Origin IGS: taagtccacttcaacgatactttaaagtatatatttcaaggagagaatgcatctgcgttctctcctttttgtttgcacaaagccaaacttgcaaacgtttgcacccacattaatacttattataaatcaagttagtgcagggaaaggaaataagttgtatatttgcgaaagcataaacaattaggataaaacaaaatcaaatcatcatt .........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 aatgatgatttgattttgttttatcctaattgtttatgctttcgcaaatatacaacttatttcctttccctgcactaacttgatttataataagtattaatgtgggtgcaaacgtttgcaagtttggctttgtgcaaacaaaaaggagagaacgcagatgcattctctccttgaaatatatactttaaagtatcgttgaagtggactta Mask Tandem Repeat Region ================================================ taagtccacttcaacgatactttaaagtatatatttcaaggagagaatgcatctgcgttctctcctttttgtttgcacaaagccaaacttgcaaacgtttgcacccacattaatacttattataaatcaagttagtgcagggaaaggaaataagttgtatatttgcgaaagcataaacaattaggataaaacaaaatcaaatcatcatt Find is-nt database================================================ Query_seq: PI1811:PI1812|PI1811:PI1812:conserved hypothetical protein:possible alpha-amylase:->->:1750690..1750898 209 taagtccacttcaacgatactttaaagtatatatttcaaggagagaatgcatctgcgttctctcctttttgtttgcacaaagccaaacttgcaaacgtttgcacccacattaatacttattataaatcaagttagtgcagggaaaggaaataagttgtatatttgcgaaagcataaacaattaggataaaacaaaatcaaatcatcatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI1811:PI1812|PI1811:PI1812:conserved hypothetical protein:possible alpha-amylase:->->:1750690..1750898 209 taagtccacttcaacgatactttaaagtatatatttcaaggagagaatgcatctgcgttctctcctttttgtttgcacaaagccaaacttgcaaacgtttgcacccacattaatacttattataaatcaagttagtgcagggaaaggaaataagttgtatatttgcgaaagcataaacaattaggataaaacaaaatcaaatcatcatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI1811:PI1812|PI1811:PI1812:conserved hypothetical protein:possible alpha-amylase:->->:1750690..1750898 209 taagtccacttcaacgatactttaaagtatatatttcaaggagagaatgcatctgcgttctctcctttttgtttgcacaaagccaaacttgcaaacgtttgcacccacattaatacttattataaatcaagttagtgcagggaaaggaaataagttgtatatttgcgaaagcataaacaattaggataaaacaaaatcaaatcatcatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taagtccacttcaacgatactttaaagtatatatttcaaggagagaatgcatctgcgttctctcctttttgtttgcacaaagccaaacttgcaaacgtttgcacccacattaatacttattataaatcaagttagtgcagggaaaggaaataagttgtatatttgcgaaagcataaacaattaggataaaacaaaatcaaatcatcatt Predict ORF larger than 30AA ================================================ Protein_Len: 34 Strand: + Start: 31 End: 132 .............................. M F Q G E N A S A F S P F C L H K A K L A N V C T H I N T Y Y K S S ............................................................................. Protein_Len: 51 Strand: + Start: 29 End: 181 ............................ M Y F K E R M H L R S L L F V C T K P N L Q T F A P T L I L I I N Q V S A G K G N K L Y I C E S I N N ............................ Protein_Len: 33 Strand: - Start: 25 End: 123 ........................ L I Y K L S L I C R R E R R K T Q V F G F K C V N A G V N I S I M ...................................................................................... taagtccacttcaacgatactttaaagtatatatttcaaggagagaatgcatctgcgttctctcctttttgtttgcacaaagccaaacttgcaaacgtttgcacccacattaatacttattataaatcaagttagtgcagggaaaggaaataagttgtatatttgcgaaagcataaacaattaggataaaacaaaatcaaatcatcatt 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================================================ taagtccacttcaacgatactttaaagtatatatttcaaggagagaatgcatctgcgttctctcctttttgtttgcacaaagccaaacttgcaaacgtttgcacccacattaatacttattataaatcaagttagtgcagggaaaggaaataagttgtatatttgcgaaagcataaacaattaggataaaacaaaatcaaatcatcatt Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 100 HP_score: -14.1 Tail_Score: -5.27335 Start: 40 End: 65 Full_Region: AAGTATATATTTCAA GGAGAGAATGC ATCT GCGTTCTCTCC TTTTTGTTTGCACAA .......................................GGAGAGAATGCATCTGCGTTCTCTCC................................................................................................................................................ Find igs database================================================ Query_seq: PI1811:PI1812|PI1811:PI1812:conserved hypothetical protein:possible alpha-amylase:->->:1750690..1750898 209 taagtccacttcaacgatactttaaagtatatatttcaaggagagaatgcatctgcgttctctcctttttgtttgcacaaagccaaacttgcaaacgtttgcacccacattaatacttattataaatcaagttagtgcagggaaaggaaataagttgtatatttgcgaaagcataaacaattaggataaaacaaaatcaaatcatcatt Intra-Species Hit: Count: 1 Min: 1 Max: 209 Len: 209 Subject: pint_PI1811_PI1812|conserved hypothetical protein:possible alpha-amylase|POSITIVE:POSITIVE|[1750690,1750898]|209 HSP 1 e-value: 1.0E-115 bit: 414.0 Len: 209 Query Start:1 Query End:209 Subject Strand: POSITIVE Subject Start: 1 Subject End: 209 taagtccacttcaacgatactttaaagtatatatttcaaggagagaatgcatctgcgttctctcctttttgtttgcacaaagccaaacttgcaaacgtttgcacccacattaatacttattataaatcaagttagtgcagggaaaggaaataagttgtatatttgcgaaagcataaacaattaggataaaacaaaatcaaatcatcatt taagtccacttcaacgatactttaaagtatatatttcaaggagagaatgcatctgcgttctctcctttttgtttgcacaaagccaaacttgcaaacgtttgcacccacattaatacttattataaatcaagttagtgcagggaaaggaaataagttgtatatttgcgaaagcataaacaattaggataaaacaaaatcaaatcatcatt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAGUCCACUUCAACGAUACUUUAAAGUAUAUAUUUCAAGGAGAGAAUGCAUCUGCGUUCUCUCCUUUUUGUUUGCACAAAGCCAAACUUGCAAACGUUUGCACCCACAUUAAUACUUAUUAUAAAUCAAGUUAGUGCAGGGAAAGGAAAUAAGUUGUAUAUUUGCGAAAGCAUAAACAAUUAGGAUAAAACAAAAUCAAAUCAUCAUU ...((((....((((.(((((....))))).((((((.((((((((((((....))))))))))))....(((((((............))))))).......(((.(((((((................)))))))..)))....)))))).))))......(((....)))..........))))...................... (-52.29) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUGAUGAUUUGAUUUUGUUUUAUCCUAAUUGUUUAUGCUUUCGCAAAUAUACAACUUAUUUCCUUUCCCUGCACUAACUUGAUUUAUAAUAAGUAUUAAUGUGGGUGCAAACGUUUGCAAGUUUGGCUUUGUGCAAACAAAAAGGAGAGAACGCAGAUGCAUUCUCUCCUUGAAAUAUAUACUUUAAAGUAUCGUUGAAGUGGACUUA ...(((((..(......)..)))))......((((((((....)).......((((.((((((.......((((((.(((((((...........))))).)).))))))...(((((((((.....))...)))))))...((((((((((.((....)).)))))))))))))))).(((((....))))).))))..))))))... (-46.70) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 402 90 42 209 152 pint:PI0537|5end_alanyl-tRNA_synthetase_(alanine--tRNA_ligase)_489756..489986_POSITIVE 303 94 55 47 1 pint:PI1845|5end_hypothetical_protein_1791457..1791687_POSITIVE 298 159 116 195 149 pint:PI1873|5end_hypothetical_protein_1817878..1818108_POSITIVE 298 108 62 225 172 pint:PI0028|5end_aminopeptidase_31559..31789_POSITIVE 286 108 64 108 54 pint:PI0410|5end_glutamyl-tRNA_synthetase_(glutamate--tRNA_ligase)_375947..376177_POSITIVE 284 72 38 154 118 