Origin IGS: cttctaactttttaagctatttttagtagtttaatacgatttgtttcttacgcattctattgatatttcaagtgcaaaggtactgtaaactaagaaaatagcaaaataaaaactatatta .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 taatatagtttttattttgctattttcttagtttacagtacctttgcacttgaaatatcaatagaatgcgtaagaaacaaatcgtattaaactactaaaaatagcttaaaaagttagaag Mask Tandem Repeat Region ================================================ cttctaactttttaagctatttttagtagtttaatacgatttgtttcttacgcattctattgatatttcaagtgcaaaggtactgtaaactaagaaaatagcaaaataaaaactatatta Find is-nt database================================================ Query_seq: PI0015:PI0016|PI0015:PI0016:possible transport protein:magnesium chelatase, subunit ChlI:->->:20211..20330 120 cttctaactttttaagctatttttagtagtttaatacgatttgtttcttacgcattctattgatatttcaagtgcaaaggtactgtaaactaagaaaatagcaaaataaaaactatatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI0015:PI0016|PI0015:PI0016:possible transport protein:magnesium chelatase, subunit ChlI:->->:20211..20330 120 cttctaactttttaagctatttttagtagtttaatacgatttgtttcttacgcattctattgatatttcaagtgcaaaggtactgtaaactaagaaaatagcaaaataaaaactatatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI0015:PI0016|PI0015:PI0016:possible transport protein:magnesium chelatase, subunit ChlI:->->:20211..20330 120 cttctaactttttaagctatttttagtagtttaatacgatttgtttcttacgcattctattgatatttcaagtgcaaaggtactgtaaactaagaaaatagcaaaataaaaactatatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 cttctaactttttaagctatttttagtagtttaatacgatttgtttcttacgcattctattgatatttcaagtgcaaaggtactgtaaactaagaaaatagcaaaataaaaactatatta Predict ORF larger than 30AA ================================================ cttctaactttttaagctatttttagtagtttaatacgatttgtttcttacgcattctattgatatttcaagtgcaaaggtactgtaaactaagaaaatagcaaaataaaaactatatta 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================================================ cttctaactttttaagctatttttagtagtttaatacgatttgtttcttacgcattctattgatatttcaagtgcaaaggtactgtaaactaagaaaatagcaaaataaaaactatatta Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PI0015:PI0016|PI0015:PI0016:possible transport protein:magnesium chelatase, subunit ChlI:->->:20211..20330 120 cttctaactttttaagctatttttagtagtttaatacgatttgtttcttacgcattctattgatatttcaagtgcaaaggtactgtaaactaagaaaatagcaaaataaaaactatatta Intra-Species Hit: Count: 1 Min: 1 Max: 120 Len: 120 Subject: pint_PI0015_PI0016|possible transport protein:magnesium chelatase, subunit ChlI|POSITIVE:POSITIVE|[20211,20330]|120 HSP 1 e-value: 3.0E-62 bit: 238.0 Len: 120 Query Start:1 Query End:120 Subject Strand: POSITIVE Subject Start: 1 Subject End: 120 cttctaactttttaagctatttttagtagtttaatacgatttgtttcttacgcattctattgatatttcaagtgcaaaggtactgtaaactaagaaaatagcaaaataaaaactatatta cttctaactttttaagctatttttagtagtttaatacgatttgtttcttacgcattctattgatatttcaagtgcaaaggtactgtaaactaagaaaatagcaaaataaaaactatatta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUUCUAACUUUUUAAGCUAUUUUUAGUAGUUUAAUACGAUUUGUUUCUUACGCAUUCUAUUGAUAUUUCAAGUGCAAAGGUACUGUAAACUAAGAAAAUAGCAAAAUAAAAACUAUAUUA ...............(((((((((..(((((((.(((..(((((..(((......((....))......))).))))).)))...))))))).))))))))).................. (-21.10) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAUAUAGUUUUUAUUUUGCUAUUUUCUUAGUUUACAGUACCUUUGCACUUGAAAUAUCAAUAGAAUGCGUAAGAAACAAAUCGUAUUAAACUACUAAAAAUAGCUUAAAAAGUUAGAAG ........((((((....((((((((..(((((((..((((.((((..((((.....((....)).....))))...))))..)))))))))))...)))))))).))))))........ (-17.90) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 267 66 25 184 134 pint:PI0402|5end_conserved_hypothetical_protein_367892..368122_POSITIVE 255 59 17 172 133 pint:PI1183|5end_conserved_hypothetical_protein_1104442..1104672_POSITIVE 246 89 52 183 147 pint:PI1692|5end_alanine_racemase_1605691..1605921_POSITIVE 239 58 12 160 106 pint:PI0081|5end_hypothetical_protein_80423..80653_POSITIVE 231 86 42 157 116 pint:PI2124|5end_excinuclease_ABC,_subunit_C_2072584..2072814_POSITIVE 228 103 69 104 74 pint:PI1858|5end_conserved_hypothetical_protein_1804400..1804630_POSITIVE 225 89 41 158 114 pint:PI0307|5end_RNA_polymerase_sigma-70_factor,_ECF_subfamily_290042..290272_POSITIVE 217 87 43 214 168 pint:PI1266|5end_hypothetical_protein_1185351..1185581_POSITIVE 215 86 41 69 35 pint:PI1390|5end_hypothetical_protein_1311154..1311384_POSITIVE 211 97 67 122 87 pint:PI1584|5end_A/G-specific_adenine_glycosylase_1511898..1512128_POSITIVE 211 91 58 88 56 pint:PI0114|5end_hypothetical_protein_108139..108369_POSITIVE 209 87 44 185 140 pint:PI1707|5end_GTP-binding_protein_1623795..1624025_POSITIVE 209 80 37 60 19 pint:PI0563|5end_possible_integral_membrane_protein_510248..510478_POSITIVE 208 103 66 166 129 pint:PI1314|5end_hypothetical_protein_1231188..1231418_POSITIVE 207 85 43 107 58 pint:PI1689|5end_conserved_hypothetical_protein_1604310..1604540_POSITIVE 205 110 61 113 66 pint:PI2004|5end_1-deoxy-D-xylulose_5-phosphate_synthase_1960954..1961184_POSITIVE 205 85 41 87 52 pint:PI1744|5end_chromosome_partitioning_protein_1665635..1665865_POSITIVE 204 89 41 216 166 pint:PI1772|5end_pullulanase_1702257..1702487_POSITIVE 202 91 64 212 187 pint:PI0456|5end_30S_ribosomal_protein_S12_428759..428989_POSITIVE 198 100 71 90 58 pint:PI2038|5end_conserved_hypothetical_protein;_possible_internalin-related_protein_1990463..1990693_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 246 89 52 148 112 pint:PI1691|3end_hypothetical_protein_1605736..1605886_POSITIVE 246 89 52 39 3 pint:PI1690|3end_transcription_regulator;_possible_Fe2+/Zn2+_uptake_regulation_proteins_1605627..1605777_POSITIVE 239 58 12 79 25 pint:PI0080|3end_hypothetical_protein_80422..80572_POSITIVE 230 94 52 67 18 pint:PI1267|3end_probable_integrase_1186475..1186625_POSITIVE 211 91 58 134 102 pint:PI0111|3end_hypothetical_protein_108265..108415_POSITIVE 211 91 58 81 49 pint:PI0112|3end_hypothetical_protein_108212..108362_POSITIVE 209 63 35 143 106 pint:PI0324|3end_conserved_hypothetical_protein_305680..305830_POSITIVE 208 103 66 139 102 pint:PI1313|3end_possible_POT_family_(proton-dependent_oligopeptide_transport_family)_1231241..1231391_POSITIVE 205 110 61 143 96 pint:PI2003|3end_hypothetical_protein_1961064..1961214_POSITIVE 205 85 41 42 7 pint:PI1742|3end_SpoOJ_regulator_protein_1665670..1665820_POSITIVE 203 91 58 124 96 pint:PI0984|3end_hypothetical_protein_910144..910294_POSITIVE 203 80 36 138 99 pint:PI0425|3end_hypothetical_protein_389722..389872_POSITIVE 198 80 37 146 105 pint:PI1067|3end_thymidylate_synthase_984811..984961_POSITIVE 198 87 50 147 115 pint:PI0857|3end_hypothetical_protein_790986..791136_POSITIVE 198 103 74 144 122 pint:PI0432|3end_hypothetical_protein_405037..405187_POSITIVE 197 83 41 148 110 pint:PI1774|3end_hypothetical_protein_1707031..1707181_POSITIVE 196 100 51 71 27 pint:PI0660|3end_conserved_hypothetical_protein_603997..604147_POSITIVE 194 64 25 117 68 pint:PI0757|3end_possible_hemagglutinin/protease_693741..693891_POSITIVE 194 89 52 134 94 pint:PI0031|3end_peptidylprolyl_isomerase_36131..36281_POSITIVE 192 77 50 37 7 pint:PI0333|3end_hypothetical_protein_313788..313938_POSITIVE