Origin IGS: aatatacattctccaaatatcatagaattttttatacagagcagatacgaatttacaaacagggagttatactacaccattttcttaaaaaaatcaacagcacaaaaacacagacaacaatacacatagttgacagttccattcctttagcctataataccgtcc .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 ggacggtattataggctaaaggaatggaactgtcaactatgtgtattgttgtctgtgtttttgtgctgttgatttttttaagaaaatggtgtagtataactccctgtttgtaaattcgtatctgctctgtataaaaaattctatgatatttggagaatgtatatt Mask Tandem Repeat Region ================================================ aatatacattctccaaatatcatagaattttttatacagagcagatacgaatttacaaacagggagttatactacaccattttcttaaaaaaatcaacagcacaaaaacacagacaacaatacacatagttgacagttccattcctttagcctataataccgtcc Find is-nt database================================================ Query_seq: TDE2546:TDE2547|TDE2546:TDE2547:hypothetical protein:hypothetical protein:<-->:2572852..2573016 165 aatatacattctccaaatatcatagaattttttatacagagcagatacgaatttacaaacagggagttatactacaccattttcttaaaaaaatcaacagcacaaaaacacagacaacaatacacatagttgacagttccattcctttagcctataataccgtcc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE2546:TDE2547|TDE2546:TDE2547:hypothetical protein:hypothetical protein:<-->:2572852..2573016 165 aatatacattctccaaatatcatagaattttttatacagagcagatacgaatttacaaacagggagttatactacaccattttcttaaaaaaatcaacagcacaaaaacacagacaacaatacacatagttgacagttccattcctttagcctataataccgtcc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE2546:TDE2547|TDE2546:TDE2547:hypothetical protein:hypothetical protein:<-->:2572852..2573016 165 aatatacattctccaaatatcatagaattttttatacagagcagatacgaatttacaaacagggagttatactacaccattttcttaaaaaaatcaacagcacaaaaacacagacaacaatacacatagttgacagttccattcctttagcctataataccgtcc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aatatacattctccaaatatcatagaattttttatacagagcagatacgaatttacaaacagggagttatactacaccattttcttaaaaaaatcaacagcacaaaaacacagacaacaatacacatagttgacagttccattcctttagcctataataccgtcc Predict ORF larger than 30AA ================================================ Protein_Len: 41 Strand: + Start: 4 End: 126 ... M H S P N I I E F F I Q S R Y E F T N R E L Y Y T I F L K K S T A Q K H R Q Q Y T ....................................... Protein_Len: 46 Strand: + Start: 27 End: 164 .......................... M F Y T E Q I R I Y K Q G V I L H H F L K K I N S T K T Q T T I H I V D S S I P L A Y N T V . aatatacattctccaaatatcatagaattttttatacagagcagatacgaatttacaaacagggagttatactacaccattttcttaaaaaaatcaacagcacaaaaacacagacaacaatacacatagttgacagttccattcctttagcctataataccgtcc 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: 94 Start: 129 End: 158 ................................................................................................................................GTTGACAGTTCCATTCCTTTAGCCTATAAT....... PromScan Matrix: RpoD-17 Strand: - Score: 81 Start: 69 End: 98 ....................................................................GTTGATTTTTTTAAGAAAATGGTGTAGTAT................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aatatacattctccaaatatcatagaattttttatacagagcagatacgaatttacaaacagggagttatactacaccattttcttaaaaaaatcaacagcacaaaaacacagacaacaatacacatagttgacagttccattcctttagcctataataccgtcc Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE2546:TDE2547|TDE2546:TDE2547:hypothetical protein:hypothetical protein:<-->:2572852..2573016 165 aatatacattctccaaatatcatagaattttttatacagagcagatacgaatttacaaacagggagttatactacaccattttcttaaaaaaatcaacagcacaaaaacacagacaacaatacacatagttgacagttccattcctttagcctataataccgtcc Intra-Species Hit: Count: 1 Min: 1 Max: 165 Len: 165 Subject: NC_002967_TDE2546_TDE2547|hypothetical protein:hypothetical protein|NEGATIVE:POSITIVE|[2572852,2573016]|165 HSP 1 e-value: 2.0E-76 bit: 285.0 Len: 165 Query Start:1 Query End:165 Subject Strand: POSITIVE Subject Start: 1 Subject End: 165 aatatacattctccaaatatcatagaattttttatacagagcagatacgaatttacaaacagggagttatactacaccattttcttnnnnnnntcaacagcacaaaaacacagacaacaatacacatagttgacagttccattcctttagcctataataccgtcc aatatacattctccaaatatcatagaattttttatacagagcagatacgaatttacaaacagggagttatactacaccattttcttaaaaaaatcaacagcacaaaaacacagacaacaatacacatagttgacagttccattcctttagcctataataccgtcc Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUAUACAUUCUCCAAAUAUCAUAGAAUUUUUUAUACAGAGCAGAUACGAAUUUACAAACAGGGAGUUAUACUACACCAUUUUCUUAAAAAAAUCAACAGCACAAAAACACAGACAACAAUACACAUAGUUGACAGUUCCAUUCCUUUAGCCUAUAAUACCGUCC .................(((.((((...............(.((((....)))).)....(((((((...(((.....(((((......)))))....................