Origin IGS: gtgtttctcctttggagctaaaaagctcctgccttctctatttctcggaacagactacagcccatcaagccgactaggggctgatcttagaaccgtaaatcctcccggatatttaccgtaaaaaacggcatgaggctattatatagttttttgaagattttgtatagtgcttgacaagatttacctaaaagagttttatctaaaaacttgaaattcggcggtttttcgt .........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 acgaaaaaccgccgaatttcaagtttttagataaaactcttttaggtaaatcttgtcaagcactatacaaaatcttcaaaaaactatataatagcctcatgccgttttttacggtaaatatccgggaggatttacggttctaagatcagcccctagtcggcttgatgggctgtagtctgttccgagaaatagagaaggcaggagctttttagctccaaaggagaaacac Mask Tandem Repeat Region ================================================ gtgtttctcctttggagctaaaaagctcctgccttctctatttctcggaacagactacagcccatcaagccgactaggggctgatcttagaaccgtaaatcctcccggatatttaccgtaaaaaacggcatgaggctattatatagttttttgaagattttgtatagtgcttgacaagatttacctaaaagagttttatctaaaaacttgaaattcggcggtttttcgt Find is-nt database================================================ Query_seq: TDE2347:TDE2348|TDE2347:TDE2348:30S ribosomal protein S2:maf protein:<-<-:2384469..2384697 229 gtgtttctcctttggagctaaaaagctcctgccttctctatttctcggaacagactacagcccatcaagccgactaggggctgatcttagaaccgtaaatcctcccggatatttaccgtaaaaaacggcatgaggctattatatagttttttgaagattttgtatagtgcttgacaagatttacctaaaagagttttatctaaaaacttgaaattcggcggtttttcgt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE2347:TDE2348|TDE2347:TDE2348:30S ribosomal protein S2:maf protein:<-<-:2384469..2384697 229 gtgtttctcctttggagctaaaaagctcctgccttctctatttctcggaacagactacagcccatcaagccgactaggggctgatcttagaaccgtaaatcctcccggatatttaccgtaaaaaacggcatgaggctattatatagttttttgaagattttgtatagtgcttgacaagatttacctaaaagagttttatctaaaaacttgaaattcggcggtttttcgt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE2347:TDE2348|TDE2347:TDE2348:30S ribosomal protein S2:maf protein:<-<-:2384469..2384697 229 gtgtttctcctttggagctaaaaagctcctgccttctctatttctcggaacagactacagcccatcaagccgactaggggctgatcttagaaccgtaaatcctcccggatatttaccgtaaaaaacggcatgaggctattatatagttttttgaagattttgtatagtgcttgacaagatttacctaaaagagttttatctaaaaacttgaaattcggcggtttttcgt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gtgtttctcctttggagctaaaaagctcctgccttctctatttctcggaacagactacagcccatcaagccgactaggggctgatcttagaaccgtaaatcctcccggatatttaccgtaaaaaacggcatgaggctattatatagttttttgaagattttgtatagtgcttgacaagatttacctaaaagagttttatctaaaaacttgaaattcggcggtttttcgt Predict ORF larger than 30AA ================================================ Protein_Len: 30 Strand: + Start: 29 End: 118 ............................ M P S L F L G T D Y S P S S R L G A D L R T V N P P G Y L P ............................................................................................................... gtgtttctcctttggagctaaaaagctcctgccttctctatttctcggaacagactacagcccatcaagccgactaggggctgatcttagaaccgtaaatcctcccggatatttaccgtaaaaaacggcatgaggctattatatagttttttgaagattttgtatagtgcttgacaagatttacctaaaagagttttatctaaaaacttgaaattcggcggtttttcgt Predict Promoter with matrix: RpoD-15 score > 80================================================ Predict Promoter with matrix: RpoD-16 score > 80================================================ Predict Promoter with matrix: RpoD-17 score > 80================================================ PromScan Matrix: RpoD-17 Strand: - Score: 83 Start: 138 End: 167 .........................................................................................................................................CTATACAAAATCTTCAAAAAACTATATAAT.............................................................