Origin IGS: ttcaaaggggagttcggaatacggactcccttttttttgtcaatatttttatccgccatggacggcggatgaaaaatgtacaaggatgtacattcataaatggacacggatgtccatggttccaaacttgagagttttgcgtaagcaaaactctaagattaaaaatgtacaaggatgtacatttttaatcgacccccttgtatattattcttttttttattatactgtaacgtcttgtatcttgaaaagtattatgacttttcggttttataaaatcatttaggagaaactcggcagtttgctcctaaaaatctataaagatgaggtattgatt .........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.........1.........2.........3.........4.........5.........6.........7.........8.........9 aatcaatacctcatctttatagatttttaggagcaaactgccgagtttctcctaaatgattttataaaaccgaaaagtcataatacttttcaagatacaagacgttacagtataataaaaaaaagaataatatacaagggggtcgattaaaaatgtacatccttgtacatttttaatcttagagttttgcttacgcaaaactctcaagtttggaaccatggacatccgtgtccatttatgaatgtacatccttgtacatttttcatccgccgtccatggcggataaaaatattgacaaaaaaaagggagtccgtattccgaactcccctttgaa Mask Tandem Repeat Region ================================================ ttcaaaggggagttcggaatacggactcccttttttttgtcaatatttttatccgccatggacggcggatgaaaaatgtacaaggatgtacattcataaatggacacggatgtccatggttccaaacttgagagttttgcgtaagcaaaactctaagattaaaaatgtacaaggatgtacatttttaatcgacccccttgtatattattcttttttttattatactgtaacgtcttgtatcttgaaaagtattatgacttttcggttttataaaatcatttaggagaaactcggcagtttgctcctaaaaatctataaagatgaggtattgatt Find is-nt database================================================ Query_seq: TDE1048:TDE1049|TDE1048:TDE1049:30S ribosomal protein S7:elongation factor EF-2:->->:1075093..1075426 334 ttcaaaggggagttcggaatacggactcccttttttttgtcaatatttttatccgccatggacggcggatgaaaaatgtacaaggatgtacattcataaatggacacggatgtccatggttccaaacttgagagttttgcgtaagcaaaactctaagattaaaaatgtacaaggatgtacatttttaatcgacccccttgtatattattcttttttttattatactgtaacgtcttgtatcttgaaaagtattatgacttttcggttttataaaatcatttaggagaaactcggcagtttgctcctaaaaatctataaagatgaggtattgatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE1048:TDE1049|TDE1048:TDE1049:30S ribosomal protein S7:elongation factor EF-2:->->:1075093..1075426 334 ttcaaaggggagttcggaatacggactcccttttttttgtcaatatttttatccgccatggacggcggatgaaaaatgtacaaggatgtacattcataaatggacacggatgtccatggttccaaacttgagagttttgcgtaagcaaaactctaagattaaaaatgtacaaggatgtacatttttaatcgacccccttgtatattattcttttttttattatactgtaacgtcttgtatcttgaaaagtattatgacttttcggttttataaaatcatttaggagaaactcggcagtttgctcctaaaaatctataaagatgaggtattgatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE1048:TDE1049|TDE1048:TDE1049:30S ribosomal protein S7:elongation factor EF-2:->->:1075093..1075426 334 ttcaaaggggagttcggaatacggactcccttttttttgtcaatatttttatccgccatggacggcggatgaaaaatgtacaaggatgtacattcataaatggacacggatgtccatggttccaaacttgagagttttgcgtaagcaaaactctaagattaaaaatgtacaaggatgtacatttttaatcgacccccttgtatattattcttttttttattatactgtaacgtcttgtatcttgaaaagtattatgacttttcggttttataaaatcatttaggagaaactcggcagtttgctcctaaaaatctataaagatgaggtattgatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ttcaaaggggagttcggaatacggactcccttttttttgtcaatatttttatccgccatggacggcggatgaaaaatgtacaaggatgtacattcataaatggacacggatgtccatggttccaaacttgagagttttgcgtaagcaaaactctaagattaaaaatgtacaaggatgtacatttttaatcgacccccttgtatattattcttttttttattatactgtaacgtcttgtatcttgaaaagtattatgacttttcggttttataaaatcatttaggagaaactcggcagtttgctcctaaaaatctataaagatgaggtattgatt Predict ORF larger than 30AA ================================================ Protein_Len: 32 Strand: + Start: 175 End: 270 .............................................................................................................................................................................. M Y I F N R P P C I L F F F L L Y C N V L Y L E K Y Y D F S V L ................................................................ Protein_Len: 60 Strand: + Start: 86 End: 280 ..................................................................................... M Y I H K W T R M S M V P N L R V L R K Q N S K I K N V Q G C T F L I D P L V Y Y S F F Y Y T V T S C I L K S I M T F R ...................................................... Protein_Len: 31 Strand: - Start: 97 End: 189 ................................................................................................ L H V R I D M T G F K L T K R L C F E L I L F T C P H V N K M ................................................................................................................................................. Protein_Len: 41 Strand: - Start: 3 End: 125 .. L P S N P I R V G K K K D I N K D A M S P P H F I Y L S T C E Y I S V S T W P E M ................................................................................................................................................................................................................. Protein_Len: 57 Strand: - Start: 5 End: 172 .... * L P T R F V S E R K K T L I K I R W P R R I F F T C P H V N M F P C P H G H N W V Q S N Q T L L V R L N F I Y M .................................................................................................................................................................. ttcaaaggggagttcggaatacggactcccttttttttgtcaatatttttatccgccatggacggcggatgaaaaatgtacaaggatgtacattcataaatggacacggatgtccatggttccaaacttgagagttttgcgtaagcaaaactctaagattaaaaatgtacaaggatgtacatttttaatcgacccccttgtatattattcttttttttattatactgtaacgtcttgtatcttgaaaagtattatgacttttcggttttataaaatcatttaggagaaactcggcagtttgctcctaaaaatctataaagatgaggtattgatt 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: 84 Start: 219 End: 248 ..........................................................................................................................................................................................................................TTTTCAAGATACAAGACGTTACAGTATAAT...................................................................................... PromScan Matrix: RpoD-17 Strand: + Score: 83 Start: 197 End: 226 ....................................................................................................................................................................................................CTTGTATATTATTCTTTTTTTTATTATACT............................................................................................................ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ ttcaaaggggagttcggaatacggactcccttttttttgtcaatatttttatccgccatggacggcggatgaaaaatgtacaaggatgtacattcataaatggacacggatgtccatggttccaaacttgagagttttgcgtaagcaaaactctaagattaaaaatgtacaaggatgtacatttttaatcgacccccttgtatattattcttttttttattatactgtaacgtcttgtatcttgaaaagtattatgacttttcggttttataaaatcatttaggagaaactcggcagtttgctcctaaaaatctataaagatgaggtattgatt Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 77 HP_score: -10.1 Tail_Score: -3.01712 Start: 46 End: 75 Full_Region: tacatccttgtacat ttttcatccgccg tcca tggcggataaaaa tattgacaaaaaaaa .............................................ttttcatccgccgtccatggcggataaaaa................................................................................................................................................................................................................................................................... TransTerm Strand: - Conf: 77 HP_score: -6.2 Tail_Score: -4.7254 Start: 77 End: 92 Full_Region: gtgtccatttatgaa tgtaca tcct tgtaca tttttcatccgccgt ............................................................................tgtacatccttgtaca.................................................................................................................................................................................................................................................. TransTerm Strand: - Conf: 76 HP_score: -7.6 Tail_Score: -3.9534 Start: 101 End: 116 Full_Region: tcaagtttggaacca tggaca tccg tgtcca tttatgaatgtacat ....................................................................................................tggacatccgtgtcca.......................................................................................................................................................................................................................... TransTerm Strand: - Conf: 89 HP_score: -10.7 Tail_Score: -3.54424 Start: 127 End: 157 Full_Region: ttgtacatttttaat cttagagttttgc ttac gcaaaactctcaag tttggaaccatggac ..............................................................................................................................cttagagttttgcttacgcaaaactctcaag................................................................................................................................................................................. TransTerm Strand: - Conf: 91 HP_score: -12.5 Tail_Score: -3.15768 Start: 159 End: 188 Full_Region: atacaagggggtcga ttaaaaatgtaca tcct tgtacatttttaa tcttagagttttgct ..............................................................................................................................................................ttaaaaatgtacatccttgtacatttttaa.................................................................................................................................................. TransTerm Strand: + Conf: 77 HP_score: -6.2 Tail_Score: -4.72272 Start: 166 End: 181 Full_Region: CTCTAAGATTAAAAA TGTACA AGGA TGTACA TTTTTAATCGACCCC .....................................................................................................................................................................TGTACAAGGATGTACA......................................................................................................................................................... TransTerm Strand: - Conf: 81 HP_score: -6.2 Tail_Score: -4.87626 Start: 166 End: 181 Full_Region: ggggtcgattaaaaa tgtaca tcct tgtaca tttttaatcttagag .....................................................................................................................................................................tgtacatccttgtaca......................................................................................................................................................... TransTerm Strand: + Conf: 58 HP_score: -2.5 Tail_Score: -4.41206 Start: 242 End: 265 Full_Region: GTAACGTCTTGTATC TTGAAAAGT ATTATG ACTTTTCGG TTTTATAAAATCATT .................................................................................................................................................................................................................................................TTGAAAAGTATTATGACTTTTCGG..................................................................... TransTerm Strand: + Conf: 49 HP_score: -3.8 Tail_Score: -3.24 Start: 243 End: 264 Full_Region: TAACGTCTTGTATCT TGAAAAGT ATTATG ACTTTTCG GTTTTATAAAATCAT ..................................................................................................................................................................................................................................................TGAAAAGTATTATGACTTTTCG...................................................................... TransTerm