Origin IGS: tattcacgctaaaacgaagatttcgtctccctcctgatgtttttctccctccctaacaaaggggatatagtcctcaaaaatccccttttttagggattgtgaacactgttcatttggcgtaattttgcaattgtaattttactgtttaagtagataa .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 ttatctacttaaacagtaaaattacaattgcaaaattacgccaaatgaacagtgttcacaatccctaaaaaaggggatttttgaggactatatcccctttgttagggagggagaaaaacatcaggagggagacgaaatcttcgttttagcgtgaata Mask Tandem Repeat Region ================================================ tattcacgctaaaacgaagatttcgtctccctcctgatgtttttctccctccctaacaaaggggatatagtcctcaaaaatccccttttttagggattgtgaacactgttcatttggcgtaattttgcaattgtaattttactgtttaagtagataa Find is-nt database================================================ Query_seq: TF2602:TF2603|TF2602:TF2603:tRNA-(5-methylaminomethyl-2-thiouridylate) methyltransferase:transcriptional regulator, AraC family:->->:2776561..2776717 157 tattcacgctaaaacgaagatttcgtctccctcctgatgtttttctccctccctaacaaaggggatatagtcctcaaaaatccccttttttagggattgtgaacactgttcatttggcgtaattttgcaattgtaattttactgtttaagtagataa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF2602:TF2603|TF2602:TF2603:tRNA-(5-methylaminomethyl-2-thiouridylate) methyltransferase:transcriptional regulator, AraC family:->->:2776561..2776717 157 tattcacgctaaaacgaagatttcgtctccctcctgatgtttttctccctccctaacaaaggggatatagtcctcaaaaatccccttttttagggattgtgaacactgttcatttggcgtaattttgcaattgtaattttactgtttaagtagataa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF2602:TF2603|TF2602:TF2603:tRNA-(5-methylaminomethyl-2-thiouridylate) methyltransferase:transcriptional regulator, AraC family:->->:2776561..2776717 157 tattcacgctaaaacgaagatttcgtctccctcctgatgtttttctccctccctaacaaaggggatatagtcctcaaaaatccccttttttagggattgtgaacactgttcatttggcgtaattttgcaattgtaattttactgtttaagtagataa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tattcacgctaaaacgaagatttcgtctccctcctgatgtttttctccctccctaacaaaggggatatagtcctcaaaaatccccttttttagggattgtgaacactgttcatttggcgtaattttgcaattgtaattttactgtttaagtagataa Predict ORF larger than 30AA ================================================ Protein_Len: 39 Strand: - Start: 7 End: 123 ...... A L V F I E D G E Q H K E G E R V F P I Y D E F I G K K L S Q S C Q E N P T M .................................. tattcacgctaaaacgaagatttcgtctccctcctgatgtttttctccctccctaacaaaggggatatagtcctcaaaaatccccttttttagggattgtgaacactgttcatttggcgtaattttgcaattgtaattttactgtttaagtagataa 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================================================ tattcacgctaaaacgaagatttcgtctccctcctgatgtttttctccctccctaacaaaggggatatagtcctcaaaaatccccttttttagggattgtgaacactgttcatttggcgtaattttgcaattgtaattttactgtttaagtagataa Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 80 HP_score: -11.1 Tail_Score: -3.31248 Start: 50 End: 96 Full_Region: TGATGTTTTTCTCCC TCCCTAACAAAGGGGATAT AGTCCTCAA AAATCCCCTTTTTTAGGGA TTGTGAACACTGTTC .................................................TCCCTAACAAAGGGGATATAGTCCTCAAAAATCCCCTTTTTTAGGGA............................................................. Find igs database================================================ Query_seq: TF2602:TF2603|TF2602:TF2603:tRNA-(5-methylaminomethyl-2-thiouridylate) methyltransferase:transcriptional regulator, AraC family:->->:2776561..2776717 157 tattcacgctaaaacgaagatttcgtctccctcctgatgtttttctccctccctaacaaaggggatatagtcctcaaaaatccccttttttagggattgtgaacactgttcatttggcgtaattttgcaattgtaattttactgtttaagtagataa Intra-Species Hit: Count: 1 Min: 1 Max: 157 Len: 157 Subject: tfor_TF2602_TF2603|tRNA-(5-methylaminomethyl-2-thiouridylate) methyltransferase:transcriptional regulator, AraC family|POSITIVE:POSITIVE|[2776561,2776717]|157 HSP 1 e-value: 4.0E-84 bit: 311.0 Len: 157 Query Start:1 Query End:157 Subject Strand: POSITIVE Subject Start: 1 Subject End: 157 tattcacgctaaaacgaagatttcgtctccctcctgatgtttttctccctccctaacaaaggggatatagtcctcaaaaatccccttttttagggattgtgaacactgttcatttggcgtaattttgcaattgtaattttactgtttaagtagataa tattcacgctaaaacgaagatttcgtctccctcctgatgtttttctccctccctaacaaaggggatatagtcctcaaaaatccccttttttagggattgtgaacactgttcatttggcgtaattttgcaattgtaattttactgtttaagtagataa Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAUUCACGCUAAAACGAAGAUUUCGUCUCCCUCCUGAUGUUUUUCUCCCUCCCUAACAAAGGGGAUAUAGUCCUCAAAAAUCCCCUUUUUUAGGGAUUGUGAACACUGUUCAUUUGGCGUAAUUUUGCAAUUGUAAUUUUACUGUUUAAGUAGAUAA .....