Origin IGS: taaaaaagatgccaggtgcagataaggagacgctggtggagcaatatacccacggtcgaacaatccatctgcgtgagacttccatgcaggagtacaatacg .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 cgtattgtactcctgcatggaagtctcacgcagatggattgttcgaccgtgggtatattgctccaccagcgtctccttatctgcacctggcatctttttta Mask Tandem Repeat Region ================================================ taaaaaagatgccaggtgcagataaggagacgctggtggagcaatatacccacggtcgaacaatccatctgcgtgagacttccatgcaggagtacaatacg Find is-nt database================================================ Query_seq: PI0338:PI0339|PI0338:PI0339:hypothetical protein:hypothetical protein:->->:315774..315874 101 taaaaaagatgccaggtgcagataaggagacgctggtggagcaatatacccacggtcgaacaatccatctgcgtgagacttccatgcaggagtacaatacg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI0338:PI0339|PI0338:PI0339:hypothetical protein:hypothetical protein:->->:315774..315874 101 taaaaaagatgccaggtgcagataaggagacgctggtggagcaatatacccacggtcgaacaatccatctgcgtgagacttccatgcaggagtacaatacg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI0338:PI0339|PI0338:PI0339:hypothetical protein:hypothetical protein:->->:315774..315874 101 taaaaaagatgccaggtgcagataaggagacgctggtggagcaatatacccacggtcgaacaatccatctgcgtgagacttccatgcaggagtacaatacg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taaaaaagatgccaggtgcagataaggagacgctggtggagcaatatacccacggtcgaacaatccatctgcgtgagacttccatgcaggagtacaatacg Predict ORF larger than 30AA ================================================ Protein_Len: 31 Strand: + Start: 9 End: 101 ........ M P G A D K E T L V E Q Y T H G R T I H L R E T S M Q E Y N T Protein_Len: 32 Strand: - Start: 3 End: 98 .. F L H W T C I L L R Q H L L I G V T S C D M Q T L S G H L L V M ... Protein_Len: 32 Strand: - Start: 2 End: 97 . F F I G P A S L S V S T S C Y V W P R V I W R R S V E M C S Y M .... taaaaaagatgccaggtgcagataaggagacgctggtggagcaatatacccacggtcgaacaatccatctgcgtgagacttccatgcaggagtacaatacg 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================================================ taaaaaagatgccaggtgcagataaggagacgctggtggagcaatatacccacggtcgaacaatccatctgcgtgagacttccatgcaggagtacaatacg Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PI0338:PI0339|PI0338:PI0339:hypothetical protein:hypothetical protein:->->:315774..315874 101 taaaaaagatgccaggtgcagataaggagacgctggtggagcaatatacccacggtcgaacaatccatctgcgtgagacttccatgcaggagtacaatacg Intra-Species Hit: Count: 1 Min: 1 Max: 101 Len: 101 Subject: pint_PI0338_PI0339|hypothetical protein:hypothetical protein|POSITIVE:POSITIVE|[315774,315874]|101 HSP 1 e-value: 6.0E-51 bit: 200.0 Len: 101 Query Start:1 Query End:101 Subject Strand: POSITIVE Subject Start: 1 Subject End: 101 taaaaaagatgccaggtgcagataaggagacgctggtggagcaatatacccacggtcgaacaatccatctgcgtgagacttccatgcaggagtacaatacg taaaaaagatgccaggtgcagataaggagacgctggtggagcaatatacccacggtcgaacaatccatctgcgtgagacttccatgcaggagtacaatacg Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAAAAAGAUGCCAGGUGCAGAUAAGGAGACGCUGGUGGAGCAAUAUACCCACGGUCGAACAAUCCAUCUGCGUGAGACUUCCAUGCAGGAGUACAAUACG ...............((((......(((..((.(.((((..........)))).).)).....))).((((((((.(....))))))))).))))...... (-24.00) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CGUAUUGUACUCCUGCAUGGAAGUCUCACGCAGAUGGAUUGUUCGACCGUGGGUAUAUUGCUCCACCAGCGUCUCCUUAUCUGCACCUGGCAUCUUUUUUA ..........(((.....))).(((....(((((((((.....((...((((((.....)).))))...))..)))..))))))