Origin IGS: acttttctttaccttgtttaaacaaagaccgttgtagtcttttctttacatttctattgcaaatatacgaaataatttgcactctattgtctaactatcaagtttttattacttttgcataaaaataaatataatat .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 atattatatttatttttatgcaaaagtaataaaaacttgatagttagacaatagagtgcaaattatttcgtatatttgcaatagaaatgtaaagaaaagactacaacggtctttgtttaaacaaggtaaagaaaagt Mask Tandem Repeat Region ================================================ acttttctttaccttgtttaaacaaagaccgttgtagtcttttctttacatttctattgcaaatatacgaaataatttgcactctattgtctaactatcaagtttttattacttttgcataaaaataaatataatat Find is-nt database================================================ Query_seq: PI0961:PI0962|PI0961:PI0962:conserved hypothetical protein:phosphoglycerate mutase:->->:892104..892240 137 acttttctttaccttgtttaaacaaagaccgttgtagtcttttctttacatttctattgcaaatatacgaaataatttgcactctattgtctaactatcaagtttttattacttttgcataaaaataaatataatat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI0961:PI0962|PI0961:PI0962:conserved hypothetical protein:phosphoglycerate mutase:->->:892104..892240 137 acttttctttaccttgtttaaacaaagaccgttgtagtcttttctttacatttctattgcaaatatacgaaataatttgcactctattgtctaactatcaagtttttattacttttgcataaaaataaatataatat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI0961:PI0962|PI0961:PI0962:conserved hypothetical protein:phosphoglycerate mutase:->->:892104..892240 137 acttttctttaccttgtttaaacaaagaccgttgtagtcttttctttacatttctattgcaaatatacgaaataatttgcactctattgtctaactatcaagtttttattacttttgcataaaaataaatataatat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 acttttctttaccttgtttaaacaaagaccgttgtagtcttttctttacatttctattgcaaatatacgaaataatttgcactctattgtctaactatcaagtttttattacttttgcataaaaataaatataatat Predict ORF larger than 30AA ================================================ acttttctttaccttgtttaaacaaagaccgttgtagtcttttctttacatttctattgcaaatatacgaaataatttgcactctattgtctaactatcaagtttttattacttttgcataaaaataaatataatat 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================================================ acttttctttaccttgtttaaacaaagaccgttgtagtcttttctttacatttctattgcaaatatacgaaataatttgcactctattgtctaactatcaagtttttattacttttgcataaaaataaatataatat Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PI0961:PI0962|PI0961:PI0962:conserved hypothetical protein:phosphoglycerate mutase:->->:892104..892240 137 acttttctttaccttgtttaaacaaagaccgttgtagtcttttctttacatttctattgcaaatatacgaaataatttgcactctattgtctaactatcaagtttttattacttttgcataaaaataaatataatat Intra-Species Hit: Count: 1 Min: 1 Max: 137 Len: 137 Subject: pint_PI0961_PI0962|conserved hypothetical protein:phosphoglycerate mutase|POSITIVE:POSITIVE|[892104,892240]|137 HSP 1 e-value: 3.0E-72 bit: 272.0 Len: 137 Query Start:1 Query End:137 Subject Strand: POSITIVE Subject Start: 1 Subject End: 137 acttttctttaccttgtttaaacaaagaccgttgtagtcttttctttacatttctattgcaaatatacgaaataatttgcactctattgtctaactatcaagtttttattacttttgcataaaaataaatataatat acttttctttaccttgtttaaacaaagaccgttgtagtcttttctttacatttctattgcaaatatacgaaataatttgcactctattgtctaactatcaagtttttattacttttgcataaaaataaatataatat Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACUUUUCUUUACCUUGUUUAAACAAAGACCGUUGUAGUCUUUUCUUUACAUUUCUAUUGCAAAUAUACGAAAUAAUUUGCACUCUAUUGUCUAACUAUCAAGUUUUUAUUACUUUUGCAUAAAAAUAAAUAUAAUAU ............((((.(((.(((((((....(((((........))))).......(((((((..........))))))).))).)))).)))....))))....(((((..((((........))))..))))). (-12.90) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUAUUAUAUUUAUUUUUAUGCAAAAGUAAUAAAAACUUGAUAGUUAGACAAUAGAGUGCAAAUUAUUUCGUAUAUUUGCAAUAGAAAUGUAAAGAAAAGACUACAACGGUCUUUGUUUAAACAAGGUAAAGAAAAGU .........((((((((....))))))))......((((....((((((.......(((((((..........)))))))...............(((((((.....))))))))))))).))))