Origin IGS: aaaaacctcccaaaacaaaggtcaaattttgaatataaccgcaagggacgaaaaaaacgctaaaatttttaattgcatttatttataaattgcttacacagccttgacggtttactcccatattccgttcttccattatacatcaaaaaaattaaaataccaagcaaaatttggaaaaa .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tttttccaaattttgcttggtattttaatttttttgatgtataatggaagaacggaatatgggagtaaaccgtcaaggctgtgtaagcaatttataaataaatgcaattaaaaattttagcgtttttttcgtcccttgcggttatattcaaaatttgacctttgttttgggaggttttt Mask Tandem Repeat Region ================================================ aaaaacctcccaaaacaaaggtcaaattttgaatataaccgcaagggacgaaaaaaacgctaaaatttttaattgcatttatttataaattgcttacacagccttgacggtttactcccatattccgttcttccattatacatcaaaaaaattaaaataccaagcaaaatttggaaaaa Find is-nt database================================================ Query_seq: TDE2242:TDE2243|TDE2242:TDE2243:antigen, putative:CutC family protein:<-<-:2282125..2282303 179 aaaaacctcccaaaacaaaggtcaaattttgaatataaccgcaagggacgaaaaaaacgctaaaatttttaattgcatttatttataaattgcttacacagccttgacggtttactcccatattccgttcttccattatacatcaaaaaaattaaaataccaagcaaaatttggaaaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE2242:TDE2243|TDE2242:TDE2243:antigen, putative:CutC family protein:<-<-:2282125..2282303 179 aaaaacctcccaaaacaaaggtcaaattttgaatataaccgcaagggacgaaaaaaacgctaaaatttttaattgcatttatttataaattgcttacacagccttgacggtttactcccatattccgttcttccattatacatcaaaaaaattaaaataccaagcaaaatttggaaaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE2242:TDE2243|TDE2242:TDE2243:antigen, putative:CutC family protein:<-<-:2282125..2282303 179 aaaaacctcccaaaacaaaggtcaaattttgaatataaccgcaagggacgaaaaaaacgctaaaatttttaattgcatttatttataaattgcttacacagccttgacggtttactcccatattccgttcttccattatacatcaaaaaaattaaaataccaagcaaaatttggaaaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aaaaacctcccaaaacaaaggtcaaattttgaatataaccgcaagggacgaaaaaaacgctaaaatttttaattgcatttatttataaattgcttacacagccttgacggtttactcccatattccgttcttccattatacatcaaaaaaattaaaataccaagcaaaatttggaaaaa Predict ORF larger than 30AA ================================================ Protein_Len: 35 Strand: + Start: 73 End: 177 ........................................................................ M H L F I N C L H S L D G L L P Y S V L P L Y I K K I K I P S K I W K .. Protein_Len: 30 Strand: + Start: 89 End: 178 ........................................................................................ M A Y T A L T V Y S H I P F F H Y T S K K L K Y Q A K F G K . Protein_Len: 33 Strand: - Start: 72 End: 170 ....................................................................... N C K N I F Q K C L R S P K S G Y E T R G N Y M L F I L I G L L M ......... aaaaacctcccaaaacaaaggtcaaattttgaatataaccgcaagggacgaaaaaaacgctaaaatttttaattgcatttatttataaattgcttacacagccttgacggtttactcccatattccgttcttccattatacatcaaaaaaattaaaataccaagcaaaatttggaaaaa 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: 88 Start: 135 End: 164 ......................................................................................................................................CTTGGTATTTTAATTTTTTTGATGTATAAT............... