Origin IGS: ctggaacgggaagcaggaaagaggcgtggaggagtaaaggacggtaaaagggattttccggtatttcagcgactatcagggggcatagaaaaaaacagcggaatgtgatagaatagtacttgatgttgtggttactttaacggcaaaattgggagacact .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 agtgtctcccaattttgccgttaaagtaaccacaacatcaagtactattctatcacattccgctgtttttttctatgccccctgatagtcgctgaaataccggaaaatcccttttaccgtcctttactcctccacgcctctttcctgcttcccgttccag Mask Tandem Repeat Region ================================================ ctggaacgggaagcaggaaagaggcgtggaggagtaaaggacggtaaaagggattttccggtatttcagcgactatcagggggcatagaaaaaaacagcggaatgtgatagaatagtacttgatgttgtggttactttaacggcaaaattgggagacact Find is-nt database================================================ Query_seq: TDE0908:TDE0909|TDE0908:TDE0909:ABC transporter, ATP-binding/permease protein:type II DNA modification methyltransferase M.TdeIII:->->:927146..927305 160 ctggaacgggaagcaggaaagaggcgtggaggagtaaaggacggtaaaagggattttccggtatttcagcgactatcagggggcatagaaaaaaacagcggaatgtgatagaatagtacttgatgttgtggttactttaacggcaaaattgggagacact Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE0908:TDE0909|TDE0908:TDE0909:ABC transporter, ATP-binding/permease protein:type II DNA modification methyltransferase M.TdeIII:->->:927146..927305 160 ctggaacgggaagcaggaaagaggcgtggaggagtaaaggacggtaaaagggattttccggtatttcagcgactatcagggggcatagaaaaaaacagcggaatgtgatagaatagtacttgatgttgtggttactttaacggcaaaattgggagacact Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE0908:TDE0909|TDE0908:TDE0909:ABC transporter, ATP-binding/permease protein:type II DNA modification methyltransferase M.TdeIII:->->:927146..927305 160 ctggaacgggaagcaggaaagaggcgtggaggagtaaaggacggtaaaagggattttccggtatttcagcgactatcagggggcatagaaaaaaacagcggaatgtgatagaatagtacttgatgttgtggttactttaacggcaaaattgggagacact Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ctggaacgggaagcaggaaagaggcgtggaggagtaaaggacggtaaaagggattttccggtatttcagcgactatcagggggcatagaaaaaaacagcggaatgtgatagaatagtacttgatgttgtggttactttaacggcaaaattgggagacact Predict ORF larger than 30AA ================================================ Protein_Len: 35 Strand: + Start: 1 End: 105 M E R E A G K R R G G V K D G K R D F P V F Q R L S G G I E K N S G M ....................................................... Protein_Len: 41 Strand: - Start: 2 End: 124 . P V P L L F S A H L L L P R Y F P N E P I E A V I L P C L F F C R F T I S Y Y K M .................................... ctggaacgggaagcaggaaagaggcgtggaggagtaaaggacggtaaaagggattttccggtatttcagcgactatcagggggcatagaaaaaaacagcggaatgtgatagaatagtacttgatgttgtggttactttaacggcaaaattgggagacact 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================================================ ctggaacgggaagcaggaaagaggcgtggaggagtaaaggacggtaaaagggattttccggtatttcagcgactatcagggggcatagaaaaaaacagcggaatgtgatagaatagtacttgatgttgtggttactttaacggcaaaattgggagacact Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 43 HP_score: -3.1 Tail_Score: -2.98493 Start: 42 End: 60 Full_Region: tagtcgctgaaatac cggaaaa tccct tttaccg tcctttactcctcca .........................................cggaaaatcccttttaccg.................................................................................................... Find igs database================================================ Query_seq: TDE0908:TDE0909|TDE0908:TDE0909:ABC transporter, ATP-binding/permease protein:type II DNA modification methyltransferase M.TdeIII:->->:927146..927305 160 ctggaacgggaagcaggaaagaggcgtggaggagtaaaggacggtaaaagggattttccggtatttcagcgactatcagggggcatagaaaaaaacagcggaatgtgatagaatagtacttgatgttgtggttactttaacggcaaaattgggagacact Intra-Species Hit: Count: 1 Min: 1 Max: 160 Len: 160 Subject: NC_002967_TDE0908_TDE0909|ABC transporter, ATP-binding/permease protein:type II DNA modification methyltransferase M.TdeIII|POSITIVE:POSITIVE|[927146,927305]|160 HSP 1 e-value: 2.0E-73 bit: 276.0 Len: 160 Query Start:1 Query End:160 Subject Strand: POSITIVE Subject Start: 1 Subject End: 160 ctggaacgggaagcaggaaagaggcgtggaggagtaaaggacggtaaaagggattttccggtatttcagcgactatcagggggcatagnnnnnnncagcggaatgtgatagaatagtacttgatgttgtggttactttaacggcaaaattgggagacact ctggaacgggaagcaggaaagaggcgtggaggagtaaaggacggtaaaagggattttccggtatttcagcgactatcagggggcatagaaaaaaacagcggaatgtgatagaatagtacttgatgttgtggttactttaacggcaaaattgggagacact Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUGGAACGGGAAGCAGGAAAGAGGCGUGGAGGAGUAAAGGACGGUAAAAGGGAUUUUCCGGUAUUUCAGCGACUAUCAGGGGGCAUAGAAAAAAACAGCGGAAUGUGAUAGAAUAGUACUUGAUGUUGUGGUUACUUUAACGGCAAAAUUGGGAGACACU ............