Origin IGS: tcggggctataccgaaacaagggtaggggctatccccctaagggctgtgcagcaatcaccggatttgtgcacagcctttttcgcatacagcccggatggatttggaaggagaaagtattgtgaggtggccaaagagagagaaaaaaaacgatacatatttcggaacttatttttccggccgggaaaagtttccccgacagctaacaaaaataaattttccggccggaaaatct .........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 agattttccggccggaaaatttatttttgttagctgtcggggaaacttttcccggccggaaaaataagttccgaaatatgtatcgttttttttctctctctttggccacctcacaatactttctccttccaaatccatccgggctgtatgcgaaaaaggctgtgcacaaatccggtgattgctgcacagcccttagggggatagcccctacccttgtttcggtatagccccga Mask Tandem Repeat Region ================================================ tcggggctataccgaaacaagggtaggggctatccccctaagggctgtgcagcaatcaccggatttgtgcacagcctttttcgcatacagcccggatggatttggaaggagaaagtattgtgaggtggccaaagagagagaaaaaaaacgatacatatttcggaacttatttttccggccgggaaaagtttccccgacagctaacaaaaataaattttccggccggaaaatct Find is-nt database================================================ Query_seq: PG0721:PG0722|PG0721:PG0722:NLP/P60 family protein:hypothetical protein:-><-:774596..774828 233 tcggggctataccgaaacaagggtaggggctatccccctaagggctgtgcagcaatcaccggatttgtgcacagcctttttcgcatacagcccggatggatttggaaggagaaagtattgtgaggtggccaaagagagagaaaaaaaacgatacatatttcggaacttatttttccggccgggaaaagtttccccgacagctaacaaaaataaattttccggccggaaaatct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG0721:PG0722|PG0721:PG0722:NLP/P60 family protein:hypothetical protein:-><-:774596..774828 233 tcggggctataccgaaacaagggtaggggctatccccctaagggctgtgcagcaatcaccggatttgtgcacagcctttttcgcatacagcccggatggatttggaaggagaaagtattgtgaggtggccaaagagagagaaaaaaaacgatacatatttcggaacttatttttccggccgggaaaagtttccccgacagctaacaaaaataaattttccggccggaaaatct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG0721:PG0722|PG0721:PG0722:NLP/P60 family protein:hypothetical protein:-><-:774596..774828 233 tcggggctataccgaaacaagggtaggggctatccccctaagggctgtgcagcaatcaccggatttgtgcacagcctttttcgcatacagcccggatggatttggaaggagaaagtattgtgaggtggccaaagagagagaaaaaaaacgatacatatttcggaacttatttttccggccgggaaaagtttccccgacagctaacaaaaataaattttccggccggaaaatct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tcggggctataccgaaacaagggtaggggctatccccctaagggctgtgcagcaatcaccggatttgtgcacagcctttttcgcatacagcccggatggatttggaaggagaaagtattgtgaggtggccaaagagagagaaaaaaaacgatacatatttcggaacttatttttccggccgggaaaagtttccccgacagctaacaaaaataaattttccggccggaaaatct Predict ORF larger than 30AA ================================================ Protein_Len: 60 Strand: + Start: 32 End: 232 ............................... M P L R A V Q Q S P D L C T A F F A Y S P D G F G R R K Y C E V A K E R E K K R Y I F R N L F F R P G K V S P T A N K N . Protein_Len: 60 Strand: + Start: 45 End: 233 ............................................ M C S N H R I C A Q P F S H T A R M D L E G E S I V R W P K R E K K N D T Y F G T Y F S G R E K F P R Q L T K I N F P A Protein_Len: 56 Strand: - Start: 33 End: 200 ................................ G G L P Q A A I V P N T C L R K R M C G P H I Q F S F T N H P P W L S L F F V I C I E S S I K G A P F L K G S M ................................. Protein_Len: 60 Strand: - Start: 10 End: 231 ......... C D G S K H V A K K A Y L G S P N P L L F Y Q S T A L S L S F F R Y M N R F K N K R G P F T E G V A L L F L N E P R F M .. tcggggctataccgaaacaagggtaggggctatccccctaagggctgtgcagcaatcaccggatttgtgcacagcctttttcgcatacagcccggatggatttggaaggagaaagtattgtgaggtggccaaagagagagaaaaaaaacgatacatatttcggaacttatttttccggccgggaaaagtttccccgacagctaacaaaaataaattttccggccggaaaatct 