Origin IGS: gatggggtatcgcttgattgctgataaatcttcttctttcattgtgatatgttttaattgaattgattaaataatttttgtttgaatgataatgatgtgtttgaatgatagttgaatggtagttgaatgattattgaaagaaaatctcttttcccaagtttttcccctccaaactttttcatctttcttcttactacatactattttaagttaagtaattgatttacaatgtatttttgtagtaccaagtcatactacgaacttacaacatacggctacta .........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 tagtagccgtatgttgtaagttcgtagtatgacttggtactacaaaaatacattgtaaatcaattacttaacttaaaatagtatgtagtaagaagaaagatgaaaaagtttggaggggaaaaacttgggaaaagagattttctttcaataatcattcaactaccattcaactatcattcaaacacatcattatcattcaaacaaaaattatttaatcaattcaattaaaacatatcacaatgaaagaagaagatttatcagcaatcaagcgataccccatc Mask Tandem Repeat Region ================================================ gatggggtatcgcttgattgctgataaatcttcttctttcattgtgatatgttttaattgaattgattaaataatttttgtttgaatgataatgatgtgtnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnntattgaaagaaaatctcttttcccaagtttttcccctccaaactttttcatctttcttcttactacatactattttaagttaagtaattgatttacaatgtatttttgtagtaccaagtcatactacgaacttacaacatacggctacta Find is-nt database================================================ Query_seq: PI1546:PI1548|PI1546:PI1548:mobilizable transposon, excision protein:conserved hypothetical protein:->->:1465160..1465440 281 gatggggtatcgcttgattgctgataaatcttcttctttcattgtgatatgttttaattgaattgattaaataatttttgtttgaatgataatgatgtgtttgaatgatagttgaatggtagttgaatgattattgaaagaaaatctcttttcccaagtttttcccctccaaactttttcatctttcttcttactacatactattttaagttaagtaattgatttacaatgtatttttgtagtaccaagtcatactacgaacttacaacatacggctacta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI1546:PI1548|PI1546:PI1548:mobilizable transposon, excision protein:conserved hypothetical protein:->->:1465160..1465440 281 gatggggtatcgcttgattgctgataaatcttcttctttcattgtgatatgttttaattgaattgattaaataatttttgtttgaatgataatgatgtgtttgaatgatagttgaatggtagttgaatgattattgaaagaaaatctcttttcccaagtttttcccctccaaactttttcatctttcttcttactacatactattttaagttaagtaattgatttacaatgtatttttgtagtaccaagtcatactacgaacttacaacatacggctacta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI1546:PI1548|PI1546:PI1548:mobilizable transposon, excision protein:conserved hypothetical protein:->->:1465160..1465440 281 gatggggtatcgcttgattgctgataaatcttcttctttcattgtgatatgttttaattgaattgattaaataatttttgtttgaatgataatgatgtgtttgaatgatagttgaatggtagttgaatgattattgaaagaaaatctcttttcccaagtttttcccctccaaactttttcatctttcttcttactacatactattttaagttaagtaattgatttacaatgtatttttgtagtaccaagtcatactacgaacttacaacatacggctacta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gatggggtatcgcttgattgctgataaatcttcttctttcattgtgatatgttttaattgaattgattaaataatttttgtttgaatgataatgatgtgtttgaatgatagttgaatggtagttgaatgattattgaaagaaaatctcttttcccaagtttttcccctccaaactttttcatctttcttcttactacatactattttaagttaagtaattgatttacaatgtatttttgtagtaccaagtcatactacgaacttacaacatacggctacta Predict ORF larger than 30AA ================================================ Protein_Len: 31 Strand: + Start: 127 End: 219 .............................................................................................................................. M I I E R K S L F P S F S P P N F F I F L L T T Y Y F K L S N .............................................................. Protein_Len: 45 Strand: - Start: 70 End: 204 ..................................................................... I I K T Q I I I I H K F S L Q I T T S H N N F S F R K E W T K G R W V K E D K K K S C V M ............................................................................. Protein_Len: 42 Strand: - Start: 57 End: 182 ........................................................ N F Q N F L K Q K F S L S T N S H Y N F P L Q I I I S L F D R K G L K E G G F K K M ................................................................................................... Protein_Len: 36 Strand: - Start: 2 End: 109 . H P I A Q N S I F R R R E N H Y T K I S N I L Y N K N S H Y H H T Q I M ............................................................................................................................................................................ gatggggtatcgcttgattgctgataaatcttcttctttcattgtgatatgttttaattgaattgattaaataatttttgtttgaatgataatgatgtgtttgaatgatagttgaatggtagttgaatgattattgaaagaaaatctcttttcccaagtttttcccctccaaactttttcatctttcttcttactacatactattttaagttaagtaattgatttacaatgtatttttgtagtaccaagtcatactacgaacttacaacatacggctacta 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================================================ gatggggtatcgcttgattgctgataaatcttcttctttcattgtgatatgttttaattgaattgattaaataatttttgtttgaatgataatgatgtgtttgaatgatagttgaatggtagttgaatgattattgaaagaaaatctcttttcccaagtttttcccctccaaactttttcatctttcttcttactacatactattttaagttaagtaattgatttacaatgtatttttgtagtaccaagtcatactacgaacttacaacatacggctacta Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PI1546:PI1548|PI1546:PI1548:mobilizable transposon, excision protein:conserved hypothetical protein:->->:1465160..1465440 281 gatggggtatcgcttgattgctgataaatcttcttctttcattgtgatatgttttaattgaattgattaaataatttttgtttgaatgataatgatgtgtttgaatgatagttgaatggtagttgaatgattattgaaagaaaatctcttttcccaagtttttcccctccaaactttttcatctttcttcttactacatactattttaagttaagtaattgatttacaatgtatttttgtagtaccaagtcatactacgaacttacaacatacggctacta Intra-Species Hit: Count: 3 Min: 1 Max: 281 Len: 281 Subject: pint_PI1546_PI1548|mobilizable transposon, excision protein:conserved hypothetical protein|POSITIVE:POSITIVE|[1465160,1465440]|281 HSP 1 e-value: 2.0E-87 bit: 323.0 Len: 163 Query Start:119 Query End:281 Subject Strand: POSITIVE Subject Start: 119 Subject End: 281 ......................................................................................................................gtagttgaatgattattgaaagaaaatctcttttcccaagtttttcccctccaaactttttcatctttcttcttactacatactattttaagttaagtaattgatttacaatgtatttttgtagtaccaagtcatactacgaacttacaacatacggctacta ......................................................................................................................gtagttgaatgattattgaaagaaaatctcttttcccaagtttttcccctccaaactttttcatctttcttcttactacatactattttaagttaagtaattgatttacaatgtatttttgtagtaccaagtcatactacgaacttacaacatacggctacta HSP 2 e-value: 2.0E-16 bit: 87.7 Len: 44 Query Start:1 Query End:44 Subject Strand: POSITIVE Subject Start: 1 Subject End: 44 gatggggtatcgcttgattgctgataaatcttcttctttcattg............................................................................................................................................................................................................................................. gatggggtatcgcttgattgctgataaatcttcttctttcattg............................................................................................................................................................................................................................................. Subject: pint_PI0743_PI0744|hypothetical protein:DNA primase/mobilizable transposon, excision protein|POSITIVE:POSITIVE|[673087,674310]|1224 HSP 1 e-value: 8.0E-22 bit: 105.0 Len: 65 Query Start:145 Query End:209 Subject Strand: NEGATIVE Subject Start: 1032 Subject End: 1096 ................................................................................................................................................tctcttttcccaagtttttcccctccaaactttttcatctttcttcttactacatactattttaa........................................................................ ................................................................................................................................................tctcttttcctaagtttttcccttccaaacttttccatctttcttcttactacatactattttaa........................................................................ HSP 2 e-value: 7.0E-7 bit: 56.0 Len: 44 Query Start:1 Query End:44 Subject Strand: NEGATIVE Subject Start: 1181 Subject End: 1224 gatggggtatcgcttgattgctgataaatcttcttctttcattg............................................................................................................................................................................................................................................. gatggggtatcgcttgatgagtgataaatcttcttctgtcattg............................................................................................................................................................................................................................................. Subject: pint_PI0377_PI0378|DNA primase/mobilizable transposon, excision protein:conserved hypothetical protein; possible helicase|POSITIVE:POSITIVE|[347884,348165]|282 HSP 1 e-value: 2.0E-16 bit: 87.7 Len: 48 Query Start:160 Query End:207 Subject Strand: POSITIVE Subject Start: 173 Subject End: 220 ...............................................................................................................................................................ttttcccctccaaactttttcatctttcttcttactacatactatttt.......................................................................... ...............................................................................................................................................................ttttcccctccaaactttttcatctttcttcttaccacatactatttt.......................................................................... HSP 2 e-value: 7.0E-7 bit: 56.0 Len: 44 Query Start:1 Query End:44 Subject Strand: POSITIVE Subject Start: 58 Subject End: 101 gatggggtatcgcttgattgctgataaatcttcttctttcattg............................................................................................................................................................................................................................................. gatgggatatcgcttgataagtgataaatcttcttctttcattg............................................................................................................................................................................................................................................. Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAUGGGGUAUCGCUUGAUUGCUGAUAAAUCUUCUUCUUUCAUUGUGAUAUGUUUUAAUUGAAUUGAUUAAAUAAUUUUUGUUUGAAUGAUAAUGAUGUGUUUGAAUGAUAGUUGAAUGGUAGUUGAAUGAUUAUUGAAAGAAAAUCUCUUUUCCCAAGUUUUUCCCCUCCAAACUUUUUCAUCUUUCUUCUUACUACAUACUAUUUUAAGUUAAGUAAUUGAUUUACAAUGUAUUUUUGUAGUACCAAGUCAUACUACGAACUUACAACAUACGGCUACUA ...((.(((((((.(((..(..((.......))..)..)))..))))))).)).....(((((..((((..(((((((((((.....)))))..((((((..(((.((.((.(((((((.((..(((.((((...((((((.....))))))....)))).)))..)))))......)))).)).)))))..)).))))........))))))..))))..)))))...((((..(((((((((........)))))))))..)))).............. (-49.30) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAGUAGCCGUAUGUUGUAAGUUCGUAGUAUGACUUGGUACUACAAAAAUACAUUGUAAAUCAAUUACUUAACUUAAAAUAGUAUGUAGUAAGAAGAAAGAUGAAAAAGUUUGGAGGGGAAAAACUUGGGAAAAGAGAUUUUCUUUCAAUAAUCAUUCAACUACCAUUCAACUAUCAUUCAAACACAUCAUUAUCAUUCAAACAAAAAUUAUUUAAUCAAUUCAAUUAAAACAUAUCACAAUGAAAGAAGAAGAUUUAUCAGCAAUCAAGCGAUACCCCAUC ..(((..(((.(((((((((((.(((((((......))))))).......((((((......(((((...(((......)))..)))))..(((....(((((....(((((((.((........(((.....((((((..........))))..)).....)))........)).)))))))...)))))....)))......................................)))))).........)))))).))))).....))).)))