((((..........))))..)))...)))))))....)))).)))...... ( -9.10) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GGACGGUAUUAUAGGCUAAAGGAAUGGAACUGUCAACUAUGUGUAUUGUUGUCUGUGUUUUUGUGCUGUUGAUUUUUUUAAGAAAAUGGUGUAGUAUAACUCCCUGUUUGUAAAUUCGUAUCUGCUCUGUAUAAAAAAUUCUAUGAUAUUUGGAGAAUGUAUAUU .(((((((((((((.....((........)).....))))).)))))))).......(((((((((.((.(((...((((...((((((.(.((.....)).))))))).)))).....))).))...))))))))).(((((.......))))).......... (-25.10) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 817 80 31 171 122 NC_002967:TDE2546|5end_hypothetical_protein_2572761..2572991_NEGATIVE 224 153 125 165 132 NC_002967:TDE0248|5end_hypothetical_protein_282068..282298_POSITIVE 216 75 32 224 183 NC_002967:TDE0048|5end_hypothetical_protein_57822..58052_NEGATIVE 214 147 120 100 66 NC_002967:TDE0847|5end_hypothetical_protein_870894..871124_POSITIVE 207 70 22 61 10 NC_002967:TDE2670|5end_glycosyl_transferase,_group_4_family_protein_2708034..2708264_NEGATIVE 205 148 118 197 164 NC_002967:TDE1856|5end_radical_SAM_domain_protein_1883133..1883363_POSITIVE 199 78 33 70 31 NC_002967:TDE2419|5end_hypothetical_protein_2444769..2444999_NEGATIVE 198 140 100 65 26 NC_002967:TDE2629|5end_peptide_ABC_transporter,_periplasmic_peptide-binding_protein,_putative_2669329..2669559_POSITIVE 195 152 124 71 39 NC_002967:TDE0152|5end_amino_acid_permease_family_protein_174477..174707_NEGATIVE 194 66 28 224 182 NC_002967:TDE0448|5end_deoxyribose-phosphate_aldolase_505796..506026_POSITIVE 192 49 4 120 73 NC_002967:TDE2649|5end_ABC_transporter,_ATP-binding_protein_2688648..2688878_NEGATIVE 191 153 128 44 20 NC_002967:TDE0135|5end_pyridine_nucleotide-disulphide_oxidoreductase_family_protein_154927..155157_POSITIVE 190 78 34 225 178 NC_002967:TDE1386|5end_methyl-accepting_chemotaxis_protein_1424941..1425171_POSITIVE 188 76 38 198 156 NC_002967:TDE1787|5end_hypothetical_protein_1826635..1826865_NEGATIVE 188 80 36 59 13 NC_002967:TDE0537|5end_hypothetical_protein_579024..579254_POSITIVE 184 153 115 102 64 NC_002967:TDE0082|5end_transcriptional_regulator,_MerR_family_94251..94481_NEGATIVE 183 154 129 208 185 NC_002967:TDE0991|5end_ribosomal_protein_L28_1018065..1018295_NEGATIVE 181 80 37 71 38 NC_002967:TDE1639|5end_sporulation_related_repeat_protein_1689563..1689793_POSITIVE 181 153 112 83 51 NC_002967:TDE0759|5end_hypothetical_protein_799499..799729_NEGATIVE 181 130 94 47 15 NC_002967:TDE0252|5end_hypothetical_protein_286263..286493_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 201 64 31 78 49 NC_002967:TDE0459|3end_hypothetical_protein_515241..515391_POSITIVE 195 152 124 60 28 NC_002967:TDE0153|3end_coenzyme_A_disulfide_reductase,_putative_174488..174638_NEGATIVE 193 68 21 135 79 NC_002967:TDE2456|3end_hypothetical_protein_2484136..2484286_NEGATIVE 192 49 4 102 55 NC_002967:TDE2650|3end_transcriptional_regulator,_putative_2688666..2688816_NEGATIVE 191 153 128 47 23 NC_002967:TDE0134|3end_oxidoreductase,_FAD-dependent_155010..155160_POSITIVE 188 141 112 30 1 NC_002967:TDE1104|3end_tRNA_pseudouridine_synthase_B_1136713..1136863_NEGATIVE 184 153 115 99 61 NC_002967:TDE0083|3end_GTP-binding_protein_EngA_94254..94404_NEGATIVE 182 159 120 118 75 NC_002967:TDE0417|3end_hypothetical_protein_469489..469639_NEGATIVE 181 80 37 61 28 NC_002967:TDE1638|3end_dephospho-CoA_kinase,_putative_1689633..1689783_POSITIVE 180 153 130 97 64 NC_002967:TDE0475|3end_ABC_transporter,_ATP-binding_protein_531153..531303_NEGATIVE 179 45 6 53 2 NC_002967:TDE2298|3end_galactokinase,_putative_2337113..2337263_NEGATIVE 178 155 123 107 67 NC_002967:TDE0551|3end_hypothetical_protein_587743..587893_NEGATIVE 178 83 62 105 82 NC_002967:TDE0515|3end_hypothetical_protein_562770..562920_NEGATIVE 177 47 5 133 91 NC_002967:TDE1588|3end_tryptophanyl-tRNA_synthetase_1636966..1637116_POSITIVE 177 153 124 91 50 NC_002967:TDE0111|3end_hypothetical_protein_132114..132264_POSITIVE 176 77 38 106 56 NC_002967:TDE2141|3end_hypothetical_protein_2175583..2175733_NEGATIVE 176 73 38 97 64 NC_002967:TDE1284|3end_methyl-accepting_chemotaxis_protein,_putative_1320923..1321073_POSITIVE 176 150 111 108 73 NC_002967:TDE0738|3end_hypothetical_protein_775674..775824_NEGATIVE 176 149 108 109 73 NC_002967:TDE0260|3end_iron-sulfur_cluster-binding_protein_294725..294875_POSITIVE 174 156 118 65 28 NC_002967:TDE2472|3end_ISTde1,_transposase_2496226..2496376_POSITIVE