Origin IGS: aagaatcaagaggatacaagcctcaaaggtgatcccaccgaaaaatctctttggggccggacagaatgtttgagcatggctggcaaaaacgaagagggtgctgcaaagacgaaacgcttgcagcaccctcttgagctttcagccttttatcctccggc .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 gccggaggataaaaggctgaaagctcaagagggtgctgcaagcgtttcgtctttgcagcaccctcttcgtttttgccagccatgctcaaacattctgtccggccccaaagagatttttcggtgggatcacctttgaggcttgtatcctcttgattctt Mask Tandem Repeat Region ================================================ aagaatcaagaggatacaagcctcaaaggtgatcccaccgaaaaatctctttggggccggacagaatgtttgagcatggctggcaaaaacgaagagggtgctgcaaagacgaaacgcttgcagcaccctcttgagctttcagccttttatcctccggc Find is-nt database================================================ Query_seq: PG1003:PG1004|PG1003:PG1004:hypothetical protein:prolyl oligopeptidase family protein:-><-:1060365..1060522 158 aagaatcaagaggatacaagcctcaaaggtgatcccaccgaaaaatctctttggggccggacagaatgtttgagcatggctggcaaaaacgaagagggtgctgcaaagacgaaacgcttgcagcaccctcttgagctttcagccttttatcctccggc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG1003:PG1004|PG1003:PG1004:hypothetical protein:prolyl oligopeptidase family protein:-><-:1060365..1060522 158 aagaatcaagaggatacaagcctcaaaggtgatcccaccgaaaaatctctttggggccggacagaatgtttgagcatggctggcaaaaacgaagagggtgctgcaaagacgaaacgcttgcagcaccctcttgagctttcagccttttatcctccggc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG1003:PG1004|PG1003:PG1004:hypothetical protein:prolyl oligopeptidase family protein:-><-:1060365..1060522 158 aagaatcaagaggatacaagcctcaaaggtgatcccaccgaaaaatctctttggggccggacagaatgtttgagcatggctggcaaaaacgaagagggtgctgcaaagacgaaacgcttgcagcaccctcttgagctttcagccttttatcctccggc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aagaatcaagaggatacaagcctcaaaggtgatcccaccgaaaaatctctttggggccggacagaatgtttgagcatggctggcaaaaacgaagagggtgctgcaaagacgaaacgcttgcagcaccctcttgagctttcagccttttatcctccggc Predict ORF larger than 30AA ================================================ Protein_Len: 39 Strand: - Start: 26 End: 142 ......................... L H D W R F I E K P G S L I N S C P Q C F R L P H Q L S S V S A A G E Q A K M ................ Protein_Len: 42 Strand: - Start: 1 End: 126 L I L L I C A E F T I G G F F R K P A P C F T Q A H S A F V F L T S C L R F A Q L M ................................ aagaatcaagaggatacaagcctcaaaggtgatcccaccgaaaaatctctttggggccggacagaatgtttgagcatggctggcaaaaacgaagagggtgctgcaaagacgaaacgcttgcagcaccctcttgagctttcagccttttatcctccggc 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================================================ aagaatcaagaggatacaagcctcaaaggtgatcccaccgaaaaatctctttggggccggacagaatgtttgagcatggctggcaaaaacgaagagggtgctgcaaagacgaaacgcttgcagcaccctcttgagctttcagccttttatcctccggc Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 100 HP_score: -14.9 Tail_Score: -4.57073 Start: 90 End: 133 Full_Region: aaaaggctgaaagct caagagggtgctgcaagcg ttt cgtctttgcagcaccctcttcg tttttgccagccatg .........................................................................................caagagggtgctgcaagcgtttcgtctttgcagcaccctcttcg......................... TransTerm Strand: - Conf: 100 HP_score: -16.8 Tail_Score: -3.80855 Start: 94 End: 130 Full_Region: aggctgaaagctcaa gagggtgctgcaagcg ttt cgtctttgcagcaccctc ttcgtttttgccagc .............................................................................................gagggtgctgcaagcgtttcgtctttgcagcaccctc............................ Find igs database================================================ Query_seq: PG1003:PG1004|PG1003:PG1004:hypothetical protein:prolyl oligopeptidase family protein:-><-:1060365..1060522 158 aagaatcaagaggatacaagcctcaaaggtgatcccaccgaaaaatctctttggggccggacagaatgtttgagcatggctggcaaaaacgaagagggtgctgcaaagacgaaacgcttgcagcaccctcttgagctttcagccttttatcctccggc Intra-Species Hit: Count: 1 Min: 1 Max: 158 Len: 158 Subject: NC_002950_PG1003_PG1004|hypothetical protein:prolyl oligopeptidase family protein|POSITIVE:NEGATIVE|[1060365,1060522]|158 HSP 1 e-value: 9.0E-85 bit: 313.0 Len: 158 Query Start:1 Query End:158 Subject Strand: POSITIVE Subject Start: 1 Subject End: 158 aagaatcaagaggatacaagcctcaaaggtgatcccaccgaaaaatctctttggggccggacagaatgtttgagcatggctggcaaaaacgaagagggtgctgcaaagacgaaacgcttgcagcaccctcttgagctttcagccttttatcctccggc aagaatcaagaggatacaagcctcaaaggtgatcccaccgaaaaatctctttggggccggacagaatgtttgagcatggctggcaaaaacgaagagggtgctgcaaagacgaaacgcttgcagcaccctcttgagctttcagccttttatcctccggc Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAGAAUCAAGAGGAUACAAGCCUCAAAGGUGAUCCCACCGAAAAAUCUCUUUGGGGCCGGACAGAAUGUUUGAGCAUGGCUGGCAAAAACGAAGAGGGUGCUGCAAAGACGAAACGCUUGCAGCACCCUCUUGAGCUUUCAGCCUUUUAUCCUCCGGC .........(((((((...((((((((((.(((...........)))))))))))))(((((.....))))).....((((((........(((((((((((((((.(.((...))))))))))))))))))......))))))...))))))).... (-60.24) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GCCGGAGGAUAAAAGGCUGAAAGCUCAAGAGGGUGCUGCAAGCGUUUCGUCUUUGCAGCACCCUCUUCGUUUUUGCCAGCCAUGCUCAAACAUUCUGUCCGGCCCCAAAGAGAUUUUUCGGUGGGAUCACCUUUGAGGCUUGUAUCCUCUUGAUUCUU .(.((((((((...((((((((((..((((((((((((((((((...)))..))))))))))))))).)))))...)))))...((((((......((((.(((..(((....)))...))).))))....)))))).....)))))))).)...... (-63.10) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 392 98 55 49 3 NC_002950:PG0083|5end_hypothetical_protein_96952..97182_POSITIVE 385 117 71 74 17 NC_002950:PG0145|5end_hypothetical_protein_167831..168061_POSITIVE 378 97 52 162 113 NC_002950:PG0326|5end_hypothetical_protein_360974..361204_NEGATIVE 365 79 35 220 171 NC_002950:PG1767|5end_lipoprotein,_putative_1853995..1854225_POSITIVE 365 140 91 225 178 NC_002950:PG0323|5end_hypothetical_protein_357388..357618_NEGATIVE 363 84 48 145 117 NC_002950:PG0423|5end_hypothetical_protein_462251..462481_POSITIVE 357 96 51 58 16 NC_002950:PG1427|5end_thiol_protease/hemagglutinin_PrtT_precursor,_putative_1514396..1514626_NEGATIVE 355 98 52 151 110 NC_002950:PG1497|5end_DNA-binding_protein,_histone-like_family_1574085..1574315_POSITIVE 351 136 91 124 81 NC_002950:PG1130|5end_TPR_domain_protein_1208053..1208283_POSITIVE 348 120 75 72 28 