Origin IGS: ggtggtgctctaccaactgagctacttccgcactattctcgctacgtatttttatgattagcgggtgcaaagatatggtcttttttttatattgcaagcattctgccactattttttttgaaatgcttgttggaataatggcaaaatgccgcttatcagacgtttttgcagccgatta .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 taatcggctgcaaaaacgtctgataagcggcattttgccattattccaacaagcatttcaaaaaaaatagtggcagaatgcttgcaatataaaaaaaagaccatatctttgcacccgctaatcataaaaatacgtagcgagaatagtgcggaagtagctcagttggtagagcaccacc Mask Tandem Repeat Region ================================================ ggtggtgctctaccaactgagctacttccgcactattctcgctacgtatttttatgattagcgggtgcaaagatatggtcttttttttatattgcaagcattctgccactattttttttgaaatgcttgttggaataatggcaaaatgccgcttatcagacgtttttgcagccgatta Find is-nt database================================================ Query_seq: TF1312:TF1313|TF1312:TF1313:hypothetical protein:conserved hypothetical protein:->->:1388842..1389019 178 ggtggtgctctaccaactgagctacttccgcactattctcgctacgtatttttatgattagcgggtgcaaagatatggtcttttttttatattgcaagcattctgccactattttttttgaaatgcttgttggaataatggcaaaatgccgcttatcagacgtttttgcagccgatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF1312:TF1313|TF1312:TF1313:hypothetical protein:conserved hypothetical protein:->->:1388842..1389019 178 ggtggtgctctaccaactgagctacttccgcactattctcgctacgtatttttatgattagcgggtgcaaagatatggtcttttttttatattgcaagcattctgccactattttttttgaaatgcttgttggaataatggcaaaatgccgcttatcagacgtttttgcagccgatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF1312:TF1313|TF1312:TF1313:hypothetical protein:conserved hypothetical protein:->->:1388842..1389019 178 ggtggtgctctaccaactgagctacttccgcactattctcgctacgtatttttatgattagcgggtgcaaagatatggtcttttttttatattgcaagcattctgccactattttttttgaaatgcttgttggaataatggcaaaatgccgcttatcagacgtttttgcagccgatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ggtggtgctctaccaactgagctacttccgcactattctcgctacgtatttttatgattagcgggtgcaaagatatggtcttttttttatattgcaagcattctgccactattttttttgaaatgcttgttggaataatggcaaaatgccgcttatcagacgtttttgcagccgatta Predict ORF larger than 30AA ================================================ Protein_Len: 43 Strand: + Start: 48 End: 176 ............................................... M F M I S G C K D M V F F L Y C K H S A T I F F E M L V G I M A K C R L S D V F A A D .. Protein_Len: 46 Strand: - Start: 2 End: 139 . H H E V L Q A V E A S N E S R I K I I L P H L S I T K K K Y Q L C E A V I K K S I S T P I M ....................................... ggtggtgctctaccaactgagctacttccgcactattctcgctacgtatttttatgattagcgggtgcaaagatatggtcttttttttatattgcaagcattctgccactattttttttgaaatgcttgttggaataatggcaaaatgccgcttatcagacgtttttgcagccgatta 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================================================ PromScan Matrix: RpoN Strand: - Score: 87 Start: 93 End: 109 ............................................................................................GTGGCAGAATGCTTGCA..................................................................... ggtggtgctctaccaactgagctacttccgcactattctcgctacgtatttttatgattagcgggtgcaaagatatggtcttttttttatattgcaagcattctgccactattttttttgaaatgcttgttggaataatggcaaaatgccgcttatcagacgtttttgcagccgatta Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TF1312:TF1313|TF1312:TF1313:hypothetical protein:conserved hypothetical protein:->->:1388842..1389019 178 ggtggtgctctaccaactgagctacttccgcactattctcgctacgtatttttatgattagcgggtgcaaagatatggtcttttttttatattgcaagcattctgccactattttttttgaaatgcttgttggaataatggcaaaatgccgcttatcagacgtttttgcagccgatta Intra-Species Hit: Count: 1 Min: 1 Max: 178 Len: 178 Subject: tfor_TF1312_TF1313|hypothetical protein:conserved hypothetical protein|POSITIVE:POSITIVE|[1388842,1389019]|178 HSP 1 e-value: 6.0E-68 bit: 258.0 Len: 178 Query Start:1 Query End:178 Subject Strand: POSITIVE Subject Start: 1 Subject End: 178 ggtggtgctctaccaactgagctacttccgcactattctcgctacgtatttttatgattagcgggtgcaaagatatggtcnnnnnnnnatattgcaagcattctgccactannnnnnnngaaatgcttgttggaataatggcaaaatgccgcttatcagacgtttttgcagccgatta ggtggtgctctaccaactgagctacttccgcactattctcgctacgtatttttatgattagcgggtgcaaagatatggtcttttttttatattgcaagcattctgccactattttttttgaaatgcttgttggaataatggcaaaatgccgcttatcagacgtttttgcagccgatta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GGUGGUGCUCUACCAACUGAGCUACUUCCGCACUAUUCUCGCUACGUAUUUUUAUGAUUAGCGGGUGCAAAGAUAUGGUCUUUUUUUUAUAUUGCAAGCAUUCUGCCACUAUUUUUUUUGAAAUGCUUGUUGGAAUAAUGGCAAAAUGCCGCUUAUCAGACGUUUUUGCAGCCGAUUA ((.(((((((........)))).))).))........(((((((((((....))))