Origin IGS: aacctctcccaaatttaacttttttataaatcaacaaccccgacgcgaggtcggggtacagtactcaatgtttcgcactgtatgttctcataaggtggttgcagtcggctttaatacccttcgttacgacgcaagcgtcggggtattaaaccctccgcacgaataaagccggcccctgttttaaaagccggctcagtttttgatagcttaaagca .........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 tgctttaagctatcaaaaactgagccggcttttaaaacaggggccggctttattcgtgcggagggtttaataccccgacgcttgcgtcgtaacgaagggtattaaagccgactgcaaccaccttatgagaacatacagtgcgaaacattgagtactgtaccccgacctcgcgtcggggttgttgatttataaaaaagttaaatttgggagaggtt Mask Tandem Repeat Region ================================================ aacctctcccaaatttaacttttttataaatcaacaaccccgacgcgaggtcggggtacagtactcaatgtttcgcactgtatgttctcataaggtggttgcagtcggctttaatacccttcgttacgacgcaagcgtcggggtattaaaccctccgcacgaataaagccggcccctgttttaaaagccggctcagtttttgatagcttaaagca Find is-nt database================================================ Query_seq: TDE1051:TDE1052|TDE1051:TDE1052:hypothetical protein:rubredoxin:<-<-:1078587..1078801 215 aacctctcccaaatttaacttttttataaatcaacaaccccgacgcgaggtcggggtacagtactcaatgtttcgcactgtatgttctcataaggtggttgcagtcggctttaatacccttcgttacgacgcaagcgtcggggtattaaaccctccgcacgaataaagccggcccctgttttaaaagccggctcagtttttgatagcttaaagca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE1051:TDE1052|TDE1051:TDE1052:hypothetical protein:rubredoxin:<-<-:1078587..1078801 215 aacctctcccaaatttaacttttttataaatcaacaaccccgacgcgaggtcggggtacagtactcaatgtttcgcactgtatgttctcataaggtggttgcagtcggctttaatacccttcgttacgacgcaagcgtcggggtattaaaccctccgcacgaataaagccggcccctgttttaaaagccggctcagtttttgatagcttaaagca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE1051:TDE1052|TDE1051:TDE1052:hypothetical protein:rubredoxin:<-<-:1078587..1078801 215 aacctctcccaaatttaacttttttataaatcaacaaccccgacgcgaggtcggggtacagtactcaatgtttcgcactgtatgttctcataaggtggttgcagtcggctttaatacccttcgttacgacgcaagcgtcggggtattaaaccctccgcacgaataaagccggcccctgttttaaaagccggctcagtttttgatagcttaaagca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aacctctcccaaatttaacttttttataaatcaacaaccccgacgcgaggtcggggtacagtactcaatgtttcgcactgtatgttctcataaggtggttgcagtcggctttaatacccttcgttacgacgcaagcgtcggggtattaaaccctccgcacgaataaagccggcccctgttttaaaagccggctcagtttttgatagcttaaagca Predict ORF larger than 30AA ================================================ Protein_Len: 39 Strand: + Start: 30 End: 146 ............................. M N N P D A R S G Y S T Q C F A L Y V L I R W L Q S A L I P F V T T Q A S G Y ..................................................................... Protein_Len: 46 Strand: + Start: 26 End: 163 ......................... M N Q Q P R R E V G V Q Y S M F R T V C S H K V V A V G F N T L R Y D A S V G V L N P P H E .................................................... aacctctcccaaatttaacttttttataaatcaacaaccccgacgcgaggtcggggtacagtactcaatgtttcgcactgtatgttctcataaggtggttgcagtcggctttaatacccttcgttacgacgcaagcgtcggggtattaaaccctccgcacgaataaagccggcccctgttttaaaagccggctcagtttttgatagcttaaagca 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================================================ aacctctcccaaatttaacttttttataaatcaacaaccccgacgcgaggtcggggtacagtactcaatgtttcgcactgtatgttctcataaggtggttgcagtcggctttaatacccttcgttacgacgcaagcgtcggggtattaaaccctccgcacgaataaagccggcccctgttttaaaagccggctcagtttttgatagcttaaagca Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 88 HP_score: -11.7 Tail_Score: -3.93401 Start: 38 End: 56 Full_Region: acattgagtactgta ccccgac ctcgc gtcgggg ttgttgatttataaa .....................................ccccgacctcgcgtcgggg............................................................................................................................................................... Find