Origin IGS: aaaatttatgtaatatacttttttaaattaaaaatgacactaaattacaaaaaaaatgttttttagtgtcatttttcttttagggctcaattatttaatttgcaacagccccttatttttttaaaatttaactgctataatagtaattaattaaatataaaattacattaaagtaaggaagataaaaa .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tttttatcttccttactttaatgtaattttatatttaattaattactattatagcagttaaattttaaaaaaataaggggctgttgcaaattaaataattgagccctaaaagaaaaatgacactaaaaaacattttttttgtaatttagtgtcatttttaatttaaaaaagtatattacataaatttt Mask Tandem Repeat Region ================================================ aaaatttatgtaatatacttttttaaattaaaaatgacactaaattacaaaaaaaatgttttttagtgtcatttttcttttagggctcaattatttaatttgcaacagccccttatttttttaaaatttaactgctataatagtaattaattaaatataaaattacattaaagtaaggaagataaaaa Find is-nt database================================================ Query_seq: FN0373:FN0374|FN0373:FN0374:hypothetical protein:Single-stranded-DNA-specific exonuclease recJ:->->:1002606..1002793 188 aaaatttatgtaatatacttttttaaattaaaaatgacactaaattacaaaaaaaatgttttttagtgtcatttttcttttagggctcaattatttaatttgcaacagccccttatttttttaaaatttaactgctataatagtaattaattaaatataaaattacattaaagtaaggaagataaaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: FN0373:FN0374|FN0373:FN0374:hypothetical protein:Single-stranded-DNA-specific exonuclease recJ:->->:1002606..1002793 188 aaaatttatgtaatatacttttttaaattaaaaatgacactaaattacaaaaaaaatgttttttagtgtcatttttcttttagggctcaattatttaatttgcaacagccccttatttttttaaaatttaactgctataatagtaattaattaaatataaaattacattaaagtaaggaagataaaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: FN0373:FN0374|FN0373:FN0374:hypothetical protein:Single-stranded-DNA-specific exonuclease recJ:->->:1002606..1002793 188 aaaatttatgtaatatacttttttaaattaaaaatgacactaaattacaaaaaaaatgttttttagtgtcatttttcttttagggctcaattatttaatttgcaacagccccttatttttttaaaatttaactgctataatagtaattaattaaatataaaattacattaaagtaaggaagataaaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aaaatttatgtaatatacttttttaaattaaaaatgacactaaattacaaaaaaaatgttttttagtgtcatttttcttttagggctcaattatttaatttgcaacagccccttatttttttaaaatttaactgctataatagtaattaattaaatataaaattacattaaagtaaggaagataaaaa Predict ORF larger than 30AA ================================================ aaaatttatgtaatatacttttttaaattaaaaatgacactaaattacaaaaaaaatgttttttagtgtcatttttcttttagggctcaattatttaatttgcaacagccccttatttttttaaaatttaactgctataatagtaattaattaaatataaaattacattaaagtaaggaagataaaaa 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: 83 Start: 98 End: 127 .................................................................................................ATTTGCAACAGCCCCTTATTTTTTTAAAAT............................................................. PromScan Matrix: RpoD-17 Strand: - Score: 81 Start: 44 End: 73 ...........................................AATGACACTAAAAAACATTTTTTTTGTAAT................................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aaaatttatgtaatatacttttttaaattaaaaatgacactaaattacaaaaaaaatgttttttagtgtcatttttcttttagggctcaattatttaatttgcaacagccccttatttttttaaaatttaactgctataatagtaattaattaaatataaaattacattaaagtaaggaagataaaaa Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 77 HP_score: -5.3 Tail_Score: -5.45802 Start: 35 End: 71 Full_Region: TTTTTAAATTAAAAA TGACACTAAATTACA AAAAAAA TGTTTTTTAGTGTCA TTTTTCTTTTAGGGC ..................................TGACACTAAATTACAAAAAAAATGTTTTTTAGTGTCA..................................................................................................................... TransTerm