Origin IGS: ggcataggctggtgttttacggacaggcctgatacccctcctttcgagatactccacgatgggatatcgcttgataagtgataaatcttcttctttcattgttttgatactttaatgggttgaatgataattatttatgcttgtctgttttatggttttaccgtttccaaagttttcccctccaaactttttcatctttcttcttaccacatactattttgtgataaatgattgataatcagtattactttgtagtataagacaatactacacattctacta .........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 tagtagaatgtgtagtattgtcttatactacaaagtaatactgattatcaatcatttatcacaaaatagtatgtggtaagaagaaagatgaaaaagtttggaggggaaaactttggaaacggtaaaaccataaaacagacaagcataaataattatcattcaacccattaaagtatcaaaacaatgaaagaagaagatttatcacttatcaagcgatatcccatcgtggagtatctcgaaaggaggggtatcaggcctgtccgtaaaacaccagcctatgcc Mask Tandem Repeat Region ================================================ ggcataggctggtgttttacggacaggcctgatacccctcctttcgagatactccacgatgggatatcgcttgataagtgataaatcttcttctttcattgttttgatactttaatgggttgaatgataattatttatgcttgtctgttttatggttttaccgtttccaaagttttcccctccaaactttttcatctttcttcttaccacatactattttgtgataaatgattgataatcagtattactttgtagtataagacaatactacacattctacta Find is-nt database================================================ Query_seq: PI0377:PI0378|PI0377:PI0378:DNA primase/mobilizable transposon, excision protein:conserved hypothetical protein; possible helicase:->->:347884..348165 282 ggcataggctggtgttttacggacaggcctgatacccctcctttcgagatactccacgatgggatatcgcttgataagtgataaatcttcttctttcattgttttgatactttaatgggttgaatgataattatttatgcttgtctgttttatggttttaccgtttccaaagttttcccctccaaactttttcatctttcttcttaccacatactattttgtgataaatgattgataatcagtattactttgtagtataagacaatactacacattctacta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI0377:PI0378|PI0377:PI0378:DNA primase/mobilizable transposon, excision protein:conserved hypothetical protein; possible helicase:->->:347884..348165 282 ggcataggctggtgttttacggacaggcctgatacccctcctttcgagatactccacgatgggatatcgcttgataagtgataaatcttcttctttcattgttttgatactttaatgggttgaatgataattatttatgcttgtctgttttatggttttaccgtttccaaagttttcccctccaaactttttcatctttcttcttaccacatactattttgtgataaatgattgataatcagtattactttgtagtataagacaatactacacattctacta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI0377:PI0378|PI0377:PI0378:DNA primase/mobilizable transposon, excision protein:conserved hypothetical protein; possible helicase:->->:347884..348165 282 ggcataggctggtgttttacggacaggcctgatacccctcctttcgagatactccacgatgggatatcgcttgataagtgataaatcttcttctttcattgttttgatactttaatgggttgaatgataattatttatgcttgtctgttttatggttttaccgtttccaaagttttcccctccaaactttttcatctttcttcttaccacatactattttgtgataaatgattgataatcagtattactttgtagtataagacaatactacacattctacta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ggcataggctggtgttttacggacaggcctgatacccctcctttcgagatactccacgatgggatatcgcttgataagtgataaatcttcttctttcattgttttgatactttaatgggttgaatgataattatttatgcttgtctgttttatggttttaccgtttccaaagttttcccctccaaactttttcatctttcttcttaccacatactattttgtgataaatgattgataatcagtattactttgtagtataagacaatactacacattctacta Predict ORF larger than 30AA ================================================ Protein_Len: 34 Strand: + Start: 120 End: 221 ....................................................................................................................... M N D N Y L C L S V L W F Y R F Q S F P L Q T F S S F F L P H T I L ............................................................. Protein_Len: 35 Strand: + Start: 124 End: 228 ........................................................................................................................... M I I I Y A C L F Y G F T V S K V F P S K L F H L S S Y H I L F C D K ...................................................... Protein_Len: 32 Strand: + Start: 137 End: 232 ........................................................................................................................................ M L V C F M V L P F P K F S P P N F F I F L L T T Y Y F V I N D .................................................. Protein_Len: 32 Strand: - Start: 115 End: 210 .................................................................................................................. H T S H Y N N I S T Q K I T K G N G F N E G G F K K M K R R V M ........................................................................ Protein_Len: 36 Strand: - Start: 1 End: 108 A Y A P T K R V P R I G R R E L Y E V I P Y R K I L S L D E E K M T K M .............................................................................................................................................................................. ggcataggctggtgttttacggacaggcctgatacccctcctttcgagatactccacgatgggatatcgcttgataagtgataaatcttcttctttcattgttttgatactttaatgggttgaatgataattatttatgcttgtctgttttatggttttaccgtttccaaagttttcccctccaaactttttcatctttcttcttaccacatactattttgtgataaatgattgataatcagtattactttgtagtataagacaatactacacattctacta 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================================================ ggcataggctggtgttttacggacaggcctgatacccctcctttcgagatactccacgatgggatatcgcttgataagtgataaatcttcttctttcattgttttgatactttaatgggttgaatgataattatttatgcttgtctgttttatggttttaccgtttccaaagttttcccctccaaactttttcatctttcttcttaccacatactattttgtgataaatgattgataatcagtattactttgtagtataagacaatactacacattctacta Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PI0377:PI0378|PI0377:PI0378:DNA primase/mobilizable transposon, excision protein:conserved hypothetical protein; possible helicase:->->:347884..348165 282 ggcataggctggtgttttacggacaggcctgatacccctcctttcgagatactccacgatgggatatcgcttgataagtgataaatcttcttctttcattgttttgatactttaatgggttgaatgataattatttatgcttgtctgttttatggttttaccgtttccaaagttttcccctccaaactttttcatctttcttcttaccacatactattttgtgataaatgattgataatcagtattactttgtagtataagacaatactacacattctacta Intra-Species Hit: Count: 3 Min: 1 Max: 282 Len: 282 Subject: pint_PI0377_PI0378|DNA primase/mobilizable transposon, excision protein:conserved hypothetical protein; possible helicase|POSITIVE:POSITIVE|[347884,348165]|282 HSP 1 e-value: 1.0E-158 bit: 559.0 Len: 282 Query Start:1 Query End:282 Subject Strand: POSITIVE Subject Start: 1 Subject End: 282 ggcataggctggtgttttacggacaggcctgatacccctcctttcgagatactccacgatgggatatcgcttgataagtgataaatcttcttctttcattgttttgatactttaatgggttgaatgataattatttatgcttgtctgttttatggttttaccgtttccaaagttttcccctccaaactttttcatctttcttcttaccacatactattttgtgataaatgattgataatcagtattactttgtagtataagacaatactacacattctacta ggcataggctggtgttttacggacaggcctgatacccctcctttcgagatactccacgatgggatatcgcttgataagtgataaatcttcttctttcattgttttgatactttaatgggttgaatgataattatttatgcttgtctgttttatggttttaccgtttccaaagttttcccctccaaactttttcatctttcttcttaccacatactattttgtgataaatgattgataatcagtattactttgtagtataagacaatactacacattctacta Subject: pint_PI0743_PI0744|hypothetical protein:DNA primase/mobilizable transposon, excision protein|POSITIVE:POSITIVE|[673087,674310]|1224 HSP 1 e-value: 5.0E-20 bit: 99.6 Len: 110 Query Start:173 Query End:282 Subject Strand: NEGATIVE Subject Start: 972 Subject End: 1081 ............................................................................................................................................................................ttttcccctccaaactttttcatctttcttcttaccacatactattttgtgataaatgattgataatcagtattactttgtagtataagacaatactacacattctacta ............................................................................................................................................................................ttttcccttccaaacttttccatctttcttcttactacatactattttaatataaatgattgataatcaacaatagttagtagtatatggagatactacacattctacta HSP 2 e-value: 7.0E-10 bit: 65.9 Len: 45 Query Start:58 Query End:102 Subject Strand: NEGATIVE Subject Start: 1180 Subject End: 1224 .........................................................gatgggatatcgcttgataagtgataaatcttcttctttcattgt.................................................................................................................................................................................... .........................................................gatggggtatcgcttgatgagtgataaatcttcttctgtcattgt.................................................................................................................................................................................... Subject: pint_PI1546_PI1548|mobilizable transposon, excision protein:conserved hypothetical protein|POSITIVE:POSITIVE|[1465160,1465440]|281 HSP 1 e-value: 2.0E-16 bit: 87.7 Len: 48 Query Start:173 Query End:220 Subject Strand: POSITIVE Subject Start: 160 Subject End: 207 ............................................................................................................................................................................ttttcccctccaaactttttcatctttcttcttaccacatactatttt.............................................................. ............................................................................................................................................................................ttttcccctccaaactttttcatctttcttcttactacatactatttt.............................................................. HSP 2 e-value: 2.0E-7 bit: 58.0 Len: 45 Query Start:58 Query End:102 Subject Strand: POSITIVE Subject Start: 1 Subject End: 45 .........................................................gatgggatatcgcttgataagtgataaatcttcttctttcattgt.................................................................................................................................................................................... .........................................................gatggggtatcgcttgattgctgataaatcttcttctttcattgt.................................................................................................................................................................................... Inter-species Hit: Count: 1 Min: 100 Max: 282 Len: 183 Subject: tfor_TF1633_TF1635|mobilizable transposon, excision protein:conserved hypothetical protein; possible helicase|POSITIVE:POSITIVE|[1745409,1745592]|184 HSP 1 e-value: 1.0E-85 bit: 317.0 Len: 183 Query Start:100 Query End:282 Subject Strand: POSITIVE Subject Start: 1 Subject End: 184 ...................................................................................................tgttttgatactttaatgggttgaatgataattatttatgcttgtctgtttt-atggttttaccgtttccaaagttttcccctccaaactttttcatctttcttcttaccacatactattttgtgataaatgattgataatcagtattactttgtagtataagacaatactacacattctacta ...................................................................................................tgttttgatactttaatgggttgaatgataattatttatgtttgtctgtttttatggttttaccttttccaaagttttcccctccaaactttttcatctttcttcttactacatactattttgtgataagtgattgataatcagtattactttgtagtataagacaatactacacattctacta Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGUUUUGAUACUUUAAUGGGUUGAAUGAUAAUUAUUUAUGCUUGUCUGUUUUAUGGUUUUACCGUUUCCAAAGUUUUCCCCUCCAAACUUUUUCAUCUUUCUUCUUACCACAUACUAUUUUGUGAUAAAUGAUUGAUAAUCAGUAUUACUUUGUAGUAUAAGACAAUACUACACAUUCUACUA .....(((((((.....(((..(((((((((.((....)).)))))......((((.....)))).......))))..))).............(((..((...(((.((((........)))).)))..))..)))....)))))))...((((((((......)))))))).......... (-28.80) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAGUAGAAUGUGUAGUAUUGUCUUAUACUACAAAGUAAUACUGAUUAUCAAUCAUUUAUCACAAAAUAGUAUGUGGUAAGAAGAAAGAUGAAAAAGUUUGGAGGGGAAAACUUUGGAAACGGUAAAACCAUAAAACAGACAAGCAUAAAUAAUUAUCAUUCAACCCAUUAAAGUAUCAAAACA (((((.....((((((((......))))))))......)))))...........(((((((((........)))))))))..(((.(((((.....