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ gtgtttctcctttggagctaaaaagctcctgccttctctatttctcggaacagactacagcccatcaagccgactaggggctgatcttagaaccgtaaatcctcccggatatttaccgtaaaaaacggcatgaggctattatatagttttttgaagattttgtatagtgcttgacaagatttacctaaaagagttttatctaaaaacttgaaattcggcggtttttcgt Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 74 HP_score: -4.0 Tail_Score: -5.08011 Start: 136 End: 146 Full_Region: AAAAACGGCATGAGG CTAT TAT ATAG TTTTTTGAAGATTTT .......................................................................................................................................CTATTATATAG................................................................................... Find igs database================================================ Query_seq: TDE2347:TDE2348|TDE2347:TDE2348:30S ribosomal protein S2:maf protein:<-<-:2384469..2384697 229 gtgtttctcctttggagctaaaaagctcctgccttctctatttctcggaacagactacagcccatcaagccgactaggggctgatcttagaaccgtaaatcctcccggatatttaccgtaaaaaacggcatgaggctattatatagttttttgaagattttgtatagtgcttgacaagatttacctaaaagagttttatctaaaaacttgaaattcggcggtttttcgt Intra-Species Hit: Count: 1 Min: 1 Max: 229 Len: 229 Subject: NC_002967_TDE2347_TDE2348|30S ribosomal protein S2:maf protein|NEGATIVE:NEGATIVE|[2384469,2384697]|229 HSP 1 e-value: 1.0E-127 bit: 454.0 Len: 229 Query Start:1 Query End:229 Subject Strand: POSITIVE Subject Start: 1 Subject End: 229 gtgtttctcctttggagctaaaaagctcctgccttctctatttctcggaacagactacagcccatcaagccgactaggggctgatcttagaaccgtaaatcctcccggatatttaccgtaaaaaacggcatgaggctattatatagttttttgaagattttgtatagtgcttgacaagatttacctaaaagagttttatctaaaaacttgaaattcggcggtttttcgt gtgtttctcctttggagctaaaaagctcctgccttctctatttctcggaacagactacagcccatcaagccgactaggggctgatcttagaaccgtaaatcctcccggatatttaccgtaaaaaacggcatgaggctattatatagttttttgaagattttgtatagtgcttgacaagatttacctaaaagagttttatctaaaaacttgaaattcggcggtttttcgt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GUGUUUCUCCUUUGGAGCUAAAAAGCUCCUGCCUUCUCUAUUUCUCGGAACAGACUACAGCCCAUCAAGCCGACUAGGGGCUGAUCUUAGAACCGUAAAUCCUCCCGGAUAUUUACCGUAAAAAACGGCAUGAGGCUAUUAUAUAGUUUUUUGAAGAUUUUGUAUAGUGCUUGACAAGAUUUACCUAAAAGAGUUUUAUCUAAAAACUUGAAAUUCGGCGGUUUUUCGU .((((((......((((((....)))))).(......)........)))))).....((((((.((.....))....)))))).....((((((((..((((....)))).....((((.....))))..(.((((.(((((((((..((.....))..))))))))))))).)................((((((((..........)))))))).)))))))).... (-51.40) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACGAAAAACCGCCGAAUUUCAAGUUUUUAGAUAAAACUCUUUUAGGUAAAUCUUGUCAAGCACUAUACAAAAUCUUCAAAAAACUAUAUAAUAGCCUCAUGCCGUUUUUUACGGUAAAUAUCCGGGAGGAUUUACGGUUCUAAGAUCAGCCCCUAGUCGGCUUGAUGGGCUGUAGUCUGUUCCGAGAAAUAGAGAAGGCAGGAGCUUUUUAGCUCCAAAGGAGAAACAC ..........((.......((((..((((..((((.....))))..)))).))))....))...........(((((................(((((.((((((.....))))))....((((((((((((.(((((((....(((((((.......))).)))))))))))))))).))))).))......).)))).((((((....))))))...)))))..... (-57.60) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 1041 110 61 201 152 NC_002967:TDE2347|5end_30S_ribosomal_protein_S2_2384378..2384608_NEGATIVE 354 87 41 132 86 NC_002967:TDE2491|5end_DNA_polymerase_domain_protein_2515499..2515729_NEGATIVE 353 137 92 155 103 NC_002967:TDE1314|5end_penicillin-binding_protein_1351174..1351404_POSITIVE 345 137 93 63 15 NC_002967:TDE0080|5end_betaine_aldehyde_dehydrogenase_92212..92442_NEGATIVE 326 48 2 219 175 NC_002967:TDE0898|5end_hypothetical_protein_915878..916108_POSITIVE 