Origin IGS: tgacagcgaaattttttaactcccaaaagagattctcgtcaaagagttgtgtcgcatcttgcaaaaagcaacatcagtttatagcgtagtagcggcagaaatattcctgcacgataaacaaagtca .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tgactttgtttatcgtgcaggaatatttctgccgctactacgctataaactgatgttgctttttgcaagatgcgacacaactctttgacgagaatctcttttgggagttaaaaaatttcgctgtca Mask Tandem Repeat Region ================================================ tgacagcgaaattttttaactcccaaaagagattctcgtcaaagagttgtgtcgcatcttgcaaaaagcaacatcagtttatagcgtagtagcggcagaaatattcctgcacgataaacaaagtca Find is-nt database================================================ Query_seq: TF1552:TF1553|TF1552:TF1553:conserved hypothetical protein:copper homeostasis protein:->->:1658887..1659012 126 tgacagcgaaattttttaactcccaaaagagattctcgtcaaagagttgtgtcgcatcttgcaaaaagcaacatcagtttatagcgtagtagcggcagaaatattcctgcacgataaacaaagtca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF1552:TF1553|TF1552:TF1553:conserved hypothetical protein:copper homeostasis protein:->->:1658887..1659012 126 tgacagcgaaattttttaactcccaaaagagattctcgtcaaagagttgtgtcgcatcttgcaaaaagcaacatcagtttatagcgtagtagcggcagaaatattcctgcacgataaacaaagtca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF1552:TF1553|TF1552:TF1553:conserved hypothetical protein:copper homeostasis protein:->->:1658887..1659012 126 tgacagcgaaattttttaactcccaaaagagattctcgtcaaagagttgtgtcgcatcttgcaaaaagcaacatcagtttatagcgtagtagcggcagaaatattcctgcacgataaacaaagtca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tgacagcgaaattttttaactcccaaaagagattctcgtcaaagagttgtgtcgcatcttgcaaaaagcaacatcagtttatagcgtagtagcggcagaaatattcctgcacgataaacaaagtca Predict ORF larger than 30AA ================================================ Protein_Len: 31 Strand: + Start: 32 End: 124 ............................... M L V K E L C R I L Q K A T S V Y S V V A A E I F L H D K Q S .. tgacagcgaaattttttaactcccaaaagagattctcgtcaaagagttgtgtcgcatcttgcaaaaagcaacatcagtttatagcgtagtagcggcagaaatattcctgcacgataaacaaagtca 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================================================ tgacagcgaaattttttaactcccaaaagagattctcgtcaaagagttgtgtcgcatcttgcaaaaagcaacatcagtttatagcgtagtagcggcagaaatattcctgcacgataaacaaagtca Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TF1552:TF1553|TF1552:TF1553:conserved hypothetical protein:copper homeostasis protein:->->:1658887..1659012 126 tgacagcgaaattttttaactcccaaaagagattctcgtcaaagagttgtgtcgcatcttgcaaaaagcaacatcagtttatagcgtagtagcggcagaaatattcctgcacgataaacaaagtca Intra-Species Hit: Count: 1 Min: 1 Max: 126 Len: 126 Subject: tfor_TF1552_TF1553|conserved hypothetical protein:copper homeostasis protein|POSITIVE:POSITIVE|[1658887,1659012]|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 tgacagcgaaattttttaactcccaaaagagattctcgtcaaagagttgtgtcgcatcttgcaaaaagcaacatcagtttatagcgtagtagcggcagaaatattcctgcacgataaacaaagtca tgacagcgaaattttttaactcccaaaagagattctcgtcaaagagttgtgtcgcatcttgcaaaaagcaacatcagtttatagcgtagtagcggcagaaatattcctgcacgataaacaaagtca Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGACAGCGAAAUUUUUUAACUCCCAAAAGAGAUUCUCGUCAAAGAGUUGUGUCGCAUCUUGCAAAAAGCAACAUCAGUUUAUAGCGUAGUAGCGGCAGAAAUAUUCCUGCACGAUAAACAAAGUCA .(((.((((.......((((((......(((...)))......))))))..))))...((((.....)))).....((((((.((......)).((((........))))...))))))...))). (-28.20) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGACUUUGUUUAUCGUGCAGGAAUAUUUCUGCCGCUACUACGCUAUAAACUGAUGUUGCUUUUUGCAAGAUGCGACACAACUCUUUGACGAGAAUCUCUUUUGGGAGUUAAAAAAUUUCGCUGUCA .(((...((((((((.((((((....))))))))..........))))))..((.((((.....)))).))((((...((((((..((.(((...))).))..))))))