Origin IGS: aaatagagttaagccctttttaatacagtaatcttaaaacagatctaaaaattatttttttagcaaaaaccttaccaaaagtacttgacaaaagtttgagaaaggggtatattcgctcacaccgtcagctaagacggtgtgcctagaaaagcaaagaaaacactagaaaagttttgcaagtcttgcattttca .........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 tgaaaatgcaagacttgcaaaacttttctagtgttttctttgcttttctaggcacaccgtcttagctgacggtgtgagcgaatatacccctttctcaaacttttgtcaagtacttttggtaaggtttttgctaaaaaaataatttttagatctgttttaagattactgtattaaaaagggcttaactctattt Mask Tandem Repeat Region ================================================ aaatagagttaagccctttttaatacagtaatcttaaaacagatctaaaaattatttttttagcaaaaaccttaccaaaagtacttgacaaaagtttgagaaaggggtatattcgctcacaccgtcagctaagacggtgtgcctagaaaagcaaagaaaacactagaaaagttttgcaagtcttgcattttca Find is-nt database================================================ Query_seq: TDE1191:TDE1192|TDE1191:TDE1192:hypothetical protein:hypothetical protein:->->:1219279..1219471 193 aaatagagttaagccctttttaatacagtaatcttaaaacagatctaaaaattatttttttagcaaaaaccttaccaaaagtacttgacaaaagtttgagaaaggggtatattcgctcacaccgtcagctaagacggtgtgcctagaaaagcaaagaaaacactagaaaagttttgcaagtcttgcattttca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE1191:TDE1192|TDE1191:TDE1192:hypothetical protein:hypothetical protein:->->:1219279..1219471 193 aaatagagttaagccctttttaatacagtaatcttaaaacagatctaaaaattatttttttagcaaaaaccttaccaaaagtacttgacaaaagtttgagaaaggggtatattcgctcacaccgtcagctaagacggtgtgcctagaaaagcaaagaaaacactagaaaagttttgcaagtcttgcattttca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE1191:TDE1192|TDE1191:TDE1192:hypothetical protein:hypothetical protein:->->:1219279..1219471 193 aaatagagttaagccctttttaatacagtaatcttaaaacagatctaaaaattatttttttagcaaaaaccttaccaaaagtacttgacaaaagtttgagaaaggggtatattcgctcacaccgtcagctaagacggtgtgcctagaaaagcaaagaaaacactagaaaagttttgcaagtcttgcattttca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aaatagagttaagccctttttaatacagtaatcttaaaacagatctaaaaattatttttttagcaaaaaccttaccaaaagtacttgacaaaagtttgagaaaggggtatattcgctcacaccgtcagctaagacggtgtgcctagaaaagcaaagaaaacactagaaaagttttgcaagtcttgcattttca Predict ORF larger than 30AA ================================================ Protein_Len: 31 Strand: + Start: 51 End: 143 .................................................. M I F L A K T L P K V L D K S L R K G Y I R S H R Q L R R C A .................................................. Protein_Len: 30 Strand: - Start: 23 End: 112 ...................... Y L L R L V S R F I I K K A F V K G F T S S L L K L F P Y M ................................................................................. aaatagagttaagccctttttaatacagtaatcttaaaacagatctaaaaattatttttttagcaaaaaccttaccaaaagtacttgacaaaagtttgagaaaggggtatattcgctcacaccgtcagctaagacggtgtgcctagaaaagcaaagaaaacactagaaaagttttgcaagtcttgcattttca 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: 84 End: 113 ...................................................................................CTTGACAAAAGTTTGAGAAAGGGGTATATT................................................................................ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ PromScan Matrix: RpoN Strand: - Score: 84 Start: 62 End: 78 .............................................................TTGGTAAGGTTTTTGCT................................................................................................................... aaatagagttaagccctttttaatacagtaatcttaaaacagatctaaaaattatttttttagcaaaaaccttaccaaaagtacttgacaaaagtttgagaaaggggtatattcgctcacaccgtcagctaagacggtgtgcctagaaaagcaaagaaaacactagaaaagttttgcaagtcttgcattttca Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 50 HP_score: -4.7 Tail_Score: -2.64739 Start: 45 End: 63 Full_Region: ttggtaaggtttttg ctaaaaa aataa tttttag atctgttttaagatt ............................................ctaaaaaaataatttttag.................................................................................................................................. Find igs database================================================ Query_seq: TDE1191:TDE1192|TDE1191:TDE1192:hypothetical protein:hypothetical protein:->->:1219279..1219471 193 aaatagagttaagccctttttaatacagtaatcttaaaacagatctaaaaattatttttttagcaaaaaccttaccaaaagtacttgacaaaagtttgagaaaggggtatattcgctcacaccgtcagctaagacggtgtgcctagaaaagcaaagaaaacactagaaaagttttgcaagtcttgcattttca Intra-Species Hit: Count: 2 Min: 1 Max: 193 Len: 193 Subject: NC_002967_TDE1191_TDE1192|hypothetical protein:hypothetical protein|POSITIVE:POSITIVE|[1219279,1219471]|193 HSP 1 e-value: 5.0E-93 bit: 341.0 Len: 193 Query Start:1 Query End:193 Subject Strand: POSITIVE Subject Start: 1 Subject End: 193 aaatagagttaagccctttttaatacagtaatcttaaaacagatctaaaaattannnnnnnagcaaaaaccttaccaaaagtacttgacaaaagtttgagaaaggggtatattcgctcacaccgtcagctaagacggtgtgcctagaaaagcaaagaaaacactagaaaagttttgcaagtcttgcattttca aaatagagttaagccctttttaatacagtaatcttaaaacagatctaaaaattatttttttagcaaaaaccttaccaaaagtacttgacaaaagtttgagaaaggggtatattcgctcacaccgtcagctaagacggtgtgcctagaaaagcaaagaaaacactagaaaagttttgcaagtcttgcattttca Subject: NC_002967_TDE0578_TDE0579|hypothetical protein:hypothetical protein|POSITIVE:NEGATIVE|[609738,609987]|250 HSP 1 e-value: 3.0E-48 bit: 192.0 Len: 105 Query Start:89 Query End:193 Subject Strand: POSITIVE Subject Start: 1 Subject End: 105 ........................................................................................caaaagtttgagaaaggggtatattcgctcacaccgtcagctaagacggtgtgcctagaaaagcaaagaaaacactagaaaagttttgcaagtcttgcattttca ........................................................................................caaaagtttgagaaaggggtatattcgctcacaccgtctgttaagacggtgtgcctagaaaagcaaagaaaacactagaaaagttttgcaagtcttgcattttca Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAUAGAGUUAAGCCCUUUUUAAUACAGUAAUCUUAAAACAGAUCUAAAAAUUAUUUUUUUAGCAAAAACCUUACCAAAAGUACUUGACAAAAGUUUGAGAAAGGGGUAUAUUCGCUCACACCGUCAGCUAAGACGGUGUGCCUAGAAAAGCAAAGAAAACACUAGAAAAGUUUUGCAAGUCUUGCAUUUUCA .....((((...(((((((((.......................(((((((.....)))))))...................((((.....))))....)))))))))..))))...(((((((((......)))))))))....(((((((((.((.((.(((.....))).)).....)))))).))))). (-41.00) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGAAAAUGCAAGACUUGCAAAACUUUUCUAGUGUUUUCUUUGCUUUUCUAGGCACACCGUCUUAGCUGACGGUGUGAGCGAAUAUACCCCUUUCUCAAACUUUUGUCAAGUACUUUUGGUAAGGUUUUUGCUAAAAAAAUAAUUUUUAGAUCUGUUUUAAGAUUACUGUAUUAAAAAGGGCUUAACUCUAUUU .((((((((.(((...(.....)...))).)))))))).(((((........(((((((((......))))))))))))))......((((((.......(((((.((((.(((((....))))).)))).)))))............(((((......)))))..........))))))