Origin IGS: acaaaatatttacggttcatcaatacggccagtccttcgtcctattcattccggctcctttcgaacactcattttcctgacctgatcggaatcgaagcagcttattgtta .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 taacaataagctgcttcgattccgatcaggtcaggaaaatgagtgttcgaaaggagccggaatgaataggacgaaggactggccgtattgatgaaccgtaaatattttgt Mask Tandem Repeat Region ================================================ acaaaatatttacggttcatcaatacggccagtccttcgtcctattcattccggctcctttcgaacactcattttcctgacctgatcggaatcgaagcagcttattgtta Find is-nt database================================================ Query_seq: TF0657:TF0658|TF0657:TF0658:conserved hypothetical protein:2-amino-3-ketobutyrate coenzyme A ligase:->->:703942..704051 110 acaaaatatttacggttcatcaatacggccagtccttcgtcctattcattccggctcctttcgaacactcattttcctgacctgatcggaatcgaagcagcttattgtta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF0657:TF0658|TF0657:TF0658:conserved hypothetical protein:2-amino-3-ketobutyrate coenzyme A ligase:->->:703942..704051 110 acaaaatatttacggttcatcaatacggccagtccttcgtcctattcattccggctcctttcgaacactcattttcctgacctgatcggaatcgaagcagcttattgtta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF0657:TF0658|TF0657:TF0658:conserved hypothetical protein:2-amino-3-ketobutyrate coenzyme A ligase:->->:703942..704051 110 acaaaatatttacggttcatcaatacggccagtccttcgtcctattcattccggctcctttcgaacactcattttcctgacctgatcggaatcgaagcagcttattgtta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 acaaaatatttacggttcatcaatacggccagtccttcgtcctattcattccggctcctttcgaacactcattttcctgacctgatcggaatcgaagcagcttattgtta Predict ORF larger than 30AA ================================================ Protein_Len: 30 Strand: + Start: 19 End: 108 .................. M N T A S P S S Y S F R L L S N T H F P D L I G I E A A Y C .. acaaaatatttacggttcatcaatacggccagtccttcgtcctattcattccggctcctttcgaacactcattttcctgacctgatcggaatcgaagcagcttattgtta 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================================================ acaaaatatttacggttcatcaatacggccagtccttcgtcctattcattccggctcctttcgaacactcattttcctgacctgatcggaatcgaagcagcttattgtta Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TF0657:TF0658|TF0657:TF0658:conserved hypothetical protein:2-amino-3-ketobutyrate coenzyme A ligase:->->:703942..704051 110 acaaaatatttacggttcatcaatacggccagtccttcgtcctattcattccggctcctttcgaacactcattttcctgacctgatcggaatcgaagcagcttattgtta Intra-Species Hit: Count: 1 Min: 1 Max: 110 Len: 110 Subject: tfor_TF0657_TF0658|conserved hypothetical protein:2-amino-3-ketobutyrate coenzyme A ligase|POSITIVE:POSITIVE|[703942,704051]|110 HSP 1 e-value: 3.0E-56 bit: 218.0 Len: 110 Query Start:1 Query End:110 Subject Strand: POSITIVE Subject Start: 1 Subject End: 110 acaaaatatttacggttcatcaatacggccagtccttcgtcctattcattccggctcctttcgaacactcattttcctgacctgatcggaatcgaagcagcttattgtta acaaaatatttacggttcatcaatacggccagtccttcgtcctattcattccggctcctttcgaacactcattttcctgacctgatcggaatcgaagcagcttattgtta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACAAAAUAUUUACGGUUCAUCAAUACGGCCAGUCCUUCGUCCUAUUCAUUCCGGCUCCUUUCGAACACUCAUUUUCCUGACCUGAUCGGAAUCGAAGCAGCUUAUUGUUA ....................(((((.(((.....(((((........(((((((.((...(((((........)))..))...))))))))))))))..))))))))... (-13.70) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAACAAUAAGCUGCUUCGAUUCCGAUCAGGUCAGGAAAAUGAGUGUUCGAAAGGAGCCGGAAUGAAUAGGACGAAGGACUGGCCGUAUUGAUGAACCGUAAAUAUUUUGU ...(((((.(((((((((..(((..(((..((.((..........(((....))).)).)).)))...))))))))...))))