Origin IGS: ttaaaataatttattgataaaagcatggataaaccgtgccgaaccgacatcatggtttctatatcatctttaaaacaacaaaggctgtatctctttatgagcttacagccttttttattcgtgcggagggtttaatcccccgacgcagagcgtcggggttgttgatttggtgttt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aaacaccaaatcaacaaccccgacgctctgcgtcgggggattaaaccctccgcacgaataaaaaaggctgtaagctcataaagagatacagcctttgttgttttaaagatgatatagaaaccatgatgtcggttcggcacggtttatccatgcttttatcaataaattattttaa Mask Tandem Repeat Region ================================================ ttaaaataatttattgataaaagcatggataaaccgtgccgaaccgacatcatggtttctatatcatctttaaaacaacaaaggctgtatctctttatgagcttacagccttttttattcgtgcggagggtttaatcccccgacgcagagcgtcggggttgttgatttggtgttt Find is-nt database================================================ Query_seq: TDE0201:TDE0202|TDE0201:TDE0202:hypothetical protein:hypothetical protein:-><-:235785..235959 175 ttaaaataatttattgataaaagcatggataaaccgtgccgaaccgacatcatggtttctatatcatctttaaaacaacaaaggctgtatctctttatgagcttacagccttttttattcgtgcggagggtttaatcccccgacgcagagcgtcggggttgttgatttggtgttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE0201:TDE0202|TDE0201:TDE0202:hypothetical protein:hypothetical protein:-><-:235785..235959 175 ttaaaataatttattgataaaagcatggataaaccgtgccgaaccgacatcatggtttctatatcatctttaaaacaacaaaggctgtatctctttatgagcttacagccttttttattcgtgcggagggtttaatcccccgacgcagagcgtcggggttgttgatttggtgttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE0201:TDE0202|TDE0201:TDE0202:hypothetical protein:hypothetical protein:-><-:235785..235959 175 ttaaaataatttattgataaaagcatggataaaccgtgccgaaccgacatcatggtttctatatcatctttaaaacaacaaaggctgtatctctttatgagcttacagccttttttattcgtgcggagggtttaatcccccgacgcagagcgtcggggttgttgatttggtgttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ttaaaataatttattgataaaagcatggataaaccgtgccgaaccgacatcatggtttctatatcatctttaaaacaacaaaggctgtatctctttatgagcttacagccttttttattcgtgcggagggtttaatcccccgacgcagagcgtcggggttgttgatttggtgttt Predict ORF larger than 30AA ================================================ Protein_Len: 40 Strand: + Start: 13 End: 132 ............ M D K S M D K P C R T D I M V S I S S L K Q Q R L Y L F M S L Q P F L F V R R V ........................................... Protein_Len: 46 Strand: + Start: 36 End: 173 ................................... M P N R H H G F Y I I F K T T K A V S L Y E L T A F F I R A E G L I P R R R A S G L L I W C .. Protein_Len: 32 Strand: - Start: 3 End: 98 .. F Y N I S L L M S L G H R V S M M T E I D D K F C C L S Y R K M ............................................................................. ttaaaataatttattgataaaagcatggataaaccgtgccgaaccgacatcatggtttctatatcatctttaaaacaacaaaggctgtatctctttatgagcttacagccttttttattcgtgcggagggtttaatcccccgacgcagagcgtcggggttgttgatttggtgttt 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================================================ ttaaaataatttattgataaaagcatggataaaccgtgccgaaccgacatcatggtttctatatcatctttaaaacaacaaaggctgtatctctttatgagcttacagccttttttattcgtgcggagggtttaatcccccgacgcagagcgtcggggttgttgatttggtgttt Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 85 HP_score: -4.9 Tail_Score: -5.5112 Start: 83 End: 110 Full_Region: CTTTAAAACAACAAA GGCTGTATCTC TTTAT GAGCTTACAGCC TTTTTTATTCGTGCG ..................................................................................GGCTGTATCTCTTTATGAGCTTACAGCC................................................................. TransTerm Strand: - Conf: 70 HP_score: -4.9 Tail_Score: -4.67697 Start: 83 End: 110 Full_Region: cgcacgaataaaaaa ggctgtaagctc ataaa gagatacagcc tttgttgttttaaag ..................................................................................ggctgtaagctcataaagagatacagcc................................................................. TransTerm Strand: + Conf: 100 HP_score: -18.3 Tail_Score: -3.92143 Start: 138 End: 158 Full_Region: GCGGAGGGTTTAATC CCCCGACGC AGA GCGTCGGGG TTGTTGATTTGGTGT .........................................................................................................................................CCCCGACGCAGAGCGTCGGGG................. Find igs database================================================ Query_seq: TDE0201:TDE0202|TDE0201:TDE0202:hypothetical protein:hypothetical protein:-><-:235785..235959 175 ttaaaataatttattgataaaagcatggataaaccgtgccgaaccgacatcatggtttctatatcatctttaaaacaacaaaggctgtatctctttatgagcttacagccttttttattcgtgcggagggtttaatcccccgacgcagagcgtcggggttgttgatttggtgttt Intra-Species Hit: Count: 1 Min: 1 Max: 175 Len: 175 Subject: NC_002967_TDE0201_TDE0202|hypothetical protein:hypothetical protein|POSITIVE:NEGATIVE|[235785,235959]|175 HSP 1 e-value: 8.0E-95 bit: 347.0 Len: 175 Query Start:1 Query End:175 Subject Strand: POSITIVE Subject Start: 1 Subject End: 175 ttaaaataatttattgataaaagcatggataaaccgtgccgaaccgacatcatggtttctatatcatctttaaaacaacaaaggctgtatctctttatgagcttacagccttttttattcgtgcggagggtttaatcccccgacgcagagcgtcggggttgttgatttggtgttt ttaaaataatttattgataaaagcatggataaaccgtgccgaaccgacatcatggtttctatatcatctttaaaacaacaaaggctgtatctctttatgagcttacagccttttttattcgtgcggagggtttaatcccccgacgcagagcgtcggggttgttgatttggtgttt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUAAAAUAAUUUAUUGAUAAAAGCAUGGAUAAACCGUGCCGAACCGACAUCAUGGUUUCUAUAUCAUCUUUAAAACAACAAAGGCUGUAUCUCUUUAUGAGCUUACAGCCUUUUUUAUUCGUGCGGAGGGUUUAAUCCCCCGACGCAGAGCGUCGGGGUUGUUGAUUUGGUGUUU ...(((((....((..((((..(((((((((((.......((((((......)))))).....................((((((((((.(((.....)))..))))))))))))))))))))).............(((((((((...)))))))))))))..))....))))) (-55.30) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAACACCAAAUCAACAACCCCGACGCUCUGCGUCGGGGGAUUAAACCCUCCGCACGAAUAAAAAAGGCUGUAAGCUCAUAAAGAGAUACAGCCUUUGUUGUUUUAAAGAUGAUAUAGAAACCAUGAUGUCGGUUCGGCACGGUUUAUCCAUGCUUUUAUCAAUAAAUUAUUUUAA .................(((((((((...))))))))).................((((((.((((((((((..(((.....))).)))))))))).))))))..((((((((.....((((........)))).((((.((.....)).))))...........)))))))).. (-50.20) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 771 159 111 150 103 NC_002967:TDE0538|5end_hypothetical_protein_580066..580296_POSITIVE 705 159 112 165 112 NC_002967:TDE0371|5end_hypothetical_protein_422687..422917_POSITIVE 650 155 113 152 107 NC_002967:TDE1470|5end_hypothetical_protein_1518026..1518256_NEGATIVE 617 164 124 121 76 NC_002967:TDE0830|5end_hypothetical_protein_852025..852255_NEGATIVE 605 155 115 150 110 NC_002967:TDE0167|5end_ABC_transporter,_ATP-binding_protein_196574..196804_NEGATIVE 566 165 122 168 126 