Origin IGS: agtttccccctaataaaatgtttaaaattcttaaagattaagtggactttaagactgagacattatttatctttttagcgatattgtcaagagccgtaaattattgtataatccgccgacaaaacttgggattttaaa .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tttaaaatcccaagttttgtcggcggattatacaataatttacggctcttgacaatatcgctaaaaagataaataatgtctcagtcttaaagtccacttaatctttaagaattttaaacattttattagggggaaact Mask Tandem Repeat Region ================================================ agtttccccctaataaaatgtttaaaattcttaaagattaagtggactttaagactgagacattatttatctttttagcgatattgtcaagagccgtaaattattgtataatccgccgacaaaacttgggattttaaa Find is-nt database================================================ Query_seq: TDE2194:TDE2195|TDE2194:TDE2195:8-amino-7-oxononanoate synthase, putative:RNA pseudouridylate synthase family protein:<-->:2231123..2231260 138 agtttccccctaataaaatgtttaaaattcttaaagattaagtggactttaagactgagacattatttatctttttagcgatattgtcaagagccgtaaattattgtataatccgccgacaaaacttgggattttaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE2194:TDE2195|TDE2194:TDE2195:8-amino-7-oxononanoate synthase, putative:RNA pseudouridylate synthase family protein:<-->:2231123..2231260 138 agtttccccctaataaaatgtttaaaattcttaaagattaagtggactttaagactgagacattatttatctttttagcgatattgtcaagagccgtaaattattgtataatccgccgacaaaacttgggattttaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE2194:TDE2195|TDE2194:TDE2195:8-amino-7-oxononanoate synthase, putative:RNA pseudouridylate synthase family protein:<-->:2231123..2231260 138 agtttccccctaataaaatgtttaaaattcttaaagattaagtggactttaagactgagacattatttatctttttagcgatattgtcaagagccgtaaattattgtataatccgccgacaaaacttgggattttaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 agtttccccctaataaaatgtttaaaattcttaaagattaagtggactttaagactgagacattatttatctttttagcgatattgtcaagagccgtaaattattgtataatccgccgacaaaacttgggattttaaa Predict ORF larger than 30AA ================================================ Protein_Len: 32 Strand: + Start: 42 End: 134 ......................................... M D F K T E T L F I F L A I L S R A V N Y C I I R R Q N L G F * .... agtttccccctaataaaatgtttaaaattcttaaagattaagtggactttaagactgagacattatttatctttttagcgatattgtcaagagccgtaaattattgtataatccgccgacaaaacttgggattttaaa 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: 90 Start: 83 End: 112 ..................................................................................ATTGTCAAGAGCCGTAAATTATTGTATAAT.......................... PromScan Matrix: RpoD-17 Strand: - Score: 86 Start: 62 End: 91 .............................................................CTTGACAATATCGCTAAAAAGATAAATAAT............................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ agtttccccctaataaaatgtttaaaattcttaaagattaagtggactttaagactgagacattatttatctttttagcgatattgtcaagagccgtaaattattgtataatccgccgacaaaacttgggattttaaa Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 41 HP_score: -2.0 Tail_Score: -3.10843 Start: 29 End: 54 Full_Region: taaataatgtctcag tcttaaag tccacttaat ctttaaga attttaaacatttta ............................tcttaaagtccacttaatctttaaga.................................................................................... Find igs database================================================ Query_seq: TDE2194:TDE2195|TDE2194:TDE2195:8-amino-7-oxononanoate synthase, putative:RNA pseudouridylate synthase family protein:<-->:2231123..2231260 138 agtttccccctaataaaatgtttaaaattcttaaagattaagtggactttaagactgagacattatttatctttttagcgatattgtcaagagccgtaaattattgtataatccgccgacaaaacttgggattttaaa Intra-Species Hit: Count: 1 Min: 1 Max: 138 Len: 138 Subject: NC_002967_TDE2194_TDE2195|8-amino-7-oxononanoate synthase, putative:RNA pseudouridylate synthase family protein|NEGATIVE:POSITIVE|[2231123,2231260]|138 HSP 1 e-value: 7.0E-73 bit: 274.0 Len: 138 Query Start:1 Query End:138 Subject Strand: POSITIVE Subject Start: 1 Subject End: 138 agtttccccctaataaaatgtttaaaattcttaaagattaagtggactttaagactgagacattatttatctttttagcgatattgtcaagagccgtaaattattgtataatccgccgacaaaacttgggattttaaa agtttccccctaataaaatgtttaaaattcttaaagattaagtggactttaagactgagacattatttatctttttagcgatattgtcaagagccgtaaattattgtataatccgccgacaaaacttgggattttaaa Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGUUUCCCCCUAAUAAAAUGUUUAAAAUUCUUAAAGAUUAAGUGGACUUUAAGACUGAGACAUUAUUUAUCUUUUUAGCGAUAUUGUCAAGAGCCGUAAAUUAUUGUAUAAUCCGCCGACAAAACUUGGGAUUUUAAA ....((((........(((((((...(.((((((((.((.....)))))))))).).)))))))..........(..(((..((((((((.............))).))))).)))..)