Origin IGS: tgcaaaactgtatttcccttttgcgaaacactcctttgcgtactcatacttgtatgtatggtctgtacttttatacacttggttgtattcttgtgcgcaacttgtgagaagaagcgacagaataaatgtaatgagaatattcttcttcataaatttactttgagatgcaaagttacatataattccataattaacaaagctgttactgcatttttagcaaaaaatcacttttaattatctataatctgcagttttttattaact .........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 agttaataaaaaactgcagattatagataattaaaagtgattttttgctaaaaatgcagtaacagctttgttaattatggaattatatgtaactttgcatctcaaagtaaatttatgaagaagaatattctcattacatttattctgtcgcttcttctcacaagttgcgcacaagaatacaaccaagtgtataaaagtacagaccatacatacaagtatgagtacgcaaaggagtgtttcgcaaaagggaaatacagttttgca Mask Tandem Repeat Region ================================================ tgcaaaactgtatttcccttttgcgaaacactcctttgcgtactcatacttgtatgtatggtctgtacttttatacacttggttgtattcttgtgcgcaacttgtgagaagaagcgacagaataaatgtaatgagaatattcttcttcataaatttactttgagatgcaaagttacatataattccataattaacaaagctgttactgcatttttagcaaaaaatcacttttaattatctataatctgcagttttttattaact Find is-nt database================================================ Query_seq: PI1062:PI1063|PI1062:PI1063:TPR repeat protein:excinuclease ABC, subunit B:->->:980841..981104 264 tgcaaaactgtatttcccttttgcgaaacactcctttgcgtactcatacttgtatgtatggtctgtacttttatacacttggttgtattcttgtgcgcaacttgtgagaagaagcgacagaataaatgtaatgagaatattcttcttcataaatttactttgagatgcaaagttacatataattccataattaacaaagctgttactgcatttttagcaaaaaatcacttttaattatctataatctgcagttttttattaact Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI1062:PI1063|PI1062:PI1063:TPR repeat protein:excinuclease ABC, subunit B:->->:980841..981104 264 tgcaaaactgtatttcccttttgcgaaacactcctttgcgtactcatacttgtatgtatggtctgtacttttatacacttggttgtattcttgtgcgcaacttgtgagaagaagcgacagaataaatgtaatgagaatattcttcttcataaatttactttgagatgcaaagttacatataattccataattaacaaagctgttactgcatttttagcaaaaaatcacttttaattatctataatctgcagttttttattaact Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI1062:PI1063|PI1062:PI1063:TPR repeat protein:excinuclease ABC, subunit B:->->:980841..981104 264 tgcaaaactgtatttcccttttgcgaaacactcctttgcgtactcatacttgtatgtatggtctgtacttttatacacttggttgtattcttgtgcgcaacttgtgagaagaagcgacagaataaatgtaatgagaatattcttcttcataaatttactttgagatgcaaagttacatataattccataattaacaaagctgttactgcatttttagcaaaaaatcacttttaattatctataatctgcagttttttattaact Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tgcaaaactgtatttcccttttgcgaaacactcctttgcgtactcatacttgtatgtatggtctgtacttttatacacttggttgtattcttgtgcgcaacttgtgagaagaagcgacagaataaatgtaatgagaatattcttcttcataaatttactttgagatgcaaagttacatataattccataattaacaaagctgttactgcatttttagcaaaaaatcacttttaattatctataatctgcagttttttattaact Predict ORF larger than 30AA ================================================ Protein_Len: 31 Strand: + Start: 12 End: 104 ........... M S L L R N T P L R T H T C M Y G L Y F Y T L G C I L V R N L ................................................................................................................................................................ Protein_Len: 51 Strand: + Start: 8 End: 160 ....... M Y F P F A K H S F A Y S Y L Y V W S V L L Y T W L Y S C A Q L V R R S D R I N V M R I F F F I N L L ........................................................................................................ Protein_Len: 60 Strand: + Start: 46 End: 231 ............................................. M L V C M V C T F I H L V V F L C A T C E K K R Q N K C N E N I L L H K F T L R C K V T Y N S I I N K A V T A F L A K N ................................. Protein_Len: 46 Strand: - Start: 3 End: 140 .. L V T N G K Q S V S R Q T S M S T H I T Q V K I C K T T N K H A V Q S F F R C F L H L S F M ............................................................................................................................ Protein_Len: 60 Strand: - Start: 1 End: 183 F S Y K G K A F C E K A Y E Y K Y T H D T S K Y V