pint:PI1672|5end_conserved_hypothetical_protein;_possible_DNA-binding_protein,_histone-like_family_1587027..1587257_POSITIVE 279 87 51 91 56 pint:PI0090|5end_amidophosphoribosyltransferase_88379..88609_POSITIVE 277 65 30 65 20 pint:PI0380|5end_conserved_hypothetical_protein_350162..350392_POSITIVE 276 73 40 73 27 pint:PI0695|5end_xanthine/uracil_permease_family_protein_631413..631643_POSITIVE 274 110 62 49 16 pint:PI0240|5end_conserved_hypothetical_protein_238462..238692_POSITIVE 273 72 40 112 80 pint:PI0041|5end_hypothetical_protein_41785..42015_POSITIVE 268 70 27 128 86 pint:PI0613|5end_glycerol-3-phosphate_dehydrogenase_(NAD(P)+)_562167..562397_POSITIVE 267 109 63 44 3 pint:PI1379|5end_hypothetical_protein_1301817..1302047_POSITIVE 267 80 34 193 126 pint:PI0764|5end_permease_697962..698192_POSITIVE 267 109 63 146 105 pint:PI0723|5end_conserved_hypothetical_protein_656043..656273_POSITIVE 264 84 43 198 157 pint:PI1767|5end_fructokinase,_pfkB_family_1694285..1694515_POSITIVE 264 98 52 105 48 pint:PI1363|5end_hypothetical_protein_1281666..1281896_POSITIVE 261 108 71 41 3 pint:PI0684|5end_coproporphyrinogen_III_oxidase_619357..619587_POSITIVE 260 130 81 128 69 pint:PI1727|5end__ATP-dependent_Clp_protease,_ATP-binding_subunit_1645680..1645910_POSITIVE 260 85 49 51 18 pint:PI0602|5end_conserved_hypothetical_protein_549099..549329_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 428 67 38 53 24 pint:PI1811|3end_conserved_hypothetical_protein_1750629..1750779_POSITIVE 401 85 42 140 95 pint:PI0535|3end_hypothetical_protein_489779..489929_POSITIVE 342 96 53 100 51 pint:PI0683|3end_hypothetical_protein_619797..619947_POSITIVE 284 72 38 73 37 pint:PI1670|3end_hypothetical_protein_1587026..1587176_POSITIVE 277 65 30 62 17 pint:PI0379|3end_conserved_hypothetical_protein_350239..350389_POSITIVE 273 72 40 119 87 pint:PI0040|3end_conserved_hypothetical_protein_(possible_integral_membrane_protein)_41872..42022_POSITIVE 271 157 116 151 107 pint:PI1872|3end_glycosyl_transferase,_group_2_family_protein_1817916..1818066_POSITIVE 268 70 27 83 41 pint:PI0612|3end_lysyl-tRNA_synthetase_562202..562352_POSITIVE 264 108 69 50 3 pint:PI0409|3end_3-deoxy-D-manno-octulosonic-acid_transferase_(kdotransferase)_375969..376119_POSITIVE 257 102 61 140 92 pint:PI0706|3end_pyridoxal_phosphate_biosynthetic_protein_(4-hydroxythreonine-4-phosphate_dehydrogenase)_643394..643544_POSITIVE 249 76 33 139 96 pint:PI0147|3end_HIT_family_protein_141308..141458_POSITIVE 246 77 34 141 86 pint:PI0763|3end_thymidine_kinase_698002..698152_POSITIVE 245 173 131 105 60 pint:PI0684|3end_coproporphyrinogen_III_oxidase_620507..620657_POSITIVE 241 174 138 121 81 pint:PI1644|3end_hypothetical_protein_1561030..1561180_POSITIVE 241 98 54 63 12 pint:PI0417|3end_hypothetical_protein_386730..386880_POSITIVE 240 98 51 64 11 pint:PI1633|3end_hypothetical_protein_1552955..1553105_POSITIVE 239 100 53 57 1 pint:PI1630|3end_hypothetical_protein_1552494..1552644_POSITIVE 239 174 136 96 61 pint:PI1570|3end_succinyl-diaminopimelate_desuccinylase_1494778..1494928_POSITIVE 239 92 52 64 22 pint:PI1531|3end_biotin--acetyl-CoA-carboxylase_ligase_1451734..1451884_POSITIVE 239 170 121 124 79 pint:PI1472|3end_hypothetical_protein_1395879..1396029_POSITIVE