..))))).................... (-19.50) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 402 63 24 126 67 tfor:TF0971|5end_conserved_hypothetical_protein_1021355..1021585_POSITIVE 396 55 14 210 156 tfor:TF1492|5end_ribonuclease_H-related_protein_1592017..1592247_POSITIVE 363 60 12 69 12 tfor:TF2704|5end_ribonuclease_HII_2876242..2876472_POSITIVE 332 57 11 184 130 tfor:TF2151|5end_uridine_kinase_2323033..2323263_POSITIVE 331 55 13 182 137 tfor:TF2789|5end_enoyl-[acyl-carrier-protein]_reductase_2972431..2972661_POSITIVE 331 71 31 180 143 tfor:TF2655|5end_DNA_topoisomerase_I_2824543..2824773_POSITIVE 326 100 51 47 7 tfor:TF2267|5end_lysozyme-related_protein_2434869..2435099_POSITIVE 323 59 25 68 31 tfor:TF1915|5end_NAD-dependent_protein_deacetylase,_SIR2_family_2067720..2067950_POSITIVE 319 100 51 197 134 tfor:TF2979|5end_possible_outer_membrane__protein_3190778..3191008_POSITIVE 318 96 52 91 45 tfor:TF3109|5end_hypothetical_protein_3341998..3342228_POSITIVE 318 70 26 204 150 tfor:TF1984|5end_conserved_hypothetical_protein_2135278..2135508_POSITIVE 317 95 51 89 30 tfor:TF0239|5end_conserved_hypothetical_protein_268894..269124_POSITIVE 316 58 13 182 127 tfor:TF3126|5end_glycosyltransferase,_group_2_family_3360439..3360669_POSITIVE 313 98 51 80 27 tfor:TF1908|5end_possible_phosphoglycerate_mutase_2062695..2062925_POSITIVE 312 65 25 229 197 tfor:TF2392|5end_alpha-galactosidase_2563384..2563614_POSITIVE 309 75 36 213 169 tfor:TF2598|5end_conserved_hypothetical_protein_2771032..2771262_POSITIVE 309 58 13 176 123 tfor:TF2261|5end_transfer_region-related_protein,_TraM_2430496..2430726_POSITIVE 309 58 13 53 16 tfor:TF1775|5end_oxidoreductase,_Gfo/Idh/MocA_family_1913135..1913365_POSITIVE 307 59 11 213 158 tfor:TF3151|5end_glyoxalase_family_protein_3386221..3386451_POSITIVE 306 98 51 69 28 tfor:TF0816|5end_hypothetical_protein_874217..874447_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 363 60 12 64 7 tfor:TF2703|3end_conserved_hypothetical_protein_2876317..2876467_POSITIVE 331 71 31 116 79 tfor:TF2654|3end_arginyl-tRNA_synthetase_2824559..2824709_POSITIVE 326 100 51 47 7 tfor:TF2266|3end_transfer_region-related_protein,_TraQ_2434949..2435099_POSITIVE 317 96 54 43 4 tfor:TF3108|3end_glutamine-hydrolyzing_carbamoyl-phosphate_synthase,_large_subunit_3342030..3342180_POSITIVE 317 95 51 72 13 tfor:TF0238|3end_outer_membrane_protein_268957..269107_POSITIVE 299 67 26 55 13 tfor:TF1599|3end_ribonuclease_P_protein_component_1714054..1714204_POSITIVE 296 110 61 127 73 tfor:TF0462|3end_possible_cobalamin_biosynthesis_precorrin-3_methylase_479095..479245_POSITIVE 290 67 22 114 48 tfor:TF0258|3end_hypothetical_protein_289534..289684_POSITIVE 289 70 24 113 48 tfor:TF2412|3end_outer_membrane_protein_2590393..2590543_POSITIVE 286 84 41 126 76 tfor:TF0119|3end_gluconate_aldolase_131334..131484_POSITIVE 285 61 26 55 27 tfor:TF2888|3end_50S_ribosomal_protein_L21_3078389..3078539_POSITIVE 285 64 21 61 14 tfor:TF1314|3end_conserved_hypothetical_protein_1390302..1390452_POSITIVE 284 70 25 144 101 tfor:TF2795|3end_hypothetical_protein_2980909..2981059_POSITIVE 282 99 51 83 14 tfor:TF2789|3end_enoyl-[acyl-carrier-protein]_reductase_2973365..2973515_POSITIVE 278 100 51 59 6 tfor:TF2434|3end_conserved_hypothetical_protein_2614363..2614513_POSITIVE 277 90 51 151 119 tfor:TF1902|3end_two-component_system_sensor_histidine_kinase_2059055..2059205_POSITIVE 277 65 26 54 5 tfor:TF1818|3end_conserved_hypothetical_protein_1958754..1958904_POSITIVE 276 70 26 147 102 tfor:TF2462|3end_hypothetical_protein_2642076..2642226_POSITIVE 275 63 26 41 4 tfor:TF2315|3end_thioesterase_2474498..2474648_POSITIVE 275 80 36 119 78 tfor:TF1851|3end_methionine_synthase_I_2004681..2004831_POSITIVE