Origin IGS: taaggtaaaagccgttatccgaaacaagcaaacctactttgtgcctatgcttttatatgcataaagtaggtttacaatggcaggctgggacgtgattcatcacgttcctgacaccaaggaaaaatgttttca .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tgaaaacatttttccttggtgtcaggaacgtgatgaatcacgtcccagcctgccattgtaaacctactttatgcatataaaagcataggcacaaagtaggtttgcttgtttcggataacggcttttacctta Mask Tandem Repeat Region ================================================ taaggtaaaagccgttatccgaaacaagcaaacctactttgtgcctatgcttttatatgcataaagtaggtttacaatggcaggctgggacgtgattcatcacgttcctgacaccaaggaaaaatgttttca Find is-nt database================================================ Query_seq: PI0068:PI0069|PI0068:PI0069:arginine repressor:hypothetical protein:->->:67080..67211 132 taaggtaaaagccgttatccgaaacaagcaaacctactttgtgcctatgcttttatatgcataaagtaggtttacaatggcaggctgggacgtgattcatcacgttcctgacaccaaggaaaaatgttttca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI0068:PI0069|PI0068:PI0069:arginine repressor:hypothetical protein:->->:67080..67211 132 taaggtaaaagccgttatccgaaacaagcaaacctactttgtgcctatgcttttatatgcataaagtaggtttacaatggcaggctgggacgtgattcatcacgttcctgacaccaaggaaaaatgttttca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI0068:PI0069|PI0068:PI0069:arginine repressor:hypothetical protein:->->:67080..67211 132 taaggtaaaagccgttatccgaaacaagcaaacctactttgtgcctatgcttttatatgcataaagtaggtttacaatggcaggctgggacgtgattcatcacgttcctgacaccaaggaaaaatgttttca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taaggtaaaagccgttatccgaaacaagcaaacctactttgtgcctatgcttttatatgcataaagtaggtttacaatggcaggctgggacgtgattcatcacgttcctgacaccaaggaaaaatgttttca Predict ORF larger than 30AA ================================================ taaggtaaaagccgttatccgaaacaagcaaacctactttgtgcctatgcttttatatgcataaagtaggtttacaatggcaggctgggacgtgattcatcacgttcctgacaccaaggaaaaatgttttca 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================================================ taaggtaaaagccgttatccgaaacaagcaaacctactttgtgcctatgcttttatatgcataaagtaggtttacaatggcaggctgggacgtgattcatcacgttcctgacaccaaggaaaaatgttttca Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 100 HP_score: -12.3 Tail_Score: -3.9392 Start: 28 End: 75 Full_Region: tcccagcctgccatt gtaaacctactttatgcatat aaaagc ataggcacaaagtaggtttgc ttgtttcggataacg ...........................gtaaacctactttatgcatataaaagcataggcacaaagtaggtttgc......................................................... TransTerm Strand: + Conf: 90 HP_score: -11.5 Tail_Score: -3.59979 Start: 33 End: 70 Full_Region: TCCGAAACAAGCAAA CCTACTTTGTGCCTATG CTTT TATATGCATAAAGTAGG TTTACAATGGCAGGC ................................CCTACTTTGTGCCTATGCTTTTATATGCATAAAGTAGG.............................................................. TransTerm Strand: - Conf: 79 HP_score: -8.6 Tail_Score: -4.14764 Start: 33 End: 70 Full_Region: gcctgccattgtaaa cctactttatgcatat aaaagc ataggcacaaagtagg tttgcttgtttcgga ................................cctactttatgcatataaaagcataggcacaaagtagg.............................................................. Find igs database================================================ Query_seq: PI0068:PI0069|PI0068:PI0069:arginine repressor:hypothetical protein:->->:67080..67211 132 taaggtaaaagccgttatccgaaacaagcaaacctactttgtgcctatgcttttatatgcataaagtaggtttacaatggcaggctgggacgtgattcatcacgttcctgacaccaaggaaaaatgttttca Intra-Species Hit: Count: 1 Min: 1 Max: 132 Len: 132 Subject: pint_PI0068_PI0069|arginine repressor:hypothetical protein|POSITIVE:POSITIVE|[67080,67211]|132 HSP 1 e-value: 3.0E-69 bit: 262.0 Len: 132 Query Start:1 Query End:132 Subject Strand: POSITIVE Subject Start: 1 Subject End: 132 taaggtaaaagccgttatccgaaacaagcaaacctactttgtgcctatgcttttatatgcataaagtaggtttacaatggcaggctgggacgtgattcatcacgttcctgacaccaaggaaaaatgttttca taaggtaaaagccgttatccgaaacaagcaaacctactttgtgcctatgcttttatatgcataaagtaggtttacaatggcaggctgggacgtgattcatcacgttcctgacaccaaggaaaaatgttttca Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAGGUAAAAGCCGUUAUCCGAAACAAGCAAACCUACUUUGUGCCUAUGCUUUUAUAUGCAUAAAGUAGGUUUACAAUGGCAGGCUGGGACGUGAUUCAUCACGUUCCUGACACCAAGGAAAAAUGUUUUCA ...(((....((((((...........(.(((((((((((((((.((((....)))).))))))))))))))).))))))).....