Origin IGS: gccgccctctctgcagtttattttttatttaaccgcagcgagcgcaaagcgttgagctcacgctcaacttcgcaaagtattttttttatgaaactaagaaataaacagctaaacttatgaaaaatcgaggctgtccactgccaattaattaatcgcttccactttttcttggctgagaccgc .........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 gcggtctcagccaagaaaaagtggaagcgattaattaattggcagtggacagcctcgatttttcataagtttagctgtttatttcttagtttcataaaaaaaatactttgcgaagttgagcgtgagctcaacgctttgcgctcgctgcggttaaataaaaaataaactgcagagagggcggc Mask Tandem Repeat Region ================================================ gccgccctctctgcagtttattttttatttaaccgcagcgagcgcaaagcgttgagctcacgctcaacttcgcaaagtattttttttatgaaactaagaaataaacagctaaacttatgaaaaatcgaggctgtccactgccaattaattaatcgcttccactttttcttggctgagaccgc Find is-nt database================================================ Query_seq: TDE1977:TDE1978|TDE1977:TDE1978:hypothetical protein:hypothetical protein:-><-:1991409..1991590 182 gccgccctctctgcagtttattttttatttaaccgcagcgagcgcaaagcgttgagctcacgctcaacttcgcaaagtattttttttatgaaactaagaaataaacagctaaacttatgaaaaatcgaggctgtccactgccaattaattaatcgcttccactttttcttggctgagaccgc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE1977:TDE1978|TDE1977:TDE1978:hypothetical protein:hypothetical protein:-><-:1991409..1991590 182 gccgccctctctgcagtttattttttatttaaccgcagcgagcgcaaagcgttgagctcacgctcaacttcgcaaagtattttttttatgaaactaagaaataaacagctaaacttatgaaaaatcgaggctgtccactgccaattaattaatcgcttccactttttcttggctgagaccgc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE1977:TDE1978|TDE1977:TDE1978:hypothetical protein:hypothetical protein:-><-:1991409..1991590 182 gccgccctctctgcagtttattttttatttaaccgcagcgagcgcaaagcgttgagctcacgctcaacttcgcaaagtattttttttatgaaactaagaaataaacagctaaacttatgaaaaatcgaggctgtccactgccaattaattaatcgcttccactttttcttggctgagaccgc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gccgccctctctgcagtttattttttatttaaccgcagcgagcgcaaagcgttgagctcacgctcaacttcgcaaagtattttttttatgaaactaagaaataaacagctaaacttatgaaaaatcgaggctgtccactgccaattaattaatcgcttccactttttcttggctgagaccgc Predict ORF larger than 30AA ================================================ Protein_Len: 43 Strand: - Start: 21 End: 149 .................... K K N L R L S R L A N L E R E V E C L I K K I F S L F L C S F K H F I S A T W Q W N M ................................. gccgccctctctgcagtttattttttatttaaccgcagcgagcgcaaagcgttgagctcacgctcaacttcgcaaagtattttttttatgaaactaagaaataaacagctaaacttatgaaaaatcgaggctgtccactgccaattaattaatcgcttccactttttcttggctgagaccgc 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================================================ gccgccctctctgcagtttattttttatttaaccgcagcgagcgcaaagcgttgagctcacgctcaacttcgcaaagtattttttttatgaaactaagaaataaacagctaaacttatgaaaaatcgaggctgtccactgccaattaattaatcgcttccactttttcttggctgagaccgc Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE1977:TDE1978|TDE1977:TDE1978:hypothetical protein:hypothetical protein:-><-:1991409..1991590 182 gccgccctctctgcagtttattttttatttaaccgcagcgagcgcaaagcgttgagctcacgctcaacttcgcaaagtattttttttatgaaactaagaaataaacagctaaacttatgaaaaatcgaggctgtccactgccaattaattaatcgcttccactttttcttggctgagaccgc Intra-Species Hit: Count: 1 Min: 1 Max: 182 Len: 182 Subject: NC_002967_TDE1977_TDE1978|hypothetical protein:hypothetical protein|POSITIVE:NEGATIVE|[1991409,1991590]|182 HSP 1 e-value: 1.0E-84 bit: 313.0 Len: 182 Query Start:1 Query End:182 Subject Strand: POSITIVE Subject Start: 1 Subject End: 182 gccgccctctctgcagtttattttttatttaaccgcagcgagcgcaaagcgttgagctcacgctcaacttcgcaaagtannnnnnnnatgaaactaagaaataaacagctaaacttatgaaaaatcgaggctgtccactgccaattaattaatcgcttccactttttcttggctgagaccgc gccgccctctctgcagtttattttttatttaaccgcagcgagcgcaaagcgttgagctcacgctcaacttcgcaaagtattttttttatgaaactaagaaataaacagctaaacttatgaaaaatcgaggctgtccactgccaattaattaatcgcttccactttttcttggctgagaccgc Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GCCGCCCUCUCUGCAGUUUAUUUUUUAUUUAACCGCAGCGAGCGCAAAGCGUUGAGCUCACGCUCAACUUCGCAAAGUAUUUUUUUUAUGAAACUAAGAAAUAAACAGCUAAACUUAUGAAAAAUCGAGGCUGUCCACUGCCAAUUAAUUAAUCGCUUCCACUUUUUCUUGGCUGAGACCGC ((.((.(((.((((.(((............))).)))).))).)).....(((((((....)))))))...))....((((((((..........))))))))..(((((((......((((((..(((((.......................)))))...)))))))))))))