Origin IGS: tgttttaatatctgcctgtattcctgcgcctcctccgctgtcggagcctgctatcgtaagagtttttacatagtgcataataagccatgaaagtaacaaatggtacttttcggaatagccaaaatataaggggatacaccaataaggatagataaacgcaaatgtctgtatattcgcacttcctacggcagcattacctgcatcaggttatacgggtataatctcagctcactcaatggagtggcacccctttttcggataaaccgaaagtctatctgcgtgcaaagatacgataatgttctgcaattgcaaaatttaagtcaaagtttttcctcatcaataatttttcttttattttccctttggtttgccaaaatttgcgtacatttgcaatccaactactaatttataatagaa .........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.........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 ttctattataaattagtagttggattgcaaatgtacgcaaattttggcaaaccaaagggaaaataaaagaaaaattattgatgaggaaaaactttgacttaaattttgcaattgcagaacattatcgtatctttgcacgcagatagactttcggtttatccgaaaaaggggtgccactccattgagtgagctgagattatacccgtataacctgatgcaggtaatgctgccgtaggaagtgcgaatatacagacatttgcgtttatctatccttattggtgtatccccttatattttggctattccgaaaagtaccatttgttactttcatggcttattatgcactatgtaaaaactcttacgatagcaggctccgacagcggaggaggcgcaggaatacaggcagatattaaaaca Mask Tandem Repeat Region ================================================ tgttttaatatctgcctgtattcctgcgcctcctccgctgtcggagcctgctatcgtaagagtttttacatagtgcataataagccatgaaagtaacaaatggtacttttcggaatagccaaaatataaggggatacaccaataaggatagataaacgcaaatgtctgtatattcgcacttcctacggcagcattacctgcatcaggttatacgggtataatctcagctcactcaatggagtggcacccctttttcggataaaccgaaagtctatctgcgtgcaaagatacgataatgttctgcaattgcaaaatttaagtcaaagtttttcctcatcaataatttttcttttattttccctttggtttgccaaaatttgcgtacatttgcaatccaactactaatttataatagaa Find is-nt database================================================ Query_seq: PI0047:PI0048|PI0047:PI0048:phosphomethylpyrimidine kinase:conserved hypothetical protein:->->:46842..47258 417 tgttttaatatctgcctgtattcctgcgcctcctccgctgtcggagcctgctatcgtaagagtttttacatagtgcataataagccatgaaagtaacaaatggtacttttcggaatagccaaaatataaggggatacaccaataaggatagataaacgcaaatgtctgtatattcgcacttcctacggcagcattacctgcatcaggttatacgggtataatctcagctcactcaatggagtggcacccctttttcggataaaccgaaagtctatctgcgtgcaaagatacgataatgttctgcaattgcaaaatttaagtcaaagtttttcctcatcaataatttttcttttattttccctttggtttgccaaaatttgcgtacatttgcaatccaactactaatttataatagaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI0047:PI0048|PI0047:PI0048:phosphomethylpyrimidine kinase:conserved hypothetical protein:->->:46842..47258 417 tgttttaatatctgcctgtattcctgcgcctcctccgctgtcggagcctgctatcgtaagagtttttacatagtgcataataagccatgaaagtaacaaatggtacttttcggaatagccaaaatataaggggatacaccaataaggatagataaacgcaaatgtctgtatattcgcacttcctacggcagcattacctgcatcaggttatacgggtataatctcagctcactcaatggagtggcacccctttttcggataaaccgaaagtctatctgcgtgcaaagatacgataatgttctgcaattgcaaaatttaagtcaaagtttttcctcatcaataatttttcttttattttccctttggtttgccaaaatttgcgtacatttgcaatccaactactaatttataatagaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI0047:PI0048|PI0047:PI0048:phosphomethylpyrimidine kinase:conserved hypothetical protein:->->:46842..47258 417 tgttttaatatctgcctgtattcctgcgcctcctccgctgtcggagcctgctatcgtaagagtttttacatagtgcataataagccatgaaagtaacaaatggtacttttcggaatagccaaaatataaggggatacaccaataaggatagataaacgcaaatgtctgtatattcgcacttcctacggcagcattacctgcatcaggttatacgggtataatctcagctcactcaatggagtggcacccctttttcggataaaccgaaagtctatctgcgtgcaaagatacgataatgttctgcaattgcaaaatttaagtcaaagtttttcctcatcaataatttttcttttattttccctttggtttgccaaaatttgcgtacatttgcaatccaactactaatttataatagaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tgttttaatatctgcctgtattcctgcgcctcctccgctgtcggagcctgctatcgtaagagtttttacatagtgcataataagccatgaaagtaacaaatggtacttttcggaatagccaaaatataaggggatacaccaataaggatagataaacgcaaatgtctgtatattcgcacttcctacggcagcattacctgcatcaggttatacgggtataatctcagctcactcaatggagtggcacccctttttcggataaaccgaaagtctatctgcgtgcaaagatacgataatgttctgcaattgcaaaatttaagtcaaagtttttcctcatcaataatttttcttttattttccctttggtttgccaaaatttgcgtacatttgcaatccaactactaatttataatagaa Predict ORF larger than 30AA ================================================ Protein_Len: 36 Strand: + Start: 152 End: 259 ....................................................................................................................................................... M