Origin IGS: aaaaaggtaaattcaatacccataaacgaaattataatggtgtatgaaccaagaagcaaaaaggttagaaaaacgagcactgacaagtattactgtttattggaagcacaatcgtttataccatatta .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 taatatggtataaacgattgtgcttccaataaacagtaatacttgtcagtgctcgtttttctaacctttttgcttcttggttcatacaccattataatttcgtttatgggtattgaatttaccttttt Mask Tandem Repeat Region ================================================ aaaaaggtaaattcaatacccataaacgaaattataatggtgtatgaaccaagaagcaaaaaggttagaaaaacgagcactgacaagtattactgtttattggaagcacaatcgtttataccatatta Find is-nt database================================================ Query_seq: PI1168:PI1169|PI1168:PI1169:hypothetical protein:hypothetical protein:->->:1089983..1090110 128 aaaaaggtaaattcaatacccataaacgaaattataatggtgtatgaaccaagaagcaaaaaggttagaaaaacgagcactgacaagtattactgtttattggaagcacaatcgtttataccatatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI1168:PI1169|PI1168:PI1169:hypothetical protein:hypothetical protein:->->:1089983..1090110 128 aaaaaggtaaattcaatacccataaacgaaattataatggtgtatgaaccaagaagcaaaaaggttagaaaaacgagcactgacaagtattactgtttattggaagcacaatcgtttataccatatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI1168:PI1169|PI1168:PI1169:hypothetical protein:hypothetical protein:->->:1089983..1090110 128 aaaaaggtaaattcaatacccataaacgaaattataatggtgtatgaaccaagaagcaaaaaggttagaaaaacgagcactgacaagtattactgtttattggaagcacaatcgtttataccatatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aaaaaggtaaattcaatacccataaacgaaattataatggtgtatgaaccaagaagcaaaaaggttagaaaaacgagcactgacaagtattactgtttattggaagcacaatcgtttataccatatta Predict ORF larger than 30AA ================================================ Protein_Len: 37 Strand: + Start: 16 End: 126 ............... M P I N E I I M V Y E P R S K K V R K T S T D K Y Y C L L E A Q S F I P Y .. aaaaaggtaaattcaatacccataaacgaaattataatggtgtatgaaccaagaagcaaaaaggttagaaaaacgagcactgacaagtattactgtttattggaagcacaatcgtttataccatatta 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: 85 Start: 31 End: 60 ..............................TTTGCTTCTTGGTTCATACACCATTATAAT.................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aaaaaggtaaattcaatacccataaacgaaattataatggtgtatgaaccaagaagcaaaaaggttagaaaaacgagcactgacaagtattactgtttattggaagcacaatcgtttataccatatta Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PI1168:PI1169|PI1168:PI1169:hypothetical protein:hypothetical protein:->->:1089983..1090110 128 aaaaaggtaaattcaatacccataaacgaaattataatggtgtatgaaccaagaagcaaaaaggttagaaaaacgagcactgacaagtattactgtttattggaagcacaatcgtttataccatatta Intra-Species Hit: Count: 1 Min: 1 Max: 128 Len: 128 Subject: pint_PI1168_PI1169|hypothetical protein:hypothetical protein|POSITIVE:POSITIVE|[1089983,1090110]|128 HSP 1 e-value: 6.0E-67 bit: 254.0 Len: 128 Query Start:1 Query End:128 Subject Strand: POSITIVE Subject Start: 1 Subject End: 128 aaaaaggtaaattcaatacccataaacgaaattataatggtgtatgaaccaagaagcaaaaaggttagaaaaacgagcactgacaagtattactgtttattggaagcacaatcgtttataccatatta aaaaaggtaaattcaatacccataaacgaaattataatggtgtatgaaccaagaagcaaaaaggttagaaaaacgagcactgacaagtattactgtttattggaagcacaatcgtttataccatatta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAAAGGUAAAUUCAAUACCCAUAAACGAAAUUAUAAUGGUGUAUGAACCAAGAAGCAAAAAGGUUAGAAAAACGAGCACUGACAAGUAUUACUGUUUAUUGGAAGCACAAUCGUUUAUACCAUAUUA .....((((..((((.(((((((.............)))).)))))))((((.(((((..((.(((((...........))))).....))..))))).))))...............))))...... (-19.12) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAUAUGGUAUAAACGAUUGUGCUUCCAAUAAACAGUAAUACUUGUCAGUGCUCGUUUUUCUAACCUUUUUGCUUCUUGGUUCAUACACCAUUAUAAUUUCGUUUAUGGGUAUUGAAUUUACCUUUUU ......((((.((((((..(..((..(((.............)))..))..)))))))....................(((((((((.((((.............))))))).))))))))))