............. (-41.40) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 315 147 103 124 74 NC_002967:TDE2338|5end_hypothetical_protein_2374719..2374949_NEGATIVE 315 157 113 139 84 NC_002967:TDE1285|5end_flagellar_motor_switch_protein_FliG_,_putative_1320924..1321154_POSITIVE 302 139 92 106 57 NC_002967:TDE1890|5end_hypothetical_protein_1911012..1911242_POSITIVE 300 155 113 92 51 NC_002967:TDE0848|5end_hypothetical_protein_871269..871499_POSITIVE 297 153 121 157 127 NC_002967:TDE2142|5end_methyl-accepting_chemotaxis_protein_2175769..2175999_POSITIVE 286 139 98 86 42 NC_002967:TDE2715|5end_hypothetical_protein_2772668..2772898_POSITIVE 278 146 112 129 99 NC_002967:TDE0311|5end_thymidylate_synthase_342816..343046_POSITIVE 265 90 65 231 206 NC_002967:TDE0577|5end_glutamyl-tRNA(Gln)_amidotransferase,_C_subunit_609509..609739_NEGATIVE 264 155 112 208 165 NC_002967:TDE0976|5end_hypothetical_protein_1000026..1000256_POSITIVE 261 149 104 78 32 NC_002967:TDE1736|5end_ferredoxin,_2(4Fe-4S)_1789908..1790138_POSITIVE 259 137 93 72 23 NC_002967:TDE2061|5end_hypothetical_protein_2087792..2088022_NEGATIVE 259 148 104 51 8 NC_002967:TDE1707|5end_hypothetical_protein_1763191..1763421_NEGATIVE 258 169 126 58 13 NC_002967:TDE2357|5end_iron_compound_ABC_transporter,_permease_protein_2392038..2392268_POSITIVE 258 142 103 108 74 NC_002967:TDE2134|5end_hypothetical_protein_2164447..2164677_POSITIVE 256 146 103 183 126 NC_002967:TDE1769|5end_hypothetical_protein_1814377..1814607_NEGATIVE 255 152 122 174 149 NC_002967:TDE2355|5end_carbon_storage_regulator_2390838..2391068_POSITIVE 253 144 104 193 152 NC_002967:TDE1214|5end_flagellar_basal_body_protein_1246307..1246537_POSITIVE 252 152 114 52 4 NC_002967:TDE0101|5end_alpha-amylase_family_protein_121161..121391_NEGATIVE 250 127 83 60 15 NC_002967:TDE0405|5end_major_outer_sheath_protein_455470..455700_POSITIVE 249 170 121 127 82 NC_002967:TDE1505|5end_hypothetical_protein_1553614..1553844_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 325 144 103 108 63 NC_002967:TDE2622|3end_ABC_transporter,_ATP-binding_protein_2662178..2662328_NEGATIVE 325 158 114 81 36 NC_002967:TDE0824|3end_lipoprotein,_putative_845226..845376_NEGATIVE 315 157 113 58 3 NC_002967:TDE1284|3end_methyl-accepting_chemotaxis_protein,_putative_1320923..1321073_POSITIVE 315 143 105 117 70 NC_002967:TDE1056|3end_hypothetical_protein_1085895..1086045_POSITIVE 307 141 118 61 38 NC_002967:TDE0578|3end_hypothetical_protein_609677..609827_POSITIVE 300 155 113 85 44 NC_002967:TDE0847|3end_hypothetical_protein_871342..871492_POSITIVE 287 143 104 105 59 NC_002967:TDE0210|3end_cob(I)yrinic_acid_a,c-diamide_adenosyltransferase_246146..246296_POSITIVE 278 146 112 45 15 NC_002967:TDE0310|3end_hypothetical_protein_342812..342962_POSITIVE 268 145 117 126 91 NC_002967:TDE1245|3end_hypothetical_protein_1277905..1278055_NEGATIVE 268 143 103 149 116 NC_002967:TDE0573|3end_hypothetical_protein_604910..605060_POSITIVE 267 150 103 79 33 NC_002967:TDE0793|3end_hypothetical_protein_819205..819355_POSITIVE 261 149 104 88 42 NC_002967:TDE1735|3end_hypothetical_protein_1789998..1790148_POSITIVE 259 137 93 62 13 NC_002967:TDE2062|3end_hypothetical_protein_2087802..2087952_NEGATIVE 259 148 104 54 11 NC_002967:TDE1708|3end_apolipoprotein_N-acyltransferase_1763188..1763338_NEGATIVE 249 170 121 66 21 NC_002967:TDE1504|3end_ribosomal_protein_L31_1553633..1553783_POSITIVE 248 118 77 68 20 NC_002967:TDE1193|3end_hypothetical_protein_1219526..1219676_NEGATIVE 248 118 77 68 20 NC_002967:TDE0579|3end_hypothetical_protein_609898..610048_NEGATIVE 248 159 111 66 22 NC_002967:TDE0562|3end_hypothetical_protein_595581..595731_POSITIVE 247 147 112 65 29 NC_002967:TDE0617|3end_hypothetical_protein_650093..650243_NEGATIVE 246 143 101 116 70 NC_002967:TDE0735|3end_hypothetical_protein_774746..774896_NEGATIVE