Origin IGS: cgttccgtgtagcgatttattgtgctcggaataattcattcctattgcaaatatcttcatttctaattcgtttgcgattttttaacttatatataataaactaagtgtaaagcattggcacaccgataggcacctattca .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tgaataggtgcctatcggtgtgccaatgctttacacttagtttattatatataagttaaaaaatcgcaaacgaattagaaatgaagatatttgcaataggaatgaattattccgagcacaataaatcgctacacggaacg Mask Tandem Repeat Region ================================================ cgttccgtgtagcgatttattgtgctcggaataattcattcctattgcaaatatcttcatttctaattcgtttgcgattttttaacttatatataataaactaagtgtaaagcattggcacaccgataggcacctattca Find is-nt database================================================ Query_seq: PI1796:PI1797|PI1796:PI1797:2-hydroxyhepta-2,4-diene-1,7-dioate isomerase, fumarylacetoacetate hydrolase family protein:hypothetical protein:->->:1731147..1731286 140 cgttccgtgtagcgatttattgtgctcggaataattcattcctattgcaaatatcttcatttctaattcgtttgcgattttttaacttatatataataaactaagtgtaaagcattggcacaccgataggcacctattca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI1796:PI1797|PI1796:PI1797:2-hydroxyhepta-2,4-diene-1,7-dioate isomerase, fumarylacetoacetate hydrolase family protein:hypothetical protein:->->:1731147..1731286 140 cgttccgtgtagcgatttattgtgctcggaataattcattcctattgcaaatatcttcatttctaattcgtttgcgattttttaacttatatataataaactaagtgtaaagcattggcacaccgataggcacctattca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI1796:PI1797|PI1796:PI1797:2-hydroxyhepta-2,4-diene-1,7-dioate isomerase, fumarylacetoacetate hydrolase family protein:hypothetical protein:->->:1731147..1731286 140 cgttccgtgtagcgatttattgtgctcggaataattcattcctattgcaaatatcttcatttctaattcgtttgcgattttttaacttatatataataaactaagtgtaaagcattggcacaccgataggcacctattca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 cgttccgtgtagcgatttattgtgctcggaataattcattcctattgcaaatatcttcatttctaattcgtttgcgattttttaacttatatataataaactaagtgtaaagcattggcacaccgataggcacctattca Predict ORF larger than 30AA ================================================ cgttccgtgtagcgatttattgtgctcggaataattcattcctattgcaaatatcttcatttctaattcgtttgcgattttttaacttatatataataaactaagtgtaaagcattggcacaccgataggcacctattca 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: 93 End: 122 ............................................................................................TGTGCCAATGCTTTACACTTAGTTTATTAT.................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ cgttccgtgtagcgatttattgtgctcggaataattcattcctattgcaaatatcttcatttctaattcgtttgcgattttttaacttatatataataaactaagtgtaaagcattggcacaccgataggcacctattca Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PI1796:PI1797|PI1796:PI1797:2-hydroxyhepta-2,4-diene-1,7-dioate isomerase, fumarylacetoacetate hydrolase family protein:hypothetical protein:->->:1731147..1731286 140 cgttccgtgtagcgatttattgtgctcggaataattcattcctattgcaaatatcttcatttctaattcgtttgcgattttttaacttatatataataaactaagtgtaaagcattggcacaccgataggcacctattca Intra-Species Hit: Count: 1 Min: 1 Max: 140 Len: 140 Subject: pint_PI1796_PI1797|2-hydroxyhepta-2,4-diene-1,7-dioate isomerase, fumarylacetoacetate hydrolase family protein:hypothetical protein|POSITIVE:POSITIVE|[1731147,1731286]|140 HSP 1 e-value: 5.0E-74 bit: 278.0 Len: 140 Query Start:1 Query End:140 Subject Strand: POSITIVE Subject Start: 1 Subject End: 140 cgttccgtgtagcgatttattgtgctcggaataattcattcctattgcaaatatcttcatttctaattcgtttgcgattttttaacttatatataataaactaagtgtaaagcattggcacaccgataggcacctattca cgttccgtgtagcgatttattgtgctcggaataattcattcctattgcaaatatcttcatttctaattcgtttgcgattttttaacttatatataataaactaagtgtaaagcattggcacaccgataggcacctattca Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CGUUCCGUGUAGCGAUUUAUUGUGCUCGGAAUAAUUCAUUCCUAUUGCAAAUAUCUUCAUUUCUAAUUCGUUUGCGAUUUUUUAACUUAUAUAUAAUAAACUAAGUGUAAAGCAUUGGCACACCGAUAGGCACCUAUUCA ......((((.((..(((((((((...(((((.....))))).(((((((((.................))))))))).............)))))))))...((((.....)))).)))))).(((((....))))).. (-24.03) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGAAUAGGUGCCUAUCGGUGUGCCAAUGCUUUACACUUAGUUUAUUAUAUAUAAGUUAAAAAAUCGCAAACGAAUUAGAAAUGAAGAUAUUUGCAAUAGGAAUGAAUUAUUCCGAGCACAAUAAAUCGCUACACGGAACG ....