Origin IGS: ttaaggatttggaagaatatagagaataaaccggtaacatgttgtaaattagtcgattttctatatgctgcgagtgtggcaggaaagcaattcggcacggaatattgaatcctttcagttaccaaaccgttatccgccagtttccccagtggggcgaggtaacgaaaaaggaaagatttttctggagtaggttctatctctatgttccacaacgttttgcttatcaaaggacgctttaacaacgggtaattttgcccataaaattaaagcgt .........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.........1.........2.........3.........4.........5.........6.........7.........8.........9 acgctttaattttatgggcaaaattacccgttgttaaagcgtcctttgataagcaaaacgttgtggaacatagagatagaacctactccagaaaaatctttcctttttcgttacctcgccccactggggaaactggcggataacggtttggtaactgaaaggattcaatattccgtgccgaattgctttcctgccacactcgcagcatatagaaaatcgactaatttacaacatgttaccggtttattctctatattcttccaaatccttaa Mask Tandem Repeat Region ================================================ ttaaggatttggaagaatatagagaataaaccggtaacatgttgtaaattagtcgattttctatatgctgcgagtgtggcaggaaagcaattcggcacggaatattgaatcctttcagttaccaaaccgttatccgccagtttccccagtggggcgaggtaacgaaaaaggaaagatttttctggagtaggttctatctctatgttccacaacgttttgcttatcaaaggacgctttaacaacgggtaattttgcccataaaattaaagcgt Find is-nt database================================================ Query_seq: TF0908:TF0909|TF0908:TF0909:integrase fragment:Tn5520-like integrase (transfer factor):->->:951085..951356 272 ttaaggatttggaagaatatagagaataaaccggtaacatgttgtaaattagtcgattttctatatgctgcgagtgtggcaggaaagcaattcggcacggaatattgaatcctttcagttaccaaaccgttatccgccagtttccccagtggggcgaggtaacgaaaaaggaaagatttttctggagtaggttctatctctatgttccacaacgttttgcttatcaaaggacgctttaacaacgggtaattttgcccataaaattaaagcgt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF0908:TF0909|TF0908:TF0909:integrase fragment:Tn5520-like integrase (transfer factor):->->:951085..951356 272 ttaaggatttggaagaatatagagaataaaccggtaacatgttgtaaattagtcgattttctatatgctgcgagtgtggcaggaaagcaattcggcacggaatattgaatcctttcagttaccaaaccgttatccgccagtttccccagtggggcgaggtaacgaaaaaggaaagatttttctggagtaggttctatctctatgttccacaacgttttgcttatcaaaggacgctttaacaacgggtaattttgcccataaaattaaagcgt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF0908:TF0909|TF0908:TF0909:integrase fragment:Tn5520-like integrase (transfer factor):->->:951085..951356 272 ttaaggatttggaagaatatagagaataaaccggtaacatgttgtaaattagtcgattttctatatgctgcgagtgtggcaggaaagcaattcggcacggaatattgaatcctttcagttaccaaaccgttatccgccagtttccccagtggggcgaggtaacgaaaaaggaaagatttttctggagtaggttctatctctatgttccacaacgttttgcttatcaaaggacgctttaacaacgggtaattttgcccataaaattaaagcgt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ttaaggatttggaagaatatagagaataaaccggtaacatgttgtaaattagtcgattttctatatgctgcgagtgtggcaggaaagcaattcggcacggaatattgaatcctttcagttaccaaaccgttatccgccagtttccccagtggggcgaggtaacgaaaaaggaaagatttttctggagtaggttctatctctatgttccacaacgttttgcttatcaaaggacgctttaacaacgggtaattttgcccataaaattaaagcgt Predict ORF larger than 30AA ================================================ Protein_Len: 33 Strand: + Start: 7 End: 105 ...... M W K N I E N K P V T C C K L V D F L Y A A S V A G K Q F G T E Y ....................................................................................................................................................................... Protein_Len: 