N A N V C I F A L P T A A L P A S G Y T G I I S A H S M E W H P F F G .............................................................................................................................................................. Protein_Len: 60 Strand: + Start: 142 End: 402 ............................................................................................................................................. M R I D K R K C L Y I R T S Y G S I T C I R L Y G Y N L S S L N G V A P L F R I N R K S I C V Q R Y D N V L Q L Q N L S ............... Protein_Len: 37 Strand: + Start: 306 End: 416 ................................................................................................................................................................................................................................................................................................................. M A K F K S K F F L I N N F S F I F P L V C Q N L R T F A I Q L L I Y N R . Protein_Len: 44 Strand: - Start: 275 End: 406 .................................................................................................................................................................................................................................................................................. R R A F I R Y H E A I A F N L D F N K R M L L K E K I K G K T Q W F K R V N A I W S S M ........... Protein_Len: 30 Strand: - Start: 186 End: 275 ......................................................................................................................................................................................... P L M V Q M L N Y P Y L R L E S L P T A G R K R I F R F D M .............................................................................................................................................. Protein_Len: 37 Strand: - Start: 69 End: 179 .................................................................... M T C L L G H F Y C I T S K P I A L I Y P S V G I L I S L R L H R Y I R M .............................................................................................................................................................................................................................................. Protein_Len: 52 Strand: - Start: 8 End: 163 ....... Y R G T N R R R R R Q R L R S D Y S N K C L A Y Y A M F T V F P V K R F L W F I L P Y V L L S L Y V C M .............................................................................................................................................................................................................................................................. Protein_Len: 57 Strand: - Start: 1 End: 171 T K I D A Q I G A G G G S D S G A I T L T K V Y H M I L W S L L L H Y K E S Y G F Y L P I C W Y P Y I F A F T Q M ...................................................................................................................................................................................................................................................... tgttttaatatctgcctgtattcctgcgcctcctccgctgtcggagcctgctatcgtaagagtttttacatagtgcataataagccatgaaagtaacaaatggtacttttcggaatagccaaaatataaggggatacaccaataaggatagataaacgcaaatgtctgtatattcgcacttcctacggcagcattacctgcatcaggttatacgggtataatctcagctcactcaatggagtggcacccctttttcggataaaccgaaagtctatctgcgtgcaaagatacgataatgttctgcaattgcaaaatttaagtcaaagtttttcctcatcaataatttttcttttattttccctttggtttgccaaaatttgcgtacatttgcaatccaactactaatttataatagaa 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: 193 End: 222 ................................................................................................................................................................................................ATTACCTGCATCAGGTTATACGGGTATAAT................................................................................................................