Strand: - Conf: 72 HP_score: -5.3 Tail_Score: -4.98531 Start: 35 End: 71 Full_Region: gccctaaaagaaaaa tgacactaaaaaaca ttttttt tgtaatttagtgtca tttttaatttaaaaa ..................................tgacactaaaaaacattttttttgtaatttagtgtca..................................................................................................................... Find igs database================================================ Query_seq: FN0373:FN0374|FN0373:FN0374:hypothetical protein:Single-stranded-DNA-specific exonuclease recJ:->->:1002606..1002793 188 aaaatttatgtaatatacttttttaaattaaaaatgacactaaattacaaaaaaaatgttttttagtgtcatttttcttttagggctcaattatttaatttgcaacagccccttatttttttaaaatttaactgctataatagtaattaattaaatataaaattacattaaagtaaggaagataaaaa Intra-Species Hit: Count: 1 Min: 1 Max: 188 Len: 188 Subject: NC_003454_FN0373_FN0374|hypothetical protein:Single-stranded-DNA-specific exonuclease recJ|POSITIVE:POSITIVE|[1002606,1002793]|188 HSP 1 e-value: 9.0E-30 bit: 131.0 Len: 66 Query Start:123 Query End:188 Subject Strand: POSITIVE Subject Start: 123 Subject End: 188 ..........................................................................................................................aaaatttaactgctataatagtaattaattaaatataaaattacattaaagtaaggaagataaaaa ..........................................................................................................................aaaatttaactgctataatagtaattaattaaatataaaattacattaaagtaaggaagataaaaa HSP 2 e-value: 5.0E-19 bit: 95.6 Len: 48 Query Start:1 Query End:48 Subject Strand: POSITIVE Subject Start: 1 Subject End: 48 aaaatttatgtaatatacttttttaaattaaaaatgacactaaattac............................................................................................................................................ aaaatttatgtaatatacttttttaaattaaaaatgacactaaattac............................................................................................................................................ Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAAUUUAUGUAAUAUACUUUUUUAAAUUAAAAAUGACACUAAAUUACAAAAAAAAUGUUUUUUAGUGUCAUUUUUCUUUUAGGGCUCAAUUAUUUAAUUUGCAACAGCCCCUUAUUUUUUUAAAAUUUAACUGCUAUAAUAGUAAUUAAUUAAAUAUAAAAUUACAUUAAAGUAAGGAAGAUAAAAA .......................((((..(((((((((((((((..(((.......)))..)))))))))))))))..))))((((((((.........)))....))))).((((((((((..........((((.((((.((((((............)))))))))).))))))))))))))... (-35.30) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUUUAUCUUCCUUACUUUAAUGUAAUUUUAUAUUUAAUUAAUUACUAUUAUAGCAGUUAAAUUUUAAAAAAAUAAGGGGCUGUUGCAAAUUAAAUAAUUGAGCCCUAAAAGAAAAAUGACACUAAAAAACAUUUUUUUUGUAAUUUAGUGUCAUUUUUAAUUUAAAAAAGUAUAUUACAUAAAUUUU ....................((((((...(((((((..((((((.(((...))).))))))..((((((.......((((((...................)))))).....(((((((((((((((..(((.......)))..)))))))))))))))..)))))).)))))))))))))