Origin IGS: tcgattctaatttgaccgagtaaagataagacatattttttactgtaaatccataaaaaaaactaaccgaatgcaatctgctgatggaaagcgttctaaacttattttgggagcgttttttccatttttaacgcccgactttgaaaataatagatacttttgtaattaagaatattaaagtaaggaggaaacagca .........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 tgctgtttcctccttactttaatattcttaattacaaaagtatctattattttcaaagtcgggcgttaaaaatggaaaaaacgctcccaaaataagtttagaacgctttccatcagcagattgcattcggttagttttttttatggatttacagtaaaaaatatgtcttatctttactcggtcaaattagaatcga Mask Tandem Repeat Region ================================================ tcgattctaatttgaccgagtaaagataagacatattttttactgtaaatccataaaaaaaactaaccgaatgcaatctgctgatggaaagcgttctaaacttattttgggagcgttttttccatttttaacgcccgactttgaaaataatagatacttttgtaattaagaatattaaagtaaggaggaaacagca Find is-nt database================================================ Query_seq: TF2988:TF2989|TF2988:TF2989:conserved hypothetical protein:conserved hypothetical protein:->->:3205013..3205208 196 tcgattctaatttgaccgagtaaagataagacatattttttactgtaaatccataaaaaaaactaaccgaatgcaatctgctgatggaaagcgttctaaacttattttgggagcgttttttccatttttaacgcccgactttgaaaataatagatacttttgtaattaagaatattaaagtaaggaggaaacagca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF2988:TF2989|TF2988:TF2989:conserved hypothetical protein:conserved hypothetical protein:->->:3205013..3205208 196 tcgattctaatttgaccgagtaaagataagacatattttttactgtaaatccataaaaaaaactaaccgaatgcaatctgctgatggaaagcgttctaaacttattttgggagcgttttttccatttttaacgcccgactttgaaaataatagatacttttgtaattaagaatattaaagtaaggaggaaacagca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF2988:TF2989|TF2988:TF2989:conserved hypothetical protein:conserved hypothetical protein:->->:3205013..3205208 196 tcgattctaatttgaccgagtaaagataagacatattttttactgtaaatccataaaaaaaactaaccgaatgcaatctgctgatggaaagcgttctaaacttattttgggagcgttttttccatttttaacgcccgactttgaaaataatagatacttttgtaattaagaatattaaagtaaggaggaaacagca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tcgattctaatttgaccgagtaaagataagacatattttttactgtaaatccataaaaaaaactaaccgaatgcaatctgctgatggaaagcgttctaaacttattttgggagcgttttttccatttttaacgcccgactttgaaaataatagatacttttgtaattaagaatattaaagtaaggaggaaacagca Predict ORF larger than 30AA ================================================ Protein_Len: 47 Strand: + Start: 26 End: 166 ......................... M R H I F Y C K S I K K T N R M Q S A D G K R S K L I L G A F F P F L T P D F E N N R Y F C N .............................. Protein_Len: 30 Strand: - Start: 105 End: 194 ........................................................................................................ K P L T K E M K L A R S Q F Y Y I S K Y N L I N F Y P P F M .. tcgattctaatttgaccgagtaaagataagacatattttttactgtaaatccataaaaaaaactaaccgaatgcaatctgctgatggaaagcgttctaaacttattttgggagcgttttttccatttttaacgcccgactttgaaaataatagatacttttgtaattaagaatattaaagtaaggaggaaacagca 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================================================ tcgattctaatttgaccgagtaaagataagacatattttttactgtaaatccataaaaaaaactaaccgaatgcaatctgctgatggaaagcgttctaaacttattttgggagcgttttttccatttttaacgcccgactttgaaaataatagatacttttgtaattaagaatattaaagtaaggaggaaacagca Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TF2988:TF2989|TF2988:TF2989:conserved hypothetical protein:conserved hypothetical protein:->->:3205013..3205208 196 tcgattctaatttgaccgagtaaagataagacatattttttactgtaaatccataaaaaaaactaaccgaatgcaatctgctgatggaaagcgttctaaacttattttgggagcgttttttccatttttaacgcccgactttgaaaataatagatacttttgtaattaagaatattaaagtaaggaggaaacagca Intra-Species Hit: Count: 1 Min: 1 Max: 196 Len: 196 Subject: tfor_TF2988_TF2989|conserved hypothetical protein:conserved hypothetical protein|POSITIVE:POSITIVE|[3205013,3205208]|196 HSP 1 e-value: 5.0E-93 bit: 341.0 Len: 196 Query Start:1 Query End:196 Subject Strand: POSITIVE Subject Start: 1 Subject End: 196 tcgattctaatttgaccgagtaaagataagacatattttttactgtaaatccatnnnnnnnnctaaccgaatgcaatctgctgatggaaagcgttctaaacttattttgggagcgttttttccatttttaacgcccgactttgaaaataatagatacttttgtaattaagaatattaaagtaaggaggaaacagca tcgattctaatttgaccgagtaaagataagacatattttttactgtaaatccataaaaaaaactaaccgaatgcaatctgctgatggaaagcgttctaaacttattttgggagcgttttttccatttttaacgcccgactttgaaaataatagatacttttgtaattaagaatattaaagtaaggaggaaacagca Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCGAUUCUAAUUUGACCGAGUAAAGAUAAGACAUAUUUUUUACUGUAAAUCCAUAAAAAAAACUAACCGAAUGCAAUCUGCUGAUGGAAAGCGUUCUAAACUUAUUUUGGGAGCGUUUUUUCCAUUUUUAACGCCCGACUUUGAAAAUAAUAGAUACUUUUGUAAUUAAGAAUAUUAAAGUAAGGAGGAAACAGCA (((..((......)).)))...((((((((.....(((((((.((......)))))))))........((((((..(((......)))..))))))....))))))))....(((((((((((.(((((((.(.....).))))))).......((((((.(((........))).)))))).))))))))).)). (-34.20) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGCUGUUUCCUCCUUACUUUAAUAUUCUUAAUUACAAAAGUAUCUAUUAUUUUCAAAGUCGGGCGUUAAAAAUGGAAAAAACGCUCCCAAAAUAAGUUUAGAACGCUUUCCAUCAGCAGAUUGCAUUCGGUUAGUUUUUUUUAUGGAUUUACAGUAAAAAAUAUGUCUUAUCUUUACUCGGUCAAAUUAGAAUCGA ((((((.(((.(((.(((((........((..(((....)))..))........))))).)))........(((((((((((...((.............(((.((..((........))..)).)))))...))))))))))))))...)))))).....................((((((......).))))) (-29.10) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 291 141 105 216 179 tfor:TF0906|5end_conserved_hypothetical_protein_949675..949905_POSITIVE 290 118 71 124 81 tfor:TF1600|5end_uroporphyrinogen-III_synthase_1713964..1714194_POSITIVE 276 103 64 210 163 tfor:TF2880|5end_phenylalanyl-tRNA_synthetase,_beta_subunit_3069052..3069282_POSITIVE 274 117 71 135 81 tfor:TF0185|5end_4-alpha-glucanotransferase_(amylomaltase)_196486..196716_POSITIVE 273 139 92 160 120 tfor:TF3158|5end_inner_membrane_protein_3393729..3393959_POSITIVE 270 135 103 106 70 tfor:TF2004|5end_thymidylate_synthase_2156372..2156602_POSITIVE 268 114 73 52 4 tfor:TF0032|5end_sugar_phosphate_permease,_major_facilitator_superfamily_27911..28141_POSITIVE 267 140 92 126 71 tfor:TF2039|5end_possible_cell-cycle_regulation_histidine_triad_(HIT)_protein_2199318..2199548_POSITIVE 265 144 105 145 108 