Origin IGS: tctacctgcaccggaaagagagagggggacttgtattctctctctctttttgtatacttgcagaagaaagagattctaaaaaaataatgagtaaatatat .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 atatatttactcattatttttttagaatctctttcttctgcaagtatacaaaaagagagagagaatacaagtccccctctctctttccggtgcaggtaga Mask Tandem Repeat Region ================================================ tctacctgcaccggaaagagagagggggacttgtattctctctctctttttgtatacttgcagaagaaagagattctaaaaaaataatgagtaaatatat Find is-nt database================================================ Query_seq: PG1497:PG1498|PG1497:PG1498:DNA-binding protein, histone-like family:hypothetical protein:->->:1574696..1574795 100 tctacctgcaccggaaagagagagggggacttgtattctctctctctttttgtatacttgcagaagaaagagattctaaaaaaataatgagtaaatatat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG1497:PG1498|PG1497:PG1498:DNA-binding protein, histone-like family:hypothetical protein:->->:1574696..1574795 100 tctacctgcaccggaaagagagagggggacttgtattctctctctctttttgtatacttgcagaagaaagagattctaaaaaaataatgagtaaatatat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG1497:PG1498|PG1497:PG1498:DNA-binding protein, histone-like family:hypothetical protein:->->:1574696..1574795 100 tctacctgcaccggaaagagagagggggacttgtattctctctctctttttgtatacttgcagaagaaagagattctaaaaaaataatgagtaaatatat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tctacctgcaccggaaagagagagggggacttgtattctctctctctttttgtatacttgcagaagaaagagattctaaaaaaataatgagtaaatatat Predict ORF larger than 30AA ================================================ Protein_Len: 31 Strand: + Start: 6 End: 98 ..... M H R K E R G G L V F S L S F C I L A E E R D S K K I M S K Y .. Protein_Len: 32 Strand: - Start: 3 End: 98 .. V Q V P F L S P S K Y E R E R K T Y K C F F S I R F F Y H T F M .. Protein_Len: 33 Strand: - Start: 5 End: 100 .... * R C R F S L P P S T N E R E K Q I S A S S L S E L F I I L L Y M tctacctgcaccggaaagagagagggggacttgtattctctctctctttttgtatacttgcagaagaaagagattctaaaaaaataatgagtaaatatat 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================================================ tctacctgcaccggaaagagagagggggacttgtattctctctctctttttgtatacttgcagaagaaagagattctaaaaaaataatgagtaaatatat Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PG1497:PG1498|PG1497:PG1498:DNA-binding protein, histone-like family:hypothetical protein:->->:1574696..1574795 100 tctacctgcaccggaaagagagagggggacttgtattctctctctctttttgtatacttgcagaagaaagagattctaaaaaaataatgagtaaatatat Intra-Species Hit: Count: 1 Min: 1 Max: 100 Len: 100 Subject: NC_002950_PG1497_PG1498|DNA-binding protein, histone-like family:hypothetical protein|POSITIVE:POSITIVE|[1574696,1574795]|100 HSP 1 e-value: 8.0E-38 bit: 157.0 Len: 100 Query Start:1 Query End:100 Subject Strand: POSITIVE Subject Start: 1 Subject End: 100 tctacctgcaccggaaagagagagggggacttgtattctctctctctttttgtatacttgcagaagaaagagattctnnnnnnntaatgagtaaatatat tctacctgcaccggaaagagagagggggacttgtattctctctctctttttgtatacttgcagaagaaagagattctaaaaaaataatgagtaaatatat Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCUACCUGCACCGGAAAGAGAGAGGGGGACUUGUAUUCUCUCUCUCUUUUUGUAUACUUGCAGAAGAAAGAGAUUCUAAAAAAAUAAUGAGUAAAUAUAU (((..(((((.(((((((((((((((((.......)))))))))))))))))......))))).))).....((((............))))........ (-26.50) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUAUAUUUACUCAUUAUUUUUUUAGAAUCUCUUUCUUCUGCAAGUAUACAAAAAGAGAGAGAGAAUACAAGUCCCCCUCUCUCUUUCCGGUGCAGGUAGA .......................((((.....))))(((((..((((....((((((((((.(...........).))))))))))...))))