Origin IGS: taattgggaaggctggaaaggtggaaaccttcccggcttgatctcggcacacgaaaattctgactctggctgctttcttccgaacctgacctggtaaaccagacttcattgcgagggaccgaaaaggtttccattgaattaaccgcaagatttcatttcacactggcgattaagggtttgcattatgcaataagccccgccgaattgcaaatgttatctccgtatgaaagggaaagtgcccgaactttaaacaaacgaggaaaata .........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 tattttcctcgtttgtttaaagttcgggcactttccctttcatacggagataacatttgcaattcggcggggcttattgcataatgcaaacccttaatcgccagtgtgaaatgaaatcttgcggttaattcaatggaaaccttttcggtccctcgcaatgaagtctggtttaccaggtcaggttcggaagaaagcagccagagtcagaattttcgtgtgccgagatcaagccgggaaggtttccacctttccagccttcccaatta Mask Tandem Repeat Region ================================================ taattgggaaggctggaaaggtggaaaccttcccggcttgatctcggcacacgaaaattctgactctggctgctttcttccgaacctgacctggtaaaccagacttcattgcgagggaccgaaaaggtttccattgaattaaccgcaagatttcatttcacactggcgattaagggtttgcattatgcaataagccccgccgaattgcaaatgttatctccgtatgaaagggaaagtgcccgaactttaaacaaacgaggaaaata Find is-nt database================================================ Query_seq: AA02609:AA02610|AA02609:AA02610:ABC transporter, ATP-binding protein/permease:acyl-CoA thioesterase II:->->:1820245..1820510 266 taattgggaaggctggaaaggtggaaaccttcccggcttgatctcggcacacgaaaattctgactctggctgctttcttccgaacctgacctggtaaaccagacttcattgcgagggaccgaaaaggtttccattgaattaaccgcaagatttcatttcacactggcgattaagggtttgcattatgcaataagccccgccgaattgcaaatgttatctccgtatgaaagggaaagtgcccgaactttaaacaaacgaggaaaata Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: AA02609:AA02610|AA02609:AA02610:ABC transporter, ATP-binding protein/permease:acyl-CoA thioesterase II:->->:1820245..1820510 266 taattgggaaggctggaaaggtggaaaccttcccggcttgatctcggcacacgaaaattctgactctggctgctttcttccgaacctgacctggtaaaccagacttcattgcgagggaccgaaaaggtttccattgaattaaccgcaagatttcatttcacactggcgattaagggtttgcattatgcaataagccccgccgaattgcaaatgttatctccgtatgaaagggaaagtgcccgaactttaaacaaacgaggaaaata Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: AA02609:AA02610|AA02609:AA02610:ABC transporter, ATP-binding protein/permease:acyl-CoA thioesterase II:->->:1820245..1820510 266 taattgggaaggctggaaaggtggaaaccttcccggcttgatctcggcacacgaaaattctgactctggctgctttcttccgaacctgacctggtaaaccagacttcattgcgagggaccgaaaaggtttccattgaattaaccgcaagatttcatttcacactggcgattaagggtttgcattatgcaataagccccgccgaattgcaaatgttatctccgtatgaaagggaaagtgcccgaactttaaacaaacgaggaaaata Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taattgggaaggctggaaaggtggaaaccttcccggcttgatctcggcacacgaaaattctgactctggctgctttcttccgaacctgacctggtaaaccagacttcattgcgagggaccgaaaaggtttccattgaattaaccgcaagatttcatttcacactggcgattaagggtttgcattatgcaataagccccgccgaattgcaaatgttatctccgtatgaaagggaaagtgcccgaactttaaacaaacgaggaaaata Predict ORF larger than 30AA ================================================ Protein_Len: 60 Strand: + Start: 70 End: 264 ..................................................................... M L S S E P D L V N Q T S L R G T E K V S I E L T A R F H F T L A I K G L H Y A I S P A E L Q M L S P Y E R E S A R T L .. Protein_Len: 31 Strand: - Start: 173 End: 265 ............................................................................................................................................................................ P N A N H L L G R R I A F T I E T H F P F H G F K L C V L F M . Protein_Len: 44 Strand: - Start: 3 End: 134 .. N P L S S L H F G E R S S R P V R F N Q S Q S S E E S G S R T F W V E N R P V S F T E M .................................................................................................................................... Protein_Len: 50 Strand: - Start: 2 End: 151 . I P F A P F T S V K G A Q D R C V F I R V R A A K K R V Q G P L G S K M A L S R F P K W Q I L R L M ................................................................................................................... Protein_Len: 34 Strand: - Start: 1 End: 102 L Q S P Q F P P F R G P K I E A C S F E S E P Q K R G F R V Q Y V M .................................................................................................................................................................... taattgggaaggctggaaaggtggaaaccttcccggcttgatctcggcacacgaaaattctgactctggctgctttcttccgaacctgacctggtaaaccagacttcattgcgagggaccgaaaaggtttccattgaattaaccgcaagatttcatttcacactggcgattaagggtttgcattatgcaataagccccgccgaattgcaaatgttatctccgtatgaaagggaaagtgcccgaactttaaacaaacgaggaaaata 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: 81 Start: 182 End: 211 .....................................................................................................................................................................................TTTGCAATTCGGCGGGGCTTATTGCATAAT....................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ taattgggaaggctggaaaggtggaaaccttcccggcttgatctcggcacacgaaaattctgactctggctgctttcttccgaacctgacctggtaaaccagacttcattgcgagggaccgaaaaggtttccattgaattaaccgcaagatttcatttcacactggcgattaagggtttgcattatgcaataagccccgccgaattgcaaatgttatctccgtatgaaagggaaagtgcccgaactttaaacaaacgaggaaaata Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: AA02609:AA02610|AA02609:AA02610:ABC transporter, ATP-binding protein/permease:acyl-CoA thioesterase II:->->:1820245..1820510 266 taattgggaaggctggaaaggtggaaaccttcccggcttgatctcggcacacgaaaattctgactctggctgctttcttccgaacctgacctggtaaaccagacttcattgcgagggaccgaaaaggtttccattgaattaaccgcaagatttcatttcacactggcgattaagggtttgcattatgcaataagccccgccgaattgcaaatgttatctccgtatgaaagggaaagtgcccgaactttaaacaaacgaggaaaata Intra-Species Hit: Count: 1 Min: 1 Max: 266 Len: 266 Subject: aact_AA02609_AA02610|ABC transporter, ATP-binding protein/permease:acyl-CoA thioesterase II|POSITIVE:POSITIVE|[1820245,1820510]|266 HSP 1 e-value: 1.0E-149 bit: 527.0 Len: 266 Query Start:1 Query End:266 Subject Strand: POSITIVE Subject Start: 1 Subject End: 266 taattgggaaggctggaaaggtggaaaccttcccggcttgatctcggcacacgaaaattctgactctggctgctttcttccgaacctgacctggtaaaccagacttcattgcgagggaccgaaaaggtttccattgaattaaccgcaagatttcatttcacactggcgattaagggtttgcattatgcaataagccccgccgaattgcaaatgttatctccgtatgaaagggaaagtgcccgaactttaaacaaacgaggaaaata taattgggaaggctggaaaggtggaaaccttcccggcttgatctcggcacacgaaaattctgactctggctgctttcttccgaacctgacctggtaaaccagacttcattgcgagggaccgaaaaggtttccattgaattaaccgcaagatttcatttcacactggcgattaagggtttgcattatgcaataagccccgccgaattgcaaatgttatctccgtatgaaagggaaagtgcccgaactttaaacaaacgaggaaaata Inter-species Hit: Count: 3 Min: 23 Max: 145 Len: 123 Subject: NC_008309_HS_1151_HS_1152|hypothetical protein:hypothetical protein|POSITIVE:POSITIVE|[1291475,1291765]|291 HSP 1 e-value: 5.0E-23 bit: 109.0 Len: 123 Query Start:23 Query End:145 Subject Strand: POSITIVE Subject Start: 62 Subject End: 184 ......................ggaaaccttcccggcttgatctcggcacacgaaaattctgactctggctgctttcttccgaacctgacctggtaaaccagacttcattgcgagggaccgaaaaggtttccattgaattaaccg......................................................................................................................... ......................ggaaacctttccggcaggatctcggcacacagaaattccgactttggctgctttcttccgaacctgaccgagtaaatcggacactattgcgaggaaccgaaaagatttccatagaattaaccg......................................................................................................................... Subject: NC_000907_HI1155_HI1156|anaerobic ribonucleoside-triphosphate reductase activating protein:transport ATP-binding protein|NEGATIVE:NEGATIVE|[1223762,1224008]|247 HSP 1 e-value: 3.0E-18 bit: 93.7 Len: 115 Query Start:23 Query End:137 Subject Strand: NEGATIVE Subject Start: 117 Subject End: 231 ......................ggaaaccttcccggcttgatctcggcacacgaaaattctgactctggctgctttcttccgaacctgacctggtaaaccagacttcattgcgagggaccgaaaaggtttccattga................................................................................................................................. ......................ggaaaccttcccagcttcttctcggcacacagtaattccgactttggctgcttccttccggacctgaccgagtaaaccagacaccgttgcgagagaccgagaaggtttccattga................................................................................................................................. Subject: NC_007146_NTHI1324_NTHI1325|anaerobic ribonucleoside-triphosphate reductase activating protein:transport ATP-binding protein CydC|NEGATIVE:NEGATIVE|[1256692,1256938]|247 HSP 1 e-value: 7.0E-16 bit: 85.7 Len: 115 Query Start:23 Query End:137 Subject Strand: NEGATIVE Subject Start: 117 Subject End: 231 ......................ggaaaccttcccggcttgatctcggcacacgaaaattctgactctggctgctttcttccgaacctgacctggtaaaccagacttcattgcgagggaccgaaaaggtttccattga................................................................................................................................. ......................ggaaaccttcccagcttcttctcggcacacagtaattccgactttggctgcttccttccagacctgaccgagtaaaccagacaccgttgcgagagaccgagaaggtttccattga................................................................................................................................. Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GGAAACCUUCCCGGCUUGAUCUCGGCACACGAAAAUUCUGACUCUGGCUGCUUUCUUCCGAACCUGACCUGGUAAACCAGACUUCAUUGCGAGGGACCGAAAAGGUUUCCAUUGAAUUAACCG (((((((((..(((.......(((.....))).........((((.((....(((....)))......((((....))))........)).)))).)))..)))))))))............. (-32.60) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CGGUUAAUUCAAUGGAAACCUUUUCGGUCCCUCGCAAUGAAGUCUGGUUUACCAGGUCAGGUUCGGAAGAAAGCAGCCAGAGUCAGAAUUUUCGUGUGCCGAGAUCAAGCCGGGAAGGUUUCC .............(((((((((..((((..(((((((((((.((((..((....(((....(((....)))....))).))..))))...))))).)).)))).....))))