1817057..1817287_POSITIVE 210 57 23 55 21 pint:PI0272|5end_conserved_hypothetical_protein_262621..262851_POSITIVE 209 88 45 167 130 pint:PI1335|5end_Fe-S_oxidoreductase_1252818..1253048_POSITIVE 207 138 103 204 169 pint:PI2162|5end_conserved_hypothetical_protein_2108796..2109026_POSITIVE 207 65 29 231 196 pint:PI1880|5end_phosphoenolpyruvate_carboxykinase_(ATP)_1821667..1821897_POSITIVE 207 150 104 208 154 pint:PI0104|5end_hypothetical_protein_99105..99335_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 273 138 105 47 18 pint:PI1816|3end_acid_phosphatase_1755514..1755664_POSITIVE 243 140 92 68 14 pint:PI1284|3end_ATP_synthase,_delta_subunit_1200323..1200473_POSITIVE 240 139 91 87 26 pint:PI1195|3end_hypothetical_protein_1113460..1113610_POSITIVE 230 148 106 50 2 pint:PI1324|3end_conserved_hypothetical_protein_1243025..1243175_POSITIVE 230 134 92 122 82 pint:PI1308|3end_hypothetical_protein_1223717..1223867_POSITIVE 226 136 104 97 63 pint:PI0366|3end_conserved_hypothetical_protein_337894..338044_POSITIVE 225 135 97 136 97 pint:PI1121|3end_glycosyltransferase_1046707..1046857_POSITIVE 223 139 96 132 86 pint:PI1234|3end_valyl-tRNA_synthetase_(valine--tRNA_ligase)_1157129..1157279_POSITIVE 222 60 26 55 26 pint:PI1820|3end_hypothetical_protein_1760377..1760527_POSITIVE 221 80 34 78 32 pint:PI0976|3end_dihydrolipoamide_dehydrogenase_(dihydrolipoyl_dehydrogenanse)_903732..903882_POSITIVE 211 150 101 80 25 pint:PI1750|3end_sulfate_transporter_1673896..1674046_POSITIVE 211 143 104 151 109 pint:PI0821|3end_conserved_hypothetical_protein_761213..761363_POSITIVE 209 88 45 144 107 pint:PI1334|3end_ferrodoxin_1252875..1253025_POSITIVE 208 139 99 92 51 pint:PI0557|3end_conserved_hypothetical_protein_506884..507034_POSITIVE 207 138 103 79 44 pint:PI2161|3end_hypothetical_protein_2108751..2108901_POSITIVE 207 150 104 123 69 pint:PI0103|3end_conserved_hypothetical_protein;_possible_permease_99100..99250_POSITIVE 204 123 86 74 28 pint:PI1440|3end_conserved_hypothetical_protein_1363009..1363159_POSITIVE 204 139 101 45 6 pint:PI1122|3end_pyridoxal-phosphate-dependent_aminotransferase_1048059..1048209_POSITIVE 204 89 52 146 101 pint:PI0525|3end_transcriptional_regulator,_Arac_family_482275..482425_POSITIVE 203 139 100 54 11 pint:PI1321|3end_conserved_hypothetical_protein_1240401..1240551_POSITIVE