Origin IGS: ttcgacgttttgatctcccttaaccgttatcgtaatcttaggcgtaggaggcgttgaagtcggtttggttacaataaaaaccgtcgtattcgtattaaaaagatgggcatcagttaaattctgacctgaggcatcggtaagtttccatttatcgggtccgcgtcctgccgcatactggtcgattctgtcctccgcttgagcctttaattggtgccatgtg .........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 cacatggcaccaattaaaggctcaagcggaggacagaatcgaccagtatgcggcaggacgcggacccgataaatggaaacttaccgatgcctcaggtcagaatttaactgatgcccatctttttaatacgaatacgacggtttttattgtaaccaaaccgacttcaacgcctcctacgcctaagattacgataacggttaagggagatcaaaacgtcgaa Mask Tandem Repeat Region ================================================ ttcgacgttttgatctcccttaaccgttatcgtaatcttaggcgtaggaggcgttgaagtcggtttggttacaataaaaaccgtcgtattcgtattaaaaagatgggcatcagttaaattctgacctgaggcatcggtaagtttccatttatcgggtccgcgtcctgccgcatactggtcgattctgtcctccgcttgagcctttaattggtgccatgtg Find is-nt database================================================ Query_seq: TDE1232:TDE1233|TDE1232:TDE1233:hypothetical protein:hypothetical protein:<-->:1267123..1267342 220 ttcgacgttttgatctcccttaaccgttatcgtaatcttaggcgtaggaggcgttgaagtcggtttggttacaataaaaaccgtcgtattcgtattaaaaagatgggcatcagttaaattctgacctgaggcatcggtaagtttccatttatcgggtccgcgtcctgccgcatactggtcgattctgtcctccgcttgagcctttaattggtgccatgtg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE1232:TDE1233|TDE1232:TDE1233:hypothetical protein:hypothetical protein:<-->:1267123..1267342 220 ttcgacgttttgatctcccttaaccgttatcgtaatcttaggcgtaggaggcgttgaagtcggtttggttacaataaaaaccgtcgtattcgtattaaaaagatgggcatcagttaaattctgacctgaggcatcggtaagtttccatttatcgggtccgcgtcctgccgcatactggtcgattctgtcctccgcttgagcctttaattggtgccatgtg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE1232:TDE1233|TDE1232:TDE1233:hypothetical protein:hypothetical protein:<-->:1267123..1267342 220 ttcgacgttttgatctcccttaaccgttatcgtaatcttaggcgtaggaggcgttgaagtcggtttggttacaataaaaaccgtcgtattcgtattaaaaagatgggcatcagttaaattctgacctgaggcatcggtaagtttccatttatcgggtccgcgtcctgccgcatactggtcgattctgtcctccgcttgagcctttaattggtgccatgtg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ttcgacgttttgatctcccttaaccgttatcgtaatcttaggcgtaggaggcgttgaagtcggtttggttacaataaaaaccgtcgtattcgtattaaaaagatgggcatcagttaaattctgacctgaggcatcggtaagtttccatttatcgggtccgcgtcctgccgcatactggtcgattctgtcctccgcttgagcctttaattggtgccatgtg Predict ORF larger than 30AA ================================================ Protein_Len: 31 Strand: + Start: 29 End: 121 ............................ M V I L G V G G V E V G L V T I K T V V F V L K R W A S V K F ................................................................................................... Protein_Len: 60 Strand: - Start: 1 End: 183 V N Q D G K V T I T I K P T P P T S T P K T V I F V T T N T N F L H A D T L N Q G S A D T L K W K D P G R G A A Y Q D M ..................................... ttcgacgttttgatctcccttaaccgttatcgtaatcttaggcgtaggaggcgttgaagtcggtttggttacaataaaaaccgtcgtattcgtattaaaaagatgggcatcagttaaattctgacctgaggcatcggtaagtttccatttatcgggtccgcgtcctgccgcatactggtcgattctgtcctccgcttgagcctttaattggtgccatgtg 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================================================ ttcgacgttttgatctcccttaaccgttatcgtaatcttaggcgtaggaggcgttgaagtcggtttggttacaataaaaaccgtcgtattcgtattaaaaagatgggcatcagttaaattctgacctgaggcatcggtaagtttccatttatcgggtccgcgtcctgccgcatactggtcgattctgtcctccgcttgagcctttaattggtgccatgtg Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE1232:TDE1233|TDE1232:TDE1233:hypothetical protein:hypothetical protein:<-->:1267123..1267342 220 ttcgacgttttgatctcccttaaccgttatcgtaatcttaggcgtaggaggcgttgaagtcggtttggttacaataaaaaccgtcgtattcgtattaaaaagatgggcatcagttaaattctgacctgaggcatcggtaagtttccatttatcgggtccgcgtcctgccgcatactggtcgattctgtcctccgcttgagcctttaattggtgccatgtg Intra-Species Hit: Count: 1 Min: 1 Max: 220 Len: 220 Subject: NC_002967_TDE1232_TDE1233|hypothetical protein:hypothetical protein|NEGATIVE:POSITIVE|[1267123,1267342]|220 HSP 1 e-value: 1.0E-121 bit: 436.0 Len: 220 Query Start:1 Query End:220 Subject Strand: POSITIVE Subject Start: 1 Subject End: 220 ttcgacgttttgatctcccttaaccgttatcgtaatcttaggcgtaggaggcgttgaagtcggtttggttacaataaaaaccgtcgtattcgtattaaaaagatgggcatcagttaaattctgacctgaggcatcggtaagtttccatttatcgggtccgcgtcctgccgcatactggtcgattctgtcctccgcttgagcctttaattggtgccatgtg ttcgacgttttgatctcccttaaccgttatcgtaatcttaggcgtaggaggcgttgaagtcggtttggttacaataaaaaccgtcgtattcgtattaaaaagatgggcatcagttaaattctgacctgaggcatcggtaagtttccatttatcgggtccgcgtcctgccgcatactggtcgattctgtcctccgcttgagcctttaattggtgccatgtg Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUCGACGUUUUGAUCUCCCUUAACCGUUAUCGUAAUCUUAGGCGUAGGAGGCGUUGAAGUCGGUUUGGUUACAAUAAAAACCGUCGUAUUCGUAUUAAAAAGAUGGGCAUCAGUUAAAUUCUGACCUGAGGCAUCGGUAAGUUUCCAUUUAUCGGGUCCGCGUCCUGCCGCAUACUGGUCGAUUCUGUCCUCCGCUUGAGCCUUUAAUUGGUGCCAUGUG ..(((((.(((.........((((((..((((....(((..((((.....))))..))).)))).))))))......))).)))))...................(((((((((((((...(((((...(((.(((((((((....)))))))))))).(((......))).....)))))............((....)).)))))))))))))..... (-56.36) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CACAUGGCACCAAUUAAAGGCUCAAGCGGAGGACAGAAUCGACCAGUAUGCGGCAGGACGCGGACCCGAUAAAUGGAAACUUACCGAUGCCUCAGGUCAGAAUUUAACUGAUGCCCAUCUUUUUAAUACGAAUACGACGGUUUUUAUUGUAACCAAACCGACUUCAACGCCUCCUACGCCUAAGAUUACGAUAACGGUUAAGGGAGAUCAAAACGUCGAA .....((((.((.(((((..((...((.((((.....((((....((.((((......)))).)).........(....)....)))).))))..)).))..))))).)).))))...................((((((((........))))................(((((..(((...............)))...)))))........)))).. (-43.26) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 952 60 11 151 102 NC_002967:TDE1232|5end_hypothetical_protein_1267032..1267262_NEGATIVE 376 195 153 230 197 NC_002967:TDE0573|5end_hypothetical_protein_604681..604911_POSITIVE 373 193 151 76 27 NC_002967:TDE2131|5end_cobalamin_biosynthesis_protein_CbiM,_putative_2162683..2162913_NEGATIVE 372 200 154 182 136 NC_002967:TDE2777|5end_hypothetical_protein_2828312..2828542_POSITIVE 370 199 151 158 111 NC_002967:TDE0957|5end_glycerophosphoryl_diester_phosphodiesterase_family_protein_980252..980482_POSITIVE 367 195 152 180 130 NC_002967:TDE1004|5end_flagellar_filament_core_protein_1030136..1030366_NEGATIVE 366 197 154 51 11 NC_002967:TDE0675|5end_hypothetical_protein_713994..714224_POSITIVE 361 199 157 218 173 