NC_002967:TDE0017|5end_hypothetical_protein_22936..23166_NEGATIVE 565 164 121 121 81 NC_002967:TDE2691|5end_hypothetical_protein_2728838..2729068_POSITIVE 498 167 138 178 150 NC_002967:TDE0509|5end_hypothetical_protein_560373..560603_NEGATIVE 467 164 123 193 151 NC_002967:TDE1194|5end_hypothetical_protein_1224973..1225203_POSITIVE 463 169 138 88 57 NC_002967:TDE2690|5end_hypothetical_protein_2728898..2729128_NEGATIVE 444 164 132 162 124 NC_002967:TDE0580|5end_hypothetical_protein_615338..615568_POSITIVE 408 144 108 231 193 NC_002967:TDE0712|5end_hypothetical_protein_746963..747193_NEGATIVE 399 155 114 227 182 NC_002967:TDE0238|5end_thioredoxin,_selenocysteine-containing_271380..271610_POSITIVE 376 159 134 148 120 NC_002967:TDE1051|5end_hypothetical_protein_1078496..1078726_NEGATIVE 368 165 139 159 134 NC_002967:TDE0713|5end_transcription_antitermination_protein,_NusG_family_747109..747339_POSITIVE 366 160 125 68 36 NC_002967:TDE2265|5end_hypothetical_protein_2302165..2302395_POSITIVE 358 130 82 222 173 NC_002967:TDE0199|5end_hypothetical_protein_234708..234938_NEGATIVE 355 159 125 230 197 NC_002967:TDE2498|5end_metallo-beta-lactamase_family_protein_2522961..2523191_NEGATIVE 346 157 117 209 166 NC_002967:TDE0738|5end_hypothetical_protein_775934..776164_NEGATIVE 343 158 118 51 5 NC_002967:TDE0120|5end_hypothetical_protein_137648..137878_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 771 159 111 82 35 NC_002967:TDE0537|3end_hypothetical_protein_580078..580228_POSITIVE 686 159 114 68 17 NC_002967:TDE0711|3end_hypothetical_protein_745690..745840_NEGATIVE 665 159 113 89 37 NC_002967:TDE0133|3end_transcriptional_regulator,_GntR_family_153202..153352_POSITIVE 658 159 113 141 89 NC_002967:TDE2458|3end_hypothetical_protein_2485849..2485999_POSITIVE 617 164 124 51 6 NC_002967:TDE0831|3end_hypothetical_protein_852095..852245_NEGATIVE 605 155 115 57 17 NC_002967:TDE0168|3end_transcriptional_regulator,_GntR_family_196667..196817_NEGATIVE 565 164 121 51 11 NC_002967:TDE2689|3end_hypothetical_protein_2728848..2728998_POSITIVE 545 155 123 33 1 NC_002967:TDE1471|3end_hypothetical_protein_1518145..1518295_NEGATIVE 511 165 128 40 2 NC_002967:TDE0693|3end_phosphomethylpyrimidine_kinase_730831..730981_POSITIVE 498 167 138 138 110 NC_002967:TDE0510|3end_hypothetical_protein_560413..560563_NEGATIVE 493 165 122 129 80 NC_002967:TDE2459|3end_hypothetical_protein_2485764..2485914_NEGATIVE 485 165 122 94 45 NC_002967:TDE0710|3end_hypothetical_protein_745667..745817_POSITIVE 476 165 138 31 5 NC_002967:TDE0018|3end_LysM_domain_protein_23073..23223_NEGATIVE 448 143 105 151 108 NC_002967:TDE2690|3end_hypothetical_protein_2728743..2728893_NEGATIVE 424 168 122 51 1 NC_002967:TDE2139|3end_hypothetical_protein_2172897..2173047_POSITIVE 415 165 124 47 4 NC_002967:TDE0333|3end_MATE_efflux_family_protein_373083..373233_POSITIVE 411 170 140 67 33 NC_002967:TDE0370|3end_UDP-N-acetylmuramoylalanine--D-glutamate_ligase_422594..422744_POSITIVE 407 165 122 71 22 NC_002967:TDE2499|3end_hypothetical_protein_2523191..2523341_NEGATIVE 359 157 117 54 23 NC_002967:TDE0978|3end_hypothetical_protein_1002424..1002574_POSITIVE 357 168 122 91 33 NC_002967:TDE1940|3end_hypothetical_protein_1955444..1955594_NEGATIVE