Origin IGS: gttgtttccatctcacaaggctgcctttattcgtgcggagggtttaataccccgacgcttgcgtcgtaacgaagggtattaaagccgactgcaaccaccttatgagaacatacagtgcgaaacattgagctctgtaccccgatgcttgcgtcggggttgttgatttcggctgtcttgtgagatttatattttgcaagcgggagaagcttttaccgttattaaattatatttttaatatcaat .........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 attgatattaaaaatataatttaataacggtaaaagcttctcccgcttgcaaaatataaatctcacaagacagccgaaatcaacaaccccgacgcaagcatcggggtacagagctcaatgtttcgcactgtatgttctcataaggtggttgcagtcggctttaatacccttcgttacgacgcaagcgtcggggtattaaaccctccgcacgaataaaggcagccttgtgagatggaaacaac Mask Tandem Repeat Region ================================================ gttgtttccatctcacaaggctgcctttattcgtgcggagggtttaataccccgacgcttgcgtcgtaacgaagggtattaaagccgactgcaaccaccttatgagaacatacagtgcgaaacattgagctctgtaccccgatgcttgcgtcggggttgttgatttcggctgtcttgtgagatttatattttgcaagcgggagaagcttttaccgttattaaattatatttttaatatcaat Find is-nt database================================================ Query_seq: TDE0333:TDE0334|TDE0333:TDE0334:MATE efflux family protein:hypothetical protein:-><-:373144..373385 242 gttgtttccatctcacaaggctgcctttattcgtgcggagggtttaataccccgacgcttgcgtcgtaacgaagggtattaaagccgactgcaaccaccttatgagaacatacagtgcgaaacattgagctctgtaccccgatgcttgcgtcggggttgttgatttcggctgtcttgtgagatttatattttgcaagcgggagaagcttttaccgttattaaattatatttttaatatcaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE0333:TDE0334|TDE0333:TDE0334:MATE efflux family protein:hypothetical protein:-><-:373144..373385 242 gttgtttccatctcacaaggctgcctttattcgtgcggagggtttaataccccgacgcttgcgtcgtaacgaagggtattaaagccgactgcaaccaccttatgagaacatacagtgcgaaacattgagctctgtaccccgatgcttgcgtcggggttgttgatttcggctgtcttgtgagatttatattttgcaagcgggagaagcttttaccgttattaaattatatttttaatatcaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE0333:TDE0334|TDE0333:TDE0334:MATE efflux family protein:hypothetical protein:-><-:373144..373385 242 gttgtttccatctcacaaggctgcctttattcgtgcggagggtttaataccccgacgcttgcgtcgtaacgaagggtattaaagccgactgcaaccaccttatgagaacatacagtgcgaaacattgagctctgtaccccgatgcttgcgtcggggttgttgatttcggctgtcttgtgagatttatattttgcaagcgggagaagcttttaccgttattaaattatatttttaatatcaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gttgtttccatctcacaaggctgcctttattcgtgcggagggtttaataccccgacgcttgcgtcgtaacgaagggtattaaagccgactgcaaccaccttatgagaacatacagtgcgaaacattgagctctgtaccccgatgcttgcgtcggggttgttgatttcggctgtcttgtgagatttatattttgcaagcgggagaagcttttaccgttattaaattatatttttaatatcaat Predict ORF larger than 30AA ================================================ Protein_Len: 37 Strand: + Start: 132 End: 242 ................................................................................................................................... M Y P D A C V G V V D F G C L V R F I F C K R E K L L P L L N Y I F N I N Protein_Len: 50 Strand: - Start: 47 End: 196 .............................................. Y G S A Q T T V F P I L A S Q L W R I L V Y L A F C Q A R Y G S A Q T P T T S K P Q R T L N I N Q M .............................................. Protein_Len: 45 Strand: - Start: 30 End: 164 ............................. E H P P N L V G V S A D Y R L T N F G V A V V K H S C V T R F M S S Q V G I S A D P N N M .............................................................................. gttgtttccatctcacaaggctgcctttattcgtgcggagggtttaataccccgacgcttgcgtcgtaacgaagggtattaaagccgactgcaaccaccttatgagaacatacagtgcgaaacattgagctctgtaccccgatgcttgcgtcggggttgttgatttcggctgtcttgtgagatttatattttgcaagcgggagaagcttttaccgttattaaattatatttttaatatcaat 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================================================ gttgtttccatctcacaaggctgcctttattcgtgcggagggtttaataccccgacgcttgcgtcgtaacgaagggtattaaagccgactgcaaccaccttatgagaacatacagtgcgaaacattgagctctgtaccccgatgcttgcgtcggggttgttgatttcggctgtcttgtgagatttatattttgcaagcgggagaagcttttaccgttattaaattatatttttaatatcaat Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 88 HP_score: -11.4 Tail_Score: -3.89756 Start: 137 End: 156 Full_Region: ACATTGAGCTCTGTA CCCCGATG CTTG CGTCGGGG TTGTTGATTTCGGCT ........................................................................................................................................CCCCGATGCTTGCGTCGGGG...................................................................................... Find igs database================================================ Query_seq: TDE0333:TDE0334|TDE0333:TDE0334:MATE efflux family protein:hypothetical protein:-><-:373144..373385 242 gttgtttccatctcacaaggctgcctttattcgtgcggagggtttaataccccgacgcttgcgtcgtaacgaagggtattaaagccgactgcaaccaccttatgagaacatacagtgcgaaacattgagctctgtaccccgatgcttgcgtcggggttgttgatttcggctgtcttgtgagatttatattttgcaagcgggagaagcttttaccgttattaaattatatttttaatatcaat Intra-Species Hit: Count: 5 Min: 1 Max: 242 Len: 242 Subject: NC_002967_TDE0333_TDE0334|MATE efflux family protein:hypothetical protein|POSITIVE:NEGATIVE|[373144,373385]|242 HSP 1 e-value: 1.0E-134 bit: 480.0 Len: 242 Query Start:1 Query End:242 Subject Strand: POSITIVE Subject Start: 1 Subject End: 242 gttgtttccatctcacaaggctgcctttattcgtgcggagggtttaataccccgacgcttgcgtcgtaacgaagggtattaaagccgactgcaaccaccttatgagaacatacagtgcgaaacattgagctctgtaccccgatgcttgcgtcggggttgttgatttcggctgtcttgtgagatttatattttgcaagcgggagaagcttttaccgttattaaattatatttttaatatcaat gttgtttccatctcacaaggctgcctttattcgtgcggagggtttaataccccgacgcttgcgtcgtaacgaagggtattaaagccgactgcaaccaccttatgagaacatacagtgcgaaacattgagctctgtaccccgatgcttgcgtcggggttgttgatttcggctgtcttgtgagatttatattttgcaagcgggagaagcttttaccgttattaaattatatttttaatatcaat Subject: NC_002967_TDE2139_TDE2140|hypothetical protein:protease II|POSITIVE:NEGATIVE|[2172958,2173172]|215 HSP 1 e-value: 2.0E-65 bit: 250.0 Len: 138 Query Start:29 Query End:166 Subject Strand: NEGATIVE Subject Start: 40 Subject End: 177 ............................attcgtgcggagggtttaataccccgacgcttgcgtcgtaacgaagggtattaaagccgactgcaaccaccttatgagaacatacagtgcgaaacattgagctctgtaccccgatgcttgcgtcggggttgttgattt............................................................................ ............................attcgtgcggagggtttaataccccgacgcttgcgtcataacgaagggtattaaagccgactgcaaccaccttatgagaacatacagtgcgaaacattgagcactgtaccccgatgcttgcgtcggggttcttgattt............................................................................ Subject: NC_002967_TDE1051_TDE1052|hypothetical protein:rubredoxin|NEGATIVE:NEGATIVE|[1078587, 1078801]|215 HSP 1 e-value: 1.0E-60 bit: 234.0 Len: 142 Query Start:25 Query End:166 Subject Strand: NEGATIVE Subject Start: 28 Subject End: 168 ........................ctttattcgtgcggagggtttaataccccgacgcttgcgtcgtaacgaagggtattaaagccgactgcaaccaccttatgagaacatacagtgcgaaacattgagctctgtaccccgatgcttgcgtcggggttgttgattt............................................................................ ........................ctttattcgtgcggagggtttaataccccgacgcttgcgtcgtaacgaagggtattaaagccgactgcaaccaccttatgagaacatacagtgcgaaacattgagtactgtaccccga-cctcgcgtcggggttgttgattt............................................................................ Subject: NC_002967_TDE2498_TDE2499|metallo-beta-lactamase family protein:hypothetical protein|NEGATIVE:NEGATIVE|[2523052,2523280]|229 HSP 1 e-value: 3.0E-39 bit: 163.0 Len: 86 Query Start:25 Query End:110 Subject Strand: NEGATIVE Subject Start: 144 Subject End: 229 ........................ctttattcgtgcggagggtttaataccccgacgcttgcgtcgtaacgaagggtattaaagccgactgcaaccaccttatgagaaca.................................................................................................................................... ........................ctttattcgtgcggagggtttaataccccgacgcttgcgtcgtaacaaagggtattaaagccgactgcaaccaccttatgagaaca.................................................................................................................................... HSP 2 e-value: 6.0E-7 bit: 56.0 Len: 32 Query Start:135 Query End:166 Subject Strand: NEGATIVE Subject Start: 109 Subject End: 140 ......................................................................................................................................taccccgatgcttgcgtcggggttgttgattt............................................................................ ......................................................................................................................................tacccctatgcttgcgtcggggttgttgattt............................................................................ Subject: NC_002967_TDE0693_TDE0694|phosphomethylpyrimidine kinase:ABC transporter, ATP-binding protein|POSITIVE:POSITIVE|[730892,731129]|238 HSP 1 e-value: 4.0E-14 bit: 79.8 Len: 40 Query Start:27 Query End:66 Subject Strand: POSITIVE Subject Start: 34 Subject End: 73 ..........................ttattcgtgcggagggtttaataccccgacgcttgcgtcg................................................................................................................................................................................ ..........................ttattcgtgcggagggtttaataccccgacgcttgcgtcg................................................................................................................................................................................ HSP 2 e-value: 2.0E-6 bit: 54.0 Len: 31 Query Start:135 Query End:165 Subject Strand: POSITIVE Subject Start: 55 Subject End: 85 ......................................................................................................................................taccccgatgcttgcgtcggggttgttgatt............................................................................. ......................................................................................................................................taccccgacgcttgcgtcggggttgttgatt............................................................................. Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GUUGUUUCCAUCUCACAAGGCUGCCUUUAUUCGUGCGGAGGGUUUAAUACCCCGACGCUUGCGUCGUAACGAAGGGUAUUAAAGCCGACUGCAACCACCUUAUGAGAACAUACAGUGCGAAACAUUGAGCUCUGUACCCCGAUGCUUGCGUCGGGGUUGUUGAUUUCGGCUGUCUUGUGAGAUUUAUAUUUUGCAAGCGGGAGAAGCUUUUACCGUUAUUAAAUUAUAUUUUUAAUAUCAAU .........((((((((((((.(((........(((((.((.(((((((((((((((....))))).......)))))))))).))..))))).............((((.((((.((..........)).))))(((((((((....)))))))))))))......))).)))))))))))).((((.((((..(((((............)))))..)))).)))).............. (-83.41) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUUGAUAUUAAAAAUAUAAUUUAAUAACGGUAAAAGCUUCUCCCGCUUGCAAAAUAUAAAUCUCACAAGACAGCCGAAAUCAACAACCCCGACGCAAGCAUCGGGGUACAGAGCUCAAUGUUUCGCACUGUAUGUUCUCAUAAGGUGGUUGCAGUCGGCUUUAAUACCCUUCGUUACGACGCAAGCGUCGGGGUAUUAAACCCUCCGCACGAAUAAAGGCAGCCUUGUGAGAUGGAAACAAC ((((.(((((((.......))))))).))))..((((.......))))...........((((((((((.(.(((..........((((((((((..((.((((((((.((((((...(((..(.((((.((((....)))).)))))..)))...))))))..))))).......))).))..)))))))))).........((.....)).....))).).))))))))))(....)