Origin IGS: tgatattaatcctcacttctcgtgcgttttccaacttgagggaaaaaagcaaaggggggggacacaagctaataggataaaatttatatggtagactatatgctgttatcaagaaaaggtgtagtttcaagtagcaa .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 ttgctacttgaaactacaccttttcttgataacagcatatagtctaccatataaattttatcctattagcttgtgtcccccccctttgcttttttccctcaagttggaaaacgcacgagaagtgaggattaatatca Mask Tandem Repeat Region ================================================ tgatattaatcctcacttctcgtgcgttttccaacttgagggaaaaaagcaaaggggggggacacaagctaataggataaaatttatatggtagactatatgctgttatcaagaaaaggtgtagtttcaagtagcaa Find is-nt database================================================ Query_seq: TF2860:TF2861|TF2860:TF2861:hypothetical protein:conserved hypothetical protein; possible Rhs family protein:->->:3051741..3051877 137 tgatattaatcctcacttctcgtgcgttttccaacttgagggaaaaaagcaaaggggggggacacaagctaataggataaaatttatatggtagactatatgctgttatcaagaaaaggtgtagtttcaagtagcaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF2860:TF2861|TF2860:TF2861:hypothetical protein:conserved hypothetical protein; possible Rhs family protein:->->:3051741..3051877 137 tgatattaatcctcacttctcgtgcgttttccaacttgagggaaaaaagcaaaggggggggacacaagctaataggataaaatttatatggtagactatatgctgttatcaagaaaaggtgtagtttcaagtagcaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF2860:TF2861|TF2860:TF2861:hypothetical protein:conserved hypothetical protein; possible Rhs family protein:->->:3051741..3051877 137 tgatattaatcctcacttctcgtgcgttttccaacttgagggaaaaaagcaaaggggggggacacaagctaataggataaaatttatatggtagactatatgctgttatcaagaaaaggtgtagtttcaagtagcaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tgatattaatcctcacttctcgtgcgttttccaacttgagggaaaaaagcaaaggggggggacacaagctaataggataaaatttatatggtagactatatgctgttatcaagaaaaggtgtagtttcaagtagcaa Predict ORF larger than 30AA ================================================ Protein_Len: 43 Strand: - Start: 2 End: 130 . I N I R V E R A N E L K L S F L L P P P C L S I P Y F K Y P L S Y A T I L F L H L K M ....... tgatattaatcctcacttctcgtgcgttttccaacttgagggaaaaaagcaaaggggggggacacaagctaataggataaaatttatatggtagactatatgctgttatcaagaaaaggtgtagtttcaagtagcaa 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================================================ tgatattaatcctcacttctcgtgcgttttccaacttgagggaaaaaagcaaaggggggggacacaagctaataggataaaatttatatggtagactatatgctgttatcaagaaaaggtgtagtttcaagtagcaa Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TF2860:TF2861|TF2860:TF2861:hypothetical protein:conserved hypothetical protein; possible Rhs family protein:->->:3051741..3051877 137 tgatattaatcctcacttctcgtgcgttttccaacttgagggaaaaaagcaaaggggggggacacaagctaataggataaaatttatatggtagactatatgctgttatcaagaaaaggtgtagtttcaagtagcaa Intra-Species Hit: Count: 1 Min: 1 Max: 137 Len: 137 Subject: tfor_TF2860_TF2861|hypothetical protein:conserved hypothetical protein; possible Rhs family protein|POSITIVE:POSITIVE|[3051741,3051877]|137 HSP 1 e-value: 6.0E-58 bit: 224.0 Len: 137 Query Start:1 Query End:137 Subject Strand: POSITIVE Subject Start: 1 Subject End: 137 tgatattaatcctcacttctcgtgcgttttccaacttgagggaaaaaagcaaannnnnnnnacacaagctaataggataaaatttatatggtagactatatgctgttatcaagaaaaggtgtagtttcaagtagcaa tgatattaatcctcacttctcgtgcgttttccaacttgagggaaaaaagcaaaggggggggacacaagctaataggataaaatttatatggtagactatatgctgttatcaagaaaaggtgtagtttcaagtagcaa Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGAUAUUAAUCCUCACUUCUCGUGCGUUUUCCAACUUGAGGGAAAAAAGCAAAGGGGGGGGACACAAGCUAAUAGGAUAAAAUUUAUAUGGUAGACUAUAUGCUGUUAUCAAGAAAAGGUGUAGUUUCAAGUAGCAA .........(((((.(((((..(((.((((((.......))))))...))).)))))))))).....((((....(((((....(((((((....)))))))...)))))..((((........))))...)))).. (-33.70) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUGCUACUUGAAACUACACCUUUUCUUGAUAACAGCAUAUAGUCUACCAUAUAAAUUUUAUCCUAUUAGCUUGUGUCCCCCCCCUUUGCUUUUUUCCCUCAAGUUGGAAAACGCACGAGAAGUGAGGAUUAAUAUCA .......