Origin IGS: acgtaaaacaatctattcgggggacaaagataagaaagttcggccattaaccattggtcaatgacaatttttcttacctttgcgccctgaaatcagctttagacgatt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aatcgtctaaagctgatttcagggcgcaaaggtaagaaaaattgtcattgaccaatggttaatggccgaactttcttatctttgtcccccgaatagattgttttacgt Mask Tandem Repeat Region ================================================ acgtaaaacaatctattcgggggacaaagataagaaagttcggccattaaccattggtcaatgacaatttttcttacctttgcgccctgaaatcagctttagacgatt Find is-nt database================================================ Query_seq: TF1455:TF1456|TF1455:TF1456:conserved hypothetical protein:GMP synthase:->->:1541722..1541829 108 acgtaaaacaatctattcgggggacaaagataagaaagttcggccattaaccattggtcaatgacaatttttcttacctttgcgccctgaaatcagctttagacgatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF1455:TF1456|TF1455:TF1456:conserved hypothetical protein:GMP synthase:->->:1541722..1541829 108 acgtaaaacaatctattcgggggacaaagataagaaagttcggccattaaccattggtcaatgacaatttttcttacctttgcgccctgaaatcagctttagacgatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF1455:TF1456|TF1455:TF1456:conserved hypothetical protein:GMP synthase:->->:1541722..1541829 108 acgtaaaacaatctattcgggggacaaagataagaaagttcggccattaaccattggtcaatgacaatttttcttacctttgcgccctgaaatcagctttagacgatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 acgtaaaacaatctattcgggggacaaagataagaaagttcggccattaaccattggtcaatgacaatttttcttacctttgcgccctgaaatcagctttagacgatt Predict ORF larger than 30AA ================================================ acgtaaaacaatctattcgggggacaaagataagaaagttcggccattaaccattggtcaatgacaatttttcttacctttgcgccctgaaatcagctttagacgatt 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================================================ acgtaaaacaatctattcgggggacaaagataagaaagttcggccattaaccattggtcaatgacaatttttcttacctttgcgccctgaaatcagctttagacgatt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TF1455:TF1456|TF1455:TF1456:conserved hypothetical protein:GMP synthase:->->:1541722..1541829 108 acgtaaaacaatctattcgggggacaaagataagaaagttcggccattaaccattggtcaatgacaatttttcttacctttgcgccctgaaatcagctttagacgatt Intra-Species Hit: Count: 1 Min: 1 Max: 108 Len: 108 Subject: tfor_TF1455_TF1456|conserved hypothetical protein:GMP synthase|POSITIVE:POSITIVE|[1541722,1541829]|108 HSP 1 e-value: 4.0E-55 bit: 214.0 Len: 108 Query Start:1 Query End:108 Subject Strand: POSITIVE Subject Start: 1 Subject End: 108 acgtaaaacaatctattcgggggacaaagataagaaagttcggccattaaccattggtcaatgacaatttttcttacctttgcgccctgaaatcagctttagacgatt acgtaaaacaatctattcgggggacaaagataagaaagttcggccattaaccattggtcaatgacaatttttcttacctttgcgccctgaaatcagctttagacgatt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACGUAAAACAAUCUAUUCGGGGGACAAAGAUAAGAAAGUUCGGCCAUUAACCAUUGGUCAAUGACAAUUUUUCUUACCUUUGCGCCCUGAAAUCAGCUUUAGACGAUU .(((...........((((((((.(((((.((((((((((.(((((........)))))...)))....))))))).)))))).)))))))...........)))... (-29.35) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUCGUCUAAAGCUGAUUUCAGGGCGCAAAGGUAAGAAAAAUUGUCAUUGACCAAUGGUUAAUGGCCGAACUUUCUUAUCUUUGUCCCCCGAAUAGAUUGUUUUACGU ...(((..(((((....(((.(((.((((((((((((((....((((((((((...)))))))))).....)))))))))))))).))).)))