...... (-40.29) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 582 45 1 136 92 pint:PI0744|5end_DNA_primase/mobilizable_transposon,_excision_protein_674171..674401_POSITIVE 319 186 144 218 172 pint:PI0328|5end_conserved_hypothetical_protein_309476..309706_POSITIVE 294 126 93 98 58 pint:PI1589|5end_conserved_hypothetical_protein_1517358..1517588_POSITIVE 282 50 12 58 14 pint:PI1946|5end_hypothetical_protein_1902713..1902943_POSITIVE 260 40 1 230 192 pint:PI1855|5end_lipopolysaccharide_biosynthesis_protein_1801715..1801945_POSITIVE 248 277 236 218 181 pint:PI0537|5end_alanyl-tRNA_synthetase_(alanine--tRNA_ligase)_489756..489986_POSITIVE 240 139 92 119 72 pint:PI0061|5end_hypothetical_protein_60500..60730_POSITIVE 238 195 155 80 41 pint:PI1653|5end_hypothetical_protein_1565158..1565388_POSITIVE 238 190 147 172 119 pint:PI0809|5end_hypothetical_protein_746630..746860_POSITIVE 235 49 1 131 77 pint:PI1183|5end_conserved_hypothetical_protein_1104442..1104672_POSITIVE 229 119 78 160 116 pint:PI1814|5end_hypothetical_protein_1752953..1753183_POSITIVE 229 119 78 85 41 pint:PI1813|5end_hypothetical_protein_1752878..1753108_POSITIVE 229 21 1 197 178 pint:PI0792|5end_conserved_hypothetical_protein_729068..729298_POSITIVE 229 21 1 82 63 pint:PI0790|5end_hypothetical_protein_728953..729183_POSITIVE 229 23 1 35 16 pint:PI0323|5end_hypothetical_protein_305349..305579_POSITIVE 228 53 11 82 35 pint:PI1066|5end_dihydrofolate_reductase_983427..983657_POSITIVE 225 183 147 230 193 pint:PI1931|5end_alpha_glycan_phosphorylase,_maltodextrin_phosphorylase_1875456..1875686_POSITIVE 222 48 1 69 25 pint:PI1081|5end_probable_endonuclease/resolvase_1000806..1001036_POSITIVE 220 180 143 229 198 pint:PI0263|5end_conjugative_transposon_protein,_TraM_255256..255486_POSITIVE 219 190 148 195 134 pint:PI0559|5end_conserved_hypothetical_protein_507668..507898_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 409 230 181 54 2 pint:PI0741|3end_conserved_hypothetical_protein_673997..674147_POSITIVE 282 50 12 130 86 pint:PI1947|3end_hypothetical_protein_1902865..1903015_POSITIVE 238 195 155 77 38 pint:PI1652|3end_hypothetical_protein_1565235..1565385_POSITIVE 238 47 6 143 83 pint:PI1229|3end_conserved_hypothetical_protein_1151669..1151819_POSITIVE 234 279 233 137 91 pint:PI0438|3end_elongation_factor_Tu_410304..410454_POSITIVE 222 159 118 116 78 pint:PI1430|3end_subtilisin-like_serine_proteinase_1351774..1351924_POSITIVE 222 48 1 66 22 pint:PI1080|3end_conserved_hypothetical_protein;_possible_outer_membrane_lipoprotein_1000883..1001033_POSITIVE 222 46 1 141 90 pint:PI0734|3end_ABC_transporter,_ATP-binding_/_permease_668760..668910_POSITIVE 220 139 94 43 3 pint:PI0856|3end_hypothetical_protein_789927..790077_POSITIVE 214 138 93 56 9 pint:PI1425|3end_conserved_hypothetical_protein_1344849..1344999_POSITIVE 213 43 3 144 109 pint:PI0988|3end_hypothetical_protein_912753..912903_POSITIVE 213 41 2 50 16 pint:PI0479|3end_50S_ribosomal_protein_L15_441648..441798_POSITIVE 211 190 157 112 78 pint:PI0884|3end_hypothetical_protein_817669..817819_POSITIVE 211 192 157 115 84 pint:PI0010|3end_conserved_hypothetical_protein_11679..11829_POSITIVE 208 171 151 147 124 pint:PI1631|3end_hypothetical_protein_1552797..1552947_POSITIVE 208 126 86 128 80 pint:PI1427|3end_nicotinate-nucleotide_pyrophosphorylase_1346660..1346810_POSITIVE 207 50 17 87 57 pint:PI1928|3end_conserved_hypothetical_protein_1873404..1873554_POSITIVE 205 44 4 137 93 pint:PI1776|3end_probable_peptidase_of_the_M22_family_(inactive?_chaperone?))_1709425..1709575_POSITIVE 201 50 4 124 71 pint:PI1613|3end_hypothetical_protein_1540906..1541056_POSITIVE 201 278 244 62 11 pint:PI0859|3end_carbamoyl-phosphate_synthase,_small_subunit_794470..794620_POSITIVE