Origin IGS: caattatattgtatgtattatttgaaagatttactactttttataaaactataatttttcgatttcggaaagccatgttaccccttcttaattaaagccatatccggtttttccattttcatacgt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 acgtatgaaaatggaaaaaccggatatggctttaattaagaaggggtaacatggctttccgaaatcgaaaaattatagttttataaaaagtagtaaatctttcaaataatacatacaatataattg Mask Tandem Repeat Region ================================================ caattatattgtatgtattatttgaaagatttactactttttataaaactataatttttcgatttcggaaagccatgttaccccttcttaattaaagccatatccggtttttccattttcatacgt Find is-nt database================================================ Query_seq: TDE0973:TDE0974|TDE0973:TDE0974:DNA repair protein RadC:hypothetical protein:<-->:998708..998833 126 caattatattgtatgtattatttgaaagatttactactttttataaaactataatttttcgatttcggaaagccatgttaccccttcttaattaaagccatatccggtttttccattttcatacgt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE0973:TDE0974|TDE0973:TDE0974:DNA repair protein RadC:hypothetical protein:<-->:998708..998833 126 caattatattgtatgtattatttgaaagatttactactttttataaaactataatttttcgatttcggaaagccatgttaccccttcttaattaaagccatatccggtttttccattttcatacgt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE0973:TDE0974|TDE0973:TDE0974:DNA repair protein RadC:hypothetical protein:<-->:998708..998833 126 caattatattgtatgtattatttgaaagatttactactttttataaaactataatttttcgatttcggaaagccatgttaccccttcttaattaaagccatatccggtttttccattttcatacgt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 caattatattgtatgtattatttgaaagatttactactttttataaaactataatttttcgatttcggaaagccatgttaccccttcttaattaaagccatatccggtttttccattttcatacgt Predict ORF larger than 30AA ================================================ Protein_Len: 30 Strand: + Start: 3 End: 92 .. M I L Y V L F E R F T T F Y K T I I F R F R K A M L P L L N .................................. caattatattgtatgtattatttgaaagatttactactttttataaaactataatttttcgatttcggaaagccatgttaccccttcttaattaaagccatatccggtttttccattttcatacgt 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================================================ caattatattgtatgtattatttgaaagatttactactttttataaaactataatttttcgatttcggaaagccatgttaccccttcttaattaaagccatatccggtttttccattttcatacgt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE0973:TDE0974|TDE0973:TDE0974:DNA repair protein RadC:hypothetical protein:<-->:998708..998833 126 caattatattgtatgtattatttgaaagatttactactttttataaaactataatttttcgatttcggaaagccatgttaccccttcttaattaaagccatatccggtttttccattttcatacgt Intra-Species Hit: Count: 1 Min: 1 Max: 126 Len: 126 Subject: NC_002967_TDE0973_TDE0974|DNA repair protein RadC:hypothetical protein|NEGATIVE:POSITIVE|[998708,998833]|126 HSP 1 e-value: 9.0E-66 bit: 250.0 Len: 126 Query Start:1 Query End:126 Subject Strand: POSITIVE Subject Start: 1 Subject End: 126 caattatattgtatgtattatttgaaagatttactactttttataaaactataatttttcgatttcggaaagccatgttaccccttcttaattaaagccatatccggtttttccattttcatacgt caattatattgtatgtattatttgaaagatttactactttttataaaactataatttttcgatttcggaaagccatgttaccccttcttaattaaagccatatccggtttttccattttcatacgt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CAAUUAUAUUGUAUGUAUUAUUUGAAAGAUUUACUACUUUUUAUAAAACUAUAAUUUUUCGAUUUCGGAAAGCCAUGUUACCCCUUCUUAAUUAAAGCCAUAUCCGGUUUUUCCAUUUUCAUACGU ..........(((((......((((((((((.....................))))))))))....((((((((.........(((........)))........))))))))......))))).. (-15.23) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACGUAUGAAAAUGGAAAAACCGGAUAUGGCUUUAAUUAAGAAGGGGUAACAUGGCUUUCCGAAAUCGAAAAAUUAUAGUUUUAUAAAAAGUAGUAAAUCUUUCAAAUAAUACAUACAAUAUAAUUG ..(((((....((((((..(((..(((..((((......))))..)))...))).)))))).....((((..((((..((((....))))..))))...))))