Origin IGS: agtattataaagtattaataaacttatgtggatagcttgcatattcaccttattatatatacctttgcattattaaacagctttgagaagcaactttctcaacattctatatttcatatcgttccgcaa .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 ttgcggaacgatatgaaatatagaatgttgagaaagttgcttctcaaagctgtttaataatgcaaaggtatatataataaggtgaatatgcaagctatccacataagtttattaatactttataatact Mask Tandem Repeat Region ================================================ agtattataaagtattaataaacttatgtggatagcttgcatattcaccttattatatatacctttgcattattaaacagctttgagaagcaactttctcaacattctatatttcatatcgttccgcaa Find is-nt database================================================ Query_seq: PI1384:PI1385|PI1384:PI1385:conserved hypothetical protein:3-deoxy-d-manno-octulosonic acid 8-phosphate synthase (DAHP synthase, Class I):->->:1306235..1306363 129 agtattataaagtattaataaacttatgtggatagcttgcatattcaccttattatatatacctttgcattattaaacagctttgagaagcaactttctcaacattctatatttcatatcgttccgcaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI1384:PI1385|PI1384:PI1385:conserved hypothetical protein:3-deoxy-d-manno-octulosonic acid 8-phosphate synthase (DAHP synthase, Class I):->->:1306235..1306363 129 agtattataaagtattaataaacttatgtggatagcttgcatattcaccttattatatatacctttgcattattaaacagctttgagaagcaactttctcaacattctatatttcatatcgttccgcaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI1384:PI1385|PI1384:PI1385:conserved hypothetical protein:3-deoxy-d-manno-octulosonic acid 8-phosphate synthase (DAHP synthase, Class I):->->:1306235..1306363 129 agtattataaagtattaataaacttatgtggatagcttgcatattcaccttattatatatacctttgcattattaaacagctttgagaagcaactttctcaacattctatatttcatatcgttccgcaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 agtattataaagtattaataaacttatgtggatagcttgcatattcaccttattatatatacctttgcattattaaacagctttgagaagcaactttctcaacattctatatttcatatcgttccgcaa Predict ORF larger than 30AA ================================================ Protein_Len: 34 Strand: + Start: 28 End: 129 ........................... M D S L H I H L I I Y T F A L L N S F E K Q L S Q H S I F H I V P Q agtattataaagtattaataaacttatgtggatagcttgcatattcaccttattatatatacctttgcattattaaacagctttgagaagcaactttctcaacattctatatttcatatcgttccgcaa 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: 4 End: 33 ...ATCCACATAAGTTTATTAATACTTTATAAT................................................................................................ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ agtattataaagtattaataaacttatgtggatagcttgcatattcaccttattatatatacctttgcattattaaacagctttgagaagcaactttctcaacattctatatttcatatcgttccgcaa Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PI1384:PI1385|PI1384:PI1385:conserved hypothetical protein:3-deoxy-d-manno-octulosonic acid 8-phosphate synthase (DAHP synthase, Class I):->->:1306235..1306363 129 agtattataaagtattaataaacttatgtggatagcttgcatattcaccttattatatatacctttgcattattaaacagctttgagaagcaactttctcaacattctatatttcatatcgttccgcaa Intra-Species Hit: Count: 1 Min: 1 Max: 129 Len: 129 Subject: pint_PI1384_PI1385|conserved hypothetical protein:3-deoxy-d-manno-octulosonic acid 8-phosphate synthase (DAHP synthase, Class I)|POSITIVE:POSITIVE|[1306235,1306363]|129 HSP 1 e-value: 2.0E-67 bit: 256.0 Len: 129 Query Start:1 Query End:129 Subject Strand: POSITIVE Subject Start: 1 Subject End: 129 agtattataaagtattaataaacttatgtggatagcttgcatattcaccttattatatatacctttgcattattaaacagctttgagaagcaactttctcaacattctatatttcatatcgttccgcaa agtattataaagtattaataaacttatgtggatagcttgcatattcaccttattatatatacctttgcattattaaacagctttgagaagcaactttctcaacattctatatttcatatcgttccgcaa Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGUAUUAUAAAGUAUUAAUAAACUUAUGUGGAUAGCUUGCAUAUUCACCUUAUUAUAUAUACCUUUGCAUUAUUAAACAGCUUUGAGAAGCAACUUUCUCAACAUUCUAUAUUUCAUAUCGUUCCGCAA ..(((((........)))))......((((((.((((((((........................)))).........))))((((((((....))))))))....................)))))). (-17.16) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUGCGGAACGAUAUGAAAUAUAGAAUGUUGAGAAAGUUGCUUCUCAAAGCUGUUUAAUAAUGCAAAGGUAUAUAUAAUAAGGUGAAUAUGCAAGCUAUCCACAUAAGUUUAUUAAUACUUUAUAAUACU .