Origin IGS: cgtgcggggcgacctaaaaagcgttgcaaagatacaaaacttattctatattattgcaagcggcatccgtgcccggaaaagtatgctttctcttcgcccgacaggcgcttatatatgatacgttgcgcccgtcctgtctccgggtcacgacgagacgggcgggtggcgcctctgttccgtccgttctgcctta .........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 taaggcagaacggacggaacagaggcgccacccgcccgtctcgtcgtgacccggagacaggacgggcgcaacgtatcatatataagcgcctgtcgggcgaagagaaagcatacttttccgggcacggatgccgcttgcaataatatagaataagttttgtatctttgcaacgctttttaggtcgccccgcacg Mask Tandem Repeat Region ================================================ cgtgcggggcgacctaaaaagcgttgcaaagatacaaaacttattctatattattgcaagcggcatccgtgcccggaaaagtatgctttctcttcgcccgacaggcgcttatatatgatacgttgcgcccgtcctgtctccgggtcacgacgagacgggcgggtggcgcctctgttccgtccgttctgcctta Find is-nt database================================================ Query_seq: TF2078:TF2079|TF2078:TF2079:dehydrogenase:permease:->->:2245532..2245724 193 cgtgcggggcgacctaaaaagcgttgcaaagatacaaaacttattctatattattgcaagcggcatccgtgcccggaaaagtatgctttctcttcgcccgacaggcgcttatatatgatacgttgcgcccgtcctgtctccgggtcacgacgagacgggcgggtggcgcctctgttccgtccgttctgcctta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF2078:TF2079|TF2078:TF2079:dehydrogenase:permease:->->:2245532..2245724 193 cgtgcggggcgacctaaaaagcgttgcaaagatacaaaacttattctatattattgcaagcggcatccgtgcccggaaaagtatgctttctcttcgcccgacaggcgcttatatatgatacgttgcgcccgtcctgtctccgggtcacgacgagacgggcgggtggcgcctctgttccgtccgttctgcctta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF2078:TF2079|TF2078:TF2079:dehydrogenase:permease:->->:2245532..2245724 193 cgtgcggggcgacctaaaaagcgttgcaaagatacaaaacttattctatattattgcaagcggcatccgtgcccggaaaagtatgctttctcttcgcccgacaggcgcttatatatgatacgttgcgcccgtcctgtctccgggtcacgacgagacgggcgggtggcgcctctgttccgtccgttctgcctta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 cgtgcggggcgacctaaaaagcgttgcaaagatacaaaacttattctatattattgcaagcggcatccgtgcccggaaaagtatgctttctcttcgcccgacaggcgcttatatatgatacgttgcgcccgtcctgtctccgggtcacgacgagacgggcgggtggcgcctctgttccgtccgttctgcctta Predict ORF larger than 30AA ================================================ Protein_Len: 38 Strand: + Start: 2 End: 115 . M R G D L K S V A K I Q N L F Y I I A S G I R A R K S M L S L R P T G A Y I .............................................................................. Protein_Len: 56 Strand: + Start: 24 End: 191 ....................... M Q R Y K T Y S I L L Q A A S V P G K V C F L F A R Q A L I Y D T L R P S C L R V T T R R A G G A S V P S V L P .. Protein_Len: 50 Strand: + Start: 43 End: 192 .......................................... M L Y Y C K R H P C P E K Y A F S S P D R R L Y M I R C A R P V S G S R R D G R V A P L F R P F C L . Protein_Len: 35 Strand: - Start: 44 End: 148 ........................................... E I N N C A A D T G P F T H K R K A R C A S I Y S V N R G D Q R R T M ............................................. cgtgcggggcgacctaaaaagcgttgcaaagatacaaaacttattctatattattgcaagcggcatccgtgcccggaaaagtatgctttctcttcgcccgacaggcgcttatatatgatacgttgcgcccgtcctgtctccgggtcacgacgagacgggcgggtggcgcctctgttccgtccgttctgcctta 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: 23 End: 52 ......................GTTGCAAAGATACAAAACTTATTCTATATT............................................................................................................................................