........))))).......... (-17.30) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 869 110 61 201 152 NC_002967:TDE0973|5end_DNA_repair_protein_RadC_998617..998847_NEGATIVE 276 107 64 97 47 NC_002967:TDE0099|5end_adenine-specific_DNA_modification_methyltransferase_115648..115878_POSITIVE 272 108 62 203 154 NC_002967:TDE1401|5end_DedA_family_protein_1442365..1442595_POSITIVE 266 99 55 213 163 NC_002967:TDE1299|5end_hypothetical_protein_1336613..1336843_NEGATIVE 260 117 81 140 100 NC_002967:TDE1201|5end_cell_cycle_protein,_FtsW/RodA/SpoVE_family_1233049..1233279_POSITIVE 259 110 63 80 25 NC_002967:TDE1000|5end_3-hydroxyacid_dehydrogenase_family_protein_1026763..1026993_POSITIVE 255 119 71 67 11 NC_002967:TDE2556|5end_hypothetical_protein_2583161..2583391_NEGATIVE 254 120 71 136 86 NC_002967:TDE0770|5end_50S_ribosomal_protein_L2_807952..808182_POSITIVE 250 111 72 65 24 NC_002967:TDE2746|5end_type_I_restriction-modification_system,_M_subunit_2802135..2802365_NEGATIVE 246 108 64 231 189 NC_002967:TDE0898|5end_hypothetical_protein_915878..916108_POSITIVE 246 107 65 125 84 NC_002967:TDE0003|5end_hypothetical_protein_3483..3713_POSITIVE 245 99 55 99 41 NC_002967:TDE2342|5end_1-deoxy-D-xylulose_5-phosphate_reductoisomerase_2380383..2380613_NEGATIVE 240 82 55 65 35 NC_002967:TDE0598|5end_3-oxoacyl-(acyl-carrier-protein)_reductase_638101..638331_NEGATIVE 239 110 63 224 182 NC_002967:TDE1058|5end_hypothetical_protein_1086366..1086596_NEGATIVE 237 112 71 137 85 NC_002967:TDE2461|5end_selenide,_water_dikinase_(selenocysteine-containing)_2488260..2488490_NEGATIVE 236 99 53 159 113 NC_002967:TDE0596|5end_hypothetical_protein_636010..636240_NEGATIVE 236 90 44 107 65 NC_002967:TDE0223|5end_hypothetical_protein_255904..256134_NEGATIVE 234 119 77 189 148 NC_002967:TDE2397|5end_hypothetical_protein_2425564..2425794_NEGATIVE 231 80 33 128 75 NC_002967:TDE0833|5end_lipoprotein,_putative_852992..853222_POSITIVE 226 112 81 112 80 NC_002967:TDE2761|5end_hypothetical_protein_2816537..2816767_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 260 117 81 139 99 NC_002967:TDE1200|3end_UDP-N-acetylmuramoylalanyl-D-glutamyl-2,_6-diaminopimelate--D-alanyl-D-alanyl_ligase_1233128..1233278_POSITIVE 255 98 55 144 97 NC_002967:TDE2196|3end_hypothetical_protein_2231883..2232033_NEGATIVE 254 120 71 102 52 NC_002967:TDE0769|3end_ribosomal_protein_L23_807998..808148_POSITIVE 250 111 72 62 21 NC_002967:TDE2747|3end_type_I_restriction-modification_system,_R_subunit_2802138..2802288_NEGATIVE 250 98 56 144 105 NC_002967:TDE2436|3end_hypothetical_protein_2467446..2467596_POSITIVE 248 80 46 128 88 NC_002967:TDE1906|3end_hypothetical_protein_1924727..1924877_POSITIVE 246 107 65 102 61 NC_002967:TDE0002|3end_DNA_gyrase,_B_subunit_3540..3690_POSITIVE 245 99 55 99 41 NC_002967:TDE2343|3end_phosphatidate_cytidylyltransferase_2380383..2380533_NEGATIVE 241 100 55 151 106 NC_002967:TDE0975|3end_hypothetical_protein_999879..1000029_POSITIVE 240 116 73 128 80 NC_002967:TDE0081|3end_hypothetical_protein_92553..92703_NEGATIVE 239 110 63 92 50 NC_002967:TDE1059|3end_hypothetical_protein_1086498..1086648_NEGATIVE 238 110 61 120 62 NC_002967:TDE1718|3end_GMP_synthase_1773811..1773961_POSITIVE 237 112 71 92 40 NC_002967:TDE2462|3end_hypothetical_protein_2488305..2488455_NEGATIVE 236 99 53 150 104 NC_002967:TDE0597|3end_hypothetical_protein_636019..636169_NEGATIVE 234 109 61 109 44 NC_002967:TDE0490|3end_hypothetical_protein_546272..546422_NEGATIVE 233 98 56 144 105 NC_002967:TDE2265|3end_hypothetical_protein_2302634..2302784_POSITIVE 231 120 76 56 4 NC_002967:TDE1877|3end_conserved_hypothetical_protein_TIGR00046_1897660..1897810_NEGATIVE 231 80 33 131 78 NC_002967:TDE0832|3end_hypothetical_protein_853075..853225_POSITIVE 228 99 53 64 24 NC_002967:TDE1052|3end_rubredoxin_1078712..1078862_NEGATIVE 226 112 81 86 54 NC_002967:TDE2762|3end_flagellar_motor_switch_protein_FliY_2816563..2816713_NEGATIVE