Origin IGS: aaaaatcaccgcaaagccttgaacggaattgcggtgattaaatcaagaaccccgacgcaagcatcggggtacagtgctcaatgtttcgcactgtatgttctcataaggtggttgcagtcggctttaatacccttcgttatgacgcaagcgtcggggtattaaaccctccgcacgaatcaaatctaaaaatataacaagtttttttaagctgccct .........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 agggcagcttaaaaaaacttgttatatttttagatttgattcgtgcggagggtttaataccccgacgcttgcgtcataacgaagggtattaaagccgactgcaaccaccttatgagaacatacagtgcgaaacattgagcactgtaccccgatgcttgcgtcggggttcttgatttaatcaccgcaattccgttcaaggctttgcggtgattttt Mask Tandem Repeat Region ================================================ aaaaatcaccgcaaagccttgaacggaattgcggtgattaaatcaagaaccccgacgcaagcatcggggtacagtgctcaatgtttcgcactgtatgttctcataaggtggttgcagtcggctttaatacccttcgttatgacgcaagcgtcggggtattaaaccctccgcacgaatcaaatctaaaaatataacaagtttttttaagctgccct Find is-nt database================================================ Query_seq: TDE2139:TDE2140|TDE2139:TDE2140:hypothetical protein:protease II:-><-:2172958..2173172 215 aaaaatcaccgcaaagccttgaacggaattgcggtgattaaatcaagaaccccgacgcaagcatcggggtacagtgctcaatgtttcgcactgtatgttctcataaggtggttgcagtcggctttaatacccttcgttatgacgcaagcgtcggggtattaaaccctccgcacgaatcaaatctaaaaatataacaagtttttttaagctgccct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE2139:TDE2140|TDE2139:TDE2140:hypothetical protein:protease II:-><-:2172958..2173172 215 aaaaatcaccgcaaagccttgaacggaattgcggtgattaaatcaagaaccccgacgcaagcatcggggtacagtgctcaatgtttcgcactgtatgttctcataaggtggttgcagtcggctttaatacccttcgttatgacgcaagcgtcggggtattaaaccctccgcacgaatcaaatctaaaaatataacaagtttttttaagctgccct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE2139:TDE2140|TDE2139:TDE2140:hypothetical protein:protease II:-><-:2172958..2173172 215 aaaaatcaccgcaaagccttgaacggaattgcggtgattaaatcaagaaccccgacgcaagcatcggggtacagtgctcaatgtttcgcactgtatgttctcataaggtggttgcagtcggctttaatacccttcgttatgacgcaagcgtcggggtattaaaccctccgcacgaatcaaatctaaaaatataacaagtttttttaagctgccct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aaaaatcaccgcaaagccttgaacggaattgcggtgattaaatcaagaaccccgacgcaagcatcggggtacagtgctcaatgtttcgcactgtatgttctcataaggtggttgcagtcggctttaatacccttcgttatgacgcaagcgtcggggtattaaaccctccgcacgaatcaaatctaaaaatataacaagtttttttaagctgccct Predict ORF larger than 30AA ================================================ Protein_Len: 47 Strand: + Start: 19 End: 159 .................. M N G I A V I K S R T P T Q A S G Y S A Q C F A L Y V L I R W L Q S A L I P F V M T Q A S G Y ........................................................ Protein_Len: 50 Strand: + Start: 42 End: 191 ......................................... M K N P D A S I G V Q C 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 S N L K I ........................ aaaaatcaccgcaaagccttgaacggaattgcggtgattaaatcaagaaccccgacgcaagcatcggggtacagtgctcaatgtttcgcactgtatgttctcataaggtggttgcagtcggctttaatacccttcgttatgacgcaagcgtcggggtattaaaccctccgcacgaatcaaatctaaaaatataacaagtttttttaagctgccct 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================================================ aaaaatcaccgcaaagccttgaacggaattgcggtgattaaatcaagaaccccgacgcaagcatcggggtacagtgctcaatgtttcgcactgtatgttctcataaggtggttgcagtcggctttaatacccttcgttatgacgcaagcgtcggggtattaaaccctccgcacgaatcaaatctaaaaatataacaagtttttttaagctgccct Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 87 HP_score: -11.4 Tail_Score: -3.91541 Start: 50 End: 69 Full_Region: acattgagcactgta ccccgatg cttg cgtcgggg ttcttgatttaatca .................................................ccccgatgcttgcgtcgggg.................................................................................................................................................. TransTerm Strand: + Conf: 52 HP_score: -4.8 Tail_Score: -3.27951 Start: 70 End: 95 Full_Region: ACGCAAGCATCGGGG TACAGTGC TCAATGTTTC GCACTGTA TGTTCTCATAAGGTG .....................................................................TACAGTGCTCAATGTTTCGCACTGTA........................................................................................................................ Find igs database================================================ Query_seq: TDE2139:TDE2140|TDE2139:TDE2140:hypothetical protein:protease II:-><-:2172958..2173172 215 aaaaatcaccgcaaagccttgaacggaattgcggtgattaaatcaagaaccccgacgcaagcatcggggtacagtgctcaatgtttcgcactgtatgttctcataaggtggttgcagtcggctttaatacccttcgttatgacgcaagcgtcggggtattaaaccctccgcacgaatcaaatctaaaaatataacaagtttttttaagctgccct Intra-Species Hit: Count: 3 Min: 1 Max: 198 Len: 198 Subject: NC_002967_TDE2139_TDE2140|hypothetical protein:protease II|POSITIVE:NEGATIVE|[2172958,2173172]|215 HSP 1 e-value: 1.0E-108 bit: 392.0 Len: 198 Query Start:1 Query End:198 Subject Strand: POSITIVE Subject Start: 1 Subject End: 198 aaaaatcaccgcaaagccttgaacggaattgcggtgattaaatcaagaaccccgacgcaagcatcggggtacagtgctcaatgtttcgcactgtatgttctcataaggtggttgcagtcggctttaatacccttcgttatgacgcaagcgtcggggtattaaaccctccgcacgaatcaaatctaaaaatataacaag................. aaaaatcaccgcaaagccttgaacggaattgcggtgattaaatcaagaaccccgacgcaagcatcggggtacagtgctcaatgtttcgcactgtatgttctcataaggtggttgcagtcggctttaatacccttcgttatgacgcaagcgtcggggtattaaaccctccgcacgaatcaaatctaaaaatataacaag................. Subject: NC_002967_TDE0333_TDE0334|MATE efflux family protein:hypothetical protein|POSITIVE:NEGATIVE|[373144,373385]|242 HSP 1 e-value: 2.0E-65 bit: 250.0 Len: 138 Query Start:40 Query End:177 Subject Strand: NEGATIVE Subject Start: 29 Subject End: 166 .......................................aaatcaagaaccccgacgcaagcatcggggtacagtgctcaatgtttcgcactgtatgttctcataaggtggttgcagtcggctttaatacccttcgttatgacgcaagcgtcggggtattaaaccctccgcacgaat...................................... .......................................aaatcaacaaccccgacgcaagcatcggggtacagagctcaatgtttcgcactgtatgttctcataaggtggttgcagtcggctttaatacccttcgttacgacgcaagcgtcggggtattaaaccctccgcacgaat...................................... Subject: NC_002967_TDE1051_TDE1052|hypothetical protein:rubredoxin|NEGATIVE:NEGATIVE|[1078587, 1078801]|215 HSP 1 e-value: 1.0E-56 bit: 220.0 Len: 139 Query Start:39 Query End:177 Subject Strand: POSITIVE Subject Start: 27 Subject End: 164 ......................................taaatcaagaaccccgacgcaagcatcggggtacagtgctcaatgtttcgcactgtatgttctcataaggtggttgcagtcggctttaatacccttcgttatgacgcaagcgtcggggtattaaaccctccgcacgaat...................................... ......................................taaatcaacaaccccgacgcgagg-tcggggtacagtactcaatgtttcgcactgtatgttctcataaggtggttgcagtcggctttaatacccttcgttacgacgcaagcgtcggggtattaaaccctccgcacgaat...................................... Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAAAUCACCGCAAAGCCUUGAACGGAAUUGCGGUGAUUAAAUCAAGAACCCCGACGCAAGCAUCGGGGUACAGUGCUCAAUGUUUCGCACUGUAUGUUCUCAUAAGGUGGUUGCAGUCGGCUUUAAUACCCUUCGUUAUGACGCAAGCGUCGGGGUAUUAAACCCUCCGCACGAAUCAAAUCUAAAAAUAUAACAAG ...(((((((((((..((......))..))))))))))).......(.((((((((....)..))))))).).((((....(((..(.((((.((((....)))).)))))..)))...((.(((((((((((.......((((....))))))))))))))).))...))))......................... (-69.41) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUUGUUAUAUUUUUAGAUUUGAUUCGUGCGGAGGGUUUAAUACCCCGACGCUUGCGUCAUAACGAAGGGUAUUAAAGCCGACUGCAACCACCUUAUGAGAACAUACAGUGCGAAACAUUGAGCACUGUACCCCGAUGCUUGCGUCGGGGUUCUUGAUUUAAUCACCGCAAUUCCGUUCAAGGCUUUGCGGUGAUUUUU ..........................(((((.((.((((((((((.((((....))))........)))))))))).))..)))))..........((((((.((((((((..........)))))))).(((((((....))))))))))))).....(((((((((((..((......))..)))))))))))