Origin IGS: tagaatttgattaaggtttgataccaagaaatcaacataccccgacgcagagtgtcggactatgttgttctcataaggtggttgcagtcggctttaatacccttcgttacgacgcaagcgtcggggtattaaaccctccgcacgaataaagattatataaagaaggttttat .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 ataaaaccttctttatataatctttattcgtgcggagggtttaataccccgacgcttgcgtcgtaacgaagggtattaaagccgactgcaaccaccttatgagaacaacatagtccgacactctgcgtcggggtatgttgatttcttggtatcaaaccttaatcaaattcta Mask Tandem Repeat Region ================================================ tagaatttgattaaggtttgataccaagaaatcaacataccccgacgcagagtgtcggactatgttgttctcataaggtggttgcagtcggctttaatacccttcgttacgacgcaagcgtcggggtattaaaccctccgcacgaataaagattatataaagaaggttttat Find is-nt database================================================ Query_seq: TDE0370:TDE0371|TDE0370:TDE0371:UDP-N-acetylmuramoylalanine--D-glutamate ligase:hypothetical protein:->->:422655..422826 172 tagaatttgattaaggtttgataccaagaaatcaacataccccgacgcagagtgtcggactatgttgttctcataaggtggttgcagtcggctttaatacccttcgttacgacgcaagcgtcggggtattaaaccctccgcacgaataaagattatataaagaaggttttat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE0370:TDE0371|TDE0370:TDE0371:UDP-N-acetylmuramoylalanine--D-glutamate ligase:hypothetical protein:->->:422655..422826 172 tagaatttgattaaggtttgataccaagaaatcaacataccccgacgcagagtgtcggactatgttgttctcataaggtggttgcagtcggctttaatacccttcgttacgacgcaagcgtcggggtattaaaccctccgcacgaataaagattatataaagaaggttttat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE0370:TDE0371|TDE0370:TDE0371:UDP-N-acetylmuramoylalanine--D-glutamate ligase:hypothetical protein:->->:422655..422826 172 tagaatttgattaaggtttgataccaagaaatcaacataccccgacgcagagtgtcggactatgttgttctcataaggtggttgcagtcggctttaatacccttcgttacgacgcaagcgtcggggtattaaaccctccgcacgaataaagattatataaagaaggttttat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tagaatttgattaaggtttgataccaagaaatcaacataccccgacgcagagtgtcggactatgttgttctcataaggtggttgcagtcggctttaatacccttcgttacgacgcaagcgtcggggtattaaaccctccgcacgaataaagattatataaagaaggttttat Predict ORF larger than 30AA ================================================ Protein_Len: 33 Strand: + Start: 31 End: 129 .............................. M N I P R R R V S D Y V V L I R W L Q S A L I P F V T T Q A S G Y ........................................... Protein_Len: 43 Strand: + Start: 18 End: 146 ................. M I P R N Q H T P T Q S V G L C 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 .......................... tagaatttgattaaggtttgataccaagaaatcaacataccccgacgcagagtgtcggactatgttgttctcataaggtggttgcagtcggctttaatacccttcgttacgacgcaagcgtcggggtattaaaccctccgcacgaataaagattatataaagaaggttttat 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================================================ tagaatttgattaaggtttgataccaagaaatcaacataccccgacgcagagtgtcggactatgttgttctcataaggtggttgcagtcggctttaatacccttcgttacgacgcaagcgtcggggtattaaaccctccgcacgaataaagattatataaagaaggttttat Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 77 HP_score: -11.5 Tail_Score: -3.26319 Start: 28 End: 72 Full_Region: ctgcaaccaccttat gagaacaacatagtccgacac tct gcgtcggggtatgttgatttc ttggtatcaaacctt ...........................gagaacaacatagtccgacactctgcgtcggggtatgttgatttc.................................................................................................... TransTerm Strand: - Conf: 79 HP_score: -8.7 Tail_Score: -4.29106 Start: 32 End: 68 Full_Region: aaccaccttatgaga acaacatagtccgacac tct gcgtcggggtatgttga