Origin IGS: tgaacgaaaaaacgaggctaaaaacaaaaaatccgctgcttttgcttggaagtaacggattttttcgtatatttgcagtactaaagcactgaaggaatggcactctggcattttagacctaaccgccacctttgatgtaatcatacaagcgtatcgggaatgatgacctggcatttgagtccaaactatcgcccgatacgctttctta .........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 taagaaagcgtatcgggcgatagtttggactcaaatgccaggtcatcattcccgatacgcttgtatgattacatcaaaggtggcggttaggtctaaaatgccagagtgccattccttcagtgctttagtactgcaaatatacgaaaaaatccgttacttccaagcaaaagcagcggattttttgtttttagcctcgttttttcgttca Mask Tandem Repeat Region ================================================ tgaacgaaaaaacgaggctaaaaacaaaaaatccgctgcttttgcttggaagtaacggattttttcgtatatttgcagtactaaagcactgaaggaatggcactctggcattttagacctaaccgccacctttgatgtaatcatacaagcgtatcgggaatgatgacctggcatttgagtccaaactatcgcccgatacgctttctta Find is-nt database================================================ Query_seq: PI0342:PI0344|PI0342:PI0344:hypothetical protein:conserved hypothetical protein:->->:318110..318317 208 tgaacgaaaaaacgaggctaaaaacaaaaaatccgctgcttttgcttggaagtaacggattttttcgtatatttgcagtactaaagcactgaaggaatggcactctggcattttagacctaaccgccacctttgatgtaatcatacaagcgtatcgggaatgatgacctggcatttgagtccaaactatcgcccgatacgctttctta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI0342:PI0344|PI0342:PI0344:hypothetical protein:conserved hypothetical protein:->->:318110..318317 208 tgaacgaaaaaacgaggctaaaaacaaaaaatccgctgcttttgcttggaagtaacggattttttcgtatatttgcagtactaaagcactgaaggaatggcactctggcattttagacctaaccgccacctttgatgtaatcatacaagcgtatcgggaatgatgacctggcatttgagtccaaactatcgcccgatacgctttctta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI0342:PI0344|PI0342:PI0344:hypothetical protein:conserved hypothetical protein:->->:318110..318317 208 tgaacgaaaaaacgaggctaaaaacaaaaaatccgctgcttttgcttggaagtaacggattttttcgtatatttgcagtactaaagcactgaaggaatggcactctggcattttagacctaaccgccacctttgatgtaatcatacaagcgtatcgggaatgatgacctggcatttgagtccaaactatcgcccgatacgctttctta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tgaacgaaaaaacgaggctaaaaacaaaaaatccgctgcttttgcttggaagtaacggattttttcgtatatttgcagtactaaagcactgaaggaatggcactctggcattttagacctaaccgccacctttgatgtaatcatacaagcgtatcgggaatgatgacctggcatttgagtccaaactatcgcccgatacgctttctta Predict ORF larger than 30AA ================================================ Protein_Len: 34 Strand: + Start: 59 End: 160 .......................................................... M F S Y I C S T K A L K E W H S G I L D L T A T F D V I I Q A Y R E ................................................ Protein_Len: 34 Strand: - Start: 2 End: 103 . F S F V L S F V F F G S S K S P L L P N K R I N A T S F C Q L F P M ......................................................................................................... Protein_Len: 60 Strand: - Start: 1 End: 189 F S A L F L F D A A K A Q F Y R I K E Y I Q L V L A S F S H C E P M K S R V A V K S T I M C A Y R S H H G P M Q T W V M ................... tgaacgaaaaaacgaggctaaaaacaaaaaatccgctgcttttgcttggaagtaacggattttttcgtatatttgcagtactaaagcactgaaggaatggcactctggcattttagacctaaccgccacctttgatgtaatcatacaagcgtatcgggaatgatgacctggcatttgagtccaaactatcgcccgatacgctttctta 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================================================ tgaacgaaaaaacgaggctaaaaacaaaaaatccgctgcttttgcttggaagtaacggattttttcgtatatttgcagtactaaagcactgaaggaatggcactctggcattttagacctaaccgccacctttgatgtaatcatacaagcgtatcgggaatgatgacctggcatttgagtccaaactatcgcccgatacgctttctta Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 86 HP_score: -2.0 Tail_Score: -5.93252 Start: 32 End: 59 Full_Region: aaatatacgaaaaaa tccgttactt ccaagcaa aagcagcgga ttttttgtttttagc ...............................tccgttacttccaagcaaaagcagcgga..................................................................................................................................................... Find igs database================================================ Query_seq: PI0342:PI0344|PI0342:PI0344:hypothetical protein:conserved hypothetical protein:->->:318110..318317 208 tgaacgaaaaaacgaggctaaaaacaaaaaatccgctgcttttgcttggaagtaacggattttttcgtatatttgcagtactaaagcactgaaggaatggcactctggcattttagacctaaccgccacctttgatgtaatcatacaagcgtatcgggaatgatgacctggcatttgagtccaaactatcgcccgatacgctttctta Intra-Species Hit: Count: 1 Min: 32 Max: 208 Len: 177 Subject: pint_PI0342_PI0344|hypothetical protein:conserved hypothetical protein|POSITIVE:POSITIVE|[318110,318317]|208 HSP 1 e-value: 6.0E-96 bit: 351.0 Len: 177 Query Start:32 Query End:208 Subject Strand: POSITIVE Subject Start: 32 Subject End: 208 ...............................tccgctgcttttgcttggaagtaacggattttttcgtatatttgcagtactaaagcactgaaggaatggcactctggcattttagacctaaccgccacctttgatgtaatcatacaagcgtatcgggaatgatgacctggcatttgagtccaaactatcgcccgatacgctttctta ...............................tccgctgcttttgcttggaagtaacggattttttcgtatatttgcagtactaaagcactgaaggaatggcactctggcattttagacctaaccgccacctttgatgtaatcatacaagcgtatcgggaatgatgacctggcatttgagtccaaactatcgcccgatacgctttctta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCCGCUGCUUUUGCUUGGAAGUAACGGAUUUUUUCGUAUAUUUGCAGUACUAAAGCACUGAAGGAAUGGCACUCUGGCAUUUUAGACCUAACCGCCACCUUUGAUGUAAUCAUACAAGCGUAUCGGGAAUGAUGACCUGGCAUUUGAGUCCAAACUAUCGCCCGAUACGCUUUCUUA ((((.(((((((....))))))).)))).......((((..(((((((......))...(((((..((((.....(((......).)).....)))))))))..)))))..)))).(((((((((((...((((...((((......).)))...)))).)))))))))))...... (-51.20) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAGAAAGCGUAUCGGGCGAUAGUUUGGACUCAAAUGCCAGGUCAUCAUUCCCGAUACGCUUGUAUGAUUACAUCAAAGGUGGCGGUUAGGUCUAAAAUGCCAGAGUGCCAUUCCUUCAGUGCUUUAGUACUGCAAAUAUACGAAAAAAUCCGUUACUUCCAAGCAAAAGCAGCGGA .....((((((((((((.(((..(((((.(......))))))..)))...))))))))))))(((((.........(((((((((.((.(((.......))).)).)))))..))))((((((....))))))....))))).......((((((.(((........))).)))))) (-58.50) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 378 166 124 64 10 pint:PI0257|5end_conjugative_transposon_protein,_TraF_249348..249578_POSITIVE 335 170 124 61 10 pint:PI0103|5end_conserved_hypothetical_protein;_possible_permease_98136..98366_POSITIVE 331 90 41 127 76 pint:PI1647|5end_hypothetical_protein_1561564..1561794_POSITIVE 325 170 139 46 18 pint:PI0839|5end_conserved_hypothetical_protein_773843..774073_POSITIVE 318 169 123 208 165 pint:PI2011|5end_hypothetical_protein_1970429..1970659_POSITIVE 312 100 55 47 4 