Origin IGS: tgatggaagaagatgtgattagacagatacagcgagagggggcggaagcattgctcgatacaggtgtaagtgtacctctgaaggctgtgcggcttccgtttaggaagagcccctttgtgctgcgtgtgactatgaagcgtccctgtatgtccggacagctgaagattgcccggacatacctttccatgaatgtgacgagtgagcagatttggaatttcacgaaagaggaggagtttcaatttctcgttcagcagggcaaaagcctaagccgtatgatagcctacatgatatgtcgcggatatttctcgcgtaa .........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 ttacgcgagaaatatccgcgacatatcatgtaggctatcatacggcttaggcttttgccctgctgaacgagaaattgaaactcctcctctttcgtgaaattccaaatctgctcactcgtcacattcatggaaaggtatgtccgggcaatcttcagctgtccggacatacagggacgcttcatagtcacacgcagcacaaaggggctcttcctaaacggaagccgcacagccttcagaggtacacttacacctgtatcgagcaatgcttccgccccctctcgctgtatctgtctaatcacatcttcttccatca Mask Tandem Repeat Region ================================================ tgatggaagaagatgtgattagacagatacagcgagagggggcggaagcattgctcgatacaggtgtaagtgtacctctgaaggctgtgcggcttccgtttaggaagagcccctttgtgctgcgtgtgactatgaagcgtccctgtatgtccggacagctgaagattgcccggacatacctttccatgaatgtgacgagtgagcagatttggaatttcacgaaagaggaggagtttcaatttctcgttcagcagggcaaaagcctaagccgtatgatagcctacatgatatgtcgcggatatttctcgcgtaa Find is-nt database================================================ Query_seq: PI0358:PI0359|PI0358:PI0359:hypothetical protein:hypothetical protein:->->:328166..328478 313 tgatggaagaagatgtgattagacagatacagcgagagggggcggaagcattgctcgatacaggtgtaagtgtacctctgaaggctgtgcggcttccgtttaggaagagcccctttgtgctgcgtgtgactatgaagcgtccctgtatgtccggacagctgaagattgcccggacatacctttccatgaatgtgacgagtgagcagatttggaatttcacgaaagaggaggagtttcaatttctcgttcagcagggcaaaagcctaagccgtatgatagcctacatgatatgtcgcggatatttctcgcgtaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI0358:PI0359|PI0358:PI0359:hypothetical protein:hypothetical protein:->->:328166..328478 313 tgatggaagaagatgtgattagacagatacagcgagagggggcggaagcattgctcgatacaggtgtaagtgtacctctgaaggctgtgcggcttccgtttaggaagagcccctttgtgctgcgtgtgactatgaagcgtccctgtatgtccggacagctgaagattgcccggacatacctttccatgaatgtgacgagtgagcagatttggaatttcacgaaagaggaggagtttcaatttctcgttcagcagggcaaaagcctaagccgtatgatagcctacatgatatgtcgcggatatttctcgcgtaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI0358:PI0359|PI0358:PI0359:hypothetical protein:hypothetical protein:->->:328166..328478 313 tgatggaagaagatgtgattagacagatacagcgagagggggcggaagcattgctcgatacaggtgtaagtgtacctctgaaggctgtgcggcttccgtttaggaagagcccctttgtgctgcgtgtgactatgaagcgtccctgtatgtccggacagctgaagattgcccggacatacctttccatgaatgtgacgagtgagcagatttggaatttcacgaaagaggaggagtttcaatttctcgttcagcagggcaaaagcctaagccgtatgatagcctacatgatatgtcgcggatatttctcgcgtaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tgatggaagaagatgtgattagacagatacagcgagagggggcggaagcattgctcgatacaggtgtaagtgtacctctgaaggctgtgcggcttccgtttaggaagagcccctttgtgctgcgtgtgactatgaagcgtccctgtatgtccggacagctgaagattgcccggacatacctttccatgaatgtgacgagtgagcagatttggaatttcacgaaagaggaggagtttcaatttctcgttcagcagggcaaaagcctaagccgtatgatagcctacatgatatgtcgcggatatttctcgcgtaa Predict ORF larger than 30AA ================================================ Protein_Len: 60 Strand: + Start: 3 End: 311 .. M E E D V I R Q I Q R E G A E A L L D T G V S V P L K