....... (-41.10) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GCGGUCUCAGCCAAGAAAAAGUGGAAGCGAUUAAUUAAUUGGCAGUGGACAGCCUCGAUUUUUCAUAAGUUUAGCUGUUUAUUUCUUAGUUUCAUAAAAAAAAUACUUUGCGAAGUUGAGCGUGAGCUCAACGCUUUGCGCUCGCUGCGGUUAAAUAAAAAAUAAACUGCAGAGAGGGCGGC ((((.....(((((.......((....)).........))))).(((((((((...(((((.....)))))..))))))))).........................))))...(((((((....)))))))...((((.(((.((((((((............)))))))).))).)))). (-54.19) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 978 76 31 120 75 NC_002967:TDE1980|5end_hypothetical_protein_1992061..1992291_NEGATIVE 978 76 31 196 151 NC_002967:TDE1979|5end_hypothetical_protein_1991985..1992215_NEGATIVE 717 77 31 101 55 NC_002967:TDE0970|5end_hypothetical_protein_994769..994999_POSITIVE 441 89 46 49 8 NC_002967:TDE2237|5end_hypothetical_protein_2276402..2276632_NEGATIVE 401 50 17 231 198 NC_002967:TDE2098|5end_hypothetical_protein_2125085..2125315_NEGATIVE 400 78 33 54 1 NC_002967:TDE2268|5end_hypothetical_protein_2304959..2305189_NEGATIVE 396 51 27 27 1 NC_002967:TDE1905|5end_hypothetical_protein_1923877..1924107_NEGATIVE 395 180 135 127 80 NC_002967:TDE0733|5end_hypothetical_protein_774096..774326_NEGATIVE 384 74 33 164 119 NC_002967:TDE1113|5end_hypothetical_protein_1148250..1148480_NEGATIVE 354 56 27 229 198 NC_002967:TDE1061|5end_ABC_transporter,_ATP-binding/permease_protein,_HlyB_family_1086646..1086876_POSITIVE 354 56 27 102 71 NC_002967:TDE1060|5end_hypothetical_protein_1086519..1086749_POSITIVE 341 79 33 84 43 NC_002967:TDE0690|5end_tRNA_(5-methylaminomethyl-2-thiouridylate)-methyltransferase_726898..727128_POSITIVE 341 77 34 63 5 NC_002967:TDE0572|5end_hypothetical_protein_603494..603724_POSITIVE 339 77 32 168 122 NC_002967:TDE2491|5end_DNA_polymerase_domain_protein_2515499..2515729_NEGATIVE 334 78 33 229 168 NC_002967:TDE2614|5end_ApbE_family_protein_2657133..2657363_NEGATIVE 328 73 31 213 159 NC_002967:TDE0151|5end_integral_membrane_protein,_YeeE/YedE_family_173101..173331_NEGATIVE 317 70 21 141 91 NC_002967:TDE1817|5end_hypothetical_protein_1852599..1852829_NEGATIVE 317 49 31 202 184 NC_002967:TDE0724|5end_hypothetical_protein_761853..762083_POSITIVE 316 63 27 191 164 NC_002967:TDE2435|5end_hypothetical_protein_2466462..2466692_NEGATIVE 314 50 1 64 21 NC_002967:TDE0169|5end_methyl-accepting_chemotaxis_domain_protein_198792..199022_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 552 150 103 92 45 NC_002967:TDE1904|3end_hypothetical_protein_1923197..1923347_NEGATIVE 541 77 31 142 97 NC_002967:TDE2237|3end_hypothetical_protein_2276298..2276448_NEGATIVE 468 180 139 126 85 NC_002967:TDE2097|3end_hypothetical_protein_2124478..2124628_NEGATIVE 416 78 32 82 28 NC_002967:TDE2269|3end_hypothetical_protein_2304931..2305081_NEGATIVE 412 77 31 84 31 NC_002967:TDE1529|3end_hypothetical_protein_1575067..1575217_POSITIVE 395 62 31 151 121 NC_002967:TDE2260|3end_hypothetical_protein_2297573..2297723_POSITIVE 347 74 34 42 7 NC_002967:TDE0617|3end_hypothetical_protein_650093..650243_NEGATIVE 341 79 33 78 37 NC_002967:TDE0689|3end_5-methylthioribose_kinase_726972..727122_POSITIVE 340 49 1 75 19 NC_002967:TDE1013|3end_hemerythrin-related_protein_1043977..1044127_NEGATIVE 315 47 1 104 48 NC_002967:TDE2735|3end_surface_antigen,_putative_2791616..2791766_POSITIVE 308 56 15 69 17 NC_002967:TDE0974|3end_hypothetical_protein_998875..999025_POSITIVE 305 73 33 105 67 NC_002967:TDE0977|3end_hypothetical_protein_1001640..1001790_POSITIVE 301 80 32 63 6 NC_002967:TDE1225|3end_zinc_ABC_transporter,_ATP-binding_protein_1258751..1258901_NEGATIVE 296 68 37 82 48 NC_002967:TDE2544|3end_hypothetical_protein_2570935..2571085_NEGATIVE 296 159 114 141 90 NC_002967:TDE1995|3end_magnesium_chelatase_family_protein_2014244..2014394_POSITIVE 295 41 4 122 79 NC_002967:TDE0156|3end_adenylate/guanylate_cyclase_catalytic_domain_protein_180344..180494_NEGATIVE 293 49 21 54 16 NC_002967:TDE2261|3end_hypothetical_protein_2297915..2298065_NEGATIVE 293 60 31 126 102 NC_002967:TDE2160|3end_hypothetical_protein_2193873..2194023_NEGATIVE 290 65 33 145 119 NC_002967:TDE2057|3end_hypothetical_protein_2085158..2085308_NEGATIVE 288 79 35 145 104 NC_002967:TDE2543|3end_hypothetical_protein_2570753..2570903_NEGATIVE