((.(((....(((.....((((....(((((((......)))))))..))))...)))..((....((((((.((......)).))))))..))..))).)).......................... (-17.40) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 298 68 21 112 61 pint:PI2121|5end_glucose_inhibited_division_protein_A_2069889..2070119_POSITIVE 240 68 28 146 100 pint:PI0059|5end_peptide_chain_release_factor_RF-2_57132..57362_POSITIVE 234 93 61 216 189 pint:PI1442|5end_radical-activating_enzyme_(pyruvate-formate_lyase-activating_enzyme)_1363949..1364179_POSITIVE 233 70 28 177 125 pint:PI1219|5end_UDP-N-acetylglucosamine_acyltransferase_1138529..1138759_POSITIVE 224 70 22 116 56 pint:PI1122|5end_pyridoxal-phosphate-dependent_aminotransferase_1046636..1046866_POSITIVE 224 60 28 53 22 pint:PI0580|5end_Holliday_junction_DNA_helicase_524178..524408_POSITIVE 223 80 37 140 98 pint:PI0724|5end_DNA_polymerase_III,_delta_subunit_657403..657633_POSITIVE 215 70 21 62 20 pint:PI2043|5end_hypothetical_protein_1996058..1996288_POSITIVE 214 50 1 108 61 pint:PI0165|5end_AAA_family_ATPase_159602..159832_POSITIVE 213 115 78 94 44 pint:PI1021|5end_conserved_hypothetical_protein;_possible_methyltransferase_938985..939215_POSITIVE 209 50 28 87 57 pint:PI1550|5end_conserved_hypothetical_protein_1467360..1467590_POSITIVE 209 103 61 67 21 pint:PI0708|5end_conserved_hypothetical_protein_644475..644705_POSITIVE 208 79 35 116 69 pint:PI1725|5end_hypothetical_protein_1643024..1643254_POSITIVE 207 59 11 128 70 pint:PI1428|5end_quinolinate_synthetase_A_1346626..1346856_POSITIVE 200 69 28 220 186 pint:PI1806|5end_integral_membrane_transport_protein;_possible_sugar_transport_proteins_1740777..1741007_POSITIVE 199 92 63 33 2 pint:PI1285|5end_ATP_synthase,_B_subunit_1200348..1200578_POSITIVE 197 99 55 132 84 pint:PI2139|5end_cysteinyl-tRNA_synthetase_2085266..2085496_POSITIVE 197 78 33 83 22 pint:PI1189|5end_conserved_hypothetical_protein_1107114..1107344_POSITIVE 196 68 22 180 139 pint:PI0476|5end_50S_ribosomal_protein_L18_440041..440271_POSITIVE 195 108 63 83 37 pint:PI1844|5end_hypothetical_protein_1790092..1790322_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 224 70 22 107 47 pint:PI1121|3end_glycosyltransferase_1046707..1046857_POSITIVE 221 100 54 64 11 pint:PI0723|3end_conserved_hypothetical_protein_657379..657529_POSITIVE 218 46 1 69 26 pint:PI1836|3end_conserved_hypothetical_protein_1778581..1778731_POSITIVE 215 70 21 62 20 pint:PI2042|3end_cation-transporting_ATPase_1996138..1996288_POSITIVE 210 47 22 125 101 pint:PI0587|3end_conserved_hypothetical_protein_535347..535497_POSITIVE 208 68 36 57 25 pint:PI1134|3end_ABC_transporter,_ATP-binding_protein_1062073..1062223_POSITIVE 207 59 11 82 24 pint:PI1427|3end_nicotinate-nucleotide_pyrophosphorylase_1346660..1346810_POSITIVE 203 70 25 110 57 pint:PI1926|3end_conserved_hypothetical_protein_1870977..1871127_POSITIVE 201 94 51 67 35 pint:PI2138|3end_nicotinate_phosphoribosyltransferase_2085133..2085283_POSITIVE 197 78 33 134 73 pint:PI1187|3end_conserved_hypothetical_protein_1107245..1107395_POSITIVE 195 69 22 134 90 pint:PI0813|3end_conserved_hypothetical_protein_752938..753088_POSITIVE 194 92 53 44 11 pint:PI1714|3end_ISPg3-related_transposase_1631352..1631502_POSITIVE 193 51 29 25 2 pint:PI0858|3end_carbamyl_phosphate_synthase,_large_subunit_793394..793544_POSITIVE 192 59 12 114 70 pint:PI0112|3end_hypothetical_protein_108212..108362_POSITIVE 191 108 80 146 116 pint:PI0379|3end_conserved_hypothetical_protein_350239..350389_POSITIVE 189 89 55 102 69 pint:PI1205|3end_hypothetical_protein_1127240..1127390_POSITIVE 189 89 55 71 38 pint:PI1207|3end_hypothtical_protein_1127209..1127359_POSITIVE 188 103 76 144 115 pint:PI0218|3end_conserved_hypothetical_protein_211149..211299_POSITIVE 187 53 17 67 32 pint:PI1599|3end_predicted_TPR-repeat-containing_protein_1529176..1529326_POSITIVE 185 70 25 84 28 pint:PI0302|3end_hypothetical_protein_287019..287169_POSITIVE