... (-74.60) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 967 150 101 228 179 NC_002967:TDE1051|5end_hypothetical_protein_1078496..1078726_NEGATIVE 798 160 111 226 176 NC_002967:TDE0580|5end_hypothetical_protein_615338..615568_POSITIVE 794 160 111 185 135 NC_002967:TDE2691|5end_hypothetical_protein_2728838..2729068_POSITIVE 701 150 101 175 125 NC_002967:TDE0830|5end_hypothetical_protein_852025..852255_NEGATIVE 684 177 131 174 115 NC_002967:TDE0713|5end_transcription_antitermination_protein,_NusG_family_747109..747339_POSITIVE 681 134 92 230 189 NC_002967:TDE1194|5end_hypothetical_protein_1224973..1225203_POSITIVE 637 177 132 183 142 NC_002967:TDE0017|5end_hypothetical_protein_22936..23166_NEGATIVE 470 70 22 230 183 NC_002967:TDE2498|5end_metallo-beta-lactamase_family_protein_2522961..2523191_NEGATIVE 398 70 49 170 149 NC_002967:TDE0509|5end_hypothetical_protein_560373..560603_NEGATIVE 384 159 113 152 114 NC_002967:TDE0538|5end_hypothetical_protein_580066..580296_POSITIVE 360 170 131 69 27 NC_002967:TDE0071|5end_peptidase,_U32_family_78602..78832_POSITIVE 358 153 113 150 117 NC_002967:TDE0167|5end_ABC_transporter,_ATP-binding_protein_196574..196804_NEGATIVE 337 170 123 175 131 NC_002967:TDE0371|5end_hypothetical_protein_422687..422917_POSITIVE 335 88 44 105 51 NC_002967:TDE2690|5end_hypothetical_protein_2728898..2729128_NEGATIVE 335 183 141 181 125 NC_002967:TDE2596|5end_hypothetical_protein_2632039..2632269_NEGATIVE 335 180 131 48 2 NC_002967:TDE0573|5end_hypothetical_protein_604681..604911_POSITIVE 332 126 84 53 8 NC_002967:TDE2320|5end_RNA_polymerase_sigma-24_factor,_putative_2356951..2357181_NEGATIVE 330 171 134 231 194 NC_002967:TDE0237|5end_HDIG_domain_protein_271190..271420_NEGATIVE 328 174 132 51 13 NC_002967:TDE1736|5end_ferredoxin,_2(4Fe-4S)_1789908..1790138_POSITIVE 319 87 45 72 30 NC_002967:TDE0978|5end_hypothetical_protein_1001868..1002098_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 987 160 111 92 43 NC_002967:TDE0710|3end_hypothetical_protein_745667..745817_POSITIVE 979 170 121 55 6 NC_002967:TDE0333|3end_MATE_efflux_family_protein_373083..373233_POSITIVE 911 160 111 69 20 NC_002967:TDE2499|3end_hypothetical_protein_2523191..2523341_NEGATIVE 842 177 131 144 98 NC_002967:TDE2459|3end_hypothetical_protein_2485764..2485914_NEGATIVE 794 160 111 115 65 NC_002967:TDE2689|3end_hypothetical_protein_2728848..2728998_POSITIVE 787 177 139 39 1 NC_002967:TDE1052|3end_rubredoxin_1078712..1078862_NEGATIVE 770 177 132 55 15 NC_002967:TDE0693|3end_phosphomethylpyrimidine_kinase_730831..730981_POSITIVE 701 150 101 105 55 NC_002967:TDE0831|3end_hypothetical_protein_852095..852245_NEGATIVE 637 177 132 46 5 NC_002967:TDE0018|3end_LysM_domain_protein_23073..23223_NEGATIVE 541 177 135 68 26 NC_002967:TDE2429|3end_hypothetical_protein_2456628..2456778_NEGATIVE 433 70 24 74 35 NC_002967:TDE0202|3end_hypothetical_protein_235870..236020_NEGATIVE 398 70 49 130 109 NC_002967:TDE0510|3end_hypothetical_protein_560413..560563_NEGATIVE 384 159 113 84 46 NC_002967:TDE0537|3end_hypothetical_protein_580078..580228_POSITIVE 358 153 113 57 24 NC_002967:TDE0168|3end_transcriptional_regulator,_GntR_family_196667..196817_NEGATIVE 358 169 123 111 55 NC_002967:TDE0133|3end_transcriptional_regulator,_GntR_family_153202..153352_POSITIVE 354 175 133 89 48 NC_002967:TDE2582|3end_GGDEF_domain_protein_2616164..2616314_POSITIVE 350 59 13 71 32 NC_002967:TDE1939|3end_hypothetical_protein_1955435..1955585_POSITIVE 337 170 123 78 34 NC_002967:TDE0711|3end_hypothetical_protein_745690..745840_NEGATIVE 332 126 84 56 11 NC_002967:TDE2321|3end_hypothetical_protein_2356948..2357098_NEGATIVE 328 174 132 61 23 NC_002967:TDE1735|3end_hypothetical_protein_1789998..1790148_POSITIVE