Origin IGS: atacttgataaacacataaatttattttataattaataataacatattgaattcagtaattttataaaaaaggaggatggaactttagtagttccaaggaaaaa .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tttttccttggaactactaaagttccatcctccttttttataaaattactgaattcaatatgttattattaattataaaataaatttatgtgtttatcaagtat Mask Tandem Repeat Region ================================================ atacttgataaacacataaatttattttataattaataataacatattgaattcagtaattttataaaaaaggaggatggaactttagtagttccaaggaaaaa Find is-nt database================================================ Query_seq: FN0374:FN0375|FN0374:FN0375:Single-stranded-DNA-specific exonuclease recJ:Iron(III)-binding protein:->->:1005329..1005432 104 atacttgataaacacataaatttattttataattaataataacatattgaattcagtaattttataaaaaaggaggatggaactttagtagttccaaggaaaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: FN0374:FN0375|FN0374:FN0375:Single-stranded-DNA-specific exonuclease recJ:Iron(III)-binding protein:->->:1005329..1005432 104 atacttgataaacacataaatttattttataattaataataacatattgaattcagtaattttataaaaaaggaggatggaactttagtagttccaaggaaaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: FN0374:FN0375|FN0374:FN0375:Single-stranded-DNA-specific exonuclease recJ:Iron(III)-binding protein:->->:1005329..1005432 104 atacttgataaacacataaatttattttataattaataataacatattgaattcagtaattttataaaaaaggaggatggaactttagtagttccaaggaaaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 atacttgataaacacataaatttattttataattaataataacatattgaattcagtaattttataaaaaaggaggatggaactttagtagttccaaggaaaaa Predict ORF larger than 30AA ================================================ atacttgataaacacataaatttattttataattaataataacatattgaattcagtaattttataaaaaaggaggatggaactttagtagttccaaggaaaaa 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: 91 Start: 4 End: 33 ...CTTGATAAACACATAAATTTATTTTATAAT....................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ atacttgataaacacataaatttattttataattaataataacatattgaattcagtaattttataaaaaaggaggatggaactttagtagttccaaggaaaaa Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: FN0374:FN0375|FN0374:FN0375:Single-stranded-DNA-specific exonuclease recJ:Iron(III)-binding protein:->->:1005329..1005432 104 atacttgataaacacataaatttattttataattaataataacatattgaattcagtaattttataaaaaaggaggatggaactttagtagttccaaggaaaaa Intra-Species Hit: Count: 1 Min: 1 Max: 104 Len: 104 Subject: NC_003454_FN0374_FN0375|Single-stranded-DNA-specific exonuclease recJ:Iron(III)-binding protein|POSITIVE:POSITIVE|[1005329,1005432]|104 HSP 1 e-value: 1.0E-52 bit: 206.0 Len: 104 Query Start:1 Query End:104 Subject Strand: POSITIVE Subject Start: 1 Subject End: 104 atacttgataaacacataaatttattttataattaataataacatattgaattcagtaattttataaaaaaggaggatggaactttagtagttccaaggaaaaa atacttgataaacacataaatttattttataattaataataacatattgaattcagtaattttataaaaaaggaggatggaactttagtagttccaaggaaaaa Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUACUUGAUAAACACAUAAAUUUAUUUUAUAAUUAAUAAUAACAUAUUGAAUUCAGUAAUUUUAUAAAAAAGGAGGAUGGAACUUUAGUAGUUCCAAGGAAAAA ...(((.(((((...(((((.....)))))..............(((((....)))))..)))))....))).....(((((((.....)))))))........ (-13.60) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUUUCCUUGGAACUACUAAAGUUCCAUCCUCCUUUUUUAUAAAAUUACUGAAUUCAAUAUGUUAUUAUUAAUUAUAAAAUAAAUUUAUGUGUUUAUCAAGUAU ........(((((((.....)))))))...................((((((.....(((((...(((((........)))))