Origin IGS: aaacctcttacagaggatggggcaagattaaagcaccaacccccaaaagagaaaagcgatgttcggaagagcatcgctttttttattgctgtctttcctggctgaatgcgaatcgatactgcgacggtt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aaccgtcgcagtatcgattcgcattcagccaggaaagacagcaataaaaaaagcgatgctcttccgaacatcgcttttctcttttgggggttggtgctttaatcttgccccatcctctgtaagaggttt Mask Tandem Repeat Region ================================================ aaacctcttacagaggatggggcaagattaaagcaccaacccccaaaagagaaaagcgatgttcggaagagcatcgctttttttattgctgtctttcctggctgaatgcgaatcgatactgcgacggtt Find is-nt database================================================ Query_seq: PG0090:PG0091|PG0090:PG0091:Dps family protein:transporter, putative:-><-:106144..106272 129 aaacctcttacagaggatggggcaagattaaagcaccaacccccaaaagagaaaagcgatgttcggaagagcatcgctttttttattgctgtctttcctggctgaatgcgaatcgatactgcgacggtt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG0090:PG0091|PG0090:PG0091:Dps family protein:transporter, putative:-><-:106144..106272 129 aaacctcttacagaggatggggcaagattaaagcaccaacccccaaaagagaaaagcgatgttcggaagagcatcgctttttttattgctgtctttcctggctgaatgcgaatcgatactgcgacggtt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG0090:PG0091|PG0090:PG0091:Dps family protein:transporter, putative:-><-:106144..106272 129 aaacctcttacagaggatggggcaagattaaagcaccaacccccaaaagagaaaagcgatgttcggaagagcatcgctttttttattgctgtctttcctggctgaatgcgaatcgatactgcgacggtt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aaacctcttacagaggatggggcaagattaaagcaccaacccccaaaagagaaaagcgatgttcggaagagcatcgctttttttattgctgtctttcctggctgaatgcgaatcgatactgcgacggtt Predict ORF larger than 30AA ================================================ Protein_Len: 34 Strand: + Start: 27 End: 128 .......................... M K A P T P K R E K R C S E E H R F F Y C C L S W L N A N R Y C D G . Protein_Len: 37 Strand: - Start: 3 End: 113 .. G R V S S P A L N F C W G G F S F L S T R F L M A K K I A T K G P Q I R M ................ aaacctcttacagaggatggggcaagattaaagcaccaacccccaaaagagaaaagcgatgttcggaagagcatcgctttttttattgctgtctttcctggctgaatgcgaatcgatactgcgacggtt 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================================================ aaacctcttacagaggatggggcaagattaaagcaccaacccccaaaagagaaaagcgatgttcggaagagcatcgctttttttattgctgtctttcctggctgaatgcgaatcgatactgcgacggtt Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 100 HP_score: -10.9 Tail_Score: -5.85737 Start: 56 End: 77 Full_Region: CCCCAAAAGAGAAAA GCGATGTTC GGAA GAGCATCGC TTTTTTTATTGCTGT .......................................................GCGATGTTCGGAAGAGCATCGC.................................................... TransTerm Strand: - Conf: 88 HP_score: -8.7 Tail_Score: -4.89567 Start: 56 End: 77 Full_Region: acagcaataaaaaaa gcgatgctc ttcc gaacatcgc ttttctcttttgggg .......................................................gcgatgctcttccgaacatcgc.................................................... Find igs database================================================ Query_seq: PG0090:PG0091|PG0090:PG0091:Dps family protein:transporter, putative:-><-:106144..106272 129 aaacctcttacagaggatggggcaagattaaagcaccaacccccaaaagagaaaagcgatgttcggaagagcatcgctttttttattgctgtctttcctggctgaatgcgaatcgatactgcgacggtt Intra-Species Hit: Count: 1 Min: 1 Max: 129 Len: 129 Subject: NC_002950_PG0090_PG0091|Dps family protein:transporter, putative|POSITIVE:NEGATIVE|[106144,106272]|129 HSP 1 e-value: 5.0E-55 bit: 214.0 Len: 129 Query Start:1 Query End:129 Subject Strand: POSITIVE Subject Start: 1 Subject End: 129 aaacctcttacagaggatggggcaagattaaagcaccaacccccaaaagagaaaagcgatgttcggaagagcatcgcnnnnnnnattgctgtctttcctggctgaatgcgaatcgatactgcgacggtt aaacctcttacagaggatggggcaagattaaagcaccaacccccaaaagagaaaagcgatgttcggaagagcatcgctttttttattgctgtctttcctggctgaatgcgaatcgatactgcgacggtt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAACCUCUUACAGAGGAUGGGGCAAGAUUAAAGCACCAACCCCCAAAAGAGAAAAGCGAUGUUCGGAAGAGCAUCGCUUUUUUUAUUGCUGUCUUUCCUGGCUGAAUGCGAAUCGAUACUGCGACGGUU ...((((.....)))).(((((..................)))))...((((((((((((((((....))))))))))))))))...((((((..((.(.((.....)).)...))