........)))).))). (-26.60) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 304 116 92 82 59 tfor:TF0090|5end_conserved_hypothetical_protein_96285..96515_POSITIVE 298 80 31 136 75 tfor:TF1576|5end_hypothetical_protein_1685852..1686082_POSITIVE 293 100 52 66 28 tfor:TF2962|5end_integrase/recombinase_3173659..3173889_POSITIVE 292 91 53 142 108 tfor:TF0704|5end_TPR-repeat-containing_protein_747888..748118_POSITIVE 291 108 71 41 1 tfor:TF2978|5end_conserved_hypothetical_protein_3186076..3186306_POSITIVE 289 80 34 192 141 tfor:TF1800|5end_conserved_hypothetical_protein_1941214..1941444_POSITIVE 287 94 51 158 118 tfor:TF2081|5end_phosphopantetheine_adenylyltransferase_2248475..2248705_POSITIVE 282 70 28 153 95 tfor:TF2141|5end_conserved_hypothetical_protein_2316677..2316907_POSITIVE 278 96 51 105 74 tfor:TF1257|5end_hypothetical_protein_1338118..1338348_POSITIVE 278 96 51 70 39 tfor:TF1256|5end_hypothetical_protein_1338083..1338313_POSITIVE 278 70 27 152 107 tfor:TF0931|5end_superfamily_II_DNA/RNA_helicase,_SNF2_family_970031..970261_POSITIVE 276 87 44 67 29 tfor:TF2753|5end_zinc_protease_2937543..2937773_POSITIVE 275 50 1 162 118 tfor:TF1116|5end_conserved_hypothetical_protein_1186491..1186721_POSITIVE 275 79 36 77 30 tfor:TF0263|5end_ISPg3_(IS195)_transposase_292179..292409_POSITIVE 274 100 51 184 129 tfor:TF0969|5end_oxidoreductase_1019550..1019780_POSITIVE 274 99 51 44 6 tfor:TF0826|5end_primosomal_protein_N'_883751..883981_POSITIVE 271 100 51 231 177 tfor:TF0100|5end_conserved_hypothetical_protein_111135..111365_POSITIVE 268 94 52 53 15 tfor:TF0858|5end_conserved_hypothetical_protein_910326..910556_POSITIVE 266 112 75 168 142 tfor:TF2402|5end_outer_membrane_protein,_possibly_involved_in_nutrient_binding_2574582..2574812_POSITIVE 265 99 51 178 108 tfor:TF2272|5end_conserved_hypothetical_protein_2436156..2436386_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 298 80 31 99 38 tfor:TF1575|3end_DNA-binding_response_regulator_1685895..1686045_POSITIVE 292 91 53 129 95 tfor:TF0703|3end_conserved_hypothetical_protein_747955..748105_POSITIVE 282 70 28 135 77 tfor:TF2140|3end_hypothetical_protein_2316739..2316889_POSITIVE 278 96 51 58 27 tfor:TF1255|3end_conserved_hypothetical_protein_1338151..1338301_POSITIVE 275 50 1 135 91 tfor:TF1115|3end_lantibiotic_biosynthesis_protein_1186544..1186694_POSITIVE 274 99 51 63 25 tfor:TF0825|3end_hypothetical_protein_883850..884000_POSITIVE 271 100 51 140 86 tfor:TF0099|3end_glycosyltransferase_of_PMT_family_111124..111274_POSITIVE 265 99 51 129 59 tfor:TF2271|3end_conserved_hypothetical_protein_2436187..2436337_POSITIVE 265 120 83 51 13 tfor:TF1160|3end_MutT/nudix_family_protein_1241008..1241158_POSITIVE 262 96 51 59 12 tfor:TF1807|3end_thioesterase_family_protein_1949425..1949575_POSITIVE 261 96 51 86 37 tfor:TF3153|3end_conserved_hypothetical_protein_3389324..3389474_POSITIVE 259 68 22 56 11 tfor:TF2703|3end_conserved_hypothetical_protein_2876317..2876467_POSITIVE 259 89 43 59 13 tfor:TF1928|3end_conserved_hypothetical_protein_2076124..2076274_POSITIVE 255 110 65 131 76 tfor:TF0165|3end_conserved_hypothetical_protein_175821..175971_POSITIVE 252 97 55 139 96 tfor:TF1786|3end_hypothetical_protein_1926425..1926575_POSITIVE 251 65 21 150 103 tfor:TF3050|3end_conserved_hypothetical_protein_3277708..3277858_POSITIVE 249 115 83 145 111 tfor:TF0636|3end_beta-galactosidase_673284..673434_POSITIVE 248 70 22 61 10 tfor:TF2978|3end_conserved_hypothetical_protein_3190862..3191012_POSITIVE 247 60 35 24 1 tfor:TF2112|3end_glycine_cleavage_H_protein_2282573..2282723_POSITIVE 246 100 54 50 1 tfor:TF1643|3end_conserved_hypothetical_protein_1752718..1752868_POSITIVE