Origin IGS: tttattgatttctgttttctcctttcaaaagaagcattttacttttcaaagaaagtctaaattcaaccgattctttgttctagccctaaagttatacatttcaattttttcaacaagctcaacttgctaaaaaaatcttcctttt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aaaaggaagatttttttagcaagttgagcttgttgaaaaaattgaaatgtataactttagggctagaacaaagaatcggttgaatttagactttctttgaaaagtaaaatgcttcttttgaaaggagaaaacagaaatcaataaa Mask Tandem Repeat Region ================================================ tttattgatttctgttttctcctttcaaaagaagcattttacttttcaaagaaagtctaaattcaaccgattctttgttctagccctaaagttatacatttcaattttttcaacaagctcaacttgctaaaaaaatcttcctttt Find is-nt database================================================ Query_seq: TDE1819:TDE1820|TDE1819:TDE1820:hypothetical protein:hypothetical protein:<-<-:1854242..1854386 145 tttattgatttctgttttctcctttcaaaagaagcattttacttttcaaagaaagtctaaattcaaccgattctttgttctagccctaaagttatacatttcaattttttcaacaagctcaacttgctaaaaaaatcttcctttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE1819:TDE1820|TDE1819:TDE1820:hypothetical protein:hypothetical protein:<-<-:1854242..1854386 145 tttattgatttctgttttctcctttcaaaagaagcattttacttttcaaagaaagtctaaattcaaccgattctttgttctagccctaaagttatacatttcaattttttcaacaagctcaacttgctaaaaaaatcttcctttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE1819:TDE1820|TDE1819:TDE1820:hypothetical protein:hypothetical protein:<-<-:1854242..1854386 145 tttattgatttctgttttctcctttcaaaagaagcattttacttttcaaagaaagtctaaattcaaccgattctttgttctagccctaaagttatacatttcaattttttcaacaagctcaacttgctaaaaaaatcttcctttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tttattgatttctgttttctcctttcaaaagaagcattttacttttcaaagaaagtctaaattcaaccgattctttgttctagccctaaagttatacatttcaattttttcaacaagctcaacttgctaaaaaaatcttcctttt Predict ORF larger than 30AA ================================================ Protein_Len: 41 Strand: + Start: 5 End: 127 .... M I S V F S F Q K K H F T F Q R K S K F N R F F V L A L K L Y I S I F S T S S T C .................. tttattgatttctgttttctcctttcaaaagaagcattttacttttcaaagaaagtctaaattcaaccgattctttgttctagccctaaagttatacatttcaattttttcaacaagctcaacttgctaaaaaaatcttcctttt 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================================================ tttattgatttctgttttctcctttcaaaagaagcattttacttttcaaagaaagtctaaattcaaccgattctttgttctagccctaaagttatacatttcaattttttcaacaagctcaacttgctaaaaaaatcttcctttt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE1819:TDE1820|TDE1819:TDE1820:hypothetical protein:hypothetical protein:<-<-:1854242..1854386 145 tttattgatttctgttttctcctttcaaaagaagcattttacttttcaaagaaagtctaaattcaaccgattctttgttctagccctaaagttatacatttcaattttttcaacaagctcaacttgctaaaaaaatcttcctttt Intra-Species Hit: Count: 1 Min: 1 Max: 128 Len: 128 Subject: NC_002967_TDE1819_TDE1820|hypothetical protein:hypothetical protein|NEGATIVE:NEGATIVE|[1854242,1854386]|145 HSP 1 e-value: 7.0E-67 bit: 254.0 Len: 128 Query Start:1 Query End:128 Subject Strand: POSITIVE Subject Start: 1 Subject End: 128 tttattgatttctgttttctcctttcaaaagaagcattttacttttcaaagaaagtctaaattcaaccgattctttgttctagccctaaagttatacatttcaattttttcaacaagctcaacttgct................. tttattgatttctgttttctcctttcaaaagaagcattttacttttcaaagaaagtctaaattcaaccgattctttgttctagccctaaagttatacatttcaattttttcaacaagctcaacttgct................. Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUAUUGAUUUCUGUUUUCUCCUUUCAAAAGAAGCAUUUUACUUUUCAAAGAAAGUCUAAAUUCAACCGAUUCUUUGUUCUAGCCCUAAAGUUAUACAUUUCAAUUUUUUCAACAAGCUCAACUUGCU ...(((((....((((((............)))))).....((...((((((..(((...........)))))))))....)).................)))))........((((.....)))).. ( -8.80) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGCAAGUUGAGCUUGUUGAAAAAAUUGAAAUGUAUAACUUUAGGGCUAGAACAAAGAAUCGGUUGAAUUUAGACUUUCUUUGAAAAGUAAAAUGCUUCUUUUGAAAGGAGAAAACAGAAAUCAAUAAA ((((((.....))))))......(((((..(((...........(((....(((((((..((((.......)))))))))))...)))......((((((....))))))...)))....)))))