Origin IGS: aagcgataaaaaatcattaaaattcatattgttattatgtaataatcgtaaaataaagtcaatcgtcgggattatggtttgtactcccttcccctaatacctaatctgtcccacttgaaaacttaaccttttcatattataatctttcctcgtattttaaaacgattggagaaaaca .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tgttttctccaatcgttttaaaatacgaggaaagattataatatgaaaaggttaagttttcaagtgggacagattaggtattaggggaagggagtacaaaccataatcccgacgattgactttattttacgattattacataataacaatatgaattttaatgattttttatcgctt Mask Tandem Repeat Region ================================================ aagcgataaaaaatcattaaaattcatattgttattatgtaataatcgtaaaataaagtcaatcgtcgggattatggtttgtactcccttcccctaatacctaatctgtcccacttgaaaacttaaccttttcatattataatctttcctcgtattttaaaacgattggagaaaaca Find is-nt database================================================ Query_seq: TDE1363:TDE1364|TDE1363:TDE1364:nitroreductase family protein:valyl-tRNA synthetase:<-->:1404726..1404902 177 aagcgataaaaaatcattaaaattcatattgttattatgtaataatcgtaaaataaagtcaatcgtcgggattatggtttgtactcccttcccctaatacctaatctgtcccacttgaaaacttaaccttttcatattataatctttcctcgtattttaaaacgattggagaaaaca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE1363:TDE1364|TDE1363:TDE1364:nitroreductase family protein:valyl-tRNA synthetase:<-->:1404726..1404902 177 aagcgataaaaaatcattaaaattcatattgttattatgtaataatcgtaaaataaagtcaatcgtcgggattatggtttgtactcccttcccctaatacctaatctgtcccacttgaaaacttaaccttttcatattataatctttcctcgtattttaaaacgattggagaaaaca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE1363:TDE1364|TDE1363:TDE1364:nitroreductase family protein:valyl-tRNA synthetase:<-->:1404726..1404902 177 aagcgataaaaaatcattaaaattcatattgttattatgtaataatcgtaaaataaagtcaatcgtcgggattatggtttgtactcccttcccctaatacctaatctgtcccacttgaaaacttaaccttttcatattataatctttcctcgtattttaaaacgattggagaaaaca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aagcgataaaaaatcattaaaattcatattgttattatgtaataatcgtaaaataaagtcaatcgtcgggattatggtttgtactcccttcccctaatacctaatctgtcccacttgaaaacttaaccttttcatattataatctttcctcgtattttaaaacgattggagaaaaca Predict ORF larger than 30AA ================================================ aagcgataaaaaatcattaaaattcatattgttattatgtaataatcgtaaaataaagtcaatcgtcgggattatggtttgtactcccttcccctaatacctaatctgtcccacttgaaaacttaaccttttcatattataatctttcctcgtattttaaaacgattggagaaaaca 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: 92 Start: 114 End: 143 .................................................................................................................CTTGAAAACTTAACCTTTTCATATTATAAT.................................. PromScan Matrix: RpoD-17 Strand: - Score: 85 Start: 34 End: 63 .................................ATTGACTTTATTTTACGATTATTACATAAT.................................................................................................................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aagcgataaaaaatcattaaaattcatattgttattatgtaataatcgtaaaataaagtcaatcgtcgggattatggtttgtactcccttcccctaatacctaatctgtcccacttgaaaacttaaccttttcatattataatctttcctcgtattttaaaacgattggagaaaaca Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE1363:TDE1364|TDE1363:TDE1364:nitroreductase family protein:valyl-tRNA synthetase:<-->:1404726..1404902 177 aagcgataaaaaatcattaaaattcatattgttattatgtaataatcgtaaaataaagtcaatcgtcgggattatggtttgtactcccttcccctaatacctaatctgtcccacttgaaaacttaaccttttcatattataatctttcctcgtattttaaaacgattggagaaaaca Intra-Species Hit: Count: 1 Min: 1 Max: 177 Len: 177 Subject: NC_002967_TDE1363_TDE1364|nitroreductase family protein:valyl-tRNA synthetase|NEGATIVE:POSITIVE|[1404726,1404902]|177 HSP 1 e-value: 5.0E-96 bit: 351.0 Len: 177 Query Start:1 Query End:177 Subject Strand: POSITIVE Subject Start: 1 Subject End: 177 aagcgataaaaaatcattaaaattcatattgttattatgtaataatcgtaaaataaagtcaatcgtcgggattatggtttgtactcccttcccctaatacctaatctgtcccacttgaaaacttaaccttttcatattataatctttcctcgtattttaaaacgattggagaaaaca aagcgataaaaaatcattaaaattcatattgttattatgtaataatcgtaaaataaagtcaatcgtcgggattatggtttgtactcccttcccctaatacctaatctgtcccacttgaaaacttaaccttttcatattataatctttcctcgtattttaaaacgattggagaaaaca Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAGCGAUAAAAAAUCAUUAAAAUUCAUAUUGUUAUUAUGUAAUAAUCGUAAAAUAAAGUCAAUCGUCGGGAUUAUGGUUUGUACUCCCUUCCCCUAAUACCUAAUCUGUCCCACUUGAAAACUUAACCUUUUCAUAUUAUAAUCUUUCCUCGUAUUUUAAAACGAUUGGAGAAAACA ....(((.....))).......(((...(((((.(((((.......))))))))))..((((((((.(((((...((((.(((..............)))