((..(((.......)))..))...((.....)).......................))))).)))...................... (-31.80) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 275 77 42 114 79 pint:PI1480|5end_xanthine/uracil_permease_family_protein_1402675..1402905_POSITIVE 267 70 39 165 133 pint:PI0871|5end_hypothetical_protein_806834..807064_POSITIVE 256 69 37 126 91 pint:PI1649|5end_hypothetical_protein_1563080..1563310_POSITIVE 256 69 37 126 91 pint:PI0354|5end_hypothetical_protein_325886..326116_POSITIVE 254 105 62 205 170 pint:PI0328|5end_conserved_hypothetical_protein_309476..309706_POSITIVE 245 59 37 231 206 pint:PI1650|5end_N-acetylmuramoyl-L-alanine_amidase_1563195..1563425_POSITIVE 243 83 43 64 16 pint:PI2064|5end_conserved_hypothetical_protein;_possible_type_I_restriction-modification_system,_S_subunit_2025076..2025306_POSITIVE 242 62 32 172 142 pint:PI0081|5end_hypothetical_protein_80423..80653_POSITIVE 239 108 62 79 31 pint:PI1653|5end_hypothetical_protein_1565158..1565388_POSITIVE 235 60 12 186 134 pint:PI1576|5end_serine_protease_precursor_1502172..1502402_POSITIVE 231 80 38 96 58 pint:PI1840|5end_conserved_hypothetical_protein_1782856..1783086_POSITIVE 228 85 53 225 189 pint:PI0883|5end_para-aminobenzoate_synthase_component_I_816131..816361_POSITIVE 227 116 71 166 111 pint:PI0068|5end_arginine_repressor_66586..66816_POSITIVE 226 80 39 209 167 pint:PI1049|5end_hypothetical_protein_967172..967402_POSITIVE 226 87 41 173 125 pint:PI0365|5end_hypothetical_protein_335721..335951_POSITIVE 222 85 42 169 117 pint:PI0268|5end_lysozyme-related_protein_259198..259428_POSITIVE 220 85 41 127 84 pint:PI0248|5end_protein_associated_with_conjugate_transformation/chromosome_partioning_246139..246369_POSITIVE 219 77 40 219 188 pint:PI1396|5end_urocanate_hydratase_1315799..1316029_POSITIVE 218 85 44 117 83 pint:PI2044|5end_hypothetical_protein_1996999..1997229_POSITIVE 218 64 22 216 163 pint:PI0849|5end_hypothetical_protein_783193..783423_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 463 140 94 47 1 pint:PI0741|3end_conserved_hypothetical_protein_673997..674147_POSITIVE 275 77 42 106 71 pint:PI1479|3end_xanthine_phosphoribosyltransferase_1402747..1402897_POSITIVE 267 70 39 145 113 pint:PI0870|3end_branched-chain_amino_acid_aminotransferase_806894..807044_POSITIVE 256 69 37 94 59 pint:PI1646|3end_hypothetical_protein_1563128..1563278_POSITIVE 256 69 37 94 59 pint:PI0352|3end_hypothetical_protein_325934..326084_POSITIVE 251 89 42 151 98 pint:PI0713|3end_hypothetical_protein_650529..650679_POSITIVE 244 73 32 55 10 pint:PI1487|3end_hypothetical_protein_1407940..1408090_POSITIVE 243 83 43 64 16 pint:PI2063|3end_conserved_hypothetical_protein_2025156..2025306_POSITIVE 242 62 32 91 61 pint:PI0080|3end_hypothetical_protein_80422..80572_POSITIVE 239 108 62 76 28 pint:PI1652|3end_hypothetical_protein_1565235..1565385_POSITIVE 229 85 54 147 111 pint:PI1631|3end_hypothetical_protein_1552797..1552947_POSITIVE 227 116 71 86 31 pint:PI0067|3end_hypothetical_protein_66586..66736_POSITIVE 226 80 39 150 108 pint:PI1048|3end_1,4-dihydroxy-2-naphthoate_octaprenyltransferase_967193..967343_POSITIVE 220 85 41 140 97 pint:PI0247|3end_conjugative_transposon_protein,_TraA_246232..246382_POSITIVE 216 87 41 133 80 pint:PI0745|3end_conserved_hypothetical_protein_675670..675820_POSITIVE 214 110 63 125 56 pint:PI0884|3end_hypothetical_protein_817669..817819_POSITIVE 211 108 63 51 2 pint:PI0593|3end_NAD-specific_glutamate_dehydrogenase_544369..544519_POSITIVE 211 106 72 115 84 pint:PI0010|3end_conserved_hypothetical_protein_11679..11829_POSITIVE 210 77 31 92 54 pint:PI1187|3end_conserved_hypothetical_protein_1107245..1107395_POSITIVE 207 80 46 76 37 pint:PI1759|3end_hypothetical_protein_1684386..1684536_POSITIVE