Origin IGS: gcctctcgttttgccgaggacgacgtattgttccggttaggacgaccctccgtctgttttaggtcgtcctaatcgttctgttaggtcgacctaaatgctccgcaaggtcgaccttaccggccgtttaggtcgaccttactttttgtcggggtcggcgtgtgtggtttattgtctcgtagtgtgcagatca .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tgatctgcacactacgagacaataaaccacacacgccgaccccgacaaaaagtaaggtcgacctaaacggccggtaaggtcgaccttgcggagcatttaggtcgacctaacagaacgattaggacgacctaaaacagacggagggtcgtcctaaccggaacaatacgtcgtcctcggcaaaacgagaggc Mask Tandem Repeat Region ================================================ gcctctcgttttgccgaggacgacgtattgttccggttaggacgaccctccgtctgttttaggtcgtcctaatcgttctgttaggtcgacctaaatgctccgcaaggtcgaccttaccggccgtttaggtcgaccttactttttgtcggggtcggcgtgtgtggtttattgtctcgtagtgtgcagatca Find is-nt database================================================ Query_seq: TF0862:TF0864|TF0862:TF0864:conserved hypothetical protein fragment:O-succinylbenzoate--CoA ligase:->->:914520..914709 190 gcctctcgttttgccgaggacgacgtattgttccggttaggacgaccctccgtctgttttaggtcgtcctaatcgttctgttaggtcgacctaaatgctccgcaaggtcgaccttaccggccgtttaggtcgaccttactttttgtcggggtcggcgtgtgtggtttattgtctcgtagtgtgcagatca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF0862:TF0864|TF0862:TF0864:conserved hypothetical protein fragment:O-succinylbenzoate--CoA ligase:->->:914520..914709 190 gcctctcgttttgccgaggacgacgtattgttccggttaggacgaccctccgtctgttttaggtcgtcctaatcgttctgttaggtcgacctaaatgctccgcaaggtcgaccttaccggccgtttaggtcgaccttactttttgtcggggtcggcgtgtgtggtttattgtctcgtagtgtgcagatca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF0862:TF0864|TF0862:TF0864:conserved hypothetical protein fragment:O-succinylbenzoate--CoA ligase:->->:914520..914709 190 gcctctcgttttgccgaggacgacgtattgttccggttaggacgaccctccgtctgttttaggtcgtcctaatcgttctgttaggtcgacctaaatgctccgcaaggtcgaccttaccggccgtttaggtcgaccttactttttgtcggggtcggcgtgtgtggtttattgtctcgtagtgtgcagatca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gcctctcgttttgccgaggacgacgtattgttccggttaggacgaccctccgtctgttttaggtcgtcctaatcgttctgttaggtcgacctaaatgctccgcaaggtcgaccttaccggccgtttaggtcgaccttactttttgtcggggtcggcgtgtgtggtttattgtctcgtagtgtgcagatca Predict ORF larger than 30AA ================================================ Protein_Len: 32 Strand: + Start: 95 End: 190 .............................................................................................. M L R K V D L T G R L G R P Y F L S G S A C V V Y C L V V C R S gcctctcgttttgccgaggacgacgtattgttccggttaggacgaccctccgtctgttttaggtcgtcctaatcgttctgttaggtcgacctaaatgctccgcaaggtcgaccttaccggccgtttaggtcgaccttactttttgtcggggtcggcgtgtgtggtttattgtctcgtagtgtgcagatca 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================================================ gcctctcgttttgccgaggacgacgtattgttccggttaggacgaccctccgtctgttttaggtcgtcctaatcgttctgttaggtcgacctaaatgctccgcaaggtcgaccttaccggccgtttaggtcgaccttactttttgtcggggtcggcgtgtgtggtttattgtctcgtagtgtgcagatca Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 68 HP_score: -8.1 Tail_Score: -3.68988 Start: 34 End: 75 Full_Region: GACGACGTATTGTTC CGGTTAGGACGACCC TCCGTCTGTTTT AGGTCGTCCTAATCG TTCTGTTAGGTCGAC .................................CGGTTAGGACGACCCTCCGTCTGTTTTAGGTCGTCCTAATCG................................................................................................................... TransTerm Strand: + Conf: 60 HP_score: -5.7 Tail_Score: -3.65827 Start: 74 End: 123 Full_Region: TTAGGTCGTCCTAAT CGTTCTGTTAGGTCGACCT AAATGCTCCGCA AGGTCGACCTTACCGGCCG TTTAGGTCGACCTTA .........................................................................CGTTCTGTTAGGTCGACCTAAATGCTCCGCAAGGTCGACCTTACCGGCCG................................................................... TransTerm Strand: + Conf: 100 HP_score: -17.4 Tail_Score: -3.88001 Start: 84 End: 135 Full_Region: CTAATCGTTCTGTTA GGTCGACCTAAATGCTCCGCAAGG TCGA CCTTACCGGCCGTTTAGGTCGACC TTACTTTTTGTCGGG ...................................................................................GGTCGACCTAAATGCTCCGCAAGGTCGACCTTACCGGCCGTTTAGGTCGACC....................................................... TransTerm Strand: + Conf: 100 HP_score: -11.3 Tail_Score: -4.84359 Start: 102 End: 139 Full_Region: CGACCTAAATGCTCC GCAAGGTCGACCTTACC GGCC GTTTAGGTCGACCTTAC TTTTTGTCGGGGTCG .....................................................................................................GCAAGGTCGACCTTACCGGCCGTTTAGGTCGACCTTAC................................................... Find igs database================================================ Query_seq: TF0862:TF0864|TF0862:TF0864:conserved hypothetical protein fragment:O-succinylbenzoate--CoA ligase:->->:914520..914709 190 gcctctcgttttgccgaggacgacgtattgttccggttaggacgaccctccgtctgttttaggtcgtcctaatcgttctgttaggtcgacctaaatgctccgcaaggtcgaccttaccggccgtttaggtcgaccttactttttgtcggggtcggcgtgtgtggtttattgtctcgtagtgtgcagatca Intra-Species Hit: Count: 2 Min: 1 Max: 190 Len: 190 Subject: tfor_TF0862_TF0864|conserved hypothetical protein fragment:O-succinylbenzoate--CoA ligase|POSITIVE:POSITIVE|[914520,914709]|190 HSP 1 e-value: 1.0E-104 bit: 377.0 Len: 190 Query Start:1 Query End:190 Subject Strand: POSITIVE Subject Start: 1 Subject End: 190 gcctctcgttttgccgaggacgacgtattgttccggttaggacgaccctccgtctgttttaggtcgtcctaatcgttctgttaggtcgacctaaatgctccgcaaggtcgaccttaccggccgtttaggtcgaccttactttttgtcggggtcggcgtgtgtggtttattgtctcgtagtgtgcagatca gcctctcgttttgccgaggacgacgtattgttccggttaggacgaccctccgtctgttttaggtcgtcctaatcgttctgttaggtcgacctaaatgctccgcaaggtcgaccttaccggccgtttaggtcgaccttactttttgtcggggtcggcgtgtgtggtttattgtctcgtagtgtgcagatca Subject: tfor_TF0883_TF0884|hypothetical protein:hypothetical protein|POSITIVE:POSITIVE|[937533,937742]|210 HSP 1 e-value: 2.0E-24 bit: 113.0 Len: 149 Query Start:32 Query End:180 Subject Strand: POSITIVE Subject Start: 62 Subject End: 210 ...............................tccggttaggacgaccctccgtctgttttaggtcgtcctaatcgttctgttaggtcgacctaaatgctccgcaaggtcgaccttaccggccgtttaggtcgaccttactttttgtcggggtcggcgtgtgtggtttattgtctcgtagt.......... ...............................tccggttaggacgaccttccgtccgttttaggtcgacctaaccgctctgtaaggacgacctatttgctccgtaaggtcgacctaaacgctcggttaggtcgacctgactttctgtcagggtcgacgtatgcggtttattccctcgtagt.......... Inter-species Hit: Count: 3 Min: 9 Max: 186 Len: 178 Subject: NC_002950_PG0665_PG0668|beta-galactosidase:TonB-dependent receptor|POSITIVE:POSITIVE|[715306,717590]|2285 HSP 1 e-value: 4.0E-32 bit: 139.0 Len: 166 Query Start:19 Query End:184 Subject Strand: POSITIVE Subject Start: 1416 Subject End: 1581 ..................gacgacgtattgttccggttaggacgaccctccgtctgttttaggtcgtcctaatcgttctgttaggtcgacctaaatgctccgcaaggtcgaccttaccggccgtttaggtcgaccttactttttgtcggggtcggcgtgtgtggtttattgtctcgtagtgtgc...... ..................gacgacgtactgctccggttaggacgaccttccgtccgttttaggtcgacctaatcgctctgtaaggacgacctatttgctccgcaaggtcgacctaaacgctcggttaggtcgacctgacttcttgtcagggtcgacgtatgcggtttattcccttgtagtgtgc...... Subject: NC_002950_PG1496_PG1497|hypothetical protein:DNA-binding protein, histone-like