..)))).)))))...((((((.......))))))...........................)))))))).))).... (-22.84) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGUUUUCUCCAAUCGUUUUAAAAUACGAGGAAAGAUUAUAAUAUGAAAAGGUUAAGUUUUCAAGUGGGACAGAUUAGGUAUUAGGGGAAGGGAGUACAAACCAUAAUCCCGACGAUUGACUUUAUUUUACGAUUAUUACAUAAUAACAAUAUGAAUUUUAAUGAUUUUUUAUCGCUU .........................(((.((((((((((........(((((.(((((.((...(((((........(((((..........))))).........)))))..))..))))).)))))..........((((.......)))).......)))))))))).)))... (-23.13) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 920 110 61 201 152 NC_002967:TDE1363|5end_nitroreductase_family_protein_1404635..1404865_NEGATIVE 377 97 55 228 190 NC_002967:TDE2260|5end_hypothetical_protein_2297338..2297568_POSITIVE 311 107 65 188 148 NC_002967:TDE2259|5end_hypothetical_protein_2297237..2297467_NEGATIVE 310 101 63 229 197 NC_002967:TDE2738|5end_oligoendopeptidase_F,_putative_2792763..2792993_POSITIVE 308 107 62 187 143 NC_002967:TDE2735|5end_surface_antigen,_putative_2790154..2790384_POSITIVE 300 117 75 103 64 NC_002967:TDE2265|5end_hypothetical_protein_2302165..2302395_POSITIVE 300 117 75 82 43 NC_002967:TDE0402|5end_hypothetical_protein_454352..454582_NEGATIVE 300 117 75 204 165 NC_002967:TDE0401|5end_adenylate/guanylate_cyclase_catalytic_domain_protein_454230..454460_NEGATIVE 296 115 75 92 51 NC_002967:TDE1892|5end_hypothetical_protein_1912065..1912295_POSITIVE 294 70 25 110 65 NC_002967:TDE1977|5end_hypothetical_protein_1990078..1990308_POSITIVE 284 101 62 223 189 NC_002967:TDE1393|5end_hypothetical_protein_1432494..1432724_POSITIVE 273 92 58 200 162 NC_002967:TDE2583|5end_hypothetical_protein_2616322..2616552_POSITIVE 259 131 92 105 68 NC_002967:TDE1144|5end_hypothetical_protein_1182855..1183085_NEGATIVE 256 90 54 133 100 NC_002967:TDE0739|5end_hypothetical_protein_775790..776020_POSITIVE 249 109 63 97 47 NC_002967:TDE0838|5end_Na(+)-translocating_NADH-quinone_reductase,_A_subunit_858551..858781_NEGATIVE 247 113 76 180 136 NC_002967:TDE0741|5end_hypothetical_protein_778158..778388_NEGATIVE 245 118 77 59 9 NC_002967:TDE2156|5end_translation_initiation_factor_IF-3_2190719..2190949_NEGATIVE 244 108 62 127 71 NC_002967:TDE1593|5end_Fe-hydrogenase_1642999..1643229_NEGATIVE 243 113 79 45 13 NC_002967:TDE0370|5end_UDP-N-acetylmuramoylalanine--D-glutamate_ligase_421084..421314_POSITIVE 239 110 65 207 167 NC_002967:TDE2024|5end_hypothetical_protein_2051021..2051251_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 315 109 63 85 44 NC_002967:TDE2737|3end_hypothetical_protein_2792690..2792840_POSITIVE 273 103 62 150 124 NC_002967:TDE1740|3end_hypothetical_protein_1792630..1792780_NEGATIVE 262 95 60 74 28 NC_002967:TDE2170|3end_hypothetical_protein_2201606..2201756_NEGATIVE 259 131 92 92 55 NC_002967:TDE1145|3end_hypothetical_protein_1182868..1183018_NEGATIVE 252 111 74 100 65 NC_002967:TDE1893|3end_GTP-binding_protein_LepA_1912212..1912362_NEGATIVE 251 110 62 89 43 NC_002967:TDE1564|3end_hypothetical_protein_1616704..1616854_POSITIVE 246 116 72 107 65 NC_002967:TDE0241|3end_hypothetical_protein_274701..274851_NEGATIVE 244 108 62 133 77 NC_002967:TDE1594|3end_pyridine_nucleotide-disulphide_oxidoreductase_family_protein_1642993..1643143_NEGATIVE 242 90 55 135 99 NC_002967:TDE2089|3end_signal_recognition_particle_protein_2116232..2116382_NEGATIVE 238 89 47 105 57 NC_002967:TDE2542|3end_antigen,_putative_2569441..2569591_NEGATIVE 238 108 68 100 61 NC_002967:TDE1048|3end_30S_ribosomal_protein_S7_1075032..1075182_POSITIVE 238 107 65 139 100 NC_002967:TDE0239|3end_glycine_reductase_complex_protein_GrdD_271828..271978_NEGATIVE 235 104 64 146 111 NC_002967:TDE0780|3end_ribosomal_protein_S14_812629..812779_POSITIVE 234 98 51 95 38 NC_002967:TDE1243|3end_hemolysin_C_1275891..1276041_POSITIVE 231 90 45 141 97 NC_002967:TDE2528|3end_hypothetical_protein_2556220..2556370_NEGATIVE 231 108 67 97 45 NC_002967:TDE0111|3end_hypothetical_protein_132114..132264_POSITIVE 229 107 63 55 2 NC_002967:TDE1355|3end_hypothetical_protein_1395527..1395677_POSITIVE 229 112 76 53 20 NC_002967:TDE1059|3end_hypothetical_protein_1086498..1086648_NEGATIVE 226 95 58 143 106 NC_002967:TDE0872|3end_recA_protein_896165..896315_POSITIVE 221 89 45 92 38 NC_002967:TDE0567|3end_hypothetical_protein_598916..599066_POSITIVE