tttcttggtatcaaa ...............................acaacatagtccgacactctgcgtcggggtatgttga........................................................................................................ TransTerm Strand: + Conf: 85 HP_score: -12.2 Tail_Score: -3.4178 Start: 33 End: 67 Full_Region: TTGATACCAAGAAAT CAACATACCCCGACGC AGA GTGTCGGACTATGTTG TTCTCATAAGGTGGT ................................CAACATACCCCGACGCAGAGTGTCGGACTATGTTG......................................................................................................... TransTerm Strand: - Conf: 81 HP_score: -12.2 Tail_Score: -3.16982 Start: 33 End: 67 Full_Region: accaccttatgagaa caacatagtccgacac tct gcgtcggggtatgttg atttcttggtatcaa ................................caacatagtccgacactctgcgtcggggtatgttg......................................................................................................... TransTerm Strand: + Conf: 74 HP_score: -8.1 Tail_Score: -3.84674 Start: 36 End: 64 Full_Region: ATACCAAGAAATCAA CATACCCCGACGC AGA GTGTCGGACTATG TTGTTCTCATAAGGT ...................................CATACCCCGACGCAGAGTGTCGGACTATG............................................................................................................ Find igs database================================================ Query_seq: TDE0370:TDE0371|TDE0370:TDE0371:UDP-N-acetylmuramoylalanine--D-glutamate ligase:hypothetical protein:->->:422655..422826 172 tagaatttgattaaggtttgataccaagaaatcaacataccccgacgcagagtgtcggactatgttgttctcataaggtggttgcagtcggctttaatacccttcgttacgacgcaagcgtcggggtattaaaccctccgcacgaataaagattatataaagaaggttttat Intra-Species Hit: Count: 1 Min: 1 Max: 172 Len: 172 Subject: NC_002967_TDE0370_TDE0371|UDP-N-acetylmuramoylalanine--D-glutamate ligase:hypothetical protein|POSITIVE:POSITIVE|[422655,422826]|172 HSP 1 e-value: 5.0E-93 bit: 341.0 Len: 172 Query Start:1 Query End:172 Subject Strand: POSITIVE Subject Start: 1 Subject End: 172 tagaatttgattaaggtttgataccaagaaatcaacataccccgacgcagagtgtcggactatgttgttctcataaggtggttgcagtcggctttaatacccttcgttacgacgcaagcgtcggggtattaaaccctccgcacgaataaagattatataaagaaggttttat tagaatttgattaaggtttgataccaagaaatcaacataccccgacgcagagtgtcggactatgttgttctcataaggtggttgcagtcggctttaatacccttcgttacgacgcaagcgtcggggtattaaaccctccgcacgaataaagattatataaagaaggttttat Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAGAAUUUGAUUAAGGUUUGAUACCAAGAAAUCAACAUACCCCGACGCAGAGUGUCGGACUAUGUUGUUCUCAUAAGGUGGUUGCAGUCGGCUUUAAUACCCUUCGUUACGACGCAAGCGUCGGGGUAUUAAACCCUCCGCACGAAUAAAGAUUAUAUAAAGAAGGUUUUAU ((((((((..((..(((((((((((..((...(((((((..(((((((...)))))))..)))))))...))..((((..((((.((....)).))))..)))).....(((((....))))).))))))))))).((.....))..............))..)))))))). (-48.70) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUAAAACCUUCUUUAUAUAAUCUUUAUUCGUGCGGAGGGUUUAAUACCCCGACGCUUGCGUCGUAACGAAGGGUAUUAAAGCCGACUGCAACCACCUUAUGAGAACAACAUAGUCCGACACUCUGCGUCGGGGUAUGUUGAUUUCUUGGUAUCAAACCUUAAUCAAAUUCUA ..............................(((((.((.(((((((((((((((....))))).......)))))))))).))..)))))...(((....((((.(((((((.((((((.......)))))).))))))).))))..)))