....... (-35.71) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 651 90 41 217 168 NC_003454:FN0372|5end_Transposase_1002479..1002709_NEGATIVE 578 100 51 226 177 NC_003454:FN1339|5end_Transposase_1991669..1991899_POSITIVE 578 100 51 226 177 NC_003454:FN0529|5end_Transposase_1186369..1186599_NEGATIVE 578 100 51 226 177 NC_003454:FN0403|5end_Transposase_1042307..1042537_NEGATIVE 578 100 51 226 177 NC_003454:FN1511|5end_Transposase_14217..14447_POSITIVE 441 106 61 231 186 NC_003454:FN0028|5end_Transposase_664913..665143_POSITIVE 307 113 79 188 152 NC_003454:FN1477|5end_Hypothetical_membrane-spanning_protein_2159504..2159734_POSITIVE 301 118 82 173 129 NC_003454:FN2104|5end_hypothetical_protein_614237..614467_POSITIVE 276 118 83 143 106 NC_003454:FN1269|5end_Hypothetical_lipoprotein_1926242..1926472_NEGATIVE 269 125 83 162 117 NC_003454:FN1446|5end_Transposase_2116033..2116263_POSITIVE 239 95 55 162 121 NC_003454:FN0812|5end_Hypothetical_cytosolic_protein_1471051..1471281_POSITIVE 238 76 31 95 51 NC_003454:FN0531|5end_hypothetical_protein_1186389..1186619_POSITIVE 238 76 31 116 72 NC_003454:FN1509|5end_hypothetical_protein_14176..14406_NEGATIVE 230 121 82 162 120 NC_003454:FN0740|5end_imidazolonepropionase_1398914..1399144_NEGATIVE 225 89 42 153 112 NC_003454:FN0930|5end_Glycerol-3-phosphate_cytidylyltransferase_1583964..1584194_NEGATIVE 225 142 101 167 128 NC_003454:FN1711|5end_Methyltransferase_206325..206555_POSITIVE 224 121 91 173 137 NC_003454:FN1935|5end_Adenine-specific_methyltransferase_437061..437291_NEGATIVE 214 119 72 204 160 NC_003454:FN0369|5end_Ribosomal-protein-alanine_acetyltransferase_998895..999125_NEGATIVE 212 99 56 56 17 NC_003454:FN0552|5end_Serine_racemase_1204715..1204945_NEGATIVE 208 88 45 182 140 NC_003454:FN1580|5end_2-C-methyl-D-erythritol_4-phosphate_cytidylyltransferase_90919..91149_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 694 110 61 81 32 NC_003454:FN0532|3end_Hypothetical_membrane-spanning_protein_1186524..1186674_NEGATIVE 694 110 61 78 29 NC_003454:FN0405|3end_tryptophanyl-tRNA_synthetase_1042465..1042615_NEGATIVE 694 110 61 56 7 NC_003454:FN1508|3end_3,4-dihydroxy-2-butanone-4-phosphate_synthase_14117..14267_POSITIVE 575 114 72 78 36 NC_003454:FN0026|3end_Hypothetical_exported_24-amino_acid_repeat_protein_664832..664982_POSITIVE 322 114 83 83 39 NC_003454:FN1907|3end_Thymidylate_synthase_400546..400696_POSITIVE 301 114 89 89 65 NC_003454:FN0029|3end_Flavodoxin_666596..666746_NEGATIVE 301 118 82 65 21 NC_003454:FN2103|3end_RecA_protein_614209..614359_POSITIVE 300 121 89 92 63 NC_003454:FN1340|3end_Glutamyl-tRNA_synthetase_1993353..1993503_NEGATIVE 299 125 81 86 49 NC_003454:FN1427|3end_Phenazine_biosynthesis_protein_phzF_2096763..2096913_POSITIVE 292 125 83 85 22 NC_003454:FN1908|3end_Glycerophosphoryl_diester_phosphodiesterase_400596..400746_NEGATIVE 288 113 94 30 11 NC_003454:FN1476|3end_N-acetylmannosamine-6-phosphate_2-epimerase_2159426..2159576_POSITIVE 284 114 89 68 44 NC_003454:FN0528|3end_Cold_shock_protein_1184746..1184896_POSITIVE 276 118 83 59 22 NC_003454:FN1270|3end_Hypothetical_cytosolic_protein_1926326..1926476_NEGATIVE 264 118 89 68 40 NC_003454:FN0371|3end_hypothetical_protein_1000840..1000990_POSITIVE 252 130 82 93 48 NC_003454:FN1006|3end_Acetyltransferase_1660998..1661148_NEGATIVE 239 95 55 139 98 NC_003454:FN0811|3end_hypothetical_protein_1471108..1471258_POSITIVE 238 76 31 61 17 NC_003454:FN0530|3end_hypothetical_protein_1186435..1186585_POSITIVE 238 76 31 61 17 NC_003454:FN0404|3end_hypothetical_protein_1042373..1042523_POSITIVE 238 76 31 61 17 NC_003454:FN1510|3end_hypothetical_protein_14231..14381_NEGATIVE 230 133 98 118 72 NC_003454:FN1277|3end_Aminoacyl-histidine_dipeptidase_1935294..1935444_NEGATIVE