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================================================ tcggggctataccgaaacaagggtaggggctatccccctaagggctgtgcagcaatcaccggatttgtgcacagcctttttcgcatacagcccggatggatttggaaggagaaagtattgtgaggtggccaaagagagagaaaaaaaacgatacatatttcggaacttatttttccggccgggaaaagtttccccgacagctaacaaaaataaattttccggccggaaaatct Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 100 HP_score: -12.5 Tail_Score: -4.62069 Start: 43 End: 76 Full_Region: GGCTATCCCCCTAAG GGCTGTGCAGCAATC ACCG GATTTGTGCACAGCC TTTTTCGCATACAGC ..........................................GGCTGTGCAGCAATCACCGGATTTGTGCACAGCC............................................................................................................................................................. Find igs database================================================ Query_seq: PG0721:PG0722|PG0721:PG0722:NLP/P60 family protein:hypothetical protein:-><-:774596..774828 233 tcggggctataccgaaacaagggtaggggctatccccctaagggctgtgcagcaatcaccggatttgtgcacagcctttttcgcatacagcccggatggatttggaaggagaaagtattgtgaggtggccaaagagagagaaaaaaaacgatacatatttcggaacttatttttccggccgggaaaagtttccccgacagctaacaaaaataaattttccggccggaaaatct Intra-Species Hit: Count: 1 Min: 1 Max: 233 Len: 233 Subject: NC_002950_PG0721_PG0722|NLP/P60 family protein:hypothetical protein|POSITIVE:NEGATIVE|[774596,774828]|233 HSP 1 e-value: 1.0E-115 bit: 414.0 Len: 233 Query Start:1 Query End:233 Subject Strand: POSITIVE Subject Start: 1 Subject End: 233 tcggggctataccgaaacaagggtaggggctatccccctaagggctgtgcagcaatcaccggatttgtgcacagcctttttcgcatacagcccggatggatttggaaggagaaagtattgtgaggtggccaaagagagagnnnnnnnncgatacatatttcggaacttatttttccggccgggaaaagtttccccgacagctaacaaaaataaattttccggccggaaaatct tcggggctataccgaaacaagggtaggggctatccccctaagggctgtgcagcaatcaccggatttgtgcacagcctttttcgcatacagcccggatggatttggaaggagaaagtattgtgaggtggccaaagagagagaaaaaaaacgatacatatttcggaacttatttttccggccgggaaaagtttccccgacagctaacaaaaataaattttccggccggaaaatct Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCGGGGCUAUACCGAAACAAGGGUAGGGGCUAUCCCCCUAAGGGCUGUGCAGCAAUCACCGGAUUUGUGCACAGCCUUUUUCGCAUACAGCCCGGAUGGAUUUGGAAGGAGAAAGUAUUGUGAGGUGGCCAAAGAGAGAGAAAAAAAACGAUACAUAUUUCGGAACUUAUUUUUCCGGCCGGGAAAAGUUUCCCCGACAGCUAACAAAAAUAAAUUUUCCGGCCGGAAAAUCU ((.(((((.((.(((((......((((((.....)))))).((((((((((..((((....))))..)))))))))).)))))..)).))))).))....(((.((((......(((((((....(..((.......).)..)....)))))))...)))).))).....((((((((((((((((((((........))))............))))))))))))))))... (-75.80) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGAUUUUCCGGCCGGAAAAUUUAUUUUUGUUAGCUGUCGGGGAAACUUUUCCCGGCCGGAAAAAUAAGUUCCGAAAUAUGUAUCGUUUUUUUUCUCUCUCUUUGGCCACCUCACAAUACUUUCUCCUUCCAAAUCCAUCCGGGCUGUAUGCGAAAAAGGCUGUGCACAAAUCCGGUGAUUGCUGCACAGCCCUUAGGGGGAUAGCCCCUACCCUUGUUUCGGUAUAGCCCCGA .........(((((((.(((((((((((.(.....((((((((.....)))))))).).))))))))))).(((........)))...............)))))))..............................((.(((((((((.(((((..(((((((((..((((....))))..)))))))))..((((((.....))))))