......)))))). (-42.27) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AACCGUCGCAGUAUCGAUUCGCAUUCAGCCAGGAAAGACAGCAAUAAAAAAAGCGAUGCUCUUCCGAACAUCGCUUUUCUCUUUUGGGGGUUGGUGCUUUAAUCUUGCCCCAUCCUCUGUAAGAGGUUU .......((.((.....((.((.....)).)).....)).))......((((((((((.((....)).))))))))))(((((.((((((.(((.((.........)).))).)))))).))))).... (-35.40) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 393 60 11 219 167 NC_002950:PG0526|5end_putative_inner_membrane_protein_translocase_component_YidC_570746..570976_POSITIVE 327 79 32 81 26 NC_002950:PG1728|5end_cytidine/deoxycytidylate_deaminase_family_protein_1817644..1817874_POSITIVE 324 60 14 46 1 NC_002950:PG1855|5end_carboxyl-terminal_protease_1955476..1955706_NEGATIVE 317 77 44 184 142 NC_002950:PG0488|5end_Holliday_junction_DNA_helicase_RuvB_528169..528399_POSITIVE 314 110 62 202 155 NC_002950:PG1760|5end_ABC_transporter,_ATP-binding_protein_1846507..1846737_POSITIVE 312 96 51 167 118 NC_002950:PG1369|5end_glycerol-3-phosphate_dehydrogenase_(NAD(P)+)_1450407..1450637_NEGATIVE 306 66 21 162 118 NC_002950:PG2087|5end_hypothetical_protein_2186990..2187220_POSITIVE 304 64 21 135 85 NC_002950:PG2030|5end_hypothetical_protein_2129747..2129977_POSITIVE 301 78 32 60 6 NC_002950:PG0295|5end_DNA_processing_protein_DprA,_putative_331300..331530_NEGATIVE 300 76 33 191 143 NC_002950:PG1162|5end_ATP:cob(I)alamin_adenosyltransferase,_putative_1242039..1242269_NEGATIVE 299 79 39 150 105 NC_002950:PG0189|5end_hypothetical_protein_225291..225521_POSITIVE 299 44 3 44 11 NC_002950:PG0049|5end_hypothetical_protein_60740..60970_NEGATIVE 299 44 3 227 194 NC_002950:PG0048|5end_conserved_hypothetical_protein_TIGR00092_60557..60787_NEGATIVE 297 99 53 104 59 NC_002950:PG0715|5end_transporter_769596..769826_NEGATIVE 297 59 15 61 14 NC_002950:PG0670|5end_lipoprotein,_putative_720752..720982_POSITIVE 297 118 71 126 73 NC_002950:PG0425|5end_esterase,_putative_463989..464219_NEGATIVE 296 110 61 215 153 NC_002950:PG2189|5end_aspartate_kinase_2297151..2297381_NEGATIVE 295 109 61 88 35 NC_002950:PG2123|5end_hypothetical_protein_2229891..2230121_POSITIVE 293 112 79 75 38 NC_002950:PG0893|5end_hydroxylamine_reductase_955853..956083_NEGATIVE 292 45 6 156 121 NC_002950:PG0237|5end_uracil-DNA_glycosylase_274778..275008_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 393 60 11 91 39 NC_002950:PG0525|3end_CTP_synthetase_570698..570848_POSITIVE 356 83 44 41 3 NC_002950:PG0090|3end_Dps_family_protein_106083..106233_POSITIVE 351 109 63 49 1 NC_002950:PG1760|3end_ABC_transporter,_ATP-binding_protein_1847216..1847366_POSITIVE 325 83 41 87 42 NC_002950:PG0179|3end_hypothetical_protein_202837..202987_POSITIVE 312 96 51 81 32 NC_002950:PG1370|3end_lysyl-tRNA_synthetase_1450493..1450643_NEGATIVE 307 108 63 82 31 NC_002950:PG1310|3end_exsB_protein_1389826..1389976_POSITIVE 301 78 32 67 13 NC_002950:PG0296|3end_phosphoribosylformylglycinamidine_synthase_331293..331443_NEGATIVE 295 60 19 38 1 NC_002950:PG1856|3end_cytidine/deoxycytidylate_deaminase_family_protein_1955484..1955634_NEGATIVE 294 116 71 149 117 NC_002950:PG0526|3end_putative_inner_membrane_protein_translocase_component_YidC_572709..572859_POSITIVE 292 45 6 122 87 NC_002950:PG0236|3end_hypothetical_protein_274824..274974_POSITIVE 288 93 56 145 107 NC_002950:PG0800|3end_hypothetical_protein_854719..854869_NEGATIVE 286 93 51 71 32 NC_002950:PG0231|3end_hypothetical_protein_267409..267559_POSITIVE 285 77 36 147 115 NC_002950:PG0250|3end_hypothetical_protein_283905..284055_NEGATIVE 284 78 33 73 28 NC_002950:PG1020|3end_hypothetical_protein_1083458..1083608_POSITIVE 284 110 63 70 12 NC_002950:PG0098|3end_hypothetical_protein_115745..115895_NEGATIVE 283 100 54 53 1 NC_002950:PG1788|3end_cysteine_peptidase,_putative_1877327..1877477_POSITIVE 283 79 33 91 47 NC_002950:PG1561|3end_dTDP-4-dehydrorhamnose_reductase_1640138..1640288_NEGATIVE 282 87 45 63 16 NC_002950:PG1910|3end_ribosomal_protein_L17_2010282..2010432_NEGATIVE 280 99 55 145 111 NC_002950:PG1975|3end_hemagglutinin_protein_HagC_2064350..2064500_POSITIVE 280 99 55 145 111 NC_002950:PG1972|3end_hemagglutinin_protein_HagB_2061203..2061353_POSITIVE