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aaaaacctcccaaaacaaaggtcaaattttgaatataaccgcaagggacgaaaaaaacgctaaaatttttaattgcatttatttataaattgcttacacagccttgacggtttactcccatattccgttcttccattatacatcaaaaaaattaaaataccaagcaaaatttggaaaaa Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE2242:TDE2243|TDE2242:TDE2243:antigen, putative:CutC family protein:<-<-:2282125..2282303 179 aaaaacctcccaaaacaaaggtcaaattttgaatataaccgcaagggacgaaaaaaacgctaaaatttttaattgcatttatttataaattgcttacacagccttgacggtttactcccatattccgttcttccattatacatcaaaaaaattaaaataccaagcaaaatttggaaaaa Intra-Species Hit: Count: 1 Min: 1 Max: 179 Len: 179 Subject: NC_002967_TDE2242_TDE2243|antigen, putative:CutC family protein|NEGATIVE:NEGATIVE|[2282125,2282303]|179 HSP 1 e-value: 4.0E-72 bit: 272.0 Len: 179 Query Start:1 Query End:179 Subject Strand: POSITIVE Subject Start: 1 Subject End: 179 aaaaacctcccaaaacaaaggtcaaattttgaatataaccgcaagggacgnnnnnnncgctaaaatttttaattgcatttatttataaattgcttacacagccttgacggtttactcccatattccgttcttccattatacatcnnnnnnnttaaaataccaagcaaaatttggaaaaa aaaaacctcccaaaacaaaggtcaaattttgaatataaccgcaagggacgaaaaaaacgctaaaatttttaattgcatttatttataaattgcttacacagccttgacggtttactcccatattccgttcttccattatacatcaaaaaaattaaaataccaagcaaaatttggaaaaa Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAAACCUCCCAAAACAAAGGUCAAAUUUUGAAUAUAACCGCAAGGGACGAAAAAAACGCUAAAAUUUUUAAUUGCAUUUAUUUAUAAAUUGCUUACACAGCCUUGACGGUUUACUCCCAUAUUCCGUUCUUCCAUUAUACAUCAAAAAAAUUAAAAUACCAAGCAAAAUUUGGAAAAA .........(((((.(((((......))))).......((....))............(((.....((((((((.........(((((...(((.....)))...(((((..((......))..)))))......))))).........)))))))).....)))....)))))..... (-24.17) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUUUCCAAAUUUUGCUUGGUAUUUUAAUUUUUUUGAUGUAUAAUGGAAGAACGGAAUAUGGGAGUAAACCGUCAAGGCUGUGUAAGCAAUUUAUAAAUAAAUGCAAUUAAAAAUUUUAGCGUUUUUUUCGUCCCUUGCGGUUAUAUUCAAAAUUUGACCUUUGUUUUGGGAGGUUUUU ...((((...((((.(...((((.((((.....)))).))))...).))))..)))).....((((((((((.(((((.(((....)))......(((.((((((..............)))))).)))....)))))))))).))))).......(((((((......)))))))... (-33.54) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 904 140 91 231 182 NC_002967:TDE2242|5end_antigen,_putative_2282034..2282264_NEGATIVE 441 170 127 176 133 NC_002967:TDE2104|5end_hypothetical_protein_2131083..2131313_NEGATIVE 359 130 89 54 10 NC_002967:TDE0623|5end_precorrin-3B_C17-methyltransferase_655783..656013_POSITIVE 275 134 97 86 40 NC_002967:TDE1885|5end_hypothetical_protein_1906857..1907087_POSITIVE 265 130 88 206 147 NC_002967:TDE2469|5end_hexokinase_family_protein_2492549..2492779_NEGATIVE 265 60 17 180 139 NC_002967:TDE2264|5end_ABC_transporter,_ATP-binding/permease_protein_2302033..2302263_NEGATIVE 264 49 6 205 151 NC_002967:TDE0957|5end_glycerophosphoryl_diester_phosphodiesterase_family_protein_980252..980482_POSITIVE 263 70 21 108 57 NC_002967:TDE1060|5end_hypothetical_protein_1086519..1086749_POSITIVE 262 134 98 166 120 NC_002967:TDE0741|5end_hypothetical_protein_778158..778388_NEGATIVE 261 136 91 166 124 