..))))))))) (-44.20) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 359 51 14 55 9 aact:AA00075|5end_conserved_hypothetical_protein_54963..55193_POSITIVE 341 97 55 217 175 aact:AA01232|5end_30S_ribosomal_protein_S8_840445..840675_POSITIVE 339 60 11 227 182 aact:AA01589|5end_conserved_hypothetical_protein_1070300..1070530_POSITIVE 333 60 11 214 150 aact:AA01421|5end_phosphoglycolate_phosphatase_955055..955285_POSITIVE 330 90 41 171 122 aact:AA00887|5end_hypothetical_protein_616739..616969_POSITIVE 320 100 56 200 139 aact:AA01259|5end_protoporphyrinogen_oxidase_854354..854584_POSITIVE 319 59 21 185 138 aact:AA01724|5end_valyl-tRNA_synthetase_1164446..1164676_POSITIVE 313 69 22 80 33 aact:AA00164|5end_dephospho-CoA_kinase_(dephosphocoenzyme_A_kinase)_116745..116975_POSITIVE 310 70 23 229 157 aact:AA01886|5end_UDP-glucose-4-epimerase_1271464..1271694_POSITIVE 309 56 11 135 80 aact:AA01066|5end_conserved_hypothetical_protein_738380..738610_POSITIVE 302 60 19 55 5 aact:AA01159|5end_phosphatase_792828..793058_POSITIVE 301 40 1 115 75 aact:AA00989|5end_hypothetical_protein_692319..692549_POSITIVE 299 53 11 63 17 aact:AA02231|5end_probable_dethiobiotin_synthetase_1_1517650..1517880_POSITIVE 299 60 11 154 107 aact:AA00894|5end_selenium_transferase_(Cysteinyl-tRNA(Sec)_selenium_transferase)_619879..620109_POSITIVE 296 99 60 59 20 aact:AA01772|5end_shikimate_5-dehydrogenase_protein_1194050..1194280_POSITIVE 296 50 1 111 60 aact:AA01274|5end_hypothetical_protein_864519..864749_POSITIVE 295 66 24 212 179 aact:AA02515|5end_flavodoxin_1748721..1748951_POSITIVE 294 90 43 193 142 aact:AA00237|5end_hypothetical_protein_170934..171164_POSITIVE 292 49 5 71 26 aact:AA02892|5end_oligopeptide_ABC_transporter,_periplasmic-binding_protein_2026402..2026632_POSITIVE 290 50 1 59 7 aact:AA01861|5end_phosphomethylpyrimidine_kinase_1251806..1252036_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 309 56 11 67 12 aact:AA01064|3end_conserved_hypothetical_protein_(possible_aminomethyltransferase)_738392..738542_POSITIVE 296 50 1 100 49 aact:AA01273|3end_hypothetical_protein_864588..864738_POSITIVE 291 57 11 98 43 aact:AA00534|3end_hypothetical_protein_365594..365744_POSITIVE 290 50 1 63 11 aact:AA01859|3end_hypothetical_protein_1251890..1252040_POSITIVE 289 90 44 77 22 aact:AA01304|3end_penicillin-binding_protein_1A_885580..885730_POSITIVE 284 60 12 144 91 aact:AA01875|3end_PTS_system,_glucose-specific_enzyme_II,_A_component_1263506..1263656_POSITIVE 284 99 58 81 22 aact:AA00551|3end_hypothetical_protein_377403..377553_POSITIVE 283 41 3 74 31 aact:AA02480|3end_excinuclease_ABC_subunit_B_1718442..1718592_POSITIVE 279 51 12 139 96 aact:AA01769|3end_hypothetical_protein_1193132..1193282_POSITIVE 279 50 3 75 13 aact:AA00419|3end_conserved_hypothetical_protein_(possible_phosphatidylethanolamine-binding_protein)_284911..285061_POSITIVE 278 60 12 76 20 aact:AA01890|3end_cell-cycle_protein_1275967..1276117_POSITIVE 278 60 12 63 29 aact:AA01269|3end_hypothetical_protein_863413..863563_POSITIVE 276 60 17 149 97 aact:AA00541|3end_conserved_hypothetical_protein_371344..371494_POSITIVE 276 70 24 101 43 aact:AA00518|3end_conserved_hypothetical_protein_357213..357363_POSITIVE 274 62 21 37 3 aact:AA02350|3end_possible_lipoprotein_1609179..1609329_POSITIVE 273 101 61 146 96 aact:AA01169|3end_hypothetical_protein_802229..802379_POSITIVE 270 98 55 147 104 aact:AA00892|3end_selenocysteine-specific_elongation_factor_(SelB_translation_factor)_619959..620109_POSITIVE 269 52 14 74 37 aact:AA01726|3end_conserved_hypothetical_protein_(possible_HipA-like_protein_1168304..1168454_POSITIVE 268 60 12 49 3 aact:AA01817|3end_hypothetical_protein_1224400..1224550_POSITIVE 265 50 1 145 81 aact:AA02937|3end_conserved_hypothetical_protein_2056947..2057097_POSITIVE