family|POSITIVE:POSITIVE|[1573758,1574224]|467 HSP 1 e-value: 9.0E-27 bit: 121.0 Len: 153 Query Start:32 Query End:184 Subject Strand: NEGATIVE Subject Start: 117 Subject End: 269 ...............................tccggttaggacgaccctccgtctgttttaggtcgtcctaatcgttctgttaggtcgacctaaatgctccgcaaggtcgaccttaccggccgtttaggtcgaccttactttttgtcggggtcggcgtgtgtggtttattgtctcgtagtgtgc...... ...............................tccggttaggtcgaccttccgtccgttttaggtcgacctaaacgctctgtaaggacgacctatttgctccgtaaggtcgacctaaacggccggttatgtcgacctgactttctgtcagggtcgacgtatgcggtttattccctcgtagtgtgc...... HSP 2 e-value: 2.0E-6 bit: 54.0 Len: 35 Query Start:105 Query End:139 Subject Strand: POSITIVE Subject Start: 165 Subject End: 199 ........................................................................................................aggtcgaccttaccggccgtttaggtcgaccttac................................................... ........................................................................................................aggtcgacataaccggccgtttaggtcgaccttac................................................... Subject: NC_002950_PG1519_PG1521|hypothetical protein:O-succinylbenzoic acid--CoA ligase|POSITIVE:NEGATIVE|[1597486,1598143]|658 HSP 1 e-value: 3.0E-20 bit: 99.6 Len: 58 Query Start:9 Query End:66 Subject Strand: POSITIVE Subject Start: 535 Subject End: 592 ........ttttgccgaggacgacgtattgttccggttaggacgaccctccgtctgttttaggtcg............................................................................................................................ ........ttttgccggggacgacgtatcgttccggttaggacgaccctccgtctgttttaggtcg............................................................................................................................ HSP 2 e-value: 2.0E-18 bit: 93.7 Len: 63 Query Start:124 Query End:186 Subject Strand: POSITIVE Subject Start: 584 Subject End: 646 ...........................................................................................................................tttaggtcgaccttactttttgtcggggtcggcgtgtgtggtttattgtctcgtagtgtgcag.... ...........................................................................................................................tttaggtcgacctgactttctgtcagggtcggcgtgtgtggtttattgtctcgtaatgtgcag.... Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUUGCCGAGGACGACGUAUUGUUCCGGUUAGGACGACCCUCCGUCUGUUUUAGGUCGUCCUAAUCGUUCUGUUAGGUCGACCUAAAUGCUCCGCAAGGUCGACCUUACCGGCCGUUUAGGUCGACCUUACUUUUUGUCGGGGUCGGCGUGUGUGGUUUAUUGUCUCGUAGUGUGCAG ....(((((...(((((........((((((((((((((..............))))))))))))))....((.(((((((((((((((..(((.((((....))))..))).))))))))))))))).))....)))))...))))).......((.(((((.....))))).)).. (-72.84) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUGCACACUACGAGACAAUAAACCACACACGCCGACCCCGACAAAAAGUAAGGUCGACCUAAACGGCCGGUAAGGUCGACCUUGCGGAGCAUUUAGGUCGACCUAACAGAACGAUUAGGACGACCUAAAACAGACGGAGGGUCGUCCUAACCGGAACAAUACGUCGUCCUCGGCAAAA ..............................(((((...((((.....((.(((((((((((((..(((.((((((....)))))).).)).))))))))))))).))....((.((((((((((((............)))))))))))).)).........))))