Q N Y E Q A C S T L L L S L I F T I L I N K K M F K S Q S A F N C I M ................................................................................. tgcaaaactgtatttcccttttgcgaaacactcctttgcgtactcatacttgtatgtatggtctgtacttttatacacttggttgtattcttgtgcgcaacttgtgagaagaagcgacagaataaatgtaatgagaatattcttcttcataaatttactttgagatgcaaagttacatataattccataattaacaaagctgttactgcatttttagcaaaaaatcacttttaattatctataatctgcagttttttattaact 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================================================ tgcaaaactgtatttcccttttgcgaaacactcctttgcgtactcatacttgtatgtatggtctgtacttttatacacttggttgtattcttgtgcgcaacttgtgagaagaagcgacagaataaatgtaatgagaatattcttcttcataaatttactttgagatgcaaagttacatataattccataattaacaaagctgttactgcatttttagcaaaaaatcacttttaattatctataatctgcagttttttattaact Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 42 HP_score: -2.6 Tail_Score: -2.91276 Start: 155 End: 175 Full_Region: ttatggaattatatg taactttg catct caaagtaa atttatgaagaagaa ..........................................................................................................................................................taactttgcatctcaaagtaa......................................................................................... Find igs database================================================ Query_seq: PI1062:PI1063|PI1062:PI1063:TPR repeat protein:excinuclease ABC, subunit B:->->:980841..981104 264 tgcaaaactgtatttcccttttgcgaaacactcctttgcgtactcatacttgtatgtatggtctgtacttttatacacttggttgtattcttgtgcgcaacttgtgagaagaagcgacagaataaatgtaatgagaatattcttcttcataaatttactttgagatgcaaagttacatataattccataattaacaaagctgttactgcatttttagcaaaaaatcacttttaattatctataatctgcagttttttattaact Intra-Species Hit: Count: 1 Min: 1 Max: 264 Len: 264 Subject: pint_PI1062_PI1063|TPR repeat protein:excinuclease ABC, subunit B|POSITIVE:POSITIVE|[980841,981104]|264 HSP 1 e-value: 1.0E-148 bit: 523.0 Len: 264 Query Start:1 Query End:264 Subject Strand: POSITIVE Subject Start: 1 Subject End: 264 tgcaaaactgtatttcccttttgcgaaacactcctttgcgtactcatacttgtatgtatggtctgtacttttatacacttggttgtattcttgtgcgcaacttgtgagaagaagcgacagaataaatgtaatgagaatattcttcttcataaatttactttgagatgcaaagttacatataattccataattaacaaagctgttactgcatttttagcaaaaaatcacttttaattatctataatctgcagttttttattaact tgcaaaactgtatttcccttttgcgaaacactcctttgcgtactcatacttgtatgtatggtctgtacttttatacacttggttgtattcttgtgcgcaacttgtgagaagaagcgacagaataaatgtaatgagaatattcttcttcataaatttactttgagatgcaaagttacatataattccataattaacaaagctgttactgcatttttagcaaaaaatcacttttaattatctataatctgcagttttttattaact Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGCAAAACUGUAUUUCCCUUUUGCGAAACACUCCUUUGCGUACUCAUACUUGUAUGUAUGGUCUGUACUUUUAUACACUUGGUUGUAUUCUUGUGCGCAACUUGUGAGAAGAAGCGACAGAAUAAAUGUAAUGAGAAUAUUCUUCUUCAUAAAUUUACUUUGAGAUGCAAAGUUACAUAUAAUUCCAUAAUUAACAAAGCUGUUACUGCAUUUUUAGCAAAAAAUCACUUUUAAUUAUCUAUAAUCUGCAGUUUUUUAUUAACU .((((((..(.....)..))))))....(((....((((((((.(((((......)))))....((((..(((......)))..))))....))))))))...)))..(((((((..((((....((((((((((((.....))).))))......((((((.....)))))))))))........((((((((..(((.((....(((.......)))......)))))))))))))......))))..)))))))....... (-47.60) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGUUAAUAAAAAACUGCAGAUUAUAGAUAAUUAAAAGUGAUUUUUUGCUAAAAAUGCAGUAACAGCUUUGUUAAUUAUGGAAUUAUAUGUAACUUUGCAUCUCAAAGUAAAUUUAUGAAGAAGAAUAUUCUCAUUACAUUUAUUCUGUCGCUUCUUCUCACAAGUUGCGCACAAGAAUACAACCAAGUGUAUAAAAGUACAGACCAUACAUACAAGUAUGAGUACGCAAAGGAGUGUUUCGCAAAAGGGAAAUACAGUUUUGCA ((((((((((..((((((..(((((((.(((((....))))).)))).)))...))))))......)))))))))).(((......(((((((((((.....))))))......((((.(((.....)))))))))))).(((((((((((..(((.....)))..))).)).))))))...)))..(((((....))))).(((((((......))))).))..((((((..(((((((.(....).)))))))