Strand: + Conf: 49 HP_score: -5.1 Tail_Score: -2.53918 Start: 244 End: 263 Full_Region: AACGTCTTGTATCTT GAAAAGT ATTATG ACTTTTC GGTTTTATAAAATCA ...................................................................................................................................................................................................................................................GAAAAGTATTATGACTTTTC....................................................................... Find igs database================================================ Query_seq: TDE1048:TDE1049|TDE1048:TDE1049:30S ribosomal protein S7:elongation factor EF-2:->->:1075093..1075426 334 ttcaaaggggagttcggaatacggactcccttttttttgtcaatatttttatccgccatggacggcggatgaaaaatgtacaaggatgtacattcataaatggacacggatgtccatggttccaaacttgagagttttgcgtaagcaaaactctaagattaaaaatgtacaaggatgtacatttttaatcgacccccttgtatattattcttttttttattatactgtaacgtcttgtatcttgaaaagtattatgacttttcggttttataaaatcatttaggagaaactcggcagtttgctcctaaaaatctataaagatgaggtattgatt Intra-Species Hit: Count: 1 Min: 1 Max: 334 Len: 334 Subject: NC_002967_TDE1048_TDE1049|30S ribosomal protein S7:elongation factor EF-2|POSITIVE:POSITIVE|[1075093,1075426]|334 HSP 1 e-value: 1.0E-161 bit: 567.0 Len: 334 Query Start:1 Query End:334 Subject Strand: POSITIVE Subject Start: 1 Subject End: 334 ttcaaaggggagttcggaatacggactcccnnnnnnnngtcaatatttttatccgccatggacggcggatgaaaaatgtacaaggatgtacattcataaatggacacggatgtccatggttccaaacttgagagttttgcgtaagcaaaactctaagattaaaaatgtacaaggatgtacatttttaatcgacccccttgtatattattcnnnnnnnnattatactgtaacgtcttgtatcttgaaaagtattatgacttttcggttttataaaatcatttaggagaaactcggcagtttgctcctaaaaatctataaagatgaggtattgatt ttcaaaggggagttcggaatacggactcccttttttttgtcaatatttttatccgccatggacggcggatgaaaaatgtacaaggatgtacattcataaatggacacggatgtccatggttccaaacttgagagttttgcgtaagcaaaactctaagattaaaaatgtacaaggatgtacatttttaatcgacccccttgtatattattcttttttttattatactgtaacgtcttgtatcttgaaaagtattatgacttttcggttttataaaatcatttaggagaaactcggcagtttgctcctaaaaatctataaagatgaggtattgatt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUCAAAGGGGAGUUCGGAAUACGGACUCCCUUUUUUUUGUCAAUAUUUUUAUCCGCCAUGGACGGCGGAUGAAAAAUGUACAAGGAUGUACAUUCAUAAAUGGACACGGAUGUCCAUGGUUCCAAACUUGAGAGUUUUGCGUAAGCAAAACUCUAAGAUUAAAAAUGUACAAGGAUGUACAUUUUUAAUCGACCCCCUUGUAUAUUAUUCUUUUUUUUAUUAUACUGUAACGUCUUGUAUCUUGAAAAGUAUUAUGACUUUUCGGUUUUAUAAAAUCAUUUAGGAGAAACUCGGCAGUUUGCUCCUAAAAAUCUAUAAAGAUGAGGUAUUGAUU ...(((((((((((((.....)))))))))))))....((((((((.((((((((((......)))))))))).(((((((((((..............(((((((....)))))))(((..........((((((((((....))))))))))..(((((((((((((((....))))))))))))))).))).)))))))))))........................((((((.....(((((((((......))))))))).............(((((((((((((....))))).))))))))........))))))..)))))))). (-120.80) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUCAAUACCUCAUCUUUAUAGAUUUUUAGGAGCAAACUGCCGAGUUUCUCCUAAAUGAUUUUAUAAAACCGAAAAGUCAUAAUACUUUUCAAGAUACAAGACGUUACAGUAUAAUAAAAAAAAGAAUAAUAUACAAGGGGGUCGAUUAAAAAUGUACAUCCUUGUACAUUUUUAAUCUUAGAGUUUUGCUUACGCAAAACUCUCAAGUUUGGAACCAUGGACAUCCGUGUCCAUUUAUGAAUGUACAUCCUUGUACAUUUUUCAUCCGCCGUCCAUGGCGGAUAAAAAUAUUGACAAAAAAAAGGGAGUCCGUAUUCCGAACUCCCCUUUGAA .....((((......((((((((..((((((((.(((((....)))))))))))))....))))))))...(((((((......)))))))..................)))).....................((((((((..(((((((((((((((....)))))))))))))))..((((((((((....))))))))))..(((((((((..((((((..((.((((.......(((((((((....)))))))))...((((((((....)))))))).........)))).......))