Origin IGS: taatcacaacacatcggacaatgatattcctgcaaaaccggcgacacaataaaacaaagcggcagtccgttcttcaaaagaaaacgaaaatcaattacactaaaacctgtaaaaa .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tttttacaggttttagtgtaattgattttcgttttcttttgaagaacggactgccgctttgttttattgtgtcgccggttttgcaggaatatcattgtccgatgtgttgtgatta Mask Tandem Repeat Region ================================================ taatcacaacacatcggacaatgatattcctgcaaaaccggcgacacaataaaacaaagcggcagtccgttcttcaaaagaaaacgaaaatcaattacactaaaacctgtaaaaa Find is-nt database================================================ Query_seq: TF1812:TF1813|TF1812:TF1813:tryptophan synthase, beta chain:peptide methionine sulfoxide reductase:->->:1954195..1954309 115 taatcacaacacatcggacaatgatattcctgcaaaaccggcgacacaataaaacaaagcggcagtccgttcttcaaaagaaaacgaaaatcaattacactaaaacctgtaaaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF1812:TF1813|TF1812:TF1813:tryptophan synthase, beta chain:peptide methionine sulfoxide reductase:->->:1954195..1954309 115 taatcacaacacatcggacaatgatattcctgcaaaaccggcgacacaataaaacaaagcggcagtccgttcttcaaaagaaaacgaaaatcaattacactaaaacctgtaaaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF1812:TF1813|TF1812:TF1813:tryptophan synthase, beta chain:peptide methionine sulfoxide reductase:->->:1954195..1954309 115 taatcacaacacatcggacaatgatattcctgcaaaaccggcgacacaataaaacaaagcggcagtccgttcttcaaaagaaaacgaaaatcaattacactaaaacctgtaaaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taatcacaacacatcggacaatgatattcctgcaaaaccggcgacacaataaaacaaagcggcagtccgttcttcaaaagaaaacgaaaatcaattacactaaaacctgtaaaaa Predict ORF larger than 30AA ================================================ Protein_Len: 37 Strand: + Start: 3 End: 113 .. M T T H R T M I F L Q N R R H N K T K R Q S V L Q K K T K I N Y T K T C K .. Protein_Len: 31 Strand: - Start: 3 End: 95 .. D C C M P C H Y E Q L V P S V I F C L P L G N K L L F R F D M .................... taatcacaacacatcggacaatgatattcctgcaaaaccggcgacacaataaaacaaagcggcagtccgttcttcaaaagaaaacgaaaatcaattacactaaaacctgtaaaaa 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================================================ taatcacaacacatcggacaatgatattcctgcaaaaccggcgacacaataaaacaaagcggcagtccgttcttcaaaagaaaacgaaaatcaattacactaaaacctgtaaaaa Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TF1812:TF1813|TF1812:TF1813:tryptophan synthase, beta chain:peptide methionine sulfoxide reductase:->->:1954195..1954309 115 taatcacaacacatcggacaatgatattcctgcaaaaccggcgacacaataaaacaaagcggcagtccgttcttcaaaagaaaacgaaaatcaattacactaaaacctgtaaaaa Intra-Species Hit: Count: 1 Min: 1 Max: 115 Len: 115 Subject: tfor_TF1812_TF1813|tryptophan synthase, beta chain:peptide methionine sulfoxide reductase|POSITIVE:POSITIVE|[1954195,1954309]|115 HSP 1 e-value: 3.0E-59 bit: 228.0 Len: 115 Query Start:1 Query End:115 Subject Strand: POSITIVE Subject Start: 1 Subject End: 115 taatcacaacacatcggacaatgatattcctgcaaaaccggcgacacaataaaacaaagcggcagtccgttcttcaaaagaaaacgaaaatcaattacactaaaacctgtaaaaa taatcacaacacatcggacaatgatattcctgcaaaaccggcgacacaataaaacaaagcggcagtccgttcttcaaaagaaaacgaaaatcaattacactaaaacctgtaaaaa Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAUCACAACACAUCGGACAAUGAUAUUCCUGCAAAACCGGCGACACAAUAAAACAAAGCGGCAGUCCGUUCUUCAAAAGAAAACGAAAAUCAAUUACACUAAAACCUGUAAAAA .....................((((.(((..((.......))...............(((((....)))))..............))).)))).(((((........)))))... ( -9.90) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUUUACAGGUUUUAGUGUAAUUGAUUUUCGUUUUCUUUUGAAGAACGGACUGCCGCUUUGUUUUAUUGUGUCGCCGGUUUUGCAGGAAUAUCAUUGUCCGAUGUGUUGUGAUUA ...((((((................((((((........)))))).(((((......(((((...((((......))))...))))).........))))).....))))))