317 107 63 61 4 NC_002967:TDE2395|5end_Jag_protein,_putative_2423454..2423684_NEGATIVE 317 110 78 228 196 NC_002967:TDE2144|5end_hypothetical_protein_2181746..2181976_NEGATIVE 314 46 6 67 20 NC_002967:TDE1027|5end_ribonuclease_III_1057562..1057792_POSITIVE 312 119 71 64 25 NC_002967:TDE0708|5end_nitroreductase_family_protein_743900..744130_POSITIVE 308 108 62 141 88 NC_002967:TDE1312|5end_hypothetical_protein_1349088..1349318_POSITIVE 308 70 30 227 188 NC_002967:TDE0679|5end_aminotransferase,_class_V_716345..716575_POSITIVE 307 130 85 104 56 NC_002967:TDE2199|5end_racemase,_Asp/Glu/Hydantoin_family_2237150..2237380_NEGATIVE 305 72 31 230 182 NC_002967:TDE2056|5end_outer_membrane_hemin-binding_protein_A_2085070..2085300_NEGATIVE 304 98 58 189 133 NC_002967:TDE1887|5end_TPR_domain_protein_1909133..1909363_NEGATIVE 298 70 21 87 26 NC_002967:TDE0462|5end_metallo-beta-lactamase_family_protein_516987..517217_NEGATIVE 298 70 24 60 16 NC_002967:TDE0369|5end_type_I_restriction-modification_system,_M_subunit_420971..421201_NEGATIVE 296 120 74 153 107 NC_002967:TDE0797|5end_acylphosphatase_820859..821089_POSITIVE 295 90 44 161 110 NC_002967:TDE1794|5end_hypothetical_protein_1832958..1833188_NEGATIVE 294 109 67 59 33 NC_002967:TDE0682|5end_preprotein_translocase,_YajC_subunit_721078..721308_NEGATIVE 292 79 32 165 102 NC_002967:TDE1069|5end_oligopeptide/dipeptide_ABC_transporter,_permease_protein_1097699..1097929_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 354 87 41 122 76 NC_002967:TDE2492|3end_hypothetical_protein_2515509..2515659_NEGATIVE 344 80 31 76 39 NC_002967:TDE2558|3end_ABC_transporter,_ATP-binding/permease_protein_2583729..2583879_NEGATIVE 341 69 24 57 11 NC_002967:TDE2196|3end_hypothetical_protein_2231883..2232033_NEGATIVE 334 78 31 150 94 NC_002967:TDE2057|3end_hypothetical_protein_2085158..2085308_NEGATIVE 317 110 78 149 117 NC_002967:TDE2145|3end_hypothetical_protein_2181825..2181975_NEGATIVE 314 50 3 142 97 NC_002967:TDE2527|3end_hypothetical_protein_2555449..2555599_NEGATIVE 310 55 11 48 7 NC_002967:TDE1026|3end_acyl_carrier_protein_1057618..1057768_POSITIVE 304 46 5 136 84 NC_002967:TDE0475|3end_ABC_transporter,_ATP-binding_protein_531153..531303_NEGATIVE 297 89 59 87 49 NC_002967:TDE1958|3end_surface_protein,_putative_1972309..1972459_NEGATIVE 295 90 44 56 5 NC_002967:TDE1795|3end_funZ_protein,_putative_1833063..1833213_NEGATIVE 291 49 2 118 72 NC_002967:TDE1070|3end_oligopeptide/dipeptide_ABC_transporter,_permease_protein_1097700..1097850_NEGATIVE 289 54 14 60 19 NC_002967:TDE2763|3end_flagellar_motor_switch_protein_2817737..2817887_NEGATIVE 287 48 3 76 23 NC_002967:TDE2269|3end_hypothetical_protein_2304931..2305081_NEGATIVE 287 130 81 82 23 NC_002967:TDE1633|3end_citrate_lyase_acyl_carrier_protein_1682428..1682578_NEGATIVE 287 118 74 97 42 NC_002967:TDE0479|3end_hydroxylamine_reductase_535029..535179_NEGATIVE 283 105 68 144 95 NC_002967:TDE2074|3end_radical_SAM_enzyme,_Cfr_family_2101537..2101687_POSITIVE 282 97 59 102 58 NC_002967:TDE0352|3end_ribose_5-phosphate_isomerase_B_396739..396889_POSITIVE 280 48 14 67 29 NC_002967:TDE0239|3end_glycine_reductase_complex_protein_GrdD_271828..271978_NEGATIVE 279 50 1 61 10 NC_002967:TDE2207|3end_hypothetical_protein_2245366..2245516_NEGATIVE 278 96 57 62 27 NC_002967:TDE0985|3end_oligopeptide/dipeptide_ABC_transporter,_periplasmic_peptide-binding_protein,_putative_1013054..1013204_POSITIVE