..)))))).))))))))))))))))).. (-113.50) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 801 160 111 62 12 NC_002967:TDE1890|5end_hypothetical_protein_1911012..1911242_POSITIVE 775 129 81 212 164 NC_002967:TDE2134|5end_hypothetical_protein_2164447..2164677_POSITIVE 588 180 131 99 51 NC_002967:TDE1923|5end_hypothetical_protein_1941692..1941922_NEGATIVE 518 179 131 227 175 NC_002967:TDE2237|5end_hypothetical_protein_2276402..2276632_NEGATIVE 508 180 131 152 99 NC_002967:TDE2548|5end_hypothetical_protein_2573198..2573428_NEGATIVE 489 135 98 231 191 NC_002967:TDE1891|5end_hypothetical_protein_1911206..1911436_POSITIVE 473 170 121 165 112 NC_002967:TDE2338|5end_hypothetical_protein_2374719..2374949_NEGATIVE 381 186 145 42 1 NC_002967:TDE1934|5end_hypothetical_protein_1952614..1952844_POSITIVE 368 146 105 201 157 NC_002967:TDE1935|5end_hypothetical_protein_1952994..1953224_POSITIVE 367 179 131 187 138 NC_002967:TDE1847|5end_hypothetical_protein_1875664..1875894_POSITIVE 331 98 53 87 49 NC_002967:TDE2739|5end_hypothetical_protein_2794673..2794903_POSITIVE 329 59 14 95 49 NC_002967:TDE0295|5end_DNA_gyrase,_A_subunit_326667..326897_NEGATIVE 313 157 117 212 169 NC_002967:TDE1936|5end_hypothetical_protein_1953086..1953316_POSITIVE 310 110 63 62 7 NC_002967:TDE0256|5end_hypothetical_protein_291440..291670_NEGATIVE 301 70 22 73 21 NC_002967:TDE0778|5end_ribosomal_protein_L24_811487..811717_POSITIVE 298 307 263 142 105 NC_002967:TDE2534|5end_endonuclease_III_2560144..2560374_POSITIVE 295 68 22 179 135 NC_002967:TDE0628|5end_molecular_chaperone_DnaK_660609..660839_POSITIVE 288 87 48 136 91 NC_002967:TDE2701|5end_hypothetical_protein_2745689..2745919_POSITIVE 288 79 31 158 108 NC_002967:TDE1970|5end_sensory_box_histidine_kinase_1985744..1985974_NEGATIVE 286 90 42 52 7 NC_002967:TDE2614|5end_ApbE_family_protein_2657133..2657363_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 588 180 131 117 69 NC_002967:TDE1924|3end_hypothetical_protein_1941674..1941824_NEGATIVE 518 179 131 75 23 NC_002967:TDE2239|3end_hypothetical_protein_2276554..2276704_NEGATIVE 503 180 132 76 24 NC_002967:TDE2101|3end_hypothetical_protein_2125549..2125699_NEGATIVE 473 180 132 78 26 NC_002967:TDE0834|3end_Na(+)-translocating_NADH-quinone_reductase,_E_subunit_854291..854441_NEGATIVE 470 197 151 101 48 NC_002967:TDE1056|3end_hypothetical_protein_1085895..1086045_POSITIVE 450 120 71 83 33 NC_002967:TDE1934|3end_hypothetical_protein_1952804..1952954_POSITIVE 368 69 53 33 17 NC_002967:TDE2483|3end_hypothetical_protein_2505880..2506030_NEGATIVE 358 42 4 96 57 NC_002967:TDE1048|3end_30S_ribosomal_protein_S7_1075032..1075182_POSITIVE 352 110 64 88 44 NC_002967:TDE1937|3end_hypothetical_protein_1953448..1953598_POSITIVE 301 70 22 63 11 NC_002967:TDE0777|3end_50S_ribosomal_protein_L14_811557..811707_POSITIVE 298 106 63 67 21 NC_002967:TDE0746|3end_iron_compound_ABC_transporter,_ATP-binding_protein,_putative_780931..781081_NEGATIVE 296 95 52 108 69 NC_002967:TDE0049|3end_hypothetical_protein_58199..58349_NEGATIVE 293 132 92 65 33 NC_002967:TDE2515|3end_hypothetical_protein_2540972..2541122_NEGATIVE 289 178 134 54 8 NC_002967:TDE0945|3end_hypothetical_protein_968320..968470_POSITIVE 288 87 48 135 90 NC_002967:TDE2700|3end_citrate_carrier_protein,_CCS_family_2745768..2745918_POSITIVE 279 94 52 115 62 NC_002967:TDE2100|3end_hypothetical_protein_2125572..2125722_POSITIVE 278 71 47 60 32 NC_002967:TDE2516|3end_hypothetical_protein_2542193..2542343_POSITIVE 278 90 51 88 51 NC_002967:TDE0405|3end_major_outer_sheath_protein_457181..457331_POSITIVE 274 180 139 49 4 NC_002967:TDE0741|3end_hypothetical_protein_776185..776335_NEGATIVE 273 139 105 66 32 NC_002967:TDE2311|3end_hypothetical_protein_2348437..2348587_POSITIVE