............ (-19.70) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 252 104 65 148 111 pint:PI0455|5end_hypothetical_protein_427361..427591_POSITIVE 251 86 43 205 153 pint:PI1638|5end_conserved_hypothetical_protein_1555337..1555567_POSITIVE 246 60 12 184 132 pint:PI1786|5end_hypothetical_protein_1718124..1718354_POSITIVE 245 47 13 171 137 pint:PI0330|5end_hypothetical_protein_310447..310677_POSITIVE 229 119 76 63 16 pint:PI1371|5end_hypothetical_protein_1292359..1292589_POSITIVE 228 61 25 63 17 pint:PI1987|5end_conserved_hypothetical_protein;_possible_outer_outer_membrane_lipoprotein_Omp28_1941556..1941786_POSITIVE 222 60 22 45 1 pint:PI0173|5end_hypothetical_protein_165305..165535_POSITIVE 221 70 30 75 32 pint:PI0587|5end_conserved_hypothetical_protein_534416..534646_POSITIVE 216 117 77 119 79 pint:PI1348|5end_glycosyltransferase_1262389..1262619_POSITIVE 215 119 99 197 177 pint:PI0521|5end_hypothetical_protein_478886..479116_POSITIVE 215 119 99 66 46 pint:PI0520|5end_hypothetical_protein_478755..478985_POSITIVE 213 49 8 113 72 pint:PI0839|5end_conserved_hypothetical_protein_773843..774073_POSITIVE 213 90 47 153 113 pint:PI0411|5end_conserved_hypothetial_protein;_possible_hydrolase_377700..377930_POSITIVE 212 68 34 107 69 pint:PI0873|5end_conserved_hypothetical_protein;_possible_permease_807968..808198_POSITIVE 211 119 79 41 1 pint:PI0119|5end_hypothetical_protein_111506..111736_POSITIVE 210 85 50 71 32 pint:PI0174|5end_succinyl-CoA_synthetase_alpha_subunit_166121..166351_POSITIVE 210 80 31 225 176 pint:PI0073|5end_dihydropteroate_synthase_70956..71186_POSITIVE 207 65 28 69 27 pint:PI0714|5end_conserved_hypothetical_protein_651345..651575_POSITIVE 203 80 33 215 180 pint:PI0611|5end_hypothetical_protein_559387..559617_POSITIVE 202 47 13 175 130 pint:PI2124|5end_excinuclease_ABC,_subunit_C_2072584..2072814_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 251 86 43 72 20 pint:PI1637|3end_hypothetical_protein_1555284..1555434_POSITIVE 246 60 12 84 32 pint:PI1785|3end_conserved_hypothetical_protein_1718104..1718254_POSITIVE 231 100 52 43 1 pint:PI1610|3end_Na+/H+_anti-porter_1538002..1538152_POSITIVE 231 86 55 44 11 pint:PI0342|3end_hypothetical_protein_318049..318199_POSITIVE 215 119 99 40 20 pint:PI0519|3end_5'-nucleotidase/2',3'-cyclic_phosphodiesterase_478809..478959_POSITIVE 213 49 8 117 76 pint:PI0838|3end_DNA_replication_and_repair_protein_773927..774077_POSITIVE 211 119 79 95 55 pint:PI0118|3end_hypothetical_protein_111640..111790_POSITIVE 210 119 76 122 75 pint:PI1308|3end_hypothetical_protein_1223717..1223867_POSITIVE 198 60 11 105 54 pint:PI0141|3end_glutamine_amidotransferase_involved_in_pyridoxine_biosynthesis_133308..133458_POSITIVE 192 45 1 108 58 pint:PI2103|3end_hypothetical_protein_2057934..2058084_POSITIVE 191 60 11 94 46 pint:PI0528|3end_hypothetical_protein_483122..483272_POSITIVE 189 50 1 145 92 pint:PI1981|3end_hypothetical_protein_1938138..1938288_POSITIVE 189 70 23 143 96 pint:PI1783|3end_possible_4-diphosphocytidyl-2c-methyl-D-erythritol_synthase_1716158..1716308_POSITIVE 189 124 85 103 67 pint:PI0659|3end_hypothetical_protein_603396..603546_POSITIVE 189 66 30 146 105 pint:PI0067|3end_hypothetical_protein_66586..66736_POSITIVE 188 70 22 140 82 pint:PI1789|3end_hypothetical_protein_1719037..1719187_POSITIVE 188 99 53 105 60 pint:PI0380|3end_conserved_hypothetical_protein_350541..350691_POSITIVE 185 110 75 59 18 pint:PI0836|3end_conserved_hypothetical_protein_772373..772523_POSITIVE 184 55 11 95 48 pint:PI0341|3end_conserved_hypothetical_protein_317615..317765_POSITIVE 183 50 2 112 66 pint:PI0434|3end_possible_beta-lactamase_406890..407040_POSITIVE