Origin IGS: taatcttatctttaaagcttaactgtagcatgggattcattttttttcaagcattttttcacaaaattccatatttttgtatatagtttcgccgattgacaaaggcttccataataaataaaattaaggccg .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 cggccttaattttatttattatggaagcctttgtcaatcggcgaaactatatacaaaaatatggaattttgtgaaaaaatgcttgaaaaaaaatgaatcccatgctacagttaagctttaaagataagatta Mask Tandem Repeat Region ================================================ taatcttatctttaaagcttaactgtagcatgggattcattttttttcaagcattttttcacaaaattccatatttttgtatatagtttcgccgattgacaaaggcttccataataaataaaattaaggccg Find is-nt database================================================ Query_seq: TDE0795:TDE0796|TDE0795:TDE0796:hypothetical protein:histidinol phosphate phosphatase HisJ family protein:<-->:820065..820196 132 taatcttatctttaaagcttaactgtagcatgggattcattttttttcaagcattttttcacaaaattccatatttttgtatatagtttcgccgattgacaaaggcttccataataaataaaattaaggccg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE0795:TDE0796|TDE0795:TDE0796:hypothetical protein:histidinol phosphate phosphatase HisJ family protein:<-->:820065..820196 132 taatcttatctttaaagcttaactgtagcatgggattcattttttttcaagcattttttcacaaaattccatatttttgtatatagtttcgccgattgacaaaggcttccataataaataaaattaaggccg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE0795:TDE0796|TDE0795:TDE0796:hypothetical protein:histidinol phosphate phosphatase HisJ family protein:<-->:820065..820196 132 taatcttatctttaaagcttaactgtagcatgggattcattttttttcaagcattttttcacaaaattccatatttttgtatatagtttcgccgattgacaaaggcttccataataaataaaattaaggccg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taatcttatctttaaagcttaactgtagcatgggattcattttttttcaagcattttttcacaaaattccatatttttgtatatagtttcgccgattgacaaaggcttccataataaataaaattaaggccg Predict ORF larger than 30AA ================================================ Protein_Len: 35 Strand: - Start: 15 End: 119 .............. L K V T A H S E N K K L C K K V F N W I K T Y L K A S Q C L S G Y Y M ............. taatcttatctttaaagcttaactgtagcatgggattcattttttttcaagcattttttcacaaaattccatatttttgtatatagtttcgccgattgacaaaggcttccataataaataaaattaaggccg 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: 88 Start: 95 End: 124 ..............................................................................................ATTGACAAAGGCTTCCATAATAAATAAAAT........ PromScan Matrix: RpoD-17 Strand: - Score: 83 Start: 22 End: 51 .....................CTTGAAAAAAAATGAATCCCATGCTACAGT................................................................................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ taatcttatctttaaagcttaactgtagcatgggattcattttttttcaagcattttttcacaaaattccatatttttgtatatagtttcgccgattgacaaaggcttccataataaataaaattaaggccg Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE0795:TDE0796|TDE0795:TDE0796:hypothetical protein:histidinol phosphate phosphatase HisJ family protein:<-->:820065..820196 132 taatcttatctttaaagcttaactgtagcatgggattcattttttttcaagcattttttcacaaaattccatatttttgtatatagtttcgccgattgacaaaggcttccataataaataaaattaaggccg Intra-Species Hit: Count: 1 Min: 1 Max: 132 Len: 132 Subject: NC_002967_TDE0795_TDE0796|hypothetical protein:histidinol phosphate phosphatase HisJ family protein|NEGATIVE:POSITIVE|[820065,820196]|132 HSP 1 e-value: 5.0E-55 bit: 214.0 Len: 132 Query Start:1 Query End:132 Subject Strand: POSITIVE Subject Start: 1 Subject End: 132 taatcttatctttaaagcttaactgtagcatgggattcannnnnnnncaagcattttttcacaaaattccatatttttgtatatagtttcgccgattgacaaaggcttccataataaataaaattaaggccg taatcttatctttaaagcttaactgtagcatgggattcattttttttcaagcattttttcacaaaattccatatttttgtatatagtttcgccgattgacaaaggcttccataataaataaaattaaggccg Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAUCUUAUCUUUAAAGCUUAACUGUAGCAUGGGAUUCAUUUUUUUUCAAGCAUUUUUUCACAAAAUUCCAUAUUUUUGUAUAUAGUUUCGCCGAUUGACAAAGGCUUCCAUAAUAAAUAAAAUUAAGGCCG ................((..(((((((((.((..(.........)..)).))........((((((........)))))).)))))))..))...........(((((...((((.......))))))))). (-19.30) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CGGCCUUAAUUUUAUUUAUUAUGGAAGCCUUUGUCAAUCGGCGAAACUAUAUACAAAAAUAUGGAAUUUUGUGAAAAAAUGCUUGAAAAAAAAUGAAUCCCAUGCUACAGUUAAGCUUUAAAGAUAAGAUUA ......