A V R L P F R K S P F V L R V T M K R P C M S G Q L K I A R T Y L .. Protein_Len: 35 Strand: + Start: 209 End: 310 ................................................................................................................................................................................................................ M E F H E R G G V S I S R S A G Q K P K P Y D S L H D M S R I F L A * ... Protein_Len: 60 Strand: - Start: 3 End: 254 .. R Q L S H P K R K P L A G K H Q T H S H L T G T H G S L Q L N G P C V K G H I H R T L L N P I E R F L L L K L K E N L M ........................................................... Protein_Len: 60 Strand: - Start: 2 End: 220 . A S A N S S V P T L T G R F A T R S G N L F L G K T S R T V I F R G Q I D P C S F I A R V Y R E M F T V L S C I Q F K M ............................................................................................. tgatggaagaagatgtgattagacagatacagcgagagggggcggaagcattgctcgatacaggtgtaagtgtacctctgaaggctgtgcggcttccgtttaggaagagcccctttgtgctgcgtgtgactatgaagcgtccctgtatgtccggacagctgaagattgcccggacatacctttccatgaatgtgacgagtgagcagatttggaatttcacgaaagaggaggagtttcaatttctcgttcagcagggcaaaagcctaagccgtatgatagcctacatgatatgtcgcggatatttctcgcgtaa 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================================================ tgatggaagaagatgtgattagacagatacagcgagagggggcggaagcattgctcgatacaggtgtaagtgtacctctgaaggctgtgcggcttccgtttaggaagagcccctttgtgctgcgtgtgactatgaagcgtccctgtatgtccggacagctgaagattgcccggacatacctttccatgaatgtgacgagtgagcagatttggaatttcacgaaagaggaggagtttcaatttctcgttcagcagggcaaaagcctaagccgtatgatagcctacatgatatgtcgcggatatttctcgcgtaa Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 67 HP_score: -7.3 Tail_Score: -3.67792 Start: 144 End: 180 Full_Region: ACTATGAAGCGTCCC TGTATGTCCGGACAG CTGAAGA TTGCCCGGACATACC TTTCCATGAATGTGA ...............................................................................................................................................TGTATGTCCGGACAGCTGAAGATTGCCCGGACATACC..................................................................................................................................... TransTerm Strand: + Conf: 69 HP_score: -10.8 Tail_Score: -2.80354 Start: 145 End: 179 Full_Region: CTATGAAGCGTCCCT GTATGTCCGGACAG CTGAAGA TTGCCCGGACATAC CTTTCCATGAATGTG ................................................................................................................................................GTATGTCCGGACAGCTGAAGATTGCCCGGACATAC...................................................................................................................................... Find igs database================================================ Query_seq: PI0358:PI0359|PI0358:PI0359:hypothetical protein:hypothetical protein:->->:328166..328478 313 tgatggaagaagatgtgattagacagatacagcgagagggggcggaagcattgctcgatacaggtgtaagtgtacctctgaaggctgtgcggcttccgtttaggaagagcccctttgtgctgcgtgtgactatgaagcgtccctgtatgtccggacagctgaagattgcccggacatacctttccatgaatgtgacgagtgagcagatttggaatttcacgaaagaggaggagtttcaatttctcgttcagcagggcaaaagcctaagccgtatgatagcctacatgatatgtcgcggatatttctcgcgtaa