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ cgtgcggggcgacctaaaaagcgttgcaaagatacaaaacttattctatattattgcaagcggcatccgtgcccggaaaagtatgctttctcttcgcccgacaggcgcttatatatgatacgttgcgcccgtcctgtctccgggtcacgacgagacgggcgggtggcgcctctgttccgtccgttctgcctta Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TF2078:TF2079|TF2078:TF2079:dehydrogenase:permease:->->:2245532..2245724 193 cgtgcggggcgacctaaaaagcgttgcaaagatacaaaacttattctatattattgcaagcggcatccgtgcccggaaaagtatgctttctcttcgcccgacaggcgcttatatatgatacgttgcgcccgtcctgtctccgggtcacgacgagacgggcgggtggcgcctctgttccgtccgttctgcctta Intra-Species Hit: Count: 1 Min: 1 Max: 193 Len: 193 Subject: tfor_TF2078_TF2079|dehydrogenase:permease|POSITIVE:POSITIVE|[224553 2,2245724]|193 HSP 1 e-value: 1.0E-105 bit: 383.0 Len: 193 Query Start:1 Query End:193 Subject Strand: POSITIVE Subject Start: 1 Subject End: 193 cgtgcggggcgacctaaaaagcgttgcaaagatacaaaacttattctatattattgcaagcggcatccgtgcccggaaaagtatgctttctcttcgcccgacaggcgcttatatatgatacgttgcgcccgtcctgtctccgggtcacgacgagacgggcgggtggcgcctctgttccgtccgttctgcctta cgtgcggggcgacctaaaaagcgttgcaaagatacaaaacttattctatattattgcaagcggcatccgtgcccggaaaagtatgctttctcttcgcccgacaggcgcttatatatgatacgttgcgcccgtcctgtctccgggtcacgacgagacgggcgggtggcgcctctgttccgtccgttctgcctta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CGUGCGGGGCGACCUAAAAAGCGUUGCAAAGAUACAAAACUUAUUCUAUAUUAUUGCAAGCGGCAUCCGUGCCCGGAAAAGUAUGCUUUCUCUUCGCCCGACAGGCGCUUAUAUAUGAUACGUUGCGCCCGUCCUGUCUCCGGGUCACGACGAGACGGGCGGGUGGCGCCUCUGUUCCGUCCGUUCUGCCUUA ((..((((((((.....((((((((((((.((((..............)))).))))).(.((((....)))))........)))))))....))))))...((((((.................((((((.((((((((((.....))..))))))))))))))))))))......))..)).......... (-63.26) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAGGCAGAACGGACGGAACAGAGGCGCCACCCGCCCGUCUCGUCGUGACCCGGAGACAGGACGGGCGCAACGUAUCAUAUAUAAGCGCCUGUCGGGCGAAGAGAAAGCAUACUUUUCCGGGCACGGAUGCCGCUUGCAAUAAUAUAGAAUAAGUUUUGUAUCUUUGCAACGCUUUUUAGGUCGCCCCGCACG ....((................((((((....((((((((..(((..........)))..))))))))....((((...))))..))))))...((((((..(((((((.......((((....))))......((((((..((((((((....))))))))..)))))).)))))))...)))))).))... (-70.20) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 531 167 121 60 14 tfor:TF0710|5end_two_component_system_histidine_kinase_757250..757480_POSITIVE 519 188 141 152 96 tfor:TF2831|5end_ABC_transporter,_permease_component_3021317..3021547_POSITIVE 519 180 131 64 15 tfor:TF2220|5end_CTn_integrase-recombinase_protein_2392424..2392654_POSITIVE 507 170 121 229 172 tfor:TF2130|5end_conserved_hypothetical_protein;_possible_permease_2306486..2306716_POSITIVE 492 169 121 61 12 tfor:TF2038|5end_hypothetical_protein_2198978..2199208_POSITIVE 487 170 121 54 4 tfor:TF0888|5end_transfer_region-related_protein,_TraN_938392..938622_POSITIVE 484 170 121 228 163 tfor:TF0098|5end_permease_108103..108333_POSITIVE 473 170 121 138 75 tfor:TF2492|5end_NifU-related_protein_2666683..2666913_POSITIVE 467 189 141 181 134 