Origin IGS: tctttttttgttgtttatttaaaacttgttttttagtgaaaccaccttccctccaaggagatttcaggtaatacatcttcatataaaaaacaatcgcatcgtatcaagcctcgaacgagggagtcgaagacggtgatacgttttttatatccgtta .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 taacggatataaaaaacgtatcaccgtcttcgactccctcgttcgaggcttgatacgatgcgattgttttttatatgaagatgtattacctgaaatctccttggagggaaggtggtttcactaaaaaacaagttttaaataaacaacaaaaaaaga Mask Tandem Repeat Region ================================================ tctttttttgttgtttatttaaaacttgttttttagtgaaaccaccttccctccaaggagatttcaggtaatacatcttcatataaaaaacaatcgcatcgtatcaagcctcgaacgagggagtcgaagacggtgatacgttttttatatccgtta Find is-nt database================================================ Query_seq: TF2916:TF2917|TF2916:TF2917:conserved hypothetical protein:conserved hypothetical protein:->->:3112239..3112394 156 tctttttttgttgtttatttaaaacttgttttttagtgaaaccaccttccctccaaggagatttcaggtaatacatcttcatataaaaaacaatcgcatcgtatcaagcctcgaacgagggagtcgaagacggtgatacgttttttatatccgtta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF2916:TF2917|TF2916:TF2917:conserved hypothetical protein:conserved hypothetical protein:->->:3112239..3112394 156 tctttttttgttgtttatttaaaacttgttttttagtgaaaccaccttccctccaaggagatttcaggtaatacatcttcatataaaaaacaatcgcatcgtatcaagcctcgaacgagggagtcgaagacggtgatacgttttttatatccgtta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF2916:TF2917|TF2916:TF2917:conserved hypothetical protein:conserved hypothetical protein:->->:3112239..3112394 156 tctttttttgttgtttatttaaaacttgttttttagtgaaaccaccttccctccaaggagatttcaggtaatacatcttcatataaaaaacaatcgcatcgtatcaagcctcgaacgagggagtcgaagacggtgatacgttttttatatccgtta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tctttttttgttgtttatttaaaacttgttttttagtgaaaccaccttccctccaaggagatttcaggtaatacatcttcatataaaaaacaatcgcatcgtatcaagcctcgaacgagggagtcgaagacggtgatacgttttttatatccgtta Predict ORF larger than 30AA ================================================ Protein_Len: 36 Strand: + Start: 26 End: 133 ......................... M F F S E T T F P P R R F Q V I H L H I K N N R I V S S L E R G S R R R ....................... Protein_Len: 32 Strand: + Start: 61 End: 156 ............................................................ M S G N T S S Y K K Q S H R I K P R T R E S K T V I R F L Y P L Protein_Len: 34 Strand: - Start: 36 End: 137 ................................... H F W R G E L S I E P L V D E Y L F C D C R I L G R V L S D F V T M ................... Protein_Len: 31 Strand: - Start: 2 End: 94 . K K Q Q K N L V Q K K T F G G E R W P S K L Y Y M K M Y F V M .............................................................. tctttttttgttgtttatttaaaacttgttttttagtgaaaccaccttccctccaaggagatttcaggtaatacatcttcatataaaaaacaatcgcatcgtatcaagcctcgaacgagggagtcgaagacggtgatacgttttttatatccgtta 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================================================ tctttttttgttgtttatttaaaacttgttttttagtgaaaccaccttccctccaaggagatttcaggtaatacatcttcatataaaaaacaatcgcatcgtatcaagcctcgaacgagggagtcgaagacggtgatacgttttttatatccgtta Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TF2916:TF2917|TF2916:TF2917:conserved hypothetical protein:conserved hypothetical protein:->->:3112239..3112394 156 tctttttttgttgtttatttaaaacttgttttttagtgaaaccaccttccctccaaggagatttcaggtaatacatcttcatataaaaaacaatcgcatcgtatcaagcctcgaacgagggagtcgaagacggtgatacgttttttatatccgtta Intra-Species Hit: Count: 1 Min: 10 Max: 156 Len: 147 Subject: tfor_TF2916_TF2917|conserved hypothetical protein:conserved hypothetical protein|POSITIVE:POSITIVE|[3112239,3112394]|156 HSP 1 e-value: 3.0E-78 bit: 291.0 Len: 147 Query Start:10 Query End:156 Subject Strand: POSITIVE Subject Start: 10 Subject End: 156 .........gttgtttatttaaaacttgttttttagtgaaaccaccttccctccaaggagatttcaggtaatacatcttcatataaaaaacaatcgcatcgtatcaagcctcgaacgagggagtcgaagacggtgatacgttttttatatccgtta .........gttgtttatttaaaacttgttttttagtgaaaccaccttccctccaaggagatttcaggtaatacatcttcatataaaaaacaatcgcatcgtatcaagcctcgaacgagggagtcgaagacggtgatacgttttttatatccgtta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GUUGUUUAUUUAAAACUUGUUUUUUAGUGAAACCACCUUCCCUCCAAGGAGAUUUCAGGUAAUACAUCUUCAUAUAAAAAACAAUCGCAUCGUAUCAAGCCUCGAACGAGGGAGUCGAAGACGGUGAUACGUUUUUUAUAUCCGUUA ...(..(((..(((((.((((((((((((((...((((...(((....))).....))))........))))).)))))))))