igs database================================================ Query_seq: TDE1051:TDE1052|TDE1051:TDE1052:hypothetical protein:rubredoxin:<-<-:1078587..1078801 215 aacctctcccaaatttaacttttttataaatcaacaaccccgacgcgaggtcggggtacagtactcaatgtttcgcactgtatgttctcataaggtggttgcagtcggctttaatacccttcgttacgacgcaagcgtcggggtattaaaccctccgcacgaataaagccggcccctgttttaaaagccggctcagtttttgatagcttaaagca Intra-Species Hit: Count: 3 Min: 1 Max: 215 Len: 215 Subject: NC_002967_TDE1051_TDE1052|hypothetical protein:rubredoxin|NEGATIVE:NEGATIVE|[1078587, 1078801]|215 HSP 1 e-value: 1.0E-118 bit: 426.0 Len: 215 Query Start:1 Query End:215 Subject Strand: POSITIVE Subject Start: 1 Subject End: 215 aacctctcccaaatttaacttttttataaatcaacaaccccgacgcgaggtcggggtacagtactcaatgtttcgcactgtatgttctcataaggtggttgcagtcggctttaatacccttcgttacgacgcaagcgtcggggtattaaaccctccgcacgaataaagccggcccctgttttaaaagccggctcagtttttgatagcttaaagca aacctctcccaaatttaacttttttataaatcaacaaccccgacgcgaggtcggggtacagtactcaatgtttcgcactgtatgttctcataaggtggttgcagtcggctttaatacccttcgttacgacgcaagcgtcggggtattaaaccctccgcacgaataaagccggcccctgttttaaaagccggctcagtttttgatagcttaaagca Subject: NC_002967_TDE0333_TDE0334|MATE efflux family protein:hypothetical protein|POSITIVE:NEGATIVE|[373144,373385]|242 HSP 1 e-value: 1.0E-60 bit: 234.0 Len: 141 Query Start:28 Query End:168 Subject Strand: NEGATIVE Subject Start: 25 Subject End: 166 ...........................aaatcaacaaccccgacgcgagg-tcggggtacagtactcaatgtttcgcactgtatgttctcataaggtggttgcagtcggctttaatacccttcgttacgacgcaagcgtcggggtattaaaccctccgcacgaataaag............................................... ...........................aaatcaacaaccccgacgcaagcatcggggtacagagctcaatgtttcgcactgtatgttctcataaggtggttgcagtcggctttaatacccttcgttacgacgcaagcgtcggggtattaaaccctccgcacgaataaag............................................... Subject: NC_002967_TDE2139_TDE2140|hypothetical protein:protease II|POSITIVE:NEGATIVE|[2172958,2173172]|215 HSP 1 e-value: 1.0E-56 bit: 220.0 Len: 138 Query Start:27 Query End:164 Subject Strand: POSITIVE Subject Start: 39 Subject End: 177 ..........................taaatcaacaaccccgacgcgagg-tcggggtacagtactcaatgtttcgcactgtatgttctcataaggtggttgcagtcggctttaatacccttcgttacgacgcaagcgtcggggtattaaaccctccgcacgaat................................................... ..........................taaatcaagaaccccgacgcaagcatcggggtacagtgctcaatgtttcgcactgtatgttctcataaggtggttgcagtcggctttaatacccttcgttatgacgcaagcgtcggggtattaaaccctccgcacgaat................................................... Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AACCUCUCCCAAAUUUAACUUUUUUAUAAAUCAACAACCCCGACGCGAGGUCGGGGUACAGUACUCAAUGUUUCGCACUGUAUGUUCUCAUAAGGUGGUUGCAGUCGGCUUUAAUACCCUUCGUUACGACGCAAGCGUCGGGGUAUUAAACCCUCCGCACGAAUAAAGCCGGCCCCUGUUUUAAAAGCCGGCUCAGUUUUUGAUAGCUUAAAGCA .............................(((((..((((((((.....))))))))...((......(((..(.((((.((((....)))).)))))..)))...((.((((((((((.......(((((....))))))))))))))).))...))..((((..(((((((.............)))))))..))))))))).((.....)). (-62.33) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGCUUUAAGCUAUCAAAAACUGAGCCGGCUUUUAAAACAGGGGCCGGCUUUAUUCGUGCGGAGGGUUUAAUACCCCGACGCUUGCGUCGUAACGAAGGGUAUUAAAGCCGACUGCAACCACCUUAUGAGAACAUACAGUGCGAAACAUUGAGUACUGUACCCCGACCUCGCGUCGGGGUUGUUGAUUUAUAAAAAAGUUAAAUUUGGGAGAGGUU .((.....))...........((((((((((((.....))))))))))))......(((((.((.(((((((((((((((....))))).......)))))))))).))..)))))...(((((.........((((((((..........))))))))(((((((.....)))))))...(((((((......)))))))