..)))))). (-54.90) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 337 122 81 96 42 pint:PI0936|5end_conserved_hypothetical_protein_868329..868559_POSITIVE 299 137 91 72 19 pint:PI0566|5end_enoyl-[acyl-carrier-protein]_reductase_511832..512062_POSITIVE 268 124 81 166 119 pint:PI0520|5end_hypothetical_protein_478755..478985_POSITIVE 263 150 108 157 119 pint:PI1423|5end_hypothetical_protein_1341888..1342118_POSITIVE 263 150 108 70 32 pint:PI1421|5end_hypothetical_protein_1341801..1342031_POSITIVE 263 122 88 186 153 pint:PI0854|5end_MiaB-like_tRNA_modifying_enzyme_786513..786743_POSITIVE 263 111 76 41 8 pint:PI0079|5end_hypothetical_protein_78565..78795_POSITIVE 259 109 67 138 104 pint:PI0026|5end_two-component_system_response_regulator_29756..29986_POSITIVE 256 99 53 139 97 pint:PI2176|5end_conserved_hypothetical_protein_2116484..2116714_POSITIVE 253 119 75 53 3 pint:PI0698|5end_conserved_hypothetical_protein_635372..635602_POSITIVE 253 105 77 215 189 pint:PI0323|5end_hypothetical_protein_305349..305579_POSITIVE 252 99 63 154 107 pint:PI1102|5end_conserved_hypothetical_protein_1025316..1025546_POSITIVE 252 80 31 81 16 pint:PI0973|5end_glycine_dehydrogenase_[decarboxylating]_subunit_1_899483..899713_POSITIVE 252 49 1 180 122 pint:PI0476|5end_50S_ribosomal_protein_L18_440041..440271_POSITIVE 250 120 78 48 11 pint:PI0848|5end_glycosyl_transferase,_group_2_family_protein_782247..782477_POSITIVE 249 120 79 67 24 pint:PI1127|5end_chloride_channel_protein_1052612..1052842_POSITIVE 249 48 2 130 84 pint:PI0530|5end_possible_membrane-fusion_protein_483772..484002_POSITIVE 248 118 81 40 2 pint:PI1796|5end_2-hydroxyhepta-2,4-diene-1,7-dioate_isomerase,_fumarylacetoacetate_hydrolase_family_protein_1730452..1730682_POSITIVE 248 68 32 180 144 pint:PI0932|5end_conserved_hypothetical_protein;_possible_hemin_receptor_863854..864084_POSITIVE 247 109 61 223 166 pint:PI0260|5end_conjugative_transposon_protein,_TraJ_253023..253253_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 278 119 78 139 93 pint:PI1715|3end_conserved_hypothetical_protein;_possible_DNA-binding_protein,_histone-like_family_1632324..1632474_POSITIVE 268 124 81 140 93 pint:PI0519|3end_5'-nucleotidase/2',3'-cyclic_phosphodiesterase_478809..478959_POSITIVE 263 150 108 131 93 pint:PI1422|3end_hypothetical_protein_1341942..1342092_POSITIVE 259 70 24 102 55 pint:PI0418|3end_hypothetical_protein_386856..387006_POSITIVE 259 70 24 74 27 pint:PI0420|3end_hypothetical_protein_386828..386978_POSITIVE 259 109 67 125 91 pint:PI0025|3end_two_component_system_sensor_histidine_kinase_29823..29973_POSITIVE 258 135 92 105 61 pint:PI0375|3end_hypothetical_protein_346082..346232_POSITIVE 256 99 53 101 59 pint:PI2175|3end_RNA_polymerase_sigma-54_2116526..2116676_POSITIVE 253 61 34 68 40 pint:PI0914|3end_ATPase,_AAA_family_844992..845142_POSITIVE 252 99 63 73 26 pint:PI1101|3end_hypothetical_protein_1025315..1025465_POSITIVE 252 80 31 109 44 pint:PI0974|3end_hypothetical_protein_899591..899741_POSITIVE 251 108 61 141 86 pint:PI1441|3end_hypothetical_protein_1363673..1363823_POSITIVE 245 133 91 98 50 pint:PI1206|3end_ATP-dependent_DNA_helicase,_UvrD/PcrA/Rep_family_1127132..1127282_POSITIVE 243 86 44 149 101 pint:PI0514|3end_possible_cell_filamentation_protein_472940..473090_POSITIVE 242 128 81 147 90 pint:PI1570|3end_succinyl-diaminopimelate_desuccinylase_1494778..1494928_POSITIVE 241 115 76 62 23 pint:PI0632|3end_NusB_family_protein_(N_utilization_substance_protein_B)_579731..579881_POSITIVE 241 45 1 151 97 pint:PI0475|3end_50S_ribosomal_protein_L6_440096..440246_POSITIVE 240 120 90 41 10 pint:PI1413|3end_hypothetical_protein_1333959..1334109_POSITIVE 236 68 23 46 9 pint:PI0481|3end_translation_initiation_factor_IF-1_443409..443559_POSITIVE 234 121 82 151 96 pint:PI0811|3end_protease/hemagglutinin_PrtT,_streptopain_family_749937..750087_POSITIVE