tfor:TF1329|5end_glucose-1-phosphate_thymidyltransferase_1408578..1408808_POSITIVE 464 190 141 64 9 tfor:TF0093|5end_outer_membrane_protein,_TonB_dependent_receptor_100497..100727_POSITIVE 460 170 126 163 120 tfor:TF1243|5end_periplasmic_protease_1327243..1327473_POSITIVE 458 168 126 200 159 tfor:TF0881|5end_conserved_hypothetical_protein_934459..934689_POSITIVE 455 190 141 94 16 tfor:TF2265|5end_transfer_region-related_protein,_TraP;_DNA_primase_involved_in_conjugation_2433474..2433704_POSITIVE 455 170 125 198 129 tfor:TF1947|5end_conserved_hypothetical_protein_2095521..2095751_POSITIVE 452 188 141 55 3 tfor:TF0992|5end_hypothetical_protein_1048251..1048481_POSITIVE 451 169 125 161 116 tfor:TF1948|5end_conserved_hypothetical_protein_2095942..2096172_POSITIVE 451 168 121 148 98 tfor:TF1182|5end_hypothetical_protein_1268565..1268795_POSITIVE 447 170 121 62 7 tfor:TF0538|5end_hypothetical_protein_566891..567121_POSITIVE 442 168 122 74 35 tfor:TF1427|5end_penicillin-binding_protein_2_1511349..1511579_POSITIVE 441 158 120 222 169 tfor:TF2832|5end_possible_proton/sodium:glutamate_symporter_protein_3022660..3022890_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 541 170 121 138 75 tfor:TF2556|3end_conserved_hypothetical_protein_2737095..2737245_POSITIVE 473 170 121 130 67 tfor:TF2490|3end_4-hydroxyphenylacetate-3-hydroxylase/4-hydroxybut_yryl_dehydratase_2666755..2666905_POSITIVE 470 168 125 118 67 tfor:TF1167|3end_hypothetical_protein_1248932..1249082_POSITIVE 455 190 141 82 4 tfor:TF2264|3end_transfer_region-related_protein,_TraO_2433542..2433692_POSITIVE 452 188 141 58 6 tfor:TF0991|3end_probable_NAD(FAD)-dependent_dehydrogenase_1048334..1048484_POSITIVE 451 168 121 148 98 tfor:TF1186|3end_hypothetical_protein_1269815..1269965_POSITIVE 450 168 121 118 65 tfor:TF2921|3end_hypothetical_protein_3118790..3118940_POSITIVE 450 168 121 118 65 tfor:TF2438|3end_hypothetical_protein_2616157..2616307_POSITIVE 447 168 121 118 49 tfor:TF2640|3end_hypothetical_protein_2809533..2809683_POSITIVE 442 168 122 58 19 tfor:TF1426|3end_N-acetylymuramoylalanyl-D-glutamate-2,6-diaminopi_melate_ligase_1511413..1511563_POSITIVE 435 166 121 57 14 tfor:TF1298|3end_possible_membrane_protein_1381197..1381347_POSITIVE 434 186 141 150 99 tfor:TF0419|3end_conserved_hypothetical_protein_435794..435944_POSITIVE 433 108 63 60 6 tfor:TF1291|3end_response_regulator_(fimR__protein)_1372647..1372797_POSITIVE 425 166 121 64 1 tfor:TF2256|3end_transfer_region-related_protein,_TraI_2428614..2428764_POSITIVE 423 169 121 148 92 tfor:TF0685|3end_hypothetical_protein_731132..731282_POSITIVE 422 155 120 148 100 tfor:TF2831|3end_ABC_transporter,_permease_component_3022671..3022821_POSITIVE 420 170 121 87 30 tfor:TF3153|3end_conserved_hypothetical_protein_3389324..3389474_POSITIVE 419 149 101 149 83 tfor:TF0240|3end_conserved_hypothetical_protein;_possible_gycosyltransferase_I_family_protein_271407..271557_POSITIVE 418 190 141 54 1 tfor:TF0776|3end_ABC_transporter,_permease_component_826173..826323_POSITIVE 416 186 141 138 89 tfor:TF1947|3end_conserved_hypothetical_protein_2096023..2096173_POSITIVE