(((....)))((.((((((.....(((((...(((..((((.....))))..)))....(((....)))........))))).(((((((....((((((...))))))..))).))))....)).)))).))... (-20.50) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 295 50 1 72 24 pint:PI2014|5end_conserved_hypothetical_protein_1971471..1971701_POSITIVE 284 133 106 225 194 pint:PI1004|5end_conserved_hypothetical_protein_925820..926050_POSITIVE 263 31 1 51 21 pint:PI1271|5end_transcriptional_regulator,__AraC/XylS_family_1190755..1190985_POSITIVE 257 48 5 162 119 pint:PI1884|5end_conserved_hypothetical_protein_1826883..1827113_POSITIVE 255 131 94 134 92 pint:PI0321|5end_conserved_hypothetical_protein_302598..302828_POSITIVE 252 48 5 61 13 pint:PI0614|5end_glucose-6-phosphate_isomerase_563170..563400_POSITIVE 248 50 1 206 160 pint:PI0845|5end_peptidyl-dipeptidase_778272..778502_POSITIVE 246 139 112 50 23 pint:PI0097|5end_aspartate_aminotransferase_93235..93465_POSITIVE 240 47 1 117 67 pint:PI2130|5end_DNA_polymerase_I_2077980..2078210_POSITIVE 238 46 5 64 27 pint:PI0046|5end_thiamine_monophosphate_synthase_(thiamine-phosphate_pyrophosphorylase)_45353..45583_POSITIVE 236 139 105 124 86 pint:PI1770|5end_4-alpha-glucanotransferase_1697336..1697566_POSITIVE 234 124 86 119 72 pint:PI1375|5end_protease_IV_family,_clan_S_(peptidase_family_S49)_1295963..1296193_POSITIVE 231 132 104 42 11 pint:PI1263|5end_probable_integrase_1184502..1184732_POSITIVE 231 140 99 84 31 pint:PI0953|5end_hypothetical_protein_885119..885349_POSITIVE 231 48 1 208 169 pint:PI0260|5end_conjugative_transposon_protein,_TraJ_253023..253253_POSITIVE 230 57 12 156 116 pint:PI2099|5end_D-alanyl-D-alanine_dipeptidase_2052409..2052639_POSITIVE 230 49 6 214 179 pint:PI1559|5end_hypothetical_protein_1476506..1476736_POSITIVE 229 58 13 155 110 pint:PI1625|5end_conserved_hypothetical_protein;_possible_phage_transposase_1549316..1549546_POSITIVE 229 42 1 205 169 pint:PI0732|5end_conserved_hypothetical_protein_663598..663828_POSITIVE 229 58 13 155 110 pint:PI0332|5end_conserved_hypothetical_protein_312600..312830_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 325 135 103 115 78 pint:PI0675|3end_hypothetical_protein_613957..614107_POSITIVE 295 50 1 76 28 pint:PI2012|3end_hypothetical_protein_1971555..1971705_POSITIVE 284 133 106 43 12 pint:PI1003|3end_conserved_hypothetical_protein_925718..925868_POSITIVE 272 29 5 117 89 pint:PI0189|3end_integrase_180437..180587_POSITIVE 263 31 1 45 15 pint:PI1270|3end_probable_dipeptidyl_peptidase_1190829..1190979_POSITIVE 255 131 94 108 66 pint:PI0320|3end_probable_cobalamin_adenosyltransferase_302652..302802_POSITIVE 252 48 5 50 2 pint:PI0613|3end_glycerol-3-phosphate_dehydrogenase_(NAD(P)+)_563239..563389_POSITIVE 246 139 112 40 13 pint:PI0096|3end_glycerol-3-phosphate_cytidylyltransferase_93305..93455_POSITIVE 238 46 5 56 19 pint:PI0045|3end_thiamine_biosynthesis_protein_45425..45575_POSITIVE 233 37 1 55 16 pint:PI1653|3end_hypothetical_protein_1565714..1565864_POSITIVE 231 48 1 148 109 pint:PI0259|3end_conserved_protein_found_in_conjugation,_TraI_253043..253193_POSITIVE 230 57 12 140 100 pint:PI2098|3end_hypothetical_protein_2052473..2052623_POSITIVE 229 58 13 50 5 pint:PI0331|3end_hypothetical_protein_312575..312725_POSITIVE 227 47 6 80 38 pint:PI1903|3end_hypothetical_protein_1845569..1845719_POSITIVE 227 134 101 70 28 pint:PI1719|3end_conserved_hypothetical_protein_1636207..1636357_POSITIVE 226 79 39 104 63 pint:PI1876|3end_possible_flagellar_motor_protein,_OmpA_family_1819968..1820118_POSITIVE 226 136 102 49 10 pint:PI0546|3end_hypothetical_protein_498238..498388_POSITIVE 225 50 1 64 3 pint:PI2124|3end_excinuclease_ABC,_subunit_C_2074496..2074646_POSITIVE 222 139 105 93 44 pint:PI0624|3end_hypothetical_protein_574471..574621_POSITIVE 222 48 1 116 75 pint:PI0365|3end_hypothetical_protein_336118..336268_POSITIVE