......)))))))))))))).)) (-74.30) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 433 90 41 162 119 NC_002950:PG1088|5end_acetyltransferase,_GNAT_family_1155426..1155656_NEGATIVE 420 50 2 64 14 NC_002950:PG0877|5end_hypothetical_protein_941545..941775_NEGATIVE 412 98 59 132 85 NC_002950:PG1311|5end_hypothetical_protein_1389709..1389939_POSITIVE 401 70 21 109 48 NC_002950:PG0605|5end_hypothetical_protein_662406..662636_NEGATIVE 396 70 21 182 136 NC_002950:PG0525|5end_CTP_synthetase_568999..569229_POSITIVE 390 50 2 198 135 NC_002950:PG1840|5end_hypothetical_protein_1937102..1937332_POSITIVE 374 70 21 177 121 NC_002950:PG0934|5end_hypothetical_protein_994318..994548_NEGATIVE 371 50 1 205 153 NC_002950:PG1601|5end_biotin--acetyl-CoA-carboxylase_ligase_1681792..1682022_NEGATIVE 366 77 40 173 128 NC_002950:PG0757|5end_hypothetical_protein_806370..806600_NEGATIVE 363 112 74 204 155 NC_002950:PG1285|5end_glucosamine-6-phosphate_deaminase_1362894..1363124_POSITIVE 358 54 12 154 112 NC_002950:PG0746|5end_sensor_histidine_kinase_793903..794133_NEGATIVE 356 107 61 85 33 NC_002950:PG0679|5end_outer_membrane_efflux_protein_729594..729824_POSITIVE 353 69 26 65 23 NC_002950:PG1100|5end_hypothetical_protein_1169012..1169242_NEGATIVE 353 70 21 224 164 NC_002950:PG0093|5end_HlyD_family_secretion_protein_109638..109868_NEGATIVE 352 129 81 149 108 NC_002950:PG1481|5end_conjugative_transposon_protein_TraG_1558447..1558677_NEGATIVE 352 77 32 72 28 NC_002950:PG1270|5end_hypothetical_protein_1350207..1350437_NEGATIVE 350 48 2 81 26 NC_002950:PG0147|5end_hypothetical_protein_169667..169897_NEGATIVE 347 60 12 137 67 NC_002950:PG0738|5end_cytidine/deoxycytidylate_deaminase_family_protein_786463..786693_POSITIVE 346 96 60 80 43 NC_002950:PG1810|5end_2-oxoglutarate_oxidoreductase,_beta_subunit_1906757..1906987_NEGATIVE 346 87 41 156 107 NC_002950:PG1351|5end_hypothetical_protein_1432744..1432974_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 454 79 40 51 12 NC_002950:PG0721|3end_NLP/P60_family_protein_774535..774685_POSITIVE 439 82 41 65 27 NC_002950:PG0034|3end_thioredoxin_42235..42385_NEGATIVE 433 90 41 65 22 NC_002950:PG1089|3end_DNA-binding_response_regulator_RprY_1155523..1155673_NEGATIVE 401 70 21 64 3 NC_002950:PG0606|3end_hypothetical_protein_662451..662601_NEGATIVE 397 100 52 83 32 NC_002950:PG1757|3end_hypothetical_protein_1843931..1844081_NEGATIVE 396 70 21 66 20 NC_002950:PG0524|3end_hypothetical_protein_568963..569113_POSITIVE 389 79 40 69 33 NC_002950:PG0506|3end_arginine-specific_cysteine_proteinase_547625..547775_POSITIVE 374 81 42 90 51 NC_002950:PG0725|3end_hydrolase,_haloacid_dehalogenase-like_family_777966..778116_POSITIVE 366 77 40 76 31 NC_002950:PG0758|3end_peptidyl-dipeptidase_Dcp_806467..806617_NEGATIVE 362 90 42 52 8 NC_002950:PG1950|3end_hypothetical_protein_2040840..2040990_POSITIVE 359 83 41 72 28 NC_002950:PG0726|3end_lipoprotein,_putative_778003..778153_NEGATIVE 357 81 41 42 6 NC_002950:PG1297|3end_ribosomal_protein_S1_1377710..1377860_POSITIVE 353 88 45 43 1 NC_002950:PG1392|3end_rod_shape-determining_protein_RodA,_putative_1472959..1473109_NEGATIVE 353 69 26 68 26 NC_002950:PG1101|3end_sodium:solute_symporter_family_protein_1169009..1169159_NEGATIVE 352 77 32 65 21 NC_002950:PG1271|3end_acetylornithine_aminotransferase,_putative_1350214..1350364_NEGATIVE 350 48 2 94 39 NC_002950:PG0148|3end_sigma-54-dependent_transcriptional_regulator_169654..169804_NEGATIVE 348 120 90 133 97 NC_002950:PG1711|3end_alpha-1,2-mannosidase_family_protein_1796652..1796802_NEGATIVE 347 60 12 140 70 NC_002950:PG0737|3end_hypothetical_protein_786546..786696_POSITIVE 346 70 21 84 38 NC_002950:PG1012|3end_tRNA-i(6)A37_modification_enzyme_MiaB_1070089..1070239_NEGATIVE 345 83 41 75 29 NC_002950:PG0350|3end_internalin-related_protein_385356..385506_NEGATIVE