..... (-19.04) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 256 108 61 204 151 pint:PI0521|5end_hypothetical_protein_478886..479116_POSITIVE 256 108 61 73 20 pint:PI0520|5end_hypothetical_protein_478755..478985_POSITIVE 249 78 37 108 54 pint:PI1852|5end_conserved_hypothetical_protein_1797952..1798182_POSITIVE 233 119 79 218 177 pint:PI2073|5end_mobilization_protein_2031995..2032225_POSITIVE 232 85 42 39 1 pint:PI1595|5end_conserved_hypothetical_protein_1524399..1524629_POSITIVE 226 105 62 69 16 pint:PI1135|5end_hypothetical_protein_1061935..1062165_POSITIVE 225 89 41 114 52 pint:PI1677|5end_cell_division_protein_FtsH_1591766..1591996_POSITIVE 223 86 50 206 171 pint:PI0920|5end_xanthan_lyase_849688..849918_POSITIVE 222 79 38 175 122 pint:PI1440|5end_conserved_hypothetical_protein_1357185..1357415_POSITIVE 222 57 19 186 143 pint:PI0769|5end_phosphomannomutase_704653..704883_POSITIVE 217 117 72 219 167 pint:PI1431|5end_conserved_hypothetical_protein_1352079..1352309_POSITIVE 217 67 27 160 116 pint:PI0542|5end_hypothetical_protein_495554..495784_POSITIVE 215 110 79 157 118 pint:PI1634|5end_conserved_hypothetical_protein_1553179..1553409_POSITIVE 215 110 79 157 118 pint:PI0340|5end_conserved_hypothetical_protein_316095..316325_POSITIVE 214 66 22 126 77 pint:PI0719|5end_conserved_hypothetical_protein_653043..653273_POSITIVE 213 97 51 83 38 pint:PI0253|5end_conjugative_transposon_protein,_TraD_248294..248524_POSITIVE 212 110 63 224 187 pint:PI2091|5end_DNA_processing_protein_2048019..2048249_POSITIVE 211 95 52 77 40 pint:PI0553|5end_recombination_protein_503344..503574_POSITIVE 210 70 25 110 56 pint:PI0883|5end_para-aminobenzoate_synthase_component_I_816131..816361_POSITIVE 207 114 77 126 81 pint:PI0761|5end_hypothetical_protein_696173..696403_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 243 108 68 47 3 pint:PI0519|3end_5'-nucleotidase/2',3'-cyclic_phosphodiesterase_478809..478959_POSITIVE 226 105 62 127 74 pint:PI1134|3end_ABC_transporter,_ATP-binding_protein_1062073..1062223_POSITIVE 223 117 71 57 6 pint:PI1958|3end_hypothetical_protein_1917369..1917519_POSITIVE 222 57 19 114 71 pint:PI0768|3end_conserved_hypothetical_protein;_possible_acetyltransferase_704661..704811_POSITIVE 215 110 79 120 81 pint:PI1632|3end_hypothetical_protein_1553222..1553372_POSITIVE 215 110 79 120 81 pint:PI0339|3end_hypothetical_protein_316138..316288_POSITIVE 214 80 50 150 122 pint:PI0919|3end_conserved_hypothetical_protein_849719..849869_POSITIVE 214 66 22 123 74 pint:PI0717|3end_conserved_hypothetical_protein_653120..653270_POSITIVE 213 97 51 92 47 pint:PI0252|3end_conserved_hypothetical_protein_248383..248533_POSITIVE 210 70 25 102 48 pint:PI0882|3end_conserved_hypothetical_protein;_possible_para-aminobenzoate_synthase_component_I_816203..816353_POSITIVE 207 80 34 135 95 pint:PI0218|3end_conserved_hypothetical_protein_211149..211299_POSITIVE 206 97 51 128 79 pint:PI1894|3end_UDP-N-acetylmuramoylalanyl-D-glutamyl-2,6-diamino_pimelate_ligase_1838484..1838634_POSITIVE 206 80 42 150 109 pint:PI0549|3end_hypothetical_protein_500691..500841_POSITIVE 206 109 62 132 72 pint:PI0196|3end_hypothetical_protein_188643..188793_POSITIVE 205 80 38 124 81 pint:PI0809|3end_hypothetical_protein_747108..747258_POSITIVE 204 77 33 120 74 pint:PI1639|3end_conserved_hypothetical_protein_1558133..1558283_POSITIVE 204 110 62 105 58 pint:PI0001|3end_possible_Ton-B_receptor_2912..3062_POSITIVE 203 78 34 72 28 pint:PI0100|3end_LPS_biosynthesis_protein_(lipopolysaccharide_biosynthesis_protein)_96726..96876_POSITIVE 202 115 74 107 69 pint:PI0655|3end_Na+/H+_anitporter_599541..599691_POSITIVE 200 88 49 58 21 pint:PI1832|3end_conserved_hypothetical_protein_1774023..1774173_POSITIVE