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tgttttaatatctgcctgtattcctgcgcctcctccgctgtcggagcctgctatcgtaagagtttttacatagtgcataataagccatgaaagtaacaaatggtacttttcggaatagccaaaatataaggggatacaccaataaggatagataaacgcaaatgtctgtatattcgcacttcctacggcagcattacctgcatcaggttatacgggtataatctcagctcactcaatggagtggcacccctttttcggataaaccgaaagtctatctgcgtgcaaagatacgataatgttctgcaattgcaaaatttaagtcaaagtttttcctcatcaataatttttcttttattttccctttggtttgccaaaatttgcgtacatttgcaatccaactactaatttataatagaa Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PI0047:PI0048|PI0047:PI0048:phosphomethylpyrimidine kinase:conserved hypothetical protein:->->:46842..47258 417 tgttttaatatctgcctgtattcctgcgcctcctccgctgtcggagcctgctatcgtaagagtttttacatagtgcataataagccatgaaagtaacaaatggtacttttcggaatagccaaaatataaggggatacaccaataaggatagataaacgcaaatgtctgtatattcgcacttcctacggcagcattacctgcatcaggttatacgggtataatctcagctcactcaatggagtggcacccctttttcggataaaccgaaagtctatctgcgtgcaaagatacgataatgttctgcaattgcaaaatttaagtcaaagtttttcctcatcaataatttttcttttattttccctttggtttgccaaaatttgcgtacatttgcaatccaactactaatttataatagaa Intra-Species Hit: Count: 1 Min: 1 Max: 417 Len: 417 Subject: pint_PI0047_PI0048|phosphomethylpyrimidine kinase:conserved hypothetical protein|POSITIVE:POSITIVE|[46842,47258]|417 HSP 1 e-value: 0.0 bit: 827.0 Len: 417 Query Start:1 Query End:417 Subject Strand: POSITIVE Subject Start: 1 Subject End: 417 tgttttaatatctgcctgtattcctgcgcctcctccgctgtcggagcctgctatcgtaagagtttttacatagtgcataataagccatgaaagtaacaaatggtacttttcggaatagccaaaatataaggggatacaccaataaggatagataaacgcaaatgtctgtatattcgcacttcctacggcagcattacctgcatcaggttatacgggtataatctcagctcactcaatggagtggcacccctttttcggataaaccgaaagtctatctgcgtgcaaagatacgataatgttctgcaattgcaaaatttaagtcaaagtttttcctcatcaataatttttcttttattttccctttggtttgccaaaatttgcgtacatttgcaatccaactactaatttataatagaa tgttttaatatctgcctgtattcctgcgcctcctccgctgtcggagcctgctatcgtaagagtttttacatagtgcataataagccatgaaagtaacaaatggtacttttcggaatagccaaaatataaggggatacaccaataaggatagataaacgcaaatgtctgtatattcgcacttcctacggcagcattacctgcatcaggttatacgggtataatctcagctcactcaatggagtggcacccctttttcggataaaccgaaagtctatctgcgtgcaaagatacgataatgttctgcaattgcaaaatttaagtcaaagtttttcctcatcaataatttttcttttattttccctttggtttgccaaaatttgcgtacatttgcaatccaactactaatttataatagaa Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGUUUUAAUAUCUGCCUGUAUUCCUGCGCCUCCUCCGCUGUCGGAGCCUGCUAUCGUAAGAGUUUUUACAUAGUGCAUAAUAAGCCAUGAAAGUAACAAAUGGUACUUUUCGGAAUAGCCAAAAUAUAAGGGGAUACACCAAUAAGGAUAGAUAAACGCAAAUGUCUGUAUAUUCGCACUUCCUACGGCAGCAUUACCUGCAUCAGGUUAUACGGGUAUAAUCUCAGCUCACUCAAUGGAGUGGCACCCCUUUUUCGGAUAAACCGAAAGUCUAUCUGCGUGCAAAGAUACGAUAAUGUUCUGCAAUUGCAAAAUUUAAGUCAAAGUUUUUCCUCAUCAAUAAUUUUUCUUUUAUUUUCCCUUUGGUUUGCCAAAAUUUGCGUACAUUUGCAAUCCAACUACUAAUUUAUAAUAGAA ........(((((((((.((((((.((((...(((((....))))).........(((((....)))))...)))).......(((((...........))))).......)))))).............((......))....))).))))))...((((((((..((((.((.((((..(((...((((......))))...))).....((((((........((.(((((....)))))))......(((((((.....)))))))..)))))).)))).)).))))...........((((....(((((..(((..((((((.............)))))).)))..)))))...(((((....)))))..))))..)))))))).......................... (-89.62) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUCUAUUAUAAAUUAGUAGUUGGAUUGCAAAUGUACGCAAAUUUUGGCAAACCAAAGGGAAAAUAAAAGAAAAAUUAUUGAUGAGGAAAAACUUUGACUUAAAUUUUGCAAUUGCAGAACAUUAUCGUAUCUUUGCACGCAGAUAGACUUUCGGUUUAUCCGAAAAAGGGGUGCCACUCCAUUGAGUGAGCUGAGAUUAUACCCGUAUAACCUGAUGCAGGUAAUGCUGCCGUAGGAAGUGCGAAUAUACAGACAUUUGCGUUUAUCUAUCCUUAUUGGUGUAUCCCCUUAUAUUUUGGCUAUUCCGAAAAGUACCAUUUGUUACUUUCAUGGCUUAUUAUGCACUAUGUAAAAACUCUUACGAUAGCAGGCUCCGACAGCGGAGGAGGCGCAGGAAUACAGGCAGAUAUUAAAACA ..((((((.....))))))......((((((.(((((....((((((....))))))........................((((..((....))..))))..((((((....))))))......))))).)))))).((((((.(((((((((..((.((((((((((((.(((((((....))))).))......((((((.((((.(((((...))))).))))....(((((((((((((((........)))))))))).))))).......)))))).))))))...)))))).))..))).))))).).)))))).....((.((.((((((.(((.((((((((......)))).))))....(((((....))))).....)))