tfor:TF1246|5end_protease,_with_chaperone_function_1329390..1329620_POSITIVE 262 94 60 226 195 tfor:TF2707|5end_glutamine_amidotransferase_2878305..2878535_POSITIVE 262 138 92 229 180 tfor:TF2512|5end_possible_abortive_infection_protein_2690247..2690477_POSITIVE 261 116 78 102 60 tfor:TF0961|5end_translation_initiation_inhibitor,_endoribonuclease_activity_1010445..1010675_POSITIVE 260 99 57 106 64 tfor:TF0595|5end_hypothetical_protein_627820..628050_POSITIVE 258 109 67 58 9 tfor:TF2501|5end_DNA_mismatch_repair_protein_2676280..2676510_POSITIVE 258 137 102 63 24 tfor:TF0579|5end_DNA-binding_protein_HU_609724..609954_POSITIVE 258 117 80 207 160 tfor:TF0464|5end_precorrin_methylase_480211..480441_POSITIVE 257 137 91 162 110 tfor:TF2810|5end_conserved_hypothetical_protein_3000583..3000813_POSITIVE 256 119 77 88 41 tfor:TF1931|5end_ATPase/GTPase_2078123..2078353_POSITIVE 252 115 71 174 130 tfor:TF1295|5end_conserved_hypothetical_protein_1375854..1376084_POSITIVE 251 116 80 215 178 tfor:TF2513|5end_conserved_hypothetical_protein_2691146..2691376_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 298 143 105 140 94 tfor:TF2511|3end_RNA_binding_protein_2690232..2690382_POSITIVE 290 118 71 134 91 tfor:TF1599|3end_ribonuclease_P_protein_component_1714054..1714204_POSITIVE 276 103 64 86 39 tfor:TF2879|3end_tRNA_(guanine-N-1)-methyltransferase_3069008..3069158_POSITIVE 274 117 71 136 82 tfor:TF0183|3end_conserved_hypothetical_protein_196567..196717_POSITIVE 273 139 92 138 98 tfor:TF3157|3end_sodium/solute_symporter_3393787..3393937_POSITIVE 270 135 103 81 45 tfor:TF2003|3end_dihydrofolate_reductase_2156427..2156577_POSITIVE 270 111 72 51 21 tfor:TF0822|3end_hypothetical_protein_880764..880914_POSITIVE 267 117 75 147 99 tfor:TF2979|3end_possible_outer_membrane__protein_3193164..3193314_POSITIVE 265 144 105 137 100 tfor:TF1245|3end_LemA_protein_1329462..1329612_POSITIVE 261 116 78 83 41 tfor:TF0960|3end_beta-galactosidase_1010506..1010656_POSITIVE 260 99 57 132 90 tfor:TF0594|3end_conserved_hypothetical_protein;_possible_PAP2_superfamily_protein_627926..628076_POSITIVE 256 119 77 88 41 tfor:TF1930|3end_two-component_response_regulator_2078203..2078353_POSITIVE 251 94 53 55 13 tfor:TF2503|3end_conserved_hypothetical_protein_2680111..2680261_POSITIVE 249 129 81 140 94 tfor:TF1333|3end_probable_acylaminoacyl_peptidase;_alanyl_dipeptidyl_peptidase_1416014..1416164_POSITIVE 246 129 89 143 98 tfor:TF2240|3end__tetracycline_resistance_element_mobilization_regulatory_protein_2415417..2415567_POSITIVE 243 117 76 144 90 tfor:TF1358|3end_hypothetical_protein_1438879..1439029_POSITIVE 242 96 67 126 101 tfor:TF2336|3end_conserved_hypothetical_protein_2498159..2498309_POSITIVE 241 114 71 66 29 tfor:TF0549|3end_universal_stress_protein,_UspA_582658..582808_POSITIVE 241 136 106 122 92 tfor:TF0207|3end_conserved_hypothetical_protein_233505..233655_POSITIVE 240 137 91 64 9 tfor:TF3144|3end_phosphomannomutase/phosphoglucomutase_3381184..3381334_POSITIVE