NC_002967:TDE1543|5end_conserved_hypothetical_protein_TIGR00247_1586068..1586298_POSITIVE 260 127 91 181 143 NC_002967:TDE2405|5end_hypothetical_protein_2432050..2432280_NEGATIVE 255 60 28 189 156 NC_002967:TDE0162|5end_hypothetical_protein_187898..188128_POSITIVE 253 61 21 226 184 NC_002967:TDE1061|5end_ABC_transporter,_ATP-binding/permease_protein,_HlyB_family_1086646..1086876_POSITIVE 253 132 91 222 175 NC_002967:TDE0368|5end_type_I_restriction-modification_system,_S_subunit,_putative_418245..418475_NEGATIVE 252 113 73 228 193 NC_002967:TDE1150|5end_hypothetical_protein_1188243..1188473_NEGATIVE 251 136 99 231 192 NC_002967:TDE1919|5end_hypothetical_protein_1939890..1940120_NEGATIVE 245 49 2 163 129 NC_002967:TDE1447|5end_tRNA_delta(2)-isopentenylpyrophosphate_transferase_1492612..1492842_POSITIVE 244 135 91 102 65 NC_002967:TDE0119|5end_flagellar_protein_FliS_137498..137728_NEGATIVE 243 140 93 95 24 NC_002967:TDE1995|5end_magnesium_chelatase_family_protein_2012464..2012694_POSITIVE 243 141 101 175 132 NC_002967:TDE0863|5end_MgtC_family_protein_884526..884756_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 441 170 127 53 10 NC_002967:TDE2105|3end_hypothetical_protein_2131206..2131356_NEGATIVE 285 130 81 139 74 NC_002967:TDE1734|3end_exodeoxyribonuclease_III_1789463..1789613_POSITIVE 284 134 91 133 70 NC_002967:TDE1450|3end_MutS2_family_protein_1497856..1498006_POSITIVE 262 48 7 62 18 NC_002967:TDE1986|3end_adenylate_cyclase,_putative_2000283..2000433_NEGATIVE 262 61 21 54 13 NC_002967:TDE1529|3end_hypothetical_protein_1575067..1575217_POSITIVE 261 136 91 146 104 NC_002967:TDE1542|3end_hypothetical_protein_1586128..1586278_POSITIVE 259 50 5 136 85 NC_002967:TDE0761|3end_protease_complex-associated_polypeptide_801968..802118_POSITIVE 253 132 91 111 64 NC_002967:TDE0369|3end_type_I_restriction-modification_system,_M_subunit_418356..418506_NEGATIVE 245 60 16 125 85 NC_002967:TDE2160|3end_hypothetical_protein_2193873..2194023_NEGATIVE 245 49 2 150 116 NC_002967:TDE1446|3end_hypothetical_protein_1492679..1492829_POSITIVE 240 127 90 64 36 NC_002967:TDE2563|3end_hypothetical_protein_2590068..2590218_POSITIVE 234 134 91 108 52 NC_002967:TDE0157|3end_KHG/KDPG_family_aldolase/carbohydrate_kinase,_PfkB_family_185711..185861_POSITIVE 233 55 20 85 47 NC_002967:TDE2310|3end_hypothetical_protein_2348256..2348406_POSITIVE 231 134 92 147 107 NC_002967:TDE2165|3end_hydrogenase_accessory_protein_HypB_2197053..2197203_NEGATIVE 227 77 36 106 56 NC_002967:TDE1013|3end_hemerythrin-related_protein_1043977..1044127_NEGATIVE 226 129 100 63 30 NC_002967:TDE1537|3end_polyprenyl_synthetase_family_protein_1580472..1580622_NEGATIVE 226 137 92 122 68 NC_002967:TDE0362|3end_bacterial_Ig-like_domain_protein_407501..407651_NEGATIVE 224 146 101 88 40 NC_002967:TDE1151|3end_hypothetical_protein_1188268..1188418_NEGATIVE 223 129 87 82 41 NC_002967:TDE2573|3end_glucose-6-phosphate_isomerase_2600459..2600609_POSITIVE 222 134 99 76 43 NC_002967:TDE1396|3end_hypothetical_protein_1436127..1436277_POSITIVE