........((((((..((((....))))..(((...)))..)))))))))))..)))..).... (-29.40) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAACGGAUAUAAAAAACGUAUCACCGUCUUCGACUCCCUCGUUCGAGGCUUGAUACGAUGCGAUUGUUUUUUAUAUGAAGAUGUAUUACCUGAAAUCUCCUUGGAGGGAAGGUGGUUUCACUAAAAAACAAGUUUUAAAUAAACAAC .........(((((..(((((((..(((((.(((......))).))))).)))))))......((((((((((..((((.....(((((((....((((....))))..))))))))))).)))))))))).))))).......... (-35.20) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 355 136 91 180 128 tfor:TF2264|5end_transfer_region-related_protein,_TraO_2432890..2433120_POSITIVE 344 125 88 57 22 tfor:TF0073|5end_possible_dTDP-glucose_4,6-dehydratase,_NAD-dependent_epimerase/dehydratase_family_80946..81176_POSITIVE 341 130 87 76 27 tfor:TF0789|5end_preprotein_translocase,_secDF_family_841293..841523_POSITIVE 335 117 77 162 118 tfor:TF1051|5end_glycoside_hydrolase_1111974..1112204_POSITIVE 333 126 85 183 136 tfor:TF1179|5end_two-component_sensor_histidine_kinase_1266057..1266287_POSITIVE 328 133 94 92 51 tfor:TF3146|5end_GTP-binding_protein_Obg_3381852..3382082_POSITIVE 319 129 86 47 1 tfor:TF2931|5end_3-deoxy-D-manno-2-octulosonic_acid_(Kdo_transferase)_3134275..3134505_POSITIVE 319 123 87 91 57 tfor:TF2640|5end_hypothetical_protein_2809106..2809336_POSITIVE 315 124 85 84 36 tfor:TF1474|5end_6-phosphogluconolactonase_1567342..1567572_POSITIVE 315 125 85 227 183 tfor:TF1398|5end_conserved_hypothetical_protein_1471474..1471704_POSITIVE 315 131 91 53 11 tfor:TF0241|5end_UDP-N-acetyl_glucosamine_-2-epimerase_271321..271551_POSITIVE 314 123 82 168 118 tfor:TF2078|5end_dehydrogenase_2244306..2244536_POSITIVE 310 129 86 211 158 tfor:TF1848|5end_conserved_hypothetical_protein_1997589..1997819_POSITIVE 310 126 84 184 146 tfor:TF1830|5end_3-isopropylmalate_dehydratase,_large_subunit_1978888..1979118_POSITIVE 310 130 84 103 60 tfor:TF0606|5end_signal_peptidase_II_636816..637046_POSITIVE 308 128 81 194 132 tfor:TF0465|5end_cobalamin_biosynthesis_protein_482028..482258_POSITIVE 307 118 87 176 143 tfor:TF2925|5end_beta-N-acetylglucosaminidase_3125700..3125930_POSITIVE 304 127 88 60 13 tfor:TF3068|5end_flavodoxin_A_3292812..3293042_POSITIVE 303 126 85 148 105 tfor:TF2782|5end_conserved_hypothetical_protein_2966455..2966685_POSITIVE 303 134 91 41 5 tfor:TF1401|5end_Holliday_junction_DNA_helicase_1476502..1476732_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 344 125 88 101 66 tfor:TF0072|3end_hypothetical_protein_81070..81220_POSITIVE 341 130 87 73 24 tfor:TF0788|3end_protein-export_membrane_protein_841370..841520_POSITIVE 335 117 77 59 15 tfor:TF1050|3end_hypothetical_protein_1111951..1112101_POSITIVE 316 131 91 58 17 tfor:TF0239|3end_conserved_hypothetical_protein_270323..270473_POSITIVE 315 131 91 59 17 tfor:TF0240|3end_conserved_hypothetical_protein;_possible_gycosyltransferase_I_family_protein_271407..271557_POSITIVE 314 123 82 145 95 tfor:TF2077|3end_conserved_hypothetical_protein;_possible_chromosome_segregation_ATPase_2244363..2244513_POSITIVE 313 127 85 110 63 tfor:TF2640|3end_hypothetical_protein_2809533..2809683_POSITIVE 313 128 84 64 16 tfor:TF2263|3end_transfer_region-related_protein,_TraN_2432964..2433114_POSITIVE 311 126 81 67 15 tfor:TF1247|3end_alanyl-tRNA_synthetase_(alanine--tRNA_ligase)_1330928..1331078_POSITIVE 310 126 84 145 107 tfor:TF1829|3end_2-isopropylmalate_synthase_1978929..1979079_POSITIVE 310 130 84 90 47 tfor:TF0605|3end_conserved_hypothetical_protein_636883..637033_POSITIVE 306 129 87 139 95 tfor:TF0271|3end_oxidase/dehydrogenase_298530..298680_POSITIVE 303 126 85 139 96 tfor:TF2780|3end_hypothetical_protein_2966526..2966676_POSITIVE 303 127 84 131 90 tfor:TF1532|3end_potassium_uptake_system_protein_1639415..1639565_POSITIVE 296 135 93 147 109 tfor:TF0995|3end_conserved_hypothetical_protein_1050962..1051112_POSITIVE 294 124 83 58 3 tfor:TF2702|3end_hypothetical_protein_2876136..2876286_POSITIVE 294 127 82 150 105 tfor:TF0469|3end_hypothetical_protein_487228..487378_POSITIVE 294 127 82 110 65 tfor:TF0468|3end_hypothetical_protein_487188..487338_POSITIVE 294 128 84 67 17 tfor:TF0120|3end_hexouronate_transporter_132811..132961_POSITIVE 291 129 88 44 5 tfor:TF2930|3end_glutamyl-tRNA_synthetase_3134352..3134502_POSITIVE