NC_002967:TDE2499|5end_hypothetical_protein_2523952..2524182_NEGATIVE 360 200 153 57 11 NC_002967:TDE1247|5end_hypothetical_protein_1281623..1281853_POSITIVE 359 200 153 66 8 NC_002967:TDE2036|5end_ATPase,_AAA_family_2066638..2066868_NEGATIVE 357 196 152 191 140 NC_002967:TDE1956|5end_hypothetical_protein_1971114..1971344_POSITIVE 357 198 157 179 140 NC_002967:TDE1897|5end_phosphoribosylglycinamide_formyltransferase_1918109..1918339_NEGATIVE 357 56 13 152 95 NC_002967:TDE0259|5end_transcriptional_regulator,_MarR_family_293257..293487_POSITIVE 356 189 141 164 110 NC_002967:TDE1878|5end_hydrolase,_haloacid_dehalogenase-like_family_1900745..1900975_NEGATIVE 354 197 153 166 106 NC_002967:TDE1566|5end_hypothetical_protein_1617822..1618052_POSITIVE 352 194 152 47 6 NC_002967:TDE2268|5end_hypothetical_protein_2304959..2305189_NEGATIVE 352 194 153 142 89 NC_002967:TDE1926|5end_hypothetical_protein_1942495..1942725_POSITIVE 346 205 162 123 80 NC_002967:TDE2103|5end_glycosyl_transferase,_group_2_family_protein_2128393..2128623_NEGATIVE 346 194 153 215 158 NC_002967:TDE1380|5end_hypothetical_protein_1421284..1421514_NEGATIVE 344 193 153 61 18 NC_002967:TDE0743|5end_thioredoxin_reductase_778718..778948_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 374 199 152 53 1 NC_002967:TDE2763|3end_flagellar_motor_switch_protein_2817737..2817887_NEGATIVE 366 197 154 54 14 NC_002967:TDE0674|3end_hypothetical_protein_714077..714227_POSITIVE 357 170 121 76 33 NC_002967:TDE2736|3end_hypothetical_protein_2791702..2791852_NEGATIVE 352 194 152 75 34 NC_002967:TDE2269|3end_hypothetical_protein_2304931..2305081_NEGATIVE 344 187 141 150 97 NC_002967:TDE0638|3end_oligopeptide/dipeptide_ABC_transporter,_permease_protein_672488..672638_NEGATIVE 331 202 163 48 1 NC_002967:TDE2238|3end_hypothetical_protein_2276545..2276695_POSITIVE 330 169 121 150 99 NC_002967:TDE1850|3end_ABC_transporter,_permease_protein,_putative_1878227..1878377_NEGATIVE 327 69 29 84 38 NC_002967:TDE1623|3end_hypothetical_protein_1671018..1671168_NEGATIVE 326 191 157 60 30 NC_002967:TDE0582|3end_hypothetical_protein_621431..621581_POSITIVE 324 164 126 61 5 NC_002967:TDE1810|3end_hypothetical_protein_1845924..1846074_NEGATIVE 324 164 126 57 1 NC_002967:TDE1787|3end_hypothetical_protein_1826378..1826528_NEGATIVE 323 210 165 55 3 NC_002967:TDE2162|3end_NOL1/NOP2/sun_family_protein_2195560..2195710_POSITIVE 323 197 151 109 71 NC_002967:TDE1848|3end_hypothetical_protein_1875897..1876047_NEGATIVE 322 193 151 150 109 NC_002967:TDE0956|3end_hypothetical_protein_980330..980480_POSITIVE 320 202 166 70 35 NC_002967:TDE0689|3end_5-methylthioribose_kinase_726972..727122_POSITIVE 319 200 155 57 1 NC_002967:TDE2037|3end_ATP:guanido_phosphotransferase_domain_protein_2066647..2066797_NEGATIVE 318 198 156 37 1 NC_002967:TDE0919|3end_hypothetical_protein_939125..939275_POSITIVE 318 204 162 98 51 NC_002967:TDE0788|3end_ribosomal_protein_L36_816625..816775_POSITIVE 316 186 141 118 72 NC_002967:TDE0775|3end_ribosomal_protein_L29_810886..811036_POSITIVE 312 170 123 80 28 NC_002967:TDE0109|3end_phenylalanyl-tRNA_synthetase_alpha_subunit_128833..128983_NEGATIVE