(((((((...(((((...((((........)))).)))))....(((((((.(((((((((.............))))))))).)))))))..((((((...)))))))))))))....((((....)))).((((((.....))))))... (-44.22) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUAUCUACUUAAACAGUAAAAUUACAAUUGCAAAAUUACGCCAAAUGAACAGUGUUCACAAUCCCUAAAAAAGGGGAUUUUUGAGGACUAUAUCCCCUUUGUUAGGGAGGGAGAAAAACAUCAGGAGGGAGACGAAAUCUUCGUUUUAGCGUGAAUA ...............((((........))))....((((((....(((......(((.(..(((((((.(((((((((.............))))))))).)))))))..).))).....))).....(((((((.....))))))).))))))... (-41.32) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 397 54 16 230 187 tfor:TF0830|5end_hypothetical_protein_887610..887840_POSITIVE 346 64 28 134 97 tfor:TF3107|5end_hypothetical_protein_3338459..3338689_POSITIVE 329 63 24 231 194 tfor:TF2653|5end_hypothetical_protein_2822093..2822323_POSITIVE 317 50 6 176 133 tfor:TF2789|5end_enoyl-[acyl-carrier-protein]_reductase_2972431..2972661_POSITIVE 308 64 40 33 9 tfor:TF2746|5end_hypothetical_protein_2927996..2928226_POSITIVE 306 77 39 159 120 tfor:TF0828|5end_hypothetical_protein_887090..887320_POSITIVE 296 52 14 56 18 tfor:TF2159|5end_conserved_hypothetical_protein_2334446..2334676_POSITIVE 295 51 25 191 166 tfor:TF2861|5end_conserved_hypothetical_protein;_possible_Rhs_family_protein_3051738..3051968_POSITIVE 295 102 71 219 184 tfor:TF0394|5end_oxaloacetate_decarboxylase,_alpha_subunit_(pyruvate_carboxylase,_C-terminal_domain)_413268..413498_POSITIVE 294 49 6 195 148 tfor:TF1329|5end_glucose-1-phosphate_thymidyltransferase_1408578..1408808_POSITIVE 293 120 76 133 93 tfor:TF1720|5end_conserved_hypothetical_protein_1843679..1843909_POSITIVE 292 72 31 76 24 tfor:TF2950|5end_chloromuconate_cycloisomerase_3157399..3157629_POSITIVE 292 77 47 76 45 tfor:TF2191|5end_hypothetical_protein_2365934..2366164_POSITIVE 292 58 25 221 182 tfor:TF1348|5end_conserved_hypothetical_protein_1428170..1428400_POSITIVE 292 77 47 211 180 tfor:TF0823|5end_conserved_hypothetical_protein_880660..880890_POSITIVE 292 77 47 38 7 tfor:TF0822|5end_hypothetical_protein_880487..880717_POSITIVE 292 77 47 65 34 tfor:TF0679|5end_hypothetical_protein_721155..721385_POSITIVE 291 86 47 65 27 tfor:TF1908|5end_possible_phosphoglycerate_mutase_2062695..2062925_POSITIVE 291 65 26 135 82 tfor:TF0346|5end_hypothetical_protein_367048..367278_POSITIVE 288 57 15 228 171 tfor:TF2215|5end_conserved_hypothetical_protein_2387501..2387731_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 459 64 24 57 15 tfor:TF0828|3end_hypothetical_protein_887508..887658_POSITIVE 362 64 24 73 35 tfor:TF2651|3end_hypothetical_protein_2822014..2822164_POSITIVE 348 64 22 145 94 tfor:TF1168|3end_hypothetical_protein_1249092..1249242_POSITIVE 341 64 24 37 9 tfor:TF1169|3end_lipoprotein_ABC_transporter,_permease_component_1251573..1251723_POSITIVE 338 64 22 69 16 tfor:TF1588|3end_hypothetical_protein_1702560..1702710_POSITIVE 330 64 24 80 43 tfor:TF0821|3end_hypothetical_protein_880195..880345_POSITIVE 330 64 24 99 62 tfor:TF0370|3end_hypothetical_protein_386317..386467_POSITIVE 314 70 21 78 42 tfor:TF2480|3end_hypothetical_protein_2657708..2657858_POSITIVE 296 52 14 114 76 tfor:TF2158|3end_conserved_hypothetical_protein_2334584..2334734_POSITIVE 295 51 25 53 28 tfor:TF2860|3end_hypothetical_protein_3051680..3051830_POSITIVE 293 120 76 42 2 tfor:TF1719|3end_ribonuclease_R_1843668..1843818_POSITIVE 292 72 31 76 24 tfor:TF2949|3end_dihydroxynaphthoate_synthase_(naphthoate_synthase)_3157479..3157629_POSITIVE 288 53 15 59 14 tfor:TF0238|3end_outer_membrane_protein_268957..269107_POSITIVE 286 140 91 107 57 tfor:TF3074|3end_tonB-dependent_receptor_HmuR_3302777..3302927_POSITIVE 284 100 51 54 4 tfor:TF0384|3end_conserved_hypothetical_protein_406140..406290_POSITIVE 283 49 4 130 72 tfor:TF1909|3end_cobalamin_(5`-phosphate)_synthase_2064075..2064225_POSITIVE 275 49 3 66 5 tfor:TF1488|3end_conserved_hypothetical_protein_1588975..1589125_POSITIVE 273 102 61 69 24 tfor:TF0874|3end_transposase_926652..926802_POSITIVE 271 69 30 67 26 tfor:TF1739|3end_possible_sulfatase_1868604..1868754_POSITIVE 270 118 71 47 5 tfor:TF2171|3end_hypothetical_protein_2345792..2345942_POSITIVE