pint:PI0028|5end_aminopeptidase_31559..31789_POSITIVE 304 50 3 194 141 pint:PI0864|5end_dihydrodipicolinate_synthase_800527..800757_POSITIVE 303 170 125 62 4 pint:PI1245|5end_hypothetical_protein_1171098..1171328_POSITIVE 300 160 118 229 191 pint:PI0873|5end_conserved_hypothetical_protein;_possible_permease_807968..808198_POSITIVE 294 170 121 191 135 pint:PI1620|5end__two-component_system_sensor_protein_1543956..1544186_POSITIVE 293 46 3 205 164 pint:PI2170|5end_RNA_polymerase_sigma-70_factor,_ECF_subfamily_2112238..2112468_POSITIVE 293 49 3 229 185 pint:PI1851|5end_conserved_hypothetical_protein_1796847..1797077_POSITIVE 288 170 125 140 84 pint:PI2074|5end_conserved_hypothetical_protein_2033660..2033890_POSITIVE 288 137 92 228 165 pint:PI1980|5end_conserved_hypothetical_protein_1937470..1937700_POSITIVE 288 50 1 104 48 pint:PI0262|5end_conserved_hypothetical_protein_254685..254915_POSITIVE 286 162 129 61 23 pint:PI1090|5end_tRNA_uracil_5-methyltransferase_1014366..1014596_POSITIVE 285 100 57 198 156 pint:PI0197|5end_acetate_kinase_188602..188832_POSITIVE 284 135 94 120 76 pint:PI1380|5end_conserved_hypothetical_protein_1302587..1302817_POSITIVE 283 99 63 42 2 pint:PI2017|5end_conserved_hypothetical_protein_1974862..1975092_POSITIVE 282 169 123 204 147 pint:PI0121|5end_outer_membrane_protein,_ompH_family_112625..112855_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 378 166 124 56 2 pint:PI0256|3end_conjugative_transposon_protein,_TraE_249420..249570_POSITIVE 349 80 41 149 107 pint:PI0873|3end_conserved_hypothetical_protein;_possible_permease_808956..809106_POSITIVE 325 170 139 50 22 pint:PI0838|3end_DNA_replication_and_repair_protein_773927..774077_POSITIVE 306 159 118 109 58 pint:PI0871|3end_hypothetical_protein_807915..808065_POSITIVE 304 50 3 150 97 pint:PI0863|3end_L-asparaginase_I_800563..800713_POSITIVE 301 69 30 63 14 pint:PI0524|3end_meso-diaminopimelate_D-dehydrogenase_480849..480999_POSITIVE 288 50 1 104 48 pint:PI0261|3end_conjugative_transposon_protein,_TraK_254765..254915_POSITIVE 277 48 3 52 5 pint:PI1630|3end_hypothetical_protein_1552494..1552644_POSITIVE 276 79 36 115 59 pint:PI1819|3end_hypothetical_protein_1759879..1760029_POSITIVE 272 102 61 134 86 pint:PI0083|3end_tyrosyl-tRNA_synthetase_84115..84265_POSITIVE 269 79 31 125 81 pint:PI1884|3end_conserved_hypothetical_protein_1827457..1827607_POSITIVE 268 164 125 130 80 pint:PI0113|3end_arginyl-tRNA_synthetase_110082..110232_POSITIVE 264 86 50 64 19 pint:PI1839|3end_hypothetical_protein_1782500..1782650_POSITIVE 262 168 129 135 104 pint:PI1850|3end_prenyltransferase,_UbiA_family_1796922..1797072_POSITIVE 260 97 55 133 94 pint:PI0769|3end_phosphomannomutase_706172..706322_POSITIVE 255 169 123 78 23 pint:PI1395|3end_hypothetical_protein_1314407..1314557_POSITIVE 254 139 93 55 11 pint:PI1734|3end_possible_carboxyl-terminal_protease-related_protein_1653829..1653979_POSITIVE 253 46 1 133 93 pint:PI1746|3end_hypothetical_protein_1667606..1667756_POSITIVE 253 149 101 67 28 pint:PI1741|3end_lipid-A-disaccharide_synthase_1663856..1664006_POSITIVE 253 51 16 131 97 pint:PI0015|3end_possible__transport_protein_20150..20300_POSITIVE