...))))).....)).)))). (-12.90) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 194 97 52 169 123 NC_003454:FN1700|5end_hypothetical_protein_195799..196029_NEGATIVE 187 95 53 51 3 NC_003454:FN1981|5end_Transposase_483299..483529_POSITIVE 187 98 73 214 189 NC_003454:FN1629|5end_50S_ribosomal_protein_L6_134508..134738_NEGATIVE 170 68 21 143 101 NC_003454:FN2065|5end_Transcriptional_repressor_575850..576080_POSITIVE 167 94 71 78 54 NC_003454:FN1736|5end_V-type_sodium_ATP_synthase_subunit_A_236021..236251_NEGATIVE 165 100 52 86 50 NC_003454:FN1043|5end_hypothetical_protein_1694239..1694469_POSITIVE 165 100 51 220 163 NC_003454:FN0897|5end_Hypothetical_cytosolic_protein_1555833..1556063_POSITIVE 161 96 66 154 127 NC_003454:FN0467|5end_murein_hydrolase_exporter_1112864..1113094_POSITIVE 161 95 53 207 161 NC_003454:FN0425|5end_Hypothetical_cytosolic_protein_1068030..1068260_POSITIVE 160 94 55 146 108 NC_003454:FN1136|5end_Phosphonates_transport_ATP-binding_protein_phnC_1783057..1783287_POSITIVE 155 98 81 180 162 NC_003454:FN0176|5end_Cell_division_inhibitor_MinD_801157..801387_POSITIVE 152 96 60 139 111 NC_003454:FN2023|5end_Hypothetical_cytosolic_protein_526642..526872_NEGATIVE 151 78 36 125 83 NC_003454:FN1103|5end_Excinuclease_ABC_subunit_A_1746559..1746789_POSITIVE 151 96 59 134 102 NC_003454:FN0653|5end_hypothetical_protein_1311448..1311678_POSITIVE 149 96 51 83 46 NC_003454:FN0386|5end_hypothetical_protein_1019045..1019275_POSITIVE 148 86 42 114 67 NC_003454:FN0483|5end_Uracil_phosphoribosyltransferase_1128577..1128807_POSITIVE 148 100 51 56 4 NC_003454:FN1749|5end_Pyruvate-flavodoxin_oxidoreductase_247461..247691_POSITIVE 148 96 83 166 153 NC_003454:FN1533|5end_Electron_transfer_flavoprotein_alpha-subunit_46321..46551_NEGATIVE 145 93 69 219 191 NC_003454:FN1678|5end_hypothetical_protein_174287..174517_POSITIVE 144 97 71 47 24 NC_003454:FN0734|5end_Fe-S_oxidoreductase_1390809..1391039_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 170 98 73 98 74 NC_003454:FN0027|3end_hypothetical_protein_664763..664913_NEGATIVE 167 94 71 60 36 NC_003454:FN1737|3end_V-type_ATP_synthase_subunit_F_236039..236189_NEGATIVE 162 100 65 40 1 NC_003454:FN2109|3end_UDP-glucose_4-epimerase_621917..622067_POSITIVE 161 96 66 72 45 NC_003454:FN0466|3end_Lysyl-tRNA_synthetase_1112862..1113012_POSITIVE 160 65 21 79 36 NC_003454:FN1444|3end_GMP_synthase_[glutamine-hydrolyzing]_2113203..2113353_POSITIVE 160 94 55 68 30 NC_003454:FN1135|3end_Phosphonates-binding_protein_1783059..1783209_POSITIVE 159 100 63 67 21 NC_003454:FN0792|3end_urocanate_hydratase_1450364..1450514_POSITIVE 158 81 52 81 53 NC_003454:FN1176|3end_Hypothetical_cytosolic_protein_1837506..1837656_NEGATIVE 158 99 55 114 68 NC_003454:FN1659|3end_hypothetical_protein_155826..155976_POSITIVE 151 78 36 57 15 NC_003454:FN1102|3end_tRNA_2'phosphotransferase_1746571..1746721_POSITIVE 151 96 59 55 23 NC_003454:FN0652|3end_Glyceraldehyde_3-phosphate_dehydrogenase_1311449..1311599_POSITIVE 151 95 70 83 55 NC_003454:FN0109|3end_hypothetical_protein_744333..744483_NEGATIVE 149 95 71 89 63 NC_003454:FN1616|3end_transcription_antitermination_protein_NusB_125976..126126_NEGATIVE 148 86 42 77 30 NC_003454:FN0482|3end_LSU_ribosomal_protein_L31P_1128620..1128770_POSITIVE 148 100 51 74 22 NC_003454:FN1748|3end_Pyruvate-flavodoxin_oxidoreductase_247559..247709_POSITIVE 147 97 55 140 103 NC_003454:FN1477|3end_Hypothetical_membrane-spanning_protein_2160297..2160447_POSITIVE 147 82 44 38 2 NC_003454:FN0839|3end_hypothetical_protein_1501244..1501394_NEGATIVE 147 95 68 82 53 NC_003454:FN1515|3end_Phophatidylinositol-4-phosphate_5-kinase_20652..20802_POSITIVE 146 82 44 79 44 NC_003454:FN0500|3end_hypothetical_protein_1149592..1149742_POSITIVE 144 97 71 40 17 NC_003454:FN0733|3end_peptidase_T_1390882..1391032_POSITIVE