((((..((.(((.(((((..((((..(((..((((..((............))..))))..)))..)))).........(((..((((((........)))))).))).))))))))))..))))..... (-19.80) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 358 69 25 185 144 tfor:TF1343|5end_hypothetical_protein_1424630..1424860_POSITIVE 345 60 11 196 150 tfor:TF1840|5end_transposase_1990221..1990451_POSITIVE 339 69 21 83 28 tfor:TF2894|5end_conserved_hypothetical_protein;_possible_Fic_family_protein_3082326..3082556_POSITIVE 339 69 21 201 150 tfor:TF0542|5end_hypothetical_protein_571918..572148_POSITIVE 332 59 11 206 165 tfor:TF0536|5end_conserved_hypothetical_protein_561917..562147_POSITIVE 328 60 11 50 3 tfor:TF1842|5end_hypothetical_protein_1992571..1992801_POSITIVE 324 59 17 53 7 tfor:TF1167|5end_hypothetical_protein_1248559..1248789_POSITIVE 324 69 22 72 36 tfor:TF0680|5end_tail-specific_protease_721393..721623_POSITIVE 317 59 11 147 99 tfor:TF3107|5end_hypothetical_protein_3338459..3338689_POSITIVE 313 69 25 50 10 tfor:TF1336|5end_hypothetical_protein_1418626..1418856_POSITIVE 308 62 21 195 147 tfor:TF1182|5end_hypothetical_protein_1268565..1268795_POSITIVE 305 69 22 115 55 tfor:TF3158|5end_inner_membrane_protein_3393729..3393959_POSITIVE 302 58 11 104 52 tfor:TF2465|5end_O-methyltransferase_2643737..2643967_POSITIVE 300 39 12 48 20 tfor:TF2422|5end_hypothetical_protein_2601298..2601528_POSITIVE 300 90 54 226 192 tfor:TF0026|5end_hypothetical_protein_21877..22107_POSITIVE 296 67 22 138 98 tfor:TF0607|5end_DnaK_suppressor_protein_637441..637671_POSITIVE 296 59 11 208 163 tfor:TF0540|5end_conserved_hypothetical_protein;_possible_surface_protein_567286..567516_POSITIVE 295 63 38 224 198 tfor:TF2603|5end_transcriptional_regulator,_AraC_family_2776578..2776808_POSITIVE 293 59 16 41 4 tfor:TF0828|5end_hypothetical_protein_887090..887320_POSITIVE 291 60 11 193 139 tfor:TF2915|5end_hypothetical_protein_3110422..3110652_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 358 69 25 95 54 tfor:TF1342|3end_possible_lipoprotein_1424620..1424770_POSITIVE 339 69 21 61 10 tfor:TF0541|3end_conserved_hypothetical_protein_571858..572008_POSITIVE 324 69 22 88 52 tfor:TF0679|3end_hypothetical_protein_721489..721639_POSITIVE 320 60 11 111 65 tfor:TF0370|3end_hypothetical_protein_386317..386467_POSITIVE 305 69 22 93 33 tfor:TF3157|3end_sodium/solute_symporter_3393787..3393937_POSITIVE 296 67 22 121 81 tfor:TF0606|3end_signal_peptidase_II_637504..637654_POSITIVE 295 63 38 66 40 tfor:TF2602|3end_tRNA-(5-methylaminomethyl-2-thiouridylate)_methyltransferase_2776500..2776650_POSITIVE 286 70 22 64 26 tfor:TF1266|3end_conserved_hypothetical_protein_1354165..1354315_POSITIVE 286 60 16 59 9 tfor:TF0864|3end_O-succinylbenzoate--CoA_ligase_915708..915858_POSITIVE 286 61 22 76 28 tfor:TF0830|3end_hypothetical_protein_887845..887995_POSITIVE 284 59 18 61 12 tfor:TF0470|3end_hypothetical_protein_487518..487668_POSITIVE 283 70 21 71 3 tfor:TF2527|3end_RNA_polymerase_ECF-type_sigma_factor_2710749..2710899_POSITIVE 283 59 12 76 15 tfor:TF1599|3end_ribonuclease_P_protein_component_1714054..1714204_POSITIVE 282 59 11 90 46 tfor:TF0821|3end_hypothetical_protein_880195..880345_POSITIVE 282 58 11 80 31 tfor:TF0369|3end_hypothetical_protein_386186..386336_POSITIVE 282 60 14 144 83 tfor:TF0098|3end_permease_109280..109430_POSITIVE 279 59 11 69 20 tfor:TF0828|3end_hypothetical_protein_887508..887658_POSITIVE 277 60 16 121 64 tfor:TF1472|3end_acyl-ACP_thioesterase_1566337..1566487_POSITIVE 272 60 11 147 95 tfor:TF2950|3end_chloromuconate_cycloisomerase_3158549..3158699_POSITIVE 272 60 11 79 30 tfor:TF2860|3end_hypothetical_protein_3051680..3051830_POSITIVE