...................... (-54.51) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 987 120 71 228 179 NC_002967:TDE1051|5end_hypothetical_protein_1078496..1078726_NEGATIVE 843 90 41 144 96 NC_002967:TDE0830|5end_hypothetical_protein_852025..852255_NEGATIVE 818 130 81 226 176 NC_002967:TDE0580|5end_hypothetical_protein_615338..615568_POSITIVE 814 130 81 185 135 NC_002967:TDE2691|5end_hypothetical_protein_2728838..2729068_POSITIVE 746 100 51 226 177 NC_002967:TDE1194|5end_hypothetical_protein_1224973..1225203_POSITIVE 740 151 111 178 138 NC_002967:TDE0713|5end_transcription_antitermination_protein,_NusG_family_747109..747339_POSITIVE 687 150 110 186 145 NC_002967:TDE0017|5end_hypothetical_protein_22936..23166_NEGATIVE 390 67 22 226 180 NC_002967:TDE0167|5end_ABC_transporter,_ATP-binding_protein_196574..196804_NEGATIVE 385 67 27 228 191 NC_002967:TDE1470|5end_hypothetical_protein_1518026..1518256_NEGATIVE 384 129 83 152 114 NC_002967:TDE0538|5end_hypothetical_protein_580066..580296_POSITIVE 380 140 101 69 27 NC_002967:TDE0071|5end_peptidase,_U32_family_78602..78832_POSITIVE 350 141 104 231 194 NC_002967:TDE0237|5end_HDIG_domain_protein_271190..271420_NEGATIVE 348 67 35 175 145 NC_002967:TDE0509|5end_hypothetical_protein_560373..560603_NEGATIVE 344 125 81 52 7 NC_002967:TDE1856|5end_radical_SAM_domain_protein_1883133..1883363_POSITIVE 343 89 41 194 155 NC_002967:TDE0991|5end_ribosomal_protein_L28_1018065..1018295_NEGATIVE 334 142 111 166 125 NC_002967:TDE2596|5end_hypothetical_protein_2632039..2632269_NEGATIVE 333 58 27 227 198 NC_002967:TDE2498|5end_metallo-beta-lactamase_family_protein_2522961..2523191_NEGATIVE 331 150 123 54 26 NC_002967:TDE1692|5end_hypothetical_protein_1748293..1748523_POSITIVE 328 144 102 51 13 NC_002967:TDE1736|5end_ferredoxin,_2(4Fe-4S)_1789908..1790138_POSITIVE 323 79 31 111 54 NC_002967:TDE2730|5end_hydrolase,_TatD_family_2786586..2786816_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 1007 130 81 92 43 NC_002967:TDE0710|3end_hypothetical_protein_745667..745817_POSITIVE 1003 150 101 65 16 NC_002967:TDE0333|3end_MATE_efflux_family_protein_373083..373233_POSITIVE 931 130 81 69 20 NC_002967:TDE2499|3end_hypothetical_protein_2523191..2523341_NEGATIVE 898 147 101 52 6 NC_002967:TDE2140|3end_protease_II_2173083..2173233_NEGATIVE 891 150 101 147 98 NC_002967:TDE2459|3end_hypothetical_protein_2485764..2485914_NEGATIVE 843 90 41 74 26 NC_002967:TDE0831|3end_hypothetical_protein_852095..852245_NEGATIVE 836 150 109 42 1 NC_002967:TDE1052|3end_rubredoxin_1078712..1078862_NEGATIVE 814 130 81 115 65 NC_002967:TDE2689|3end_hypothetical_protein_2728848..2728998_POSITIVE 811 149 110 57 18 NC_002967:TDE0693|3end_phosphomethylpyrimidine_kinase_730831..730981_POSITIVE 687 150 110 49 8 NC_002967:TDE0018|3end_LysM_domain_protein_23073..23223_NEGATIVE 590 150 105 71 26 NC_002967:TDE2429|3end_hypothetical_protein_2456628..2456778_NEGATIVE 455 80 40 87 53 NC_002967:TDE0202|3end_hypothetical_protein_235870..236020_NEGATIVE 415 55 15 77 41 NC_002967:TDE1939|3end_hypothetical_protein_1955435..1955585_POSITIVE 390 67 22 133 87 NC_002967:TDE0168|3end_transcriptional_regulator,_GntR_family_196667..196817_NEGATIVE 385 67 27 109 72 NC_002967:TDE1471|3end_hypothetical_protein_1518145..1518295_NEGATIVE 384 129 83 84 46 NC_002967:TDE0537|3end_hypothetical_protein_580078..580228_POSITIVE 380 67 27 132 96 NC_002967:TDE0711|3end_hypothetical_protein_745690..745840_NEGATIVE 362 70 27 63 20 NC_002967:TDE0370|3end_UDP-N-acetylmuramoylalanine--D-glutamate_ligase_422594..422744_POSITIVE 358 139 93 111 55 NC_002967:TDE0133|3end_transcriptional_regulator,_GntR_family_153202..153352_POSITIVE 354 145 103 89 48 NC_002967:TDE2582|3end_GGDEF_domain_protein_2616164..2616314_POSITIVE