... (-20.60) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 778 100 51 191 142 NC_002967:TDE1819|5end_hypothetical_protein_1854151..1854381_NEGATIVE 290 110 71 150 115 NC_002967:TDE1772|5end_hypothetical_protein_1815817..1816047_NEGATIVE 232 60 13 67 22 NC_002967:TDE1180|5end_iron_compound_ABC_transporter,_periplasmic_iron_compound-binding_protein_1209833..1210063_NEGATIVE 225 120 77 99 57 NC_002967:TDE1660|5end_leucine_Rich_Repeat_domain_protein_1715266..1715496_NEGATIVE 221 108 64 103 46 NC_002967:TDE2240|5end_hypothetical_protein_2278422..2278652_NEGATIVE 221 108 64 178 121 NC_002967:TDE2102|5end_hypothetical_protein_2127347..2127577_NEGATIVE 220 120 81 118 72 NC_002967:TDE1086|5end_conserved_hypothetical_protein_TIGR00255_1117786..1118016_POSITIVE 216 95 51 52 3 NC_002967:TDE1880|5end_hypothetical_protein_1902535..1902765_POSITIVE 211 87 43 97 45 NC_002967:TDE2402|5end_radical_SAM_domain_protein_2427691..2427921_POSITIVE 207 77 38 151 107 NC_002967:TDE2092|5end_amino_acid_ABC_transporter,_amino_acid-binding_protein,_putative_2119563..2119793_POSITIVE 206 119 71 227 182 NC_002967:TDE1389|5end_hypothetical_protein_1428238..1428468_POSITIVE 206 37 5 36 1 NC_002967:TDE0322|5end_regulatory_protein,_P-II_family_355405..355635_NEGATIVE 206 81 42 207 158 NC_002967:TDE0318|5end_hypothetical_protein_351082..351312_POSITIVE 204 48 5 103 57 NC_002967:TDE0806|5end_hypothetical_protein_828888..829118_NEGATIVE 202 85 43 49 12 NC_002967:TDE2043|5end_signal_recognition_particle-docking_protein_FtsY_2073058..2073288_NEGATIVE 201 77 33 167 129 NC_002967:TDE1241|5end_HD_domain_protein_1272269..1272499_POSITIVE 201 97 55 123 92 NC_002967:TDE0768|5end_50S_ribosomal_protein_L4_806996..807226_POSITIVE 200 85 54 193 168 NC_002967:TDE0691|5end_ABC_transporter,_ATP-binding/permease_protein_728062..728292_POSITIVE 197 87 43 51 3 NC_002967:TDE2354|5end_hypothetical_protein_2390395..2390625_POSITIVE 196 93 65 135 110 NC_002967:TDE1291|5end_HD_domain_protein_1329213..1329443_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 256 115 71 148 101 NC_002967:TDE0670|3end_ATP-dependent_protease_La_710393..710543_POSITIVE 255 119 78 98 61 NC_002967:TDE1569|3end_hypothetical_protein_1619975..1620125_POSITIVE 236 96 65 83 53 NC_002967:TDE1791|3end_hypothetical_protein_1828308..1828458_NEGATIVE 230 87 43 85 37 NC_002967:TDE2272|3end_hypothetical_protein_2308980..2309130_NEGATIVE 220 120 81 102 56 NC_002967:TDE1085|3end_UDP-N-acetylmuramate--L-alanine_ligase_1117850..1118000_POSITIVE 207 77 38 134 90 NC_002967:TDE2091|3end_amino_acid_ABC_transporter,_amino_acid-binding_protein,_putative_2119626..2119776_POSITIVE 204 48 5 68 22 NC_002967:TDE0807|3end_hypothetical_protein_828923..829073_NEGATIVE 204 120 71 126 87 NC_002967:TDE0292|3end_hypothetical_protein_321175..321325_NEGATIVE 202 85 43 59 22 NC_002967:TDE2044|3end_lipoprotein,_putative_2073048..2073198_NEGATIVE 201 97 55 108 77 NC_002967:TDE0767|3end_ribosomal_protein_L3_807061..807211_POSITIVE 200 103 63 48 7 NC_002967:TDE1093|3end_hypothetical_protein_1128158..1128308_POSITIVE 200 85 54 129 104 NC_002967:TDE0690|3end_tRNA_(5-methylaminomethyl-2-thiouridylate)-methyltransferase_728078..728228_POSITIVE 200 105 76 147 115 NC_002967:TDE0320|3end_CBS_domain_protein_352480..352630_NEGATIVE 197 87 54 87 61 NC_002967:TDE0162|3end_hypothetical_protein_192882..193032_POSITIVE 196 93 65 34 9 NC_002967:TDE1292|3end_TldD/PmbA_family_protein_1329314..1329464_NEGATIVE 195 93 53 57 9 NC_002967:TDE2401|3end_hypothetical_protein_2427722..2427872_POSITIVE 193 87 41 88 34 NC_002967:TDE2298|3end_galactokinase,_putative_2337113..2337263_NEGATIVE 193 34 2 147 102 NC_002967:TDE1223|3end_zinc_ABC_transporter,_permease_protein_1256735..1256885_NEGATIVE 190 90 42 130 82 NC_002967:TDE0620|3end_hypothetical_protein_653373..653523_POSITIVE 190 57 11 137 98 NC_002967:TDE0177|3end_hypothetical_protein_209791..209941_NEGATIVE