44 Strand: + Start: 56 End: 187 ....................................................... M F Y M L R V W Q E S N S A R N I E S F Q L P N R Y P P V S P V G R G N E K G K I F L E ..................................................................................... Protein_Len: 60 Strand: + Start: 48 End: 236 ............................................... M S R F S I C C E C G R K A I R H G I L N P F S Y Q T V I R Q F P Q W G E V T K K E R F F W S R F Y L Y V P Q R F A Y Q .................................... Protein_Len: 44 Strand: - Start: 133 End: 264 .................................................................................................................................... G G T E G T P R P L S F P F I K R S Y T R D R H E V V N Q K D F S A K V V P L K A W L M ........ Protein_Len: 60 Strand: - Start: 3 End: 242 .. Y A A L T A P F C N P V S Y Q I R E T V L G N D A L K G L P A L Y R F L F S K E P T P E I E I N W L T K S I L P R K L M .............................. Protein_Len: 39 Strand: - Start: 2 End: 118 . L S K S S Y L S Y V P L M N Y I L R N E I H Q S H P L F A I R C P I N F G K M .......................................................................................................................................................... ttaaggatttggaagaatatagagaataaaccggtaacatgttgtaaattagtcgattttctatatgctgcgagtgtggcaggaaagcaattcggcacggaatattgaatcctttcagttaccaaaccgttatccgccagtttccccagtggggcgaggtaacgaaaaaggaaagatttttctggagtaggttctatctctatgttccacaacgttttgcttatcaaaggacgctttaacaacgggtaattttgcccataaaattaaagcgt Predict Promoter with matrix: RpoD-15 score > 80================================================ Predict Promoter with matrix: RpoD-16 score > 80================================================ Predict Promoter with matrix: RpoD-17 score > 80================================================ PromScan Matrix: RpoD-17 Strand: + Score: 82 Start: 235 End: 264 ..........................................................................................................................................................................................................................................TTTAACAACGGGTAATTTTGCCCATAAAAT........ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ ttaaggatttggaagaatatagagaataaaccggtaacatgttgtaaattagtcgattttctatatgctgcgagtgtggcaggaaagcaattcggcacggaatattgaatcctttcagttaccaaaccgttatccgccagtttccccagtggggcgaggtaacgaaaaaggaaagatttttctggagtaggttctatctctatgttccacaacgttttgcttatcaaaggacgctttaacaacgggtaattttgcccataaaattaaagcgt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TF0908:TF0909|TF0908:TF0909:integrase fragment:Tn5520-like integrase (transfer factor):->->:951085..951356 272 ttaaggatttggaagaatatagagaataaaccggtaacatgttgtaaattagtcgattttctatatgctgcgagtgtggcaggaaagcaattcggcacggaatattgaatcctttcagttaccaaaccgttatccgccagtttccccagtggggcgaggtaacgaaaaaggaaagatttttctggagtaggttctatctctatgttccacaacgttttgcttatcaaaggacgctttaacaacgggtaattttgcccataaaattaaagcgt Intra-Species Hit: Count: 1 Min: 1 Max: 272 Len: 272 Subject: tfor_TF0908_TF0909|integrase fragment:Tn5520-like integrase (transfer factor)|POSITIVE:POSITIVE|[951085,951356]|272 HSP 1 e-value: 1.0E-152 bit: 539.0 Len: 272 Query Start:1 Query End:272 Subject Strand: POSITIVE Subject Start: 1 Subject End: 272 ttaaggatttggaagaatatagagaataaaccggtaacatgttgtaaattagtcgattttctatatgctgcgagtgtggcaggaaagcaattcggcacggaatattgaatcctttcagttaccaaaccgttatccgccagtttccccagtggggcgaggtaacgaaaaaggaaagatttttctggagtaggttctatctctatgttccacaacgttttgcttatcaaaggacgctttaacaacgggtaattttgcccataaaattaaagcgt ttaaggatttggaagaatatagagaataaaccggtaacatgttgtaaattagtcgattttctatatgctgcgagtgtggcaggaaagcaattcggcacggaatattgaatcctttcagttaccaaaccgttatccgccagtttccccagtggggcgaggtaacgaaaaaggaaagatttttctggagtaggttctatctctatgttccacaacgttttgcttatcaaaggacgctttaacaacgggtaattttgcccataaaattaaagcgt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUAAGGAUUUGGAAGAAUAUAGAGAAUAAACCGGUAACAUGUUGUAAAUUAGUCGAUUUUCUAUAUGCUGCGAGUGUGGCAGGAAAGCAAUUCGGCACGGAAUAUUGAAUCCUUUCAGUUACCAAACCGUUAUCCGCCAGUUUCCCCAGUGGGGCGAGGUAACGAAAAAGGAAAGAUUUUUCUGGAGUAGGUUCUAUCUCUAUGUUCCACAACGUUUUGCUUAUCAAAGGACGCUUUAACAACGGGUAAUUUUGCCCAUAAAAUUAAAGCGU ...((((((((...(((((((((((...((((((((((.............(((((((((((...(((..(....)..)))))))))....)))))..(((........))).....))))))....(((((((((((..............)))).))))))).....(((((....)))))......))))...)))))))))))..))).)))))............(((((((((....(((((....)))))......))))))))) (-73.04) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACGCUUUAAUUUUAUGGGCAAAAUUACCCGUUGUUAAAGCGUCCUUUGAUAAGCAAAACGUUGUGGAACAUAGAGAUAGAACCUACUCCAGAAAAAUCUUUCCUUUUUCGUUACCUCGCCCCACUGGGGAAACUGGCGGAUAACGGUUUGGUAACUGAAAGGAUUCAAUAUUCCGUGCCGAAUUGCUUUCCUGCCACACUCGCAGCAUAUAGAAAAUCGACUAAUUUACAACAUGUUACCGGUUUAUUCUCUAUAUUCUUCCAAAUCCUUAA ((((((((((...(((((........))))).)))))))))).......((((.......(((.((((.(((((((..(((((......(((....))).((..(((((.........((((...))))....(((((((...((((((((((.......(((........))).))))))))))...))).))))...............)))))..))....................)))))..))))))).))))..)))...)))). (-66.30) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 395 100 51 51 1 tfor:TF2676|5end_conserved_hypothetical_protein_2849645..2849875_POSITIVE 373 108 61 69 23 tfor:TF0428|5end_methylmalonyl-CoA_mutase,_beta_subunit_447809..448039_POSITIVE 355 173 134 98 54 tfor:TF2206|5end_conserved_hypothetical_protein;_possible_sugar_phosphate_isomerase/epimerase_2379969..2380199_POSITIVE 355 160 111 212 154 tfor:TF0955|5end_conserved_hypothetical_protein_999215..999445_POSITIVE 353 159 112 212 151 tfor:TF3096|5end_conserved_hypothetical_protein_3327963..3328193_POSITIVE 353 200 155 85 33 tfor:TF0864|5end_O-succinylbenzoate--CoA_ligase_914570..914800_POSITIVE 352 164 123 217 162 tfor:TF0265|5end_conserved_hypothetical_protein,_Rhs_family_293279..293509_POSITIVE 351 189 142 140 100 tfor:TF0947|5end_extracellular_protease_990627..990857_POSITIVE 348 100 52 61 14 tfor:TF0722|5end_pyruvate_dehydrogenase_E3_component(dihydrolipoamide_dehydrogenase)_772873..773103_POSITIVE 347 