Intra-Species Hit: Count: 1 Min: 1 Max: 313 Len: 313 Subject: pint_PI0358_PI0359|hypothetical protein:hypothetical protein|POSITIVE:POSITIVE|[328166,328478]|313 HSP 1 e-value: 1.0E-177 bit: 620.0 Len: 313 Query Start:1 Query End:313 Subject Strand: POSITIVE Subject Start: 1 Subject End: 313 tgatggaagaagatgtgattagacagatacagcgagagggggcggaagcattgctcgatacaggtgtaagtgtacctctgaaggctgtgcggcttccgtttaggaagagcccctttgtgctgcgtgtgactatgaagcgtccctgtatgtccggacagctgaagattgcccggacatacctttccatgaatgtgacgagtgagcagatttggaatttcacgaaagaggaggagtttcaatttctcgttcagcagggcaaaagcctaagccgtatgatagcctacatgatatgtcgcggatatttctcgcgtaa tgatggaagaagatgtgattagacagatacagcgagagggggcggaagcattgctcgatacaggtgtaagtgtacctctgaaggctgtgcggcttccgtttaggaagagcccctttgtgctgcgtgtgactatgaagcgtccctgtatgtccggacagctgaagattgcccggacatacctttccatgaatgtgacgagtgagcagatttggaatttcacgaaagaggaggagtttcaatttctcgttcagcagggcaaaagcctaagccgtatgatagcctacatgatatgtcgcggatatttctcgcgtaa Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGAUGGAAGAAGAUGUGAUUAGACAGAUACAGCGAGAGGGGGCGGAAGCAUUGCUCGAUACAGGUGUAAGUGUACCUCUGAAGGCUGUGCGGCUUCCGUUUAGGAAGAGCCCCUUUGUGCUGCGUGUGACUAUGAAGCGUCCCUGUAUGUCCGGACAGCUGAAGAUUGCCCGGACAUACCUUUCCAUGAAUGUGACGAGUGAGCAGAUUUGGAAUUUCACGAAAGAGGAGGAGUUUCAAUUUCUCGUUCAGCAGGGCAAAAGCCUAAGCCGUAUGAUAGCCUACAUGAUAUGUCGCGGAUAUUUCUCGCGUAA ..(((((((..(((((...(((.((.(..(((((.((((((((....((((.((.(..((.(((((......))))).))..))).))))..(((((.....))))).)))))))).)))))..).)).)))....)))))...((((((((((.((((....).))).)))))))))).)))))))..((((((.((.((((((((.((((((((((.(....)....))))))))))..))).)))))...((((....))))...((((..((((..(.....)...)))))))).....)))))))).. (-110.00) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUACGCGAGAAAUAUCCGCGACAUAUCAUGUAGGCUAUCAUACGGCUUAGGCUUUUGCCCUGCUGAACGAGAAAUUGAAACUCCUCCUCUUUCGUGAAAUUCCAAAUCUGCUCACUCGUCACAUUCAUGGAAAGGUAUGUCCGGGCAAUCUUCAGCUGUCCGGACAUACAGGGACGCUUCAUAGUCACACGCAGCACAAAGGGGCUCUUCCUAAACGGAAGCCGCACAGCCUUCAGAGGUACACUUACACCUGUAUCGAGCAAUGCUUCCGCCCCCUCUCGCUGUAUCUGUCUAAUCACAUCUUCUUCCAUCA ...((((.((....))))))..........(((((....(((((((...(((....))).(((((...(.((...((((.(((((....(((((((((.........................)))))))))..(((((((((((((.........))))))))))))).)))).).))))...)).)...)))))....(((((.(((((.....)))))..(((..(((..(((..(((....)))..)))....).))..)))....))))).....)))))))..)))))................... (-90.51) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 411 68 21 168 126 pint:PI1644|5end_hypothetical_protein_1560372..1560602_POSITIVE 406 117 77 207 165 pint:PI0263|5end_conjugative_transposon_protein,_TraM_255256..255486_POSITIVE 391 69 21 63 11 pint:PI0652|5end_conserved_hypothetical_protein_592878..593108_POSITIVE 377 90 46 148 95 pint:PI2133|5end_collagenase_2081106..2081336_POSITIVE 371 128 83 175 124 pint:PI0331|5end_hypothetical_protein_311656..311886_POSITIVE 368 62 21 168 126 pint:PI0349|5end_hypothetical_protein_323144..323374_POSITIVE 367 128 84 87 35 pint:PI1705|5end_3-oxoacyl-(acyl-carrier-protein)_synthase_III_1621781..1622011_POSITIVE 359 66 21 142 103 