(((((((((((.(((..(((...((((((....)))))).((((((......))))))..)))..)))......((((((......(((.....))).......)))))).....))))))))))) (-22.52) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 800 110 61 201 152 NC_002967:TDE0795|5end_hypothetical_protein_819974..820204_NEGATIVE 290 61 23 69 25 NC_002967:TDE2695|5end_transcript_cleavage_factor/unknown_domain_fusion_protein_2739079..2739309_NEGATIVE 284 110 74 127 78 NC_002967:TDE0040|5end_AMP-binding_protein_47428..47658_NEGATIVE 279 108 71 153 117 NC_002967:TDE0450|5end_hypothetical_protein_508529..508759_NEGATIVE 273 110 65 62 15 NC_002967:TDE2574|5end_conserved_hypothetical_protein_TIGR00650_2600376..2600606_POSITIVE 263 110 74 175 134 NC_002967:TDE2499|5end_hypothetical_protein_2523952..2524182_NEGATIVE 246 107 71 201 170 NC_002967:TDE2282|5end_tRNA_synthetase,_class_II_family_protein_2319665..2319895_NEGATIVE 244 94 54 139 102 NC_002967:TDE2305|5end_hypothetical_protein_2343652..2343882_POSITIVE 238 130 91 64 17 NC_002967:TDE2562|5end_cation_ABC_transporter,_permease_protein,_putative_2588899..2589129_POSITIVE 235 109 77 70 39 NC_002967:TDE1140|5end_hypothetical_protein_1169845..1170075_NEGATIVE 232 120 78 81 43 NC_002967:TDE0623|5end_precorrin-3B_C17-methyltransferase_655783..656013_POSITIVE 231 59 16 62 21 NC_002967:TDE2165|5end_hydrogenase_accessory_protein_HypB_2197715..2197945_NEGATIVE 231 106 67 43 8 NC_002967:TDE0551|5end_hypothetical_protein_588273..588503_NEGATIVE 230 60 11 172 115 NC_002967:TDE1713|5end_hypothetical_protein_1768468..1768698_NEGATIVE 229 54 23 160 129 NC_002967:TDE1581|5end_hypothetical_protein_1630246..1630476_NEGATIVE 229 97 51 133 102 NC_002967:TDE1056|5end_hypothetical_protein_1085210..1085440_POSITIVE 228 109 69 192 145 NC_002967:TDE2149|5end_transglycosylase,_SLT_family_2187293..2187523_NEGATIVE 226 99 68 164 127 NC_002967:TDE0826|5end_hypothetical_protein_847604..847834_POSITIVE 222 118 74 97 54 NC_002967:TDE2686|5end_flagellar_biosynthetic_protein_FlhF_2727125..2727355_NEGATIVE 220 110 68 83 29 NC_002967:TDE2637|5end_hypothetical_protein_2677316..2677546_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 290 61 23 50 6 NC_002967:TDE2696|3end_TPR_domain_protein_2739098..2739248_NEGATIVE 273 110 65 65 18 NC_002967:TDE2573|3end_glucose-6-phosphate_isomerase_2600459..2600609_POSITIVE 258 110 69 132 94 NC_002967:TDE2527|3end_hypothetical_protein_2555449..2555599_NEGATIVE 244 94 54 142 105 NC_002967:TDE2304|3end_hypothetical_protein_2343735..2343885_POSITIVE 238 130 91 62 15 NC_002967:TDE2561|3end_ABC_transporter,_ATP-binding_protein_2588977..2589127_POSITIVE 235 109 77 55 24 NC_002967:TDE1141|3end_tail_fiber_domain_protein_1169860..1170010_NEGATIVE 234 110 70 46 6 NC_002967:TDE2269|3end_hypothetical_protein_2304931..2305081_NEGATIVE 229 54 23 122 91 NC_002967:TDE1582|3end_glycogen_synthase_1630284..1630434_NEGATIVE 226 99 68 120 83 NC_002967:TDE0825|3end_UDP-N-acetylmuramoylalanyl-D-glutamate-2,_6-diaminopimelate_ligase,_putative_847640..847790_POSITIVE 225 110 66 73 23 NC_002967:TDE1585|3end_hypothetical_protein_1632932..1633082_NEGATIVE 220 117 90 32 8 NC_002967:TDE0388|3end_hypothetical_protein_440050..440200_POSITIVE 219 106 67 85 46 NC_002967:TDE2372|3end_hypothetical_protein_2405199..2405349_POSITIVE 218 108 68 59 16 NC_002967:TDE0745|3end_glycine_reductase_complex_selenoprotein_GrdA_780840..780990_POSITIVE 216 54 17 108 66 NC_002967:TDE0779|3end_ribosomal_protein_L5_812432..812582_POSITIVE 214 99 51 148 95 NC_002967:TDE2626|3end_ABC_transporter,_ATP-binding/permease_protein_2666657..2666807_NEGATIVE 214 110 64 90 31 NC_002967:TDE0192|3end_hypothetical_protein_227817..227967_NEGATIVE 212 117 74 116 73 NC_002967:TDE0209|3end_arsenical_pump_membrane_protein,_putative_245561..245711_POSITIVE 208 61 22 93 41 NC_002967:TDE1981|3end_hypothetical_protein_1992437..1992587_POSITIVE 204 130 91 61 15 NC_002967:TDE1990|3end_ATP-dependent_helicase,_DinG_family_2006367..2006517_NEGATIVE 204 111 86 52 23 NC_002967:TDE0995|3end_hypothetical_protein_1022442..1022592_NEGATIVE