((...((((..((.....((((((..(((..((.......))..)))..)))))).(((((.((((((..((.((.......(((......))).......)))).))))))))))).))..))))....)).......(....)... (-31.14) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGUGUCUCCCAAUUUUGCCGUUAAAGUAACCACAACAUCAAGUACUAUUCUAUCACAUUCCGCUGUUUUUUUCUAUGCCCCCUGAUAGUCGCUGAAAUACCGGAAAAUCCCUUUUACCGUCCUUUACUCCUCCACGCCUCUUUCCUGCUUCCCGUUCCAG .(((............((.((.((((........((.....))..............(((((.((((((...((((........)))).....)))))).))))).....)))).)).))............)))......................... (-14.35) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 337 44 1 190 141 NC_002967:TDE2516|5end_hypothetical_protein_2542021..2542251_POSITIVE 326 44 2 176 126 NC_002967:TDE1941|5end_hypothetical_protein_1959285..1959515_NEGATIVE 316 80 31 92 41 NC_002967:TDE0995|5end_hypothetical_protein_1022576..1022806_NEGATIVE 311 61 22 108 62 NC_002967:TDE0760|5end_hypothetical_protein_799436..799666_POSITIVE 310 45 1 201 150 NC_002967:TDE0213|5end_TPR_domain_protein_249460..249690_NEGATIVE 301 60 12 225 170 NC_002967:TDE2701|5end_hypothetical_protein_2745689..2745919_POSITIVE 301 58 13 89 48 NC_002967:TDE1644|5end_methionyl-tRNA_formyltransferase_1695546..1695776_NEGATIVE 299 90 42 220 180 NC_002967:TDE2475|5end_MATE_efflux_family_protein_2498521..2498751_NEGATIVE 299 49 1 66 19 NC_002967:TDE1510|5end_hypothetical_protein_1557180..1557410_POSITIVE 299 48 2 157 112 NC_002967:TDE1285|5end_flagellar_motor_switch_protein_FliG_,_putative_1320924..1321154_POSITIVE 297 45 7 224 177 NC_002967:TDE0765|5end_translation_elongation_factor_Tu_804732..804962_POSITIVE 296 48 1 64 22 NC_002967:TDE1244|5end_TPR_domain_protein_1275823..1276053_POSITIVE 295 45 5 134 95 NC_002967:TDE0998|5end_hypothetical_protein_1025202..1025432_POSITIVE 295 49 1 50 7 NC_002967:TDE0089|5end_transglutaminase-like_domain_protein_108554..108784_NEGATIVE 293 60 11 177 115 NC_002967:TDE1233|5end_hypothetical_protein_1267203..1267433_POSITIVE 291 50 1 165 110 NC_002967:TDE2715|5end_hypothetical_protein_2772668..2772898_POSITIVE 288 82 42 48 2 NC_002967:TDE1657|5end_transcription_antitermination_protein_NusB_1707640..1707870_NEGATIVE 284 90 42 214 166 NC_002967:TDE0438|5end_queuine_tRNA-ribosyltransferase_494811..495041_NEGATIVE 283 79 31 71 30 NC_002967:TDE0587|5end_hypothetical_protein_625749..625979_POSITIVE 281 46 11 186 153 NC_002967:TDE1730|5end_glycosyl_hydrolase,_family_2_1785545..1785775_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 328 60 11 69 22 NC_002967:TDE2293|3end_hypothetical_protein_2329325..2329475_NEGATIVE 306 59 13 67 19 NC_002967:TDE2075|3end_GGDEF_domain/EAL_domain_protein_2101504..2101654_NEGATIVE 301 58 13 92 51 NC_002967:TDE1645|3end_polypeptide_deformylase_1695543..1695693_NEGATIVE 300 60 15 44 2 NC_002967:TDE1892|3end_hypothetical_protein_1912237..1912387_POSITIVE 299 70 22 110 59 NC_002967:TDE1487|3end_conserved_hypothetical_protein_TIGR01033_1531528..1531678_POSITIVE 299 48 2 76 31 NC_002967:TDE1284|3end_methyl-accepting_chemotaxis_protein,_putative_1320923..1321073_POSITIVE 296 48 1 52 10 NC_002967:TDE1243|3end_hemolysin_C_1275891..1276041_POSITIVE 296 34 1 140 105 NC_002967:TDE0214|3end_hypothetical_protein_249505..249655_NEGATIVE 295 49 1 60 17 NC_002967:TDE0090|3end_hypothetical_protein_108544..108694_NEGATIVE 287 47 1 88 29 NC_002967:TDE0158|3end_hypothetical_protein_185724..185874_NEGATIVE 284 100 51 44 5 NC_002967:TDE1658|3end_basic_membrane_protein,_putative_1707655..1707805_NEGATIVE 284 60 15 140 93 NC_002967:TDE0848|3end_hypothetical_protein_871558..871708_POSITIVE 284 45 1 84 37 NC_002967:TDE0740|3end_hypothetical_protein_776204..776354_POSITIVE 280 70 27 87 45 NC_002967:TDE2422|3end_ribosomal_protein_L7/L12_2452911..2453061_NEGATIVE 277 46 2 79 16 NC_002967:TDE2773|3end_hypothetical_protein_2825823..2825973_NEGATIVE 275 84 42 66 24 NC_002967:TDE1623|3end_hypothetical_protein_1671018..1671168_NEGATIVE 273 84 41 44 3 NC_002967:TDE2086|3end_DnaJ_domain_protein_2115475..2115625_POSITIVE 273 41 2 52 15 NC_002967:TDE0669|3end_hypothetical_protein_706949..707099_NEGATIVE 273 99 58 119 76 NC_002967:TDE0141|3end_hypothetical_protein_164065..164215_POSITIVE 272 60 13 60 9 NC_002967:TDE1727|3end_hypothetical_protein_1780774..1780924_NEGATIVE