(((((((((....)))))))))....)))..(((((....))))). (-45.10) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGAAAACAUUUUUCCUUGGUGUCAGGAACGUGAUGAAUCACGUCCCAGCCUGCCAUUGUAAACCUACUUUAUGCAUAUAAAAGCAUAGGCACAAAGUAGGUUUGCUUGUUUCGGAUAACGGCUUUUACCUUA (((((.(.....(((.((((((..(((.(((((....))))))))..))..))))..(((((((((((((.(((.(((......))).))).))))))))))))).......))).....).)))))..... (-39.30) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 410 128 81 131 84 pint:PI0933|5end_hypothetical_protein_865700..865930_POSITIVE 390 120 72 137 86 pint:PI2145|5end_hypothetical_protein_2092213..2092443_POSITIVE 386 109 66 219 169 pint:PI0648|5end_hypothetical_protein_589448..589678_POSITIVE 373 79 34 77 20 pint:PI2131|5end_hypothetical_protein_2080678..2080908_POSITIVE 351 120 78 177 136 pint:PI0902|5end_hypothetical_protein_832291..832521_POSITIVE 345 50 3 113 64 pint:PI0707|5end_conserved_hypothetical_protein;_possible_integral_membrane_protein_643358..643588_POSITIVE 333 121 87 223 190 pint:PI1750|5end_sulfate_transporter_1672134..1672364_POSITIVE 324 120 74 216 176 pint:PI0889|5end_pyruvate_kinase_818758..818988_POSITIVE 322 88 41 94 31 pint:PI1733|5end_hypothetical_protein_1652160..1652390_POSITIVE 319 89 41 53 12 pint:PI1588|5end_DNA_polymerase_III,_epsilon_chain_1516302..1516532_POSITIVE 318 60 13 70 26 pint:PI0845|5end_peptidyl-dipeptidase_778272..778502_POSITIVE 313 70 27 160 118 pint:PI0072|5end_conserved_hypothetical_protein_70139..70369_POSITIVE 306 110 65 202 158 pint:PI1974|5end_hypothetical_protein_1931193..1931423_POSITIVE 306 110 66 223 166 pint:PI1011|5end_cytochrome_c_biogenesis_protein_CycY_932115..932345_POSITIVE 305 79 39 231 183 pint:PI2111|5end_conserved_hypothetical_protein_2062771..2063001_POSITIVE 304 119 79 65 29 pint:PI1749|5end_conserved_hypothetical_protein_1671039..1671269_POSITIVE 303 107 65 146 90 pint:PI2109|5end_surface_antigen_BspA_2060553..2060783_POSITIVE 303 110 66 50 17 pint:PI1549|5end_conserved_hypothetical_protein_1467021..1467251_POSITIVE 302 88 43 122 69 pint:PI2002|5end_hypothetical_protein_1960662..1960892_POSITIVE 294 90 41 91 31 pint:PI0182|5end_hypothetical_protein_174093..174323_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 403 123 87 51 15 pint:PI1820|3end_hypothetical_protein_1760377..1760527_POSITIVE 390 120 72 144 93 pint:PI2144|3end_hypothetical_protein_2092300..2092450_POSITIVE 367 73 31 61 19 pint:PI0068|3end_arginine_repressor_67019..67169_POSITIVE 345 50 3 69 20 pint:PI0706|3end_pyridoxal_phosphate_biosynthetic_protein_(4-hydroxythreonine-4-phosphate_dehydrogenase)_643394..643544_POSITIVE 335 110 65 79 39 pint:PI0925|3end_ribosomal_protein_L11_methyltransferase_856638..856788_POSITIVE 320 120 80 80 42 pint:PI1440|3end_conserved_hypothetical_protein_1363009..1363159_POSITIVE 313 70 27 49 7 pint:PI0070|3end_conserved_hypothetical_protein_70108..70258_POSITIVE 311 88 41 144 102 pint:PI0345|3end_conserved_hypothetical_protein_320809..320959_POSITIVE 310 110 68 131 84 pint:PI2137|3end_RNA_methylase_SpoU_family_2083807..2083957_POSITIVE 306 110 65 100 56 pint:PI1973|3end_conserved_hypothetical_protein_1931171..1931321_POSITIVE 303 107 65 138 82 pint:PI2108|3end_cell_surface_protein;_possible_cell_surface_antigen_BspA_2060625..2060775_POSITIVE 298 97 56 142 100 pint:PI2025|3end_conserved_hypothetical_protein_1979452..1979602_POSITIVE 293 51 18 148 107 pint:PI1824|3end_ThiJ/PfpI_family_protein_1765005..1765155_POSITIVE 280 90 43 103 49 pint:PI1127|3end_chloride_channel_protein_1054485..1054635_POSITIVE 270 110 69 133 84 pint:PI0201|3end_hypothetical_protein_195398..195548_POSITIVE 268 75 33 54 13 pint:PI0999|3end_hypothetical_protein_922812..922962_POSITIVE 267 115 79 144 100 pint:PI0362|3end_hypothetical_protein_333938..334088_POSITIVE 265 113 87 52 27 pint:PI2088|3end_conserved_hypothetical_protein;_possible_PAP2_superfamily_protein_2045815..2045965_POSITIVE 263 120 79 43 7 pint:PI0264|3end_transfer_region-related_protein,_TraN_257371..257521_POSITIVE 261 107 74 67 36 pint:PI1186|3end_conserved_hypothetical_protein_1106772..1106922_POSITIVE