NC_002950:PG0476|5end_yngK_protein_518762..518992_NEGATIVE 342 100 55 224 172 NC_002950:PG0683|5end_ABC_transporter,_permease_protein,_putative_735255..735485_POSITIVE 340 85 46 47 10 NC_002950:PG0500|5end_queuine_tRNA-ribosyltransferase_539197..539427_POSITIVE 339 110 67 222 180 NC_002950:PG0684|5end_ABC_transporter,_permease_protein,_putative_737648..737878_POSITIVE 339 100 54 228 186 NC_002950:PG0091|5end_transporter,_putative_107400..107630_NEGATIVE 337 100 51 77 30 NC_002950:PG0369|5end_phosphopantetheine_adenylyltransferase_403210..403440_POSITIVE 336 58 13 214 166 NC_002950:PG2099|5end_ATP-dependent_RNA_helicase,_DEAD/DEAH_box_family_2207932..2208162_NEGATIVE 336 86 53 216 183 NC_002950:PG1156|5end_S4_domain_protein_1236735..1236965_POSITIVE 336 110 67 222 173 NC_002950:PG0597|5end_ribosomal_protein_L9_653662..653892_POSITIVE 329 120 72 173 133 NC_002950:PG2107|5end_thiamine_biosynthesis_protein_ThiH_2216658..2216888_NEGATIVE 329 138 96 227 165 NC_002950:PG0702|5end_nicotinate-nucleotide--dimethylbenzimidazole_phosphoribosyltransferase,_putative_757100..757330_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 634 140 91 52 7 NC_002950:PG0712|3end_hypothetical_protein_766784..766934_NEGATIVE 363 129 89 87 42 NC_002950:PG0725|3end_hydrolase,_haloacid_dehalogenase-like_family_777966..778116_POSITIVE 355 98 57 143 98 NC_002950:PG0046|3end_phosphatidate_cytidylyltransferase_56346..56496_NEGATIVE 348 120 75 82 38 NC_002950:PG0477|3end_pantoate--beta-alanine_ligase_518752..518902_NEGATIVE 333 120 74 63 1 NC_002950:PG0248|3end_translation_initation_factor_SUI1,_putative_281510..281660_NEGATIVE 329 140 94 150 106 NC_002950:PG2101|3end_hypothetical_protein_2210278..2210428_NEGATIVE 323 130 84 59 17 NC_002950:PG0912|3end_polysaccharide_transport_protein,_putative_973791..973941_NEGATIVE 322 144 101 75 23 NC_002950:PG0361|3end_hypothetical_protein_395481..395631_POSITIVE 320 132 91 68 26 NC_002950:PG0726|3end_lipoprotein,_putative_778003..778153_NEGATIVE 319 85 43 122 64 NC_002950:PG0453|3end_hypothetical_protein_496670..496820_POSITIVE 319 59 12 72 25 NC_002950:PG0310|3end_nitroreductase_family_protein_345020..345170_NEGATIVE 318 98 54 77 22 NC_002950:PG1723|3end_ribosomal_protein_S20_1813403..1813553_POSITIVE 318 130 88 77 27 NC_002950:PG0758|3end_peptidyl-dipeptidase_Dcp_806467..806617_NEGATIVE 318 100 56 83 30 NC_002950:PG0226|3end_transglutaminase-related_protein_259838..259988_NEGATIVE 317 98 53 120 73 NC_002950:PG0932|3end_DNA_polymerase_III,_delta_prime_subunit,_putative_989833..989983_POSITIVE 315 146 103 64 17 NC_002950:PG1786|3end_hypothetical_protein_1875322..1875472_POSITIVE 313 100 55 50 3 NC_002950:PG0232|3end_zinc_carboxypeptidase,_putative_267458..267608_NEGATIVE 312 139 92 92 53 NC_002950:PG1283|3end_hypothetical_protein_1362795..1362945_POSITIVE 311 140 92 57 3 NC_002950:PG1950|3end_hypothetical_protein_2040840..2040990_POSITIVE 311 100 53 46 1 NC_002950:PG0368|3end_DNA_topoisomerase_IV_subunit_B_403259..403409_POSITIVE