..)))))))(((((((((...((((............((..(((((.(((((.((((((................)))))).))))).))))).)).....)))))))))))))........ (-44.92) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAUCGGCUGCAAAAACGUCUGAUAAGCGGCAUUUUGCCAUUAUUCCAACAAGCAUUUCAAAAAAAAUAGUGGCAGAAUGCUUGCAAUAUAAAAAAAAGACCAUAUCUUUGCACCCGCUAAUCAUAAAAAUACGUAGCGAGAAUAGUGCGGAAGUAGCUCAGUUGGUAGAGCACCACC .....((.(((.........((((.((((((((((((((((((((....................)))))))))))))))).(((((.....................)))))..)))).))))......(((.(((((((.....(((....))).))).)))))))..)))))... (-45.35) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 554 39 1 132 92 tfor:TF1272|5end_hypothetical_protein_1355561..1355791_POSITIVE 454 47 1 197 146 tfor:TF2938|5end_conserved_hypothetical_protein;_possible_translocase_secE_subunit_3140563..3140793_POSITIVE 426 104 62 184 140 tfor:TF2548|5end_30S_ribosomal_protein_S12_2731238..2731468_POSITIVE 344 46 1 52 12 tfor:TF1873|5end_possible_hemolysin_secretion_protein_2026745..2026975_POSITIVE 344 46 1 52 12 tfor:TF1131|5end_membrane-fusion_protein;_possible_hemolysin_secretion_protein_1207611..1207841_POSITIVE 336 108 61 207 155 tfor:TF2278|5end_conserved_hypothetical_protein_2438662..2438892_POSITIVE 333 107 61 58 18 tfor:TF2738|5end_30S_ribosomal_protein_S16_2919303..2919533_POSITIVE 314 49 1 231 193 tfor:TF2937|5end_translation_elongation_factor_Tu_3139238..3139468_POSITIVE 314 84 41 221 164 tfor:TF1599|5end_ribonuclease_P_protein_component_1713564..1713794_POSITIVE 311 169 124 40 6 tfor:TF2950|5end_chloromuconate_cycloisomerase_3157399..3157629_POSITIVE 310 48 1 54 5 tfor:TF0496|5end_conserved_hypothetical_protein_522332..522562_POSITIVE 309 74 38 191 153 tfor:TF2736|5end_methylglyoxal_synthase_2917917..2918147_POSITIVE 305 68 21 227 174 tfor:TF0154|5end_conserved_hypothetical_protein_163564..163794_POSITIVE 302 163 123 231 193 tfor:TF1292|5end_sensor_histidine_protein_kinase_1372567..1372797_POSITIVE 299 47 1 153 108 tfor:TF0215|5end_tRNA/rRNA_methyltransferase,_TrmH_family_241463..241693_POSITIVE 298 169 124 55 3 tfor:TF0538|5end_hypothetical_protein_566891..567121_POSITIVE 297 34 5 208 180 tfor:TF1727|5end_hypothetical_protein_1852311..1852541_POSITIVE 293 48 1 195 141 tfor:TF0243|5end_conserved_hypothetical_protein_273728..273958_POSITIVE 289 169 121 120 66 tfor:TF1299|5end_conserved_hypothetical_protein_1380937..1381167_POSITIVE 286 43 2 82 39 tfor:TF3107|5end_hypothetical_protein_3338459..3338689_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 582 45 1 100 59 tfor:TF1271|3end_hypothetical_protein_1355462..1355612_POSITIVE 554 39 1 86 46 tfor:TF1270|3end_hypothetical_protein_1355595..1355745_POSITIVE 552 37 1 92 56 tfor:TF1272|3end_hypothetical_protein_1355823..1355973_POSITIVE 454 47 1 56 5 tfor:TF2937|3end_translation_elongation_factor_Tu_3140502..3140652_POSITIVE 420 48 1 62 9 tfor:TF0073|3end_possible_dTDP-glucose_4,6-dehydratase,_NAD-dependent_epimerase/dehydratase_family_82051..82201_POSITIVE 318 41 1 135 90 tfor:TF2953|3end_possible_TonB-dependent_outer_membrane_receptor_3161501..3161651_POSITIVE 311 169 124 40 6 tfor:TF2949|3end_dihydroxynaphthoate_synthase_(naphthoate_synthase)_3157479..3157629_POSITIVE 309 74 38 122 84 tfor:TF2735|3end_hypothetical_protein_2917928..2918078_POSITIVE 303 80 38 144 97 tfor:TF2832|3end_possible_proton/sodium:glutamate_symporter_protein_3023939..3024089_POSITIVE 297 34 5 98 70 tfor:TF1726|3end_hypothetical_protein_1852281..1852431_POSITIVE 286 43 2 151 108 tfor:TF3106|3end_hypothetical_protein_3338608..3338758_POSITIVE 284 46 24 38 16 tfor:TF1872|3end_ABC_transporter,_ATP-binding/permease_component_2026811..2026961_POSITIVE 284 46 24 38 16 tfor:TF1130|3end_ABC_transporter_ATP-binding_protein/permease_component_1207677..1207827_POSITIVE 281 170 123 144 102 tfor:TF0968|3end_hypothetical_protein_1019608..1019758_POSITIVE 269 78 36 58 18 tfor:TF0541|3end_conserved_hypothetical_protein_571858..572008_POSITIVE 268 164 125 75 34 tfor:TF1424|3end_N-acetylymuramoyl-L-alanine-D-glutamate_ligase_1508674..1508824_POSITIVE 268 97 61 61 26 tfor:TF0681|3end_sugar_kinase,_PfkB_family_724209..724359_POSITIVE 267 110 61 65 14 tfor:TF2791|3end_GTP-binding_protein_TypA_2977219..2977369_POSITIVE 266 100 59 148 110 tfor:TF0532|3end_hypothetical_protein_557924..558074_POSITIVE 265 47 8 108 52 tfor:TF2889|3end_50S_ribosomal_protein_L27_3078688..3078838_POSITIVE