..)))).)).)))).......... (-100.40) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 417 228 181 175 128 pint:PI1451|5end_outer_membrane_receptor_proteins,_tonB_dependent_(possibly_iron_transport_related)_1372931..1373161_POSITIVE 406 60 12 160 119 pint:PI1575|5end_LemA_protein_1501143..1501373_POSITIVE 400 58 13 93 33 pint:PI1637|5end_hypothetical_protein_1554500..1554730_POSITIVE 373 51 14 203 167 pint:PI1768|5end_conserved_hypothetical_protein_1695456..1695686_POSITIVE 373 60 12 64 9 pint:PI1749|5end_conserved_hypothetical_protein_1671039..1671269_POSITIVE 373 62 26 66 32 pint:PI1086|5end_pyruvate:ferredoxin_oxidoreductase_1006602..1006832_POSITIVE 368 58 12 92 46 pint:PI1625|5end_conserved_hypothetical_protein;_possible_phage_transposase_1549316..1549546_POSITIVE 368 58 12 92 46 pint:PI0332|5end_conserved_hypothetical_protein_312600..312830_POSITIVE 366 57 13 204 159 pint:PI1411|5end_conserved_hypothetical_protein_1331884..1332114_POSITIVE 358 64 25 101 46 pint:PI0715|5end_hypothetical_protein_652311..652541_POSITIVE 347 57 12 81 25 pint:PI1550|5end_conserved_hypothetical_protein_1467360..1467590_POSITIVE 346 56 11 65 6 pint:PI0341|5end_conserved_hypothetical_protein_317038..317268_POSITIVE 342 260 211 111 59 pint:PI1216|5end_probable_phosphohydrolase_1134814..1135044_POSITIVE 341 66 23 62 1 pint:PI0531|5end_ABC_transporter,_ATP-binding_protein;_possible_gliding_motility_related_484696..484926_POSITIVE 338 52 12 48 7 pint:PI1594|5end_MotA/TolQ/ExbB_proton_channel_1523528..1523758_POSITIVE 337 220 174 57 12 pint:PI1697|5end_conserved_hypothetical_protein_1612217..1612447_POSITIVE 331 57 12 60 2 pint:PI1694|5end_hypothetical_protein_1609717..1609947_POSITIVE 331 216 172 111 48 pint:PI0729|5end_integrase_661428..661658_POSITIVE 330 49 11 205 154 pint:PI1480|5end_xanthine/uracil_permease_family_protein_1402675..1402905_POSITIVE 329 56 11 196 130 pint:PI2090|5end_thioesterase_family_protein_2047570..2047800_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 417 228 181 55 8 pint:PI1450|3end_hypothetical_protein_1372891..1373041_POSITIVE 348 56 11 127 65 pint:PI0570|3end_exsB_protein;_possible_aluminum_resistance_protein_515395..515545_POSITIVE 342 260 211 88 36 pint:PI1215|3end_orotidine_5'-phosphate_decarboxylase_1134871..1135021_POSITIVE 339 55 17 52 6 pint:PI1633|3end_hypothetical_protein_1552955..1553105_POSITIVE 337 52 12 125 85 pint:PI1227|3end_conserved_hypothetical_protein;_possible_DNA-binding_protein,_histone-like_family_1148974..1149124_POSITIVE 331 216 172 111 48 pint:PI0728|3end_integrase_661508..661658_POSITIVE 325 60 12 86 32 pint:PI2016|3end_ribosomal_large_subunit_pseudouridine_synthase_D_1974933..1975083_POSITIVE 323 146 101 141 96 pint:PI2077|3end_hypothetical_protein_2036070..2036220_POSITIVE 322 56 12 147 112 pint:PI0750|3end_zinc_protease_680633..680783_POSITIVE 322 55 13 149 92 pint:PI0087|3end_conserved_hypothetical_protein_86733..86883_POSITIVE 321 63 26 59 7 pint:PI1864|3end_chromate_transport_protein_1811009..1811159_POSITIVE 321 57 15 83 26 pint:PI1734|3end_possible_carboxyl-terminal_protease-related_protein_1653829..1653979_POSITIVE 321 206 165 145 104 pint:PI1087|3end_conserved_hypothetical_protein_1011557..1011707_POSITIVE 320 49 13 130 96 pint:PI1338|3end_phosphoserine_phosphatase_1256594..1256744_POSITIVE 318 46 12 151 122 pint:PI1574|3end_conserved_hypothetical_protein_1501226..1501376_POSITIVE 318 215 173 142 100 pint:PI0811|3end_protease/hemagglutinin_PrtT,_streptopain_family_749937..750087_POSITIVE 318 56 16 65 13 pint:PI0634|3end_conserved_hypothetical_protein_581121..581271_POSITIVE 316 56 12 67 17 pint:PI0696|3end_NADH_pyrophosphatase,_MutT_family_hydrolase_(NAD+_diphosphatase)_633600..633750_POSITIVE 310 220 175 116 70 pint:PI0168|3end_methionyl-tRNA_synthetase_(methionine--tRNA_ligase)_163279..163429_POSITIVE 309 230 181 151 100 pint:PI0355|3end_probable__N-acetylmuramoyl-L-alanine_amidase_326698..326848_POSITIVE