........))))....... (-20.12) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUAAAAUCCCAAGUUUUGUCGGCGGAUUAUACAAUAAUUUACGGCUCUUGACAAUAUCGCUAAAAAGAUAAAUAAUGUCUCAGUCUUAAAGUCCACUUAAUCUUUAAGAAUUUUAAACAUUUUAUUAGGGGGAAACU .......((((..(((..((((..(((((((...))))))).))))....))).......((((..(((((.....)))))...((((((((..........))))))))...............)))).)))).... (-24.20) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 851 130 81 221 172 NC_002967:TDE2194|5end_8-amino-7-oxononanoate_synthase,_putative_2231032..2231262_NEGATIVE 307 117 79 200 161 NC_002967:TDE2553|5end_lysyl-tRNA_synthetase_2580633..2580863_NEGATIVE 307 129 83 75 24 NC_002967:TDE0175|5end_pyrrolidone-carboxylate_peptidase_208782..209012_NEGATIVE 294 119 75 117 72 NC_002967:TDE1598|5end_ABC_transporter,_ATP-binding_protein_1648910..1649140_NEGATIVE 251 117 78 92 52 NC_002967:TDE1260|5end_cholinephosphate_cytidylyltransferase/choline_kinase_1294028..1294258_POSITIVE 247 120 86 73 32 NC_002967:TDE0137|5end_carbohydrate_kinase,_FGGY_family_156640..156870_POSITIVE 246 116 79 66 31 NC_002967:TDE1052|5end_rubredoxin_1078870..1079100_NEGATIVE 244 129 81 57 21 NC_002967:TDE2364|5end_high-affinity_branched-chain_amino_acid_ABC_transporter,_ATP-binding_protein_2398949..2399179_NEGATIVE 236 118 78 63 18 NC_002967:TDE2131|5end_cobalamin_biosynthesis_protein_CbiM,_putative_2162683..2162913_NEGATIVE 234 116 71 75 30 NC_002967:TDE0369|5end_type_I_restriction-modification_system,_M_subunit_420971..421201_NEGATIVE 232 119 79 201 156 NC_002967:TDE2342|5end_1-deoxy-D-xylulose_5-phosphate_reductoisomerase_2380383..2380613_NEGATIVE 232 130 90 194 142 NC_002967:TDE0797|5end_acylphosphatase_820859..821089_POSITIVE 231 98 59 181 140 NC_002967:TDE0410|5end_peptidase,_M48_family_462053..462283_POSITIVE 229 102 61 133 89 NC_002967:TDE0681|5end_protein_export_protein_SecD_720619..720849_NEGATIVE 228 106 69 131 96 NC_002967:TDE1862|5end_hypothetical_protein_1886928..1887158_POSITIVE 228 120 76 157 119 NC_002967:TDE1820|5end_hypothetical_protein_1854692..1854922_NEGATIVE 225 118 75 54 13 NC_002967:TDE1605|5end_hypothetical_protein_1656111..1656341_NEGATIVE 224 129 81 174 117 NC_002967:TDE1656|5end_lipoprotein,_putative_1707220..1707450_NEGATIVE 223 118 79 59 25 NC_002967:TDE0623|5end_precorrin-3B_C17-methyltransferase_655783..656013_POSITIVE 220 107 68 179 144 NC_002967:TDE1882|5end_glycosyl_hydrolase,_family_1_1903544..1903774_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 307 129 83 57 6 NC_002967:TDE0176|3end_hypothetical_protein_208800..208950_NEGATIVE 294 119 75 107 62 NC_002967:TDE1599|3end_ABC_transporter,_ATP-binding/permease_protein_1648920..1649070_NEGATIVE 264 118 77 106 59 NC_002967:TDE1848|3end_hypothetical_protein_1875897..1876047_NEGATIVE 247 120 86 76 35 NC_002967:TDE0136|3end_hypothetical_protein_156723..156873_POSITIVE 244 129 81 76 40 NC_002967:TDE2365|3end_high-affinity_branched-chain_amino_acid_ABC_transporter,_permease_protein_2398930..2399080_NEGATIVE 237 45 1 38 2 NC_002967:TDE2715|3end_hypothetical_protein_2772936..2773086_POSITIVE 229 102 61 87 43 NC_002967:TDE0682|3end_preprotein_translocase,_YajC_subunit_720665..720815_NEGATIVE 218 130 91 33 4 NC_002967:TDE0837|3end_Na(+)-translocating_NADH-quinone_reductase,_B_subunit_856093..856243_NEGATIVE 215 117 78 74 45 NC_002967:TDE1644|3end_methionyl-tRNA_formyltransferase_1694578..1694728_NEGATIVE 211 119 92 39 12 NC_002967:TDE0818|3end_ABC_transporter,_ATP-binding/permease_protein_839926..840076_NEGATIVE 210 130 82 88 31 NC_002967:TDE2736|3end_hypothetical_protein_2791702..2791852_NEGATIVE 209 130 85 89 27 NC_002967:TDE0744|3end_thioredoxin_780241..780391_POSITIVE 207 119 77 76 35 NC_002967:TDE1036|3end_hypothetical_protein_1064553..1064703_POSITIVE 207 119 77 76 42 NC_002967:TDE0352|3end_ribose_5-phosphate_isomerase_B_396739..396889_POSITIVE 204 105 61 95 59 NC_002967:TDE1329|3end_ATPase,_AAA_family_1365346..1365496_POSITIVE 204 98 66 118 84 NC_002967:TDE0304|3end_hypothetical_protein_335492..335642_POSITIVE 203 97 84 144 131 NC_002967:TDE2438|3end_hypothetical_protein_2467965..2468115_NEGATIVE 202 116 72 119 80 NC_002967:TDE0448|3end_deoxyribose-phosphate_aldolase_506526..506676_POSITIVE 201 119 71 122 81 NC_002967:TDE0956|3end_hypothetical_protein_980330..980480_POSITIVE 201 105 65 127 89 NC_002967:TDE0951|3end_lipoprotein,_putative_975378..975528_POSITIVE