........))))). (-75.21) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 1048 80 31 171 122 NC_002967:TDE1051|5end_hypothetical_protein_1078496..1078726_NEGATIVE 815 160 111 198 148 NC_002967:TDE2691|5end_hypothetical_protein_2728838..2729068_POSITIVE 811 139 91 218 169 NC_002967:TDE0580|5end_hypothetical_protein_615338..615568_POSITIVE 753 168 124 178 131 NC_002967:TDE0713|5end_transcription_antitermination_protein,_NusG_family_747109..747339_POSITIVE 741 140 91 178 128 NC_002967:TDE0830|5end_hypothetical_protein_852025..852255_NEGATIVE 687 167 127 186 145 NC_002967:TDE0017|5end_hypothetical_protein_22936..23166_NEGATIVE 676 120 73 229 181 NC_002967:TDE1194|5end_hypothetical_protein_1224973..1225203_POSITIVE 469 58 22 231 190 NC_002967:TDE2498|5end_metallo-beta-lactamase_family_protein_2522961..2523191_NEGATIVE 380 157 118 69 27 NC_002967:TDE0071|5end_peptidase,_U32_family_78602..78832_POSITIVE 371 197 152 214 172 NC_002967:TDE1311|5end_ABC_transporter,_ATP-binding/permease_protein_1347371..1347601_POSITIVE 367 146 101 152 115 NC_002967:TDE0538|5end_hypothetical_protein_580066..580296_POSITIVE 366 158 111 186 132 NC_002967:TDE0371|5end_hypothetical_protein_422687..422917_POSITIVE 363 178 131 209 149 NC_002967:TDE0946|5end_hypothetical_protein_968212..968442_POSITIVE 359 209 163 42 2 NC_002967:TDE2676|5end_threonine_synthase_2714285..2714515_POSITIVE 358 140 100 150 117 NC_002967:TDE0167|5end_ABC_transporter,_ATP-binding_protein_196574..196804_NEGATIVE 351 200 160 53 4 NC_002967:TDE1995|5end_magnesium_chelatase_family_protein_2012464..2012694_POSITIVE 350 158 121 231 194 NC_002967:TDE0237|5end_HDIG_domain_protein_271190..271420_NEGATIVE 349 57 13 223 174 NC_002967:TDE1470|5end_hypothetical_protein_1518026..1518256_NEGATIVE 346 149 101 60 14 NC_002967:TDE1856|5end_radical_SAM_domain_protein_1883133..1883363_POSITIVE 346 206 167 39 1 NC_002967:TDE0903|5end_ATP-dependent_DNA_helicase_PcrA_920228..920458_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 1007 140 91 85 36 NC_002967:TDE0710|3end_hypothetical_protein_745667..745817_POSITIVE 1004 160 111 58 9 NC_002967:TDE0333|3end_MATE_efflux_family_protein_373083..373233_POSITIVE 945 169 123 91 45 NC_002967:TDE2499|3end_hypothetical_protein_2523191..2523341_NEGATIVE 908 160 113 48 1 NC_002967:TDE2140|3end_protease_II_2173083..2173233_NEGATIVE 892 160 111 140 91 NC_002967:TDE2459|3end_hypothetical_protein_2485764..2485914_NEGATIVE 836 169 127 59 18 NC_002967:TDE0693|3end_phosphomethylpyrimidine_kinase_730831..730981_POSITIVE 815 160 111 128 78 NC_002967:TDE2689|3end_hypothetical_protein_2728848..2728998_POSITIVE 741 140 91 108 58 NC_002967:TDE0831|3end_hypothetical_protein_852095..852245_NEGATIVE 687 167 127 49 8 NC_002967:TDE0018|3end_LysM_domain_protein_23073..23223_NEGATIVE 590 167 122 71 26 NC_002967:TDE2429|3end_hypothetical_protein_2456628..2456778_NEGATIVE 414 144 101 74 38 NC_002967:TDE0202|3end_hypothetical_protein_235870..236020_NEGATIVE 382 159 111 105 56 NC_002967:TDE0133|3end_transcriptional_regulator,_GntR_family_153202..153352_POSITIVE 380 173 132 117 56 NC_002967:TDE2582|3end_GGDEF_domain_protein_2616164..2616314_POSITIVE 371 197 152 103 61 NC_002967:TDE1310|3end_modulator_of_DNA_gyrase_family_protein_1347340..1347490_POSITIVE 367 146 101 84 47 NC_002967:TDE0537|3end_hypothetical_protein_580078..580228_POSITIVE 366 158 111 89 35 NC_002967:TDE0711|3end_hypothetical_protein_745690..745840_NEGATIVE 358 140 100 57 24 NC_002967:TDE0168|3end_transcriptional_regulator,_GntR_family_196667..196817_NEGATIVE 349 57 13 104 55 NC_002967:TDE1471|3end_hypothetical_protein_1518145..1518295_NEGATIVE 346 149 101 60 14 NC_002967:TDE1855|3end_hypothetical_protein_1883213..1883363_POSITIVE 342 144 103 130 93 NC_002967:TDE0510|3end_hypothetical_protein_560413..560563_NEGATIVE