..))))) (-21.70) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 358 44 8 170 124 NC_002950:PG0620|5end_ATP-dependent_protease_La_672963..673193_POSITIVE 334 60 12 50 6 NC_002950:PG1554|5end_hypothetical_protein_1635264..1635494_POSITIVE 326 45 18 156 123 NC_002950:PG1509|5end_HAD-superfamily_hydrolase,_subfamily_IA,_variant_1_family_protein_1586691..1586921_POSITIVE 323 77 31 121 71 NC_002950:PG0414|5end_hypothetical_protein_453652..453882_NEGATIVE 321 46 4 121 78 NC_002950:PG1831|5end_ATP-dependent_DNA_helicase_RecQ_1925422..1925652_NEGATIVE 309 47 8 213 171 NC_002950:PG1018|5end_hypothetical_protein_1078894..1079124_POSITIVE 300 50 2 182 139 NC_002950:PG1479|5end_conjugative_transposon_protein_TraJ_1555234..1555464_NEGATIVE 297 44 5 213 170 NC_002950:PG0366|5end_hypothetical_protein_400815..401045_NEGATIVE 296 48 12 109 70 NC_002950:PG1999|5end_hypothetical_protein_2088821..2089051_NEGATIVE 292 49 5 212 159 NC_002950:PG2136|5end_hypothetical_protein_2243360..2243590_POSITIVE 290 52 11 181 129 NC_002950:PG1328|5end_CoA_ligase_family_protein_1408680..1408910_NEGATIVE 282 37 8 140 114 NC_002950:PG1500|5end_hypothetical_protein_1576099..1576329_POSITIVE 282 41 2 185 142 NC_002950:PG0784|5end_polyprenyl_synthetase_836729..836959_NEGATIVE 281 60 11 227 169 NC_002950:PG0396|5end_transcriptional_regulator,_Crp/Fnr_family_433513..433743_POSITIVE 278 55 13 173 131 NC_002950:PG0336|5end_hypothetical_protein_371292..371522_NEGATIVE 273 42 4 58 24 NC_002950:PG1821|5end_cytochrome_c_nitrite_reductase,_small_subunit_NrfH_1916522..1916752_NEGATIVE 273 47 6 216 162 NC_002950:PG0333|5end_hypothetical_protein_367823..368053_POSITIVE 272 58 13 223 162 NC_002950:PG1791|5end_hypothetical_protein_1881166..1881396_NEGATIVE 269 40 2 171 131 NC_002950:PG1947|5end_TPR_domain_protein_2032932..2033162_POSITIVE 269 38 5 74 36 NC_002950:PG0814|5end_hypothetical_protein_876251..876481_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 415 50 1 67 5 NC_002950:PG2072|3end_UvrD/REP_helicase_domain_protein_2170757..2170907_POSITIVE 373 50 1 75 24 NC_002950:PG1497|3end_DNA-binding_protein,_histone-like_family_1574635..1574785_POSITIVE 344 60 11 112 65 NC_002950:PG0173|3end_transcriptional_regulator,_putative_194388..194538_NEGATIVE 334 60 12 53 9 NC_002950:PG1553|3end_CobN/magnesium_chelatase_family_protein_1635347..1635497_POSITIVE 333 50 5 106 50 NC_002950:PG1128|3end_exodeoxyribonuclease_VII_large_subunit_1205199..1205349_POSITIVE 326 45 18 73 40 NC_002950:PG1508|3end_hypothetical_protein_1586688..1586838_POSITIVE 324 50 4 68 15 NC_002950:PG1630|3end_hypothetical_protein_1712142..1712292_POSITIVE 323 77 31 59 9 NC_002950:PG0415|3end_peptidyl-prolyl_cis-trans_isomerase,_PPIC-type_453714..453864_NEGATIVE 317 55 13 70 23 NC_002950:PG1226|3end_peptidyl-prolyl_cis-trans_isomerase,_cyclophilin-type_1304048..1304198_POSITIVE 300 50 2 150 107 NC_002950:PG1480|3end_conjugative_transposon_protein_TraI_1555266..1555416_NEGATIVE 296 48 12 88 49 NC_002950:PG2000|3end_signal_peptidase-related_protein_2088842..2088992_NEGATIVE 289 46 2 80 38 NC_002950:PG0143|3end_hydrolase,_carbon-nitrogen_family_165747..165897_NEGATIVE 282 37 8 62 36 NC_002950:PG1499|3end_hypothetical_protein_1576101..1576251_POSITIVE 279 57 12 103 51 NC_002950:PG2023|3end_methionyl-tRNA_formyltransferase_2117565..2117715_NEGATIVE 278 55 13 88 46 NC_002950:PG0337|3end_hypothetical_protein_371377..371527_NEGATIVE 277 47 5 97 50 NC_002950:PG0172|3end_exonuclease_194355..194505_POSITIVE 275 49 5 68 6 NC_002950:PG1501|3end_transcriptional_regulator,_tetR_family_1578500..1578650_NEGATIVE 274 59 12 67 24 NC_002950:PG1134|3end_thioredoxin_reductase_1215371..1215521_POSITIVE 273 54 11 47 1 NC_002950:PG0844|3end_hypothetical_protein_905461..905611_POSITIVE 272 49 10 62 3 NC_002950:PG1949|3end_malate_dehydrogenase_2038184..2038334_NEGATIVE