... (-15.66) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 329 64 21 192 151 tfor:TF3098|5end_conserved_hypothetical_protein_3329913..3330143_POSITIVE 317 47 14 69 43 tfor:TF1740|5end_hypothetical_protein_1868645..1868875_POSITIVE 301 60 11 75 13 tfor:TF0192|5end_hypothetical_protein_207446..207676_POSITIVE 298 48 13 144 105 tfor:TF1623|5end_5-formyltetrahydrofolate_cyclo-ligase_1736698..1736928_POSITIVE 294 69 28 72 25 tfor:TF2342|5end_glutathione_peroxidase_2505963..2506193_POSITIVE 289 69 30 46 9 tfor:TF1198|5end_conserved_hypothetical_protein_1281464..1281694_POSITIVE 287 44 7 54 24 tfor:TF1241|5end_prolyl-tRNA_synthetase_1324711..1324941_POSITIVE 286 67 21 231 192 tfor:TF2908|5end_transcriptional_regulator,_AraC_family_3103696..3103926_POSITIVE 282 80 38 227 187 tfor:TF2577|5end_30S_ribosomal_protein_S13_2746308..2746538_POSITIVE 282 65 21 64 20 tfor:TF0279|5end_conserved_hypothetical_protein_307142..307372_POSITIVE 280 65 21 35 4 tfor:TF2798|5end_conserved_hypothetical_protein_2984023..2984253_POSITIVE 276 70 22 184 137 tfor:TF1426|5end_N-acetylymuramoylalanyl-D-glutamate-2,6-diaminopi_melate_ligase_1509873..1510103_POSITIVE 276 43 3 136 94 tfor:TF0816|5end_hypothetical_protein_874217..874447_POSITIVE 276 48 12 213 180 tfor:TF0634|5end_hypothetical_protein_668120..668350_POSITIVE 275 70 24 70 16 tfor:TF2906|5end_phosphatidylserine_decarboxylase_3102182..3102412_POSITIVE 273 87 42 194 141 tfor:TF2842|5end_methyltransferase_3032094..3032324_POSITIVE 273 64 27 51 8 tfor:TF2515|5end_outer_membrane_protein,_TonB_dependent_receptor_2692854..2693084_POSITIVE 273 69 32 39 2 tfor:TF1742|5end_TPR_repeat-containing_protein_1873129..1873359_POSITIVE 272 86 41 76 33 tfor:TF1775|5end_oxidoreductase,_Gfo/Idh/MocA_family_1913135..1913365_POSITIVE 271 47 16 230 204 tfor:TF1953|5end_methlytransferase,_possible_UbiE/COQ5_family_2103806..2104036_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 323 42 6 113 72 tfor:TF1774|3end_arylsulfatase_precursor_1912939..1913089_POSITIVE 301 69 21 151 97 tfor:TF2907|3end_CDP-diacylglycerol-serine-O-phosphatidyltransfera_se_3103681..3103831_POSITIVE 298 48 13 129 90 tfor:TF1622|3end_conserved_hypothetical_protein_1736763..1736913_POSITIVE 294 69 28 56 9 tfor:TF2341|3end_hypothetical_protein_2506027..2506177_POSITIVE 282 46 3 148 104 tfor:TF3097|3end_conserved_hypothetical_protein_3329961..3330111_POSITIVE 282 80 38 46 6 tfor:TF2576|3end_translation_initiation_factor_IF-1_2746207..2746357_POSITIVE 269 60 19 135 97 tfor:TF2946|3end_conserved_hypothetical_protein;_possible_ATPase_3153362..3153512_POSITIVE 267 85 45 73 37 tfor:TF0383|3end_alkyl_hydroperoxide_reductase,_subunit_C_406056..406206_POSITIVE 267 70 27 53 4 tfor:TF0281|3end_hypothetical_protein_309159..309309_POSITIVE 265 69 29 119 76 tfor:TF2882|3end_conserved_hypothetical_protein_3074401..3074551_POSITIVE 261 46 14 32 3 tfor:TF0378|3end_aspartyl-tRNA_synthetase_399520..399670_POSITIVE 257 58 12 53 12 tfor:TF2157|3end_conserved_hypothetical_protein_2333924..2334074_POSITIVE 257 67 21 125 74 tfor:TF0663|3end_conserved_hypothetical_protein_709093..709243_POSITIVE 257 80 33 78 35 tfor:TF0189|3end_phosphatidate_cytidylytransferase_(CDP-diglyceride_synthetase)_204090..204240_POSITIVE 255 43 14 145 116 tfor:TF1425|3end_phospho-N-acetylmuramoyl_pentapeptide_transferase_1509942..1510092_POSITIVE 253 70 23 112 64 tfor:TF0675|3end_conserved_hypothetical_protein_719019..719169_POSITIVE 251 44 12 49 20 tfor:TF0388|3end_conserved_hypothetical_protein;_possible_integral_membrane_protein_408846..408996_POSITIVE 251 70 21 66 21 tfor:TF0023|3end_possible_response_element_in_two_component_regulation_20233..20383_POSITIVE 249 69 27 54 6 tfor:TF1197|3end_transcriptional_regulator_1281414..1281564_POSITIVE 247 69 24 39 1 tfor:TF2912|3end_hypothetical_protein_3108000..3108150_POSITIVE