...))))).... (-72.60) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 543 131 97 170 136 tfor:TF0884|5end_hypothetical_protein_937603..937833_POSITIVE 470 158 111 183 131 tfor:TF1767|5end_3-dehydroquinate_synthase_1905492..1905722_POSITIVE 421 149 101 122 59 tfor:TF0257|5end_hypothetical_protein_287610..287840_POSITIVE 412 49 5 125 77 tfor:TF1250|5end_possible_cation_efflux_pump_1332324..1332554_POSITIVE 409 148 109 222 182 tfor:TF0428|5end_methylmalonyl-CoA_mutase,_beta_subunit_447809..448039_POSITIVE 404 48 7 231 184 tfor:TF0457|5end_beta-glucanase_precursor_474099..474329_POSITIVE 399 152 111 84 28 tfor:TF0847|5end_hypothetical_protein_897633..897863_POSITIVE 398 115 71 192 139 tfor:TF1067|5end_conserved_hypothetical_protein_1136867..1137097_POSITIVE 393 58 13 201 151 tfor:TF0960|5end_beta-galactosidase_1008618..1008848_POSITIVE 389 140 91 197 135 tfor:TF2946|5end_conserved_hypothetical_protein;_possible_ATPase_3151750..3151980_POSITIVE 382 140 93 81 25 tfor:TF2112|5end_glycine_cleavage_H_protein_2282119..2282349_POSITIVE 380 62 22 68 15 tfor:TF2704|5end_ribonuclease_HII_2876242..2876472_POSITIVE 380 130 82 210 156 tfor:TF0949|5end_conserved_hypothetical_protein_993863..994093_POSITIVE 377 150 110 67 32 tfor:TF2318|5end_conserved_hypothetical_protein_2475603..2475833_POSITIVE 377 148 101 141 88 tfor:TF1975|5end_uridylate_kinase_2121536..2121766_POSITIVE 375 156 111 53 4 tfor:TF0202|5end_folylpolyglutamate_synthase_227717..227947_POSITIVE 373 124 89 142 98 tfor:TF2674|5end_conserved_hypothetical_protein;_possible_phosphoesterase_2848176..2848406_POSITIVE 373 148 102 81 10 tfor:TF1474|5end_6-phosphogluconolactonase_1567342..1567572_POSITIVE 371 159 111 178 119 tfor:TF1181|5end_methylated-DNA--[protein]-cysteine_S-methyltransferase_1267522..1267752_POSITIVE 370 155 114 223 177 tfor:TF2560|5end_30S_ribosomal_protein_S3_2737897..2738127_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 416 67 26 57 16 tfor:TF0862|3end_conserved_hypothetical_protein_fragment_914459..914609_POSITIVE 412 49 5 77 29 tfor:TF1249|3end_phosphoglycerate_kinase_(cytosolic_phosphoglycerate_kinase)_1332356..1332506_POSITIVE 404 169 121 141 91 tfor:TF0350|3end_hypothetical_protein_371101..371251_POSITIVE 398 115 71 103 50 tfor:TF1066|3end_hypothetical_protein_1136858..1137008_POSITIVE 380 62 22 63 10 tfor:TF2703|3end_conserved_hypothetical_protein_2876317..2876467_POSITIVE 377 150 110 51 16 tfor:TF2317|3end_3-oxoacyl-[acyl-carrier-protein]_synthase_II_2475667..2475817_POSITIVE 368 170 132 141 101 tfor:TF0982|3end_conserved_hypothetical_protein_1039474..1039624_POSITIVE 364 118 74 48 4 tfor:TF2366|3end_conserved_hypothetical_protein_2531892..2532042_POSITIVE 357 148 104 58 1 tfor:TF2768|3end_ferredoxin_oxidoreductase,_beta_subunit_2955169..2955319_POSITIVE 349 49 2 126 75 tfor:TF3053|3end_conserved_hypothetical_protein_3278889..3279039_POSITIVE 347 149 104 138 93 tfor:TF0776|3end_ABC_transporter,_permease_component_826173..826323_POSITIVE 347 157 112 148 93 tfor:TF0605|3end_conserved_hypothetical_protein_636883..637033_POSITIVE 346 150 102 108 54 tfor:TF2556|3end_conserved_hypothetical_protein_2737095..2737245_POSITIVE 341 150 101 149 109 tfor:TF1186|3end_hypothetical_protein_1269815..1269965_POSITIVE 339 159 111 120 73 tfor:TF2255|3end_transfer_region-related_protein,_TraH_2427961..2428111_POSITIVE 337 160 111 90 44 tfor:TF2846|3end_cobyric_acid_synthase_3036469..3036619_POSITIVE 337 48 4 138 93 tfor:TF2406|3end_anti-sigma_factor_2581659..2581809_POSITIVE 337 148 104 149 100 tfor:TF1274|3end_hypothetical_protein_1357895..1358045_POSITIVE 336 147 110 66 32 tfor:TF2808|3end_bacterial_sugar_transferase_2999909..3000059_POSITIVE 336 46 5 148 106 tfor:TF1145|3end_anaerobic_C4-dicarboxylate_membrane_transporter_1227180..1227330_POSITIVE