100 51 140 90 tfor:TF0473|5end_cation_or_acridine_efflux_membrane-fusion_protein_491047..491277_POSITIVE 343 100 52 133 70 tfor:TF0324|5end_conserved_hypothetical_protein_351228..351458_POSITIVE 341 140 98 96 42 tfor:TF0098|5end_permease_108103..108333_POSITIVE 340 101 67 189 152 tfor:TF1586|5end_hypothetical_protein_1690971..1691201_POSITIVE 334 178 131 88 43 tfor:TF1067|5end_conserved_hypothetical_protein_1136867..1137097_POSITIVE 332 170 123 220 162 tfor:TF1068|5end_conserved_hypothetical_protein;_possible_N-acetylglucosamine_kinase_1138036..1138266_POSITIVE 330 92 51 231 187 tfor:TF0252|5end_hypothetical_protein_283530..283760_POSITIVE 330 180 131 87 45 tfor:TF0141|5end_exodeoxyribonuclease_VII,_large_subunit_148422..148652_POSITIVE 324 180 134 70 12 tfor:TF2994|5end_hypothetical_protein_3210605..3210835_POSITIVE 324 168 127 48 5 tfor:TF1798|5end_aldose_1-epimerase_1938815..1939045_POSITIVE 324 159 111 125 66 tfor:TF0257|5end_hypothetical_protein_287610..287840_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 511 270 228 88 45 tfor:TF1651|3end_integrase_1762602..1762752_POSITIVE 373 108 61 48 2 tfor:TF0427|3end_methylmalonyl-CoA_mutase,_alpha_subunit_447868..448018_POSITIVE 355 173 134 59 15 tfor:TF2205|3end_conserved_hypothetical_protein;_possible_transcriptional_regulator_2380010..2380160_POSITIVE 351 189 142 131 91 tfor:TF0946|3end_iron(III)_ABC_transporter,_periplasmic_iron-binding_protein_990698..990848_POSITIVE 347 100 51 70 20 tfor:TF0472|3end_multidrug_resistance_protein,_AcrB/AcrD/AcrF_family_(cation_efflux_pump)_491057..491207_POSITIVE 341 187 142 77 23 tfor:TF0958|3end_conserved_hypothetical_protein_1004909..1005059_POSITIVE 341 140 98 91 37 tfor:TF0096|3end_tRNA-guanine_transglycosylase_(queuine_tRNA-ribosyltransferase)_108178..108328_POSITIVE 330 92 51 150 106 tfor:TF0251|3end_conserved_hypothetical_protein;_possible_exporter_283529..283679_POSITIVE 330 180 131 68 26 tfor:TF0140|3end_exodeoxyribonuclease_VII,_small_subunit_148483..148633_POSITIVE 327 163 122 117 80 tfor:TF1629|3end_hypothetical_protein_1741915..1742065_POSITIVE 322 100 51 150 95 tfor:TF1681|3end_dTDP-4-keto-L-rhamnose_reductase_1795844..1795994_POSITIVE 322 156 118 45 6 tfor:TF1173|3end_ABC_transporter,_permease_component_1256651..1256801_POSITIVE 322 107 61 119 68 tfor:TF0242|3end_conserved_hypothetical_protein_274069..274219_POSITIVE 319 100 51 151 106 tfor:TF1467|3end_conserved_hypothetical_protein_1557837..1557987_POSITIVE 317 139 91 81 31 tfor:TF2683|3end_translation_initiation_factor_IF-2_2860756..2860906_POSITIVE 317 162 122 149 107 tfor:TF0594|3end_conserved_hypothetical_protein;_possible_PAP2_superfamily_protein_627926..628076_POSITIVE 310 90 50 151 110 tfor:TF1644|3end_conserved_hypothetical_protein_1755503..1755653_POSITIVE 308 159 111 128 81 tfor:TF2654|3end_arginyl-tRNA_synthetase_2824559..2824709_POSITIVE 307 160 111 84 19 tfor:TF2340|3end_hypothetical_protein_2500915..2501065_POSITIVE 306 100 52 63 10 tfor:TF1675|3end_hypothetical_protein_1789137..1789287_POSITIVE