pint:PI0094|5end_protoporphyrinogen_oxidase_89571..89801_POSITIVE 359 66 21 68 29 pint:PI0091|5end_hypothetical_protein_89497..89727_POSITIVE 358 68 29 231 197 pint:PI2171|5end_conserved_hypothetical_protein_2112735..2112965_POSITIVE 358 130 83 204 157 pint:PI0092|5end_regulatory_protein_RecX_89080..89310_POSITIVE 357 124 83 176 132 pint:PI1768|5end_conserved_hypothetical_protein_1695456..1695686_POSITIVE 357 58 15 202 162 pint:PI1641|5end_hypothetical_protein_1558495..1558725_POSITIVE 354 79 31 65 4 pint:PI0047|5end_phosphomethylpyrimidine_kinase_45964..46194_POSITIVE 352 110 63 70 7 pint:PI0613|5end_glycerol-3-phosphate_dehydrogenase_(NAD(P)+)_562167..562397_POSITIVE 351 78 31 212 164 pint:PI0735|5end_ABC_transporter,_ATP-binding_/_permease_668793..669023_POSITIVE 350 80 31 178 113 pint:PI1448|5end_hypothetical_protein_1371579..1371809_POSITIVE 350 142 101 210 158 pint:PI1164|5end_hypothetical_protein_1088203..1088433_POSITIVE 350 90 41 78 29 pint:PI0569|5end_phosphoglycerate_kinase_513297..513527_POSITIVE 346 159 112 203 164 pint:PI0185|5end_conserved_hypothetical_protein_176992..177222_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 377 90 46 101 48 pint:PI2132|3end_hypothetical_protein_2081139..2081289_POSITIVE 360 63 21 150 113 pint:PI1642|3end_conserved_hypothetical_protein_1560439..1560589_POSITIVE 359 66 21 142 103 pint:PI0092|3end_regulatory_protein_RecX_89651..89801_POSITIVE 356 284 241 135 81 pint:PI1884|3end_conserved_hypothetical_protein_1827457..1827607_POSITIVE 354 79 31 65 4 pint:PI0046|3end_thiamine_monophosphate_synthase_(thiamine-phosphate_pyrophosphorylase)_46044..46194_POSITIVE 351 78 31 99 51 pint:PI0734|3end_ABC_transporter,_ATP-binding_/_permease_668760..668910_POSITIVE 349 110 63 126 69 pint:PI1803|3end_conserved_hypothetical_protein_1737791..1737941_POSITIVE 338 128 84 95 42 pint:PI1460|3end_ribonucleotide_reductase,_alpha_subunit,_N-terminal_region_1384436..1384586_POSITIVE 335 66 21 150 113 pint:PI0348|3end_conserved_hypothetical_protein_323211..323361_POSITIVE 334 124 82 78 29 pint:PI0315|3end_conserved_hypothetical_protein_298186..298336_POSITIVE 334 158 111 83 41 pint:PI0287|3end_ISPg3-related_transposase_272352..272502_POSITIVE 328 130 82 62 11 pint:PI1199|3end_possible_acetyltransferase_1115746..1115896_POSITIVE 325 74 33 68 25 pint:PI2158|3end_glycosyl_transferase,_group_2_family_protein_2105347..2105497_POSITIVE 324 69 25 73 29 pint:PI1749|3end_conserved_hypothetical_protein_1671637..1671787_POSITIVE 324 123 82 83 21 pint:PI0052|3end_hypothetical_protein_52715..52865_POSITIVE 323 100 52 73 9 pint:PI1734|3end_possible_carboxyl-terminal_protease-related_protein_1653829..1653979_POSITIVE 322 78 31 101 47 pint:PI2032|3end_RNA_polymerase_sigma_factor,_ECF_subfamily_1987121..1987271_POSITIVE 320 68 26 143 93 pint:PI1230|3end_probable_metallo-beta-lactamase_family_protein_1152729..1152879_POSITIVE 320 99 51 136 80 pint:PI0955|3end_conserved_hypothetical_protein_886084..886234_POSITIVE 320 78 37 129 84 pint:PI0769|3end_phosphomannomutase_706172..706322_POSITIVE