....))).......... (-22.40) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 367 60 17 61 10 pint:PI0628|5end_phosphoribosylglycinamide_formyltransferase_576027..576257_POSITIVE 353 76 32 179 133 pint:PI1849|5end_conserved_hypothetical_protein;_possible_acyltransferase_family_protein_1794916..1795146_POSITIVE 349 63 22 188 137 pint:PI1951|5end_ABC_transporter,_ATP-binding_protein_1905823..1906053_POSITIVE 343 65 28 44 2 pint:PI0013|5end_auxin-regulated_protein_15506..15736_POSITIVE 328 60 18 40 1 pint:PI0726|5end_hypothetical_protein_659042..659272_POSITIVE 326 56 13 76 30 pint:PI1751|5end_desulfoferrodoxin_1679835..1680065_POSITIVE 324 70 26 222 183 pint:PI0266|5end_DNA_primase_(bacterial_type)_257931..258161_POSITIVE 322 59 11 108 59 pint:PI1542|5end_mobilization_protein_1461728..1461958_POSITIVE 319 59 11 177 127 pint:PI0252|5end_conserved_hypothetical_protein_247761..247991_POSITIVE 307 94 52 222 176 pint:PI1644|5end_hypothetical_protein_1560372..1560602_POSITIVE 306 42 7 199 158 pint:PI0077|5end_hypothetical_protein_76244..76474_POSITIVE 304 43 10 74 37 pint:PI1816|5end_acid_phosphatase_1754646..1754876_POSITIVE 304 57 11 75 26 pint:PI0277|5end_hypothetical_protein_264980..265210_POSITIVE 303 59 11 85 34 pint:PI1975|5end_conserved_hypothetical_protein_1931513..1931743_POSITIVE 302 94 52 222 176 pint:PI0349|5end_hypothetical_protein_323144..323374_POSITIVE 298 60 11 109 56 pint:PI0604|5end_O-succinylbenzoic_acid--CoA_ligase_550825..551055_POSITIVE 296 58 14 201 152 pint:PI2112|5end_phosphopantetheine_adenylyltransferase_2063194..2063424_POSITIVE 295 70 24 78 12 pint:PI2088|5end_conserved_hypothetical_protein;_possible_PAP2_superfamily_protein_2044437..2044667_POSITIVE 295 59 11 217 166 pint:PI0556|5end_saccharopine_dehydrogenase_504935..505165_POSITIVE 294 58 11 169 124 pint:PI0785|5end_hypothetical_protein_723744..723974_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 322 59 11 71 22 pint:PI1540|3end_hypothetical_protein_1461771..1461921_POSITIVE 319 59 11 146 96 pint:PI0251|3end_hypothetical_protein_247810..247960_POSITIVE 312 54 11 115 67 pint:PI1794|3end_conserved_hypothetical_protein_1726696..1726846_POSITIVE 312 58 16 126 85 pint:PI0431|3end_Xaa-Pro_aminopeptidase_404673..404823_POSITIVE 306 42 7 67 26 pint:PI0076|3end_conserved_hypothetical_protein_76192..76342_POSITIVE 303 59 11 79 28 pint:PI1974|3end_hypothetical_protein_1931587..1931737_POSITIVE 298 93 51 85 43 pint:PI0343|3end_hypothetical_protein_317920..318070_POSITIVE 292 57 15 44 3 pint:PI1649|3end_hypothetical_protein_1563441..1563591_POSITIVE 291 80 32 113 62 pint:PI1789|3end_hypothetical_protein_1719037..1719187_POSITIVE 287 96 53 87 52 pint:PI1635|3end_hypothetical_protein_1554306..1554456_POSITIVE 286 90 41 71 14 pint:PI0379|3end_conserved_hypothetical_protein_350239..350389_POSITIVE 283 77 32 118 71 pint:PI1487|3end_hypothetical_protein_1407940..1408090_POSITIVE 282 43 8 105 57 pint:PI0684|3end_coproporphyrinogen_III_oxidase_620507..620657_POSITIVE 277 45 7 149 112 pint:PI1579|3end_penicillin-binding_protein_2_1507913..1508063_POSITIVE 277 44 7 68 13 pint:PI0748|3end_possible_mobilization_protein_677214..677364_POSITIVE 275 74 31 71 16 pint:PI1882|3end_hypothetical_protein_1826487..1826637_POSITIVE 273 42 7 103 55 pint:PI2074|3end_conserved_hypothetical_protein_2034375..2034525_POSITIVE 273 60 13 144 90 pint:PI0732|3end_conserved_hypothetical_protein_664367..664517_POSITIVE 272 74 31 80 22 pint:PI2117|3end_fumarate_reductase/succinate_dehydrogenase_flavoprotein_subunit,_C-terminal_2066684..2066834_POSITIVE 270 56 11 147 97 pint:PI0199|3end_phosphate_acetyltransferase_190923..191073_POSITIVE