... (-73.91) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 1053 100 51 188 139 NC_002967:TDE0371|5end_hypothetical_protein_422687..422917_POSITIVE 972 80 31 166 116 NC_002967:TDE1470|5end_hypothetical_protein_1518026..1518256_NEGATIVE 906 110 61 52 3 NC_002967:TDE2690|5end_hypothetical_protein_2728898..2729128_NEGATIVE 897 80 31 164 114 NC_002967:TDE0167|5end_ABC_transporter,_ATP-binding_protein_196574..196804_NEGATIVE 774 66 24 146 100 NC_002967:TDE0538|5end_hypothetical_protein_580066..580296_POSITIVE 605 165 124 178 134 NC_002967:TDE0509|5end_hypothetical_protein_560373..560603_NEGATIVE 559 56 17 231 190 NC_002967:TDE0712|5end_hypothetical_protein_746963..747193_NEGATIVE 481 172 136 134 94 NC_002967:TDE2691|5end_hypothetical_protein_2728838..2729068_POSITIVE 481 172 136 134 94 NC_002967:TDE0830|5end_hypothetical_protein_852025..852255_NEGATIVE 457 86 47 172 139 NC_002967:TDE0017|5end_hypothetical_protein_22936..23166_NEGATIVE 435 93 51 169 134 NC_002967:TDE0713|5end_transcription_antitermination_protein,_NusG_family_747109..747339_POSITIVE 430 68 26 225 182 NC_002967:TDE0238|5end_thioredoxin,_selenocysteine-containing_271380..271610_POSITIVE 404 165 138 29 1 NC_002967:TDE0613|5end_hypothetical_protein_647966..648196_NEGATIVE 390 65 21 46 1 NC_002967:TDE0745|5end_glycine_reductase_complex_selenoprotein_GrdA_780287..780517_POSITIVE 387 180 132 75 16 NC_002967:TDE0909|5end_type_II_DNA_modification_methyltransferase_M.TdeIII_927166..927396_POSITIVE 385 172 136 206 165 NC_002967:TDE1194|5end_hypothetical_protein_1224973..1225203_POSITIVE 385 172 136 175 134 NC_002967:TDE0580|5end_hypothetical_protein_615338..615568_POSITIVE 367 180 136 184 128 NC_002967:TDE1051|5end_hypothetical_protein_1078496..1078726_NEGATIVE 365 69 23 77 23 NC_002967:TDE0353|5end_lipase/acylhydrolase,_GDSL_family_398338..398568_NEGATIVE 360 179 138 59 5 NC_002967:TDE1847|5end_hypothetical_protein_1875664..1875894_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 1053 100 51 91 42 NC_002967:TDE0711|3end_hypothetical_protein_745690..745840_NEGATIVE 1004 80 31 92 43 NC_002967:TDE0133|3end_transcriptional_regulator,_GntR_family_153202..153352_POSITIVE 1001 80 31 144 95 NC_002967:TDE2458|3end_hypothetical_protein_2485849..2485999_POSITIVE 935 100 51 67 17 NC_002967:TDE1471|3end_hypothetical_protein_1518145..1518295_NEGATIVE 897 80 31 71 21 NC_002967:TDE0168|3end_transcriptional_regulator,_GntR_family_196667..196817_NEGATIVE 840 158 116 43 1 NC_002967:TDE2139|3end_hypothetical_protein_2172897..2173047_POSITIVE 774 66 24 78 32 NC_002967:TDE0537|3end_hypothetical_protein_580078..580228_POSITIVE 732 66 23 70 23 NC_002967:TDE0202|3end_hypothetical_protein_235870..236020_NEGATIVE 605 165 124 138 94 NC_002967:TDE0510|3end_hypothetical_protein_560413..560563_NEGATIVE 504 130 86 44 1 NC_002967:TDE0370|3end_UDP-N-acetylmuramoylalanine--D-glutamate_ligase_422594..422744_POSITIVE 481 172 136 64 24 NC_002967:TDE2689|3end_hypothetical_protein_2728848..2728998_POSITIVE 481 172 136 64 24 NC_002967:TDE0831|3end_hypothetical_protein_852095..852245_NEGATIVE 457 86 47 35 2 NC_002967:TDE0018|3end_LysM_domain_protein_23073..23223_NEGATIVE 453 172 136 42 2 NC_002967:TDE0710|3end_hypothetical_protein_745667..745817_POSITIVE 452 55 26 151 122 NC_002967:TDE2690|3end_hypothetical_protein_2728743..2728893_NEGATIVE 433 88 41 53 3 NC_002967:TDE0693|3end_phosphomethylpyrimidine_kinase_730831..730981_POSITIVE 425 93 51 63 14 NC_002967:TDE2429|3end_hypothetical_protein_2456628..2456778_NEGATIVE 421 80 34 127 80 NC_002967:TDE2459|3end_hypothetical_protein_2485764..2485914_NEGATIVE 395 175 141 96 64 NC_002967:TDE1940|3end_hypothetical_protein_1955444..1955594_NEGATIVE 369 180 133 69 12 NC_002967:TDE1620|3end_hypothetical_protein_1666959..1667109_NEGATIVE