......)))))))). (-38.50) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 336 94 57 70 29 tfor:TF2533|5end_adenylosuccinate_synthetase_2715666..2715896_POSITIVE 328 86 41 125 73 tfor:TF1183|5end_hypothetical_protein_1268391..1268621_POSITIVE 328 59 11 201 149 tfor:TF0645|5end_hypothetical_protein_688673..688903_POSITIVE 321 60 11 51 3 tfor:TF1062|5end_glycosyltransferase_1131727..1131957_POSITIVE 319 100 53 189 130 tfor:TF0133|5end_transposase_element_145174..145404_POSITIVE 313 97 56 192 144 tfor:TF1286|5end_hypothetical_protein_1369199..1369429_POSITIVE 292 60 18 104 62 tfor:TF0992|5end_hypothetical_protein_1048251..1048481_POSITIVE 283 49 12 121 88 tfor:TF2874|5end_conserved_hypothetical_protein_3064920..3065150_POSITIVE 275 59 14 170 124 tfor:TF3143|5end_conserved_hypothetical_protein;_possible_membrane_protein_3377465..3377695_POSITIVE 275 64 22 227 178 tfor:TF1673|5end_ATP_synthase,_C_subunit_1787238..1787468_POSITIVE 275 88 41 50 13 tfor:TF1145|5end_anaerobic_C4-dicarboxylate_membrane_transporter_1225799..1226029_POSITIVE 272 95 69 200 174 tfor:TF2127|5end_hypothetical_protein_2304038..2304268_POSITIVE 271 91 52 117 75 tfor:TF1648|5end_hypothetical_protein_1759338..1759568_POSITIVE 271 44 1 175 138 tfor:TF0049|5end_membrane-associated_HD_superfamily_hydrolase_55245..55475_POSITIVE 268 86 41 175 117 tfor:TF2114|5end_1-hydroxy-2-methyl-2-(E)-butenyl_4-diphosphate_synthase,_GcpE_2283006..2283236_POSITIVE 266 99 51 127 81 tfor:TF1730|5end_diaminopimelate_decarboxylase_1854670..1854900_POSITIVE 266 99 51 76 30 tfor:TF1732|5end_conserved_hypothetical_protein_1854619..1854849_POSITIVE 266 58 16 198 144 tfor:TF1011|5end_cell_division_protein;_rod_shape-determining_protein_1066647..1066877_POSITIVE 264 89 41 58 13 tfor:TF1611|5end_conserved_hypothetical_protein;_possible_glycosyl_transferase_1729620..1729850_POSITIVE 260 58 12 76 30 tfor:TF2971|5end_possible_transposase_3178978..3179208_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 321 60 11 51 3 tfor:TF1061|3end_glycosyltransferase_1131807..1131957_POSITIVE 299 89 42 104 58 tfor:TF2816|3end_hypothetical_protein_3007184..3007334_POSITIVE 292 60 18 107 65 tfor:TF0991|3end_probable_NAD(FAD)-dependent_dehydrogenase_1048334..1048484_POSITIVE 283 49 12 87 54 tfor:TF2873|3end_conserved_hypothetical_protein_3064966..3065116_POSITIVE 275 59 14 135 89 tfor:TF3142|3end_conserved_hypothetical_protein_3377510..3377660_POSITIVE 272 95 69 78 52 tfor:TF2126|3end_S-adenosylhomocysteine_hydrolase_2303996..2304146_POSITIVE 271 44 1 150 113 tfor:TF0050|3end_hypothetical_protein_55300..55450_POSITIVE 266 99 51 95 49 tfor:TF1729|3end_aspartokinase_1854718..1854868_POSITIVE 260 35 7 42 9 tfor:TF2352|3end_phosphotransacetylase_2517784..2517934_POSITIVE 260 58 12 49 3 tfor:TF1769|3end_transposase_1908488..1908638_POSITIVE 256 90 45 74 28 tfor:TF1455|3end_conserved_hypothetical_protein_1541661..1541811_POSITIVE 255 54 11 50 9 tfor:TF1111|3end_glycosyltransferase_1182048..1182198_POSITIVE 247 85 41 66 22 tfor:TF1109|3end_lipoprotein_1179997..1180147_POSITIVE 244 92 56 151 110 tfor:TF1285|3end_hypothetical_protein_1369245..1369395_POSITIVE 243 93 71 24 1 tfor:TF1600|3end_uroporphyrinogen-III_synthase_1714817..1714967_POSITIVE 242 45 1 128 75 tfor:TF2973|3end_transposase_3180181..3180331_POSITIVE 242 60 13 131 67 tfor:TF2884|3end_conserved_hypothetical_protein_3075748..3075898_POSITIVE 242 45 1 149 96 tfor:TF1772|3end_ISPg4-related_transposase_(IS5_family)_1909660..1909810_POSITIVE 240 97 58 148 98 tfor:TF0291|3end_triose-phosphate_isomerase_320131..320281